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  • 1.
    Ansell, Ricky
    et al.
    Swedish National Forensic Centre, Linköping, Sweden.
    Allen, Marie
    Molekylär patologi och rättsgenetik, Uppsala universitet.
    DNA-analyser inom brottsbekämpningen2016In: Skurk, sjuk eller släkt?: vem ska ha ditt DNA? / [ed] Eva Regårdh, Sofie Pehrssoon, Stockholm: Stiftelsen för strategisk forskning , 2016, p. 18-27Chapter in book (Other academic)
    Abstract [sv]

    Idag räcker det med DNA från enstaka celler för att kunna få fram en DNA-profil som kan jämföras med per-soner eller andra DNA-spår. En DNA-träff mot ett biologiskt spår kan utgöra en mycket stark bevisning och vara avgörande för en fällande dom. DNA-teknik gör det möjligt att analysera och ta fram en DNA-profil för de allra flesta typer av humana biologiska spår som avsatts i samband med brott, såsom blod, sperma, vaginalsekret, saliv, hår och ”kontaktspår”. Teknikerna har med åren utvecklats och förfinats. På senare år har också det internationella utbytet av DNA-profiler ökat samtidigt som fortsatt teknik- och metodutveckling banar väg för fördjupade analy-ser som kan bidra till att klara upp brott. Det kan handla om att utifrån DNA-spår ringa in ungefärlig ålder, ursprung, hårfärg, ögonfärg och kroppsstorlek på en misstänkt gärningsman

  • 2.
    Arja, Katriann
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Elgland, Mathias
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Nilsson, Peter
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Synthesis and Characterization of Oligothiophene-Porphyrin-Based Molecules That Can Be Utilized for Optical Assignment of Aggregated Amyloid-beta Morphotypes2018In: Frontiers in Chemistry, E-ISSN 2296-2646, Vol. 6, article id 391Article in journal (Refereed)
    Abstract [en]

    Molecular tools for fluorescent imaging of protein aggregates are essential for understanding the significance of these pathological hallmarks in proteopathic neurodegenerative diseases, such as Alzheimers disease. Here, we report the synthesis of a series of oligothiophene porphyrin hybrids, OTPHs, and the evaluation of these dyes for fluorescent imaging of beta-amyloid aggregates in tissue sections from a transgenic mouse model with Alzheimers disease pathology. The OTPHs proved to be successful for spectral and lifetime imaging assessment of protein deposits and our findings confirm that the enhanced spectral range and distinct lifetime diversity of these novel tools allow a more precise assessment of heterogeneous amyloid morphology compared with the corresponding oligothiophene dye. In addition, the chemical identity of the porphyrin moiety, as well as the spacing between the two optical active moieties, influenced the OTPHs performance for fluorescent assignment of the protein deposits. We foresee that our findings will aid in the chemical design of dyes that can be utilized as optical tools for studying the polymorphic nature of protein aggregates associated with proteopathic neurodegenerative diseases.

  • 3.
    Aronsson, Christopher
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering.
    Tunable and modular assembly of polypeptides and polypeptide-hybrid biomaterials2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Biomaterials are materials that are specifically designed to be in contact with biological systems and have for a long time been used in medicine. Examples of biomaterials range from sophisticated prostheses used for replacing outworn body parts to ordinary contact lenses. Currently it is possible to create biomaterials that can e.g. specifically interact with cells or respond to certain stimuli. Peptides, the shorter version of proteins, are excellent molecules for fabrication of such biomaterials. By following and developing design rules it is possible to obtain peptides that can self-assemble into well-defined nanostructures and biomaterials.

    The aim of this thesis is to create ”smart” and tunable biomaterials by molecular self-assembly using dimerizing –helical polypeptides. Two different, but structurally related, polypeptide-systems have been used in this thesis. The EKIV-polypeptide system was developed in this thesis and consists of four 28-residue polypeptides that can be mixed-and-matched to self-assemble into four different coiled coil heterodimers. The dissociation constant of the different heterodimers range from μM to < nM. Due to the large difference in affinities, the polypeptides are prone to thermodynamic social self-sorting. The JR-polypeptide system, on the other hand, consists of several 42-residue de novo designed helix-loop-helix polypeptides that can dimerize into four-helix bundles. In this work, primarily the glutamic acid-rich polypeptide JR2E has been explored as a component in supramolecular materials. Dimerization was induced by exposing the polypeptide to either Zn2+, acidic conditions or the complementary polypeptide JR2K.

    By conjugating JR2E to hyaluronic acid and the EKIV-polypeptides to star-shaped poly(ethylene glycol), respectively, highly tunable hydrogels that can be self-assembled in a modular fashion have been created. In addition, self-assembly of spherical superstructures has been investigated and were obtained by linking two thiol-modified JR2E polypeptides via a disulfide bridge in the loop region. ŒThe thesis also demonstrates that the polypeptides and the polypeptide-hybrids can be used for encapsulation and release of molecules and nanoparticles. In addition, some of the hydrogels have been explored for 3D cell culture. By using supramolecular interactions combined with bio-orthogonal covalent crosslinking reactions, hydrogels were obtained that enabled facile encapsulation of cells that retained high viability.

    The results of the work presented in this thesis show that dimerizing α–helical polypeptides can be used to create modular biomaterials with properties that can be tuned by specific molecular interactions. The modularity and the tunable properties of these smart biomaterials are conceptually very interesting andmake them useful in many emerging biomedical applications, such as 3D cell culture, cell therapy, and drug delivery

    .

    List of papers
    1. Self-sorting heterodimeric coiled coil peptides with defined and tuneable self-assembly properties
    Open this publication in new window or tab >>Self-sorting heterodimeric coiled coil peptides with defined and tuneable self-assembly properties
    Show others...
    2015 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, no 14063Article in journal (Refereed) Published
    Abstract [en]

    Coiled coils with defined assembly properties and dissociation constants are highly attractive components in synthetic biology and for fabrication of peptide-based hybrid nanomaterials and nanostructures. Complex assemblies based on multiple different peptides typically require orthogonal peptides obtained by negative design. Negative design does not necessarily exclude formation of undesired species and may eventually compromise the stability of the desired coiled coils. This work describe a set of four promiscuous 28-residue de novo designed peptides that heterodimerize and fold into parallel coiled coils. The peptides are non-orthogonal and can form four different heterodimers albeit with large differences in affinities. The peptides display dissociation constants for dimerization spanning from the micromolar to the picomolar range. The significant differences in affinities for dimerization make the peptides prone to thermodynamic social self-sorting as shown by thermal unfolding and fluorescence experiments, and confirmed by simulations. The peptides self-sort with high fidelity to form the two coiled coils with the highest and lowest affinities for heterodimerization. The possibility to exploit self-sorting of mutually complementary peptides could hence be a viable approach to guide the assembly of higher order architectures and a powerful strategy for fabrication of dynamic and tuneable nanostructured materials.

    Place, publisher, year, edition, pages
    NATURE PUBLISHING GROUP, 2015
    National Category
    Physical Sciences Electrical Engineering, Electronic Engineering, Information Engineering
    Identifiers
    urn:nbn:se:liu:diva-121739 (URN)10.1038/srep14063 (DOI)000361177400001 ()26370878 (PubMedID)
    Note

    Funding Agencies|Swedish Research Council (VR); Swedish Foundation for Strategic Research (SSF)

    Available from: 2015-10-06 Created: 2015-10-05 Last updated: 2019-01-22
    2. Tailoring Supramolecular Peptide-Poly(ethylene glycol) Hydrogels by Coiled Coil Self-Assembly and Self-Sorting
    Open this publication in new window or tab >>Tailoring Supramolecular Peptide-Poly(ethylene glycol) Hydrogels by Coiled Coil Self-Assembly and Self-Sorting
    2016 (English)In: Biomacromolecules, ISSN 1525-7797, E-ISSN 1526-4602, Vol. 17, no 6, p. 2260-2267Article in journal (Refereed) Published
    Abstract [en]

    Physical hydrogels are extensively used in a wide range of biomedical applications. However, different applications require hydrogels with different mechanical and structural properties. Tailoring these properties demands exquisite control over the supramolecular peptides with different affinities for dimerization. Four different mechanical properties of hydrogels using de novo designed coiled coil interactions involved. Here we show that it is possible to control the nonorthogonal peptides, designed to fold into four different coiled coil heterodimers with dissociation constants spanning from mu M to pM, were conjugated to star-shaped 4-arm poly(ethylene glycol) (PEG). The different PEG-coiled coil conjugates self-assemble as a result of peptide heterodimerization. Different combinations of PEG peptide conjugates assemble into PEG peptide networks and hydrogels with distinctly different thermal stabilities, supramolecular, and rheological properties, reflecting the peptide dimer affinities. We also demonstrate that it is possible to rationally modulate the self-assembly process by means of thermodynamic self-sorting by sequential additions of nonpegylated peptides. The specific interactions involved in peptide dimerization thus provides means for programmable and reversible self-assembly of hydrogels with precise control over rheological properties, which can significantly facilitate optimization of their overall performance and adaption to different processing requirements and applications.

    Place, publisher, year, edition, pages
    AMER CHEMICAL SOC, 2016
    National Category
    Polymer Chemistry
    Identifiers
    urn:nbn:se:liu:diva-130135 (URN)10.1021/acs.biomac.6b00528 (DOI)000377924800038 ()27219681 (PubMedID)
    Note

    Funding Agencies|Swedish Research Council [621-2011-4319]; Swedish Foundation for Strategic Research [ICA10-0002]; Linkoping University; Swedish Government Strategic Research Area in Materials Science on Functional Materials at Linkoping University (Faculty Grant SFO-Mat-LiU) [2009 00971]

    Available from: 2016-07-12 Created: 2016-07-11 Last updated: 2019-01-22
    3. Zinc-Triggered Hierarchical Self-Assembly of Fibrous Helix-Loop-Helix Peptide Superstructures for Controlled Encapsulation and Release
    Open this publication in new window or tab >>Zinc-Triggered Hierarchical Self-Assembly of Fibrous Helix-Loop-Helix Peptide Superstructures for Controlled Encapsulation and Release
    2016 (English)In: Macromolecules, ISSN 0024-9297, E-ISSN 1520-5835, Vol. 49, no 18, p. 6997-7003Article in journal (Refereed) Published
    Abstract [en]

    We demonstrate a novel route for hierarchical self-assembly of sub-micrometer-sized peptide superstructures that respond to subtle changes in Zn2+ concentration. The self-assembly process is triggered by a specific folding-dependent coordination of Zn2+ by a de novo designed nonlinear helix-loop-helix peptide, resulting in a propagating fiber formation and formation of spherical superstructures. The superstructures further form larger assemblies that can be completely disassembled upon removal of Zn2+ or degradation of the nonlinear peptide. This flexible and reversible assembly strategy of the superstructures enables facile encapsulation of nanoparticles and drugs that can be released by means of different stimuli.

    Place, publisher, year, edition, pages
    AMER CHEMICAL SOC, 2016
    National Category
    Polymer Chemistry
    Identifiers
    urn:nbn:se:liu:diva-132215 (URN)10.1021/acs.macromol.6b01724 (DOI)000384399100030 ()
    Note

    Funding Agencies|Swedish Research Council [621-2011-4319]; Swedish Foundation for Strategic Research [ICA10-0002]; Linkoping University; Swedish Government Strategic Research Area in Materials Science on Functional Materials at Linkoping University [2009 00971]

    Available from: 2016-10-26 Created: 2016-10-21 Last updated: 2019-01-22
  • 4.
    Babu Moparthi, Satish
    et al.
    Aix Marseille University, France.
    Carlsson, Uno
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Vincentelli, Renaud
    University of Aix Marseille, France.
    Jonsson, Bengt-Harald
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Hammarström, Per
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Wenger, Jerome
    Aix Marseille University, France.
    Differential conformational modulations of MreB folding upon interactions with GroEL/ES and TRiC chaperonin components2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, no 28386Article in journal (Refereed)
    Abstract [en]

    Here, we study and compare the mechanisms of action of the GroEL/GroES and the TRiC chaperonin systems on MreB client protein variants extracted from E. coli. MreB is a homologue to actin in prokaryotes. Single-molecule fluorescence correlation spectroscopy (FCS) and time-resolved fluorescence polarization anisotropy report the binding interaction of folding MreB with GroEL, GroES and TRiC. Fluorescence resonance energy transfer (FRET) measurements on MreB variants quantified molecular distance changes occurring during conformational rearrangements within folding MreB bound to chaperonins. We observed that the MreB structure is rearranged by a binding-induced expansion mechanism in TRiC, GroEL and GroES. These results are quantitatively comparable to the structural rearrangements found during the interaction of beta-actin with GroEL and TRiC, indicating that the mechanism of chaperonins is conserved during evolution. The chaperonin-bound MreB is also significantly compacted after addition of AMP-PNP for both the GroEL/ES and TRiC systems. Most importantly, our results showed that GroES may act as an unfoldase by inducing a dramatic initial expansion of MreB (even more than for GroEL) implicating a role for MreB folding, allowing us to suggest a delivery mechanism for GroES to GroEL in prokaryotes.

  • 5.
    Bergkvist, Liza
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Amyloid-β and lysozyme proteotoxicity in Drosophila: Beneficial effects of lysozyme and serum amyloid P component in models of Alzheimer’s disease and lysozyme amyloidosis2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In the work presented this thesis, two different conditions that are classified as protein misfolding diseases: Alzheimer's disease and lysozyme amyloidosis and proteins that could have a beneficial effect in these diseases, have been studied using Drosophila melanogaster, commonly known as the fruit fly. The fruit fly has been used for over 100 years to study and better understand fundamental biological processes. Although the fruit fly, unlike humans, is an invertebrate, many of its central biological mechanisms are very similar to ours. The first transgenic flies were designed in the early 1980s, and since then, the fruit fly has been one of the most widely used model organisms in studies on the effects of over-expressed human proteins in a biological system; one can regard the fly as a living, biological test tube. For  most proteins, it is necessary that they fold into a three-dimensional structure to function properly. But sometimes the folding goes wrong; this may be due to mutations that make the protein unstable and subject to misfolding. A misfolded protein molecule can then aggregate with other misfolded proteins. In Alzheimer's disease, which is the most common form of dementia, protein aggregates are present in the brains of patients. These aggregates are composed of the amyloid-β (Aβ) peptide, a small peptide of around 42 amino acids which is cleaved from the larger, membrane-bound, protein AβPP by two different enzymes, BACE1 and γ-secretase. In the first part of this thesis, two different fly models for Alzheimer’s disease were used: the Aβ fly model, which directly expresses the Aβ peptide, and the AβPP-BACE1 fly model, in which all the components necessary to produce the Aβ peptide in the fly are expressed in the fly central nervous system (CNS). The two different fly models were compared and the results show that a significantly smaller amount of the Aβ peptide is needed to achieve the same, or an even greater, toxic effect in the AβPP-BACE1 model compared to the Aβ model. In the second part of the thesis, these two fly models for Alzheimer’s disease were again used, but now to investigate whether lysozyme, a protein involved in our innate immune system, can counteract the toxic effect of Aβ generated in the fly models. And indeed, lysozyme is able to save the flies from Aβ-induced toxicity. Aβ and lysozyme were found to interact with each other in vivo. The second misfolding disease studied in this thesis is lysozyme amyloidosis. It is a rare, dominantly inherited amyloid disease in which mutant variants of lysozyme give rise to aggregates, weighing up to several kilograms, that accumulate around the kidneys and liver, eventually leading to organ failure. In the third part of this thesis, a fly model for lysozyme amyloidosis was used to study the effect of co-expressing the serum amyloid P component (SAP), a protein that is part of all protein aggregates found within this disease class. SAP is able to rescue the toxicity induced by expressing the mutant variant of lysozyme, F57I, in the fly's CNS. To further investigate how SAP was able to do this, double-expressing lysozyme flies, which exhibit stronger disease phenotypes than those of the single-expressing lysozyme flies previously studied, were used in the fourth part of this thesis. SAP was observed to reduce F57I toxicity and promote F57I to form aggregates with more distinct amyloid characteristics. In conclusion, the work included in this thesis demonstrates that: i) Aβ generated from AβPP processing in the fly CNS results in higher proteotoxicity compared with direct expression of Aβ from the transgene, ii) lysozyme can prevent Aβ proteotoxicity in Drosophila and could thus be a potential therapeutic molecule to treat Alzheimer’s disease and iii) in a Drosophila model of lysozyme amyloidosis, SAP can prevent toxicity from the disease-associated lysozyme variant F57I and promote formation of aggregated lysozyme morphotypes with amyloid properties; this is important to take into account when a reduced level of SAP is considered as a treatment strategy for lysozyme amyloidosis.

    List of papers
    1. A beta PP processing results in greater toxicity per amount of A beta(1-42) than individually expressed and secreted A beta(1-42) in Drosophila melanogaster
    Open this publication in new window or tab >>A beta PP processing results in greater toxicity per amount of A beta(1-42) than individually expressed and secreted A beta(1-42) in Drosophila melanogaster
    2016 (English)In: BIOLOGY OPEN, ISSN 2046-6390, Vol. 5, no 8, p. 1030-1039Article in journal (Refereed) Published
    Abstract [en]

    The aggregation of the amyloid-beta (A beta) peptide into fibrillar deposits has long been considered the key neuropathological hallmark of Alzheimers disease (AD). A beta peptides are generated from proteolytic processing of the transmembrane A beta precursor protein (A beta PP) via sequential proteolysis through the beta-secretase activity of beta-site A beta PP-cleaving enzyme (BACE1) and by the intramembranous enzyme gamma-secretase. For over a decade, Drosophila melanogaster has been used as a model organism to study AD, and two different approaches have been developed to investigate the toxicity caused by AD-associated gene products in vivo. In one model, the A beta peptide is directly over-expressed fused to a signal peptide, allowing secretion of the peptide into the extracellular space. In the other model, human A beta PP is co-expressed with human BACE1, resulting in production of the A beta peptide through the processing of A beta PP by BACE1 and by endogenous fly gamma-secretase. Here, we performed a parallel study of flies that expressed the A beta(1-42) peptide alone or that co-expressed A beta PP and BACE1. Toxic effects (assessed by eye phenotype, longevity and locomotor assays) and levels of the A beta(1-42), A beta(1-40) and A beta(1-38) peptides were examined. Our data reveal that the toxic effect per amount of detected A beta(1-42) peptide was higher in the flies co-expressing A beta PP and BACE1 than in the A beta(1-42)-expressing flies, and that the co-existence of A beta(1-42) and A beta(1-40) in the flies co-expressing A beta PP and BACE1 could be of significant importance to the neurotoxic effect detected in these flies. Thus, the toxicity detected in these two fly models seems to have different modes of action and is highly dependent on how and where the peptide is generated rather than on the actual level of the A beta(1-42) peptide in the flies. This is important knowledge that needs to be taken into consideration when using Drosophila models to investigate disease mechanisms or therapeutic strategies in AD research.

    Place, publisher, year, edition, pages
    COMPANY OF BIOLOGISTS LTD, 2016
    Keywords
    Alzheimers disease; Amyloid-beta (A beta); A beta PP processing; Drosophila melanogaster; Proteotoxicity
    National Category
    Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
    Identifiers
    urn:nbn:se:liu:diva-131685 (URN)10.1242/bio.017194 (DOI)000382304400003 ()27387531 (PubMedID)
    Note

    Funding Agencies|Torsten Soderbergs Stiftelse [M26/11]; Alzheimer Foundation [03-069]; Dementia Foundation; Ahlen Foundation; Gamla Tjanarinnor [2015-00187]

    Available from: 2016-10-03 Created: 2016-09-30 Last updated: 2017-05-16
    2. Beneficial effects of increased lysozyme levels in Alzheimer’s disease modelled in Drosophila melanogaster
    Open this publication in new window or tab >>Beneficial effects of increased lysozyme levels in Alzheimer’s disease modelled in Drosophila melanogaster
    Show others...
    2016 (English)In: The FEBS Journal, ISSN 1742-464X, E-ISSN 1742-4658, Vol. 283, no 19, p. 3508-3522Article in journal (Refereed) Published
    Abstract [en]

    Genetic polymorphisms of immune genes that associate with higher risk to develop Alzheimer’s disease (AD) have led to an increased research interest on the involvement of the immune system in AD pathogenesis. A link between amyloid pathology and immune gene expression was suggested in a genome-wide gene expression study of transgenic amyloid mouse models. In this study, the gene expression of lysozyme, a major player in the innate immune system, was found to be increased in a comparable pattern as the amyloid pathology developed in transgenic mouse models of AD. A similar pattern was seen at protein levels of lysozyme in human AD brain and CSF, but this lysozyme pattern was not seen in a tau transgenic mouse model. Lysozyme was demonstrated to be beneficial for different Drosophila melanogaster models of AD. In flies that expressed Aβ1-42 or AβPP together with BACE1 in the eyes, the rough eye phenotype indicative of toxicity was completely rescued by coexpression of lysozyme. In Drosophila flies bearing the Aβ1-42 variant with the Arctic gene mutation, lysozyme increased the fly survival and decreased locomotor dysfunction dose dependently. An interaction between lysozyme and Aβ1-42 in the Drosophila eye was discovered. We propose that the increased levels of lysozyme, seen in mouse models of AD and in human AD cases, were triggered by Aβ1-42 and caused a beneficial effect by binding of lysozyme to toxic species of Aβ1-42, which prevented these from exerting their toxic effects. These results emphasize the possibility of lysozyme as biomarker and therapeutic target for AD.

    Place, publisher, year, edition, pages
    John Wiley & Sons, 2016
    Keywords
    Alzheimer’s disease, amyloid-β, Drosophila, lysozyme
    National Category
    Genetics Medical Genetics Developmental Biology Bioinformatics and Systems Biology Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
    Identifiers
    urn:nbn:se:liu:diva-131796 (URN)10.1111/febs.13830 (DOI)000386033700001 ()27562772 (PubMedID)
    Available from: 2016-10-07 Created: 2016-10-07 Last updated: 2018-03-20Bibliographically approved
    3. Serum Amyloid P Component Ameliorates Neurological Damage Caused by Expressing a Lysozyme Variant in the Central Nervous System of Drosophila melanogaster
    Open this publication in new window or tab >>Serum Amyloid P Component Ameliorates Neurological Damage Caused by Expressing a Lysozyme Variant in the Central Nervous System of Drosophila melanogaster
    2016 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 7, p. e0159294-Article in journal (Refereed) Published
    Abstract [en]

    Lysozyme amyloidosis is a hereditary disease in which mutations in the gene coding for lysozyme leads to misfolding and consequently accumulation of amyloid material. To improve understanding of the processes involved we expressed human wild type (WT) lysozyme and the disease-associated variant F57I in the central nervous system (CNS) of a Drosophila melanogaster model of lysozyme amyloidosis, with and without co-expression of serum amyloid p component (SAP). SAP is known to be a universal constituent of amyloid deposits and to associate with lysozyme fibrils. There are clear indications that SAP may play an important role in lysozyme amyloidosis, which requires further elucidation. We found that flies expressing the amyloidogenic variant F57I in the CNS have a shorter lifespan than flies expressing WT lysozyme. We also identified apoptotic cells in the brains of F57I flies demonstrating that the flies neurological functions are impaired when F57I is expressed in the nerve cells. However, co-expression of SAP in the CNS prevented cell death and restored the F57I flies lifespan. Thus, SAP has the apparent ability to protect nerve cells from damage caused by F57I. Furthermore, it was found that co-expression of SAP prevented accumulation of insoluble forms of lysozyme in both WT- and F57I-expressing flies. Our findings suggest that the F57I mutation affects the aggregation process of lysozyme resulting in the formation of cytotoxic species and that SAP is able to prevent cell death in the F57I flies by preventing accumulation of toxic F57I structures.

    Place, publisher, year, edition, pages
    PUBLIC LIBRARY SCIENCE, 2016
    National Category
    Developmental Biology
    Identifiers
    urn:nbn:se:liu:diva-131183 (URN)10.1371/journal.pone.0159294 (DOI)000380169300043 ()27428539 (PubMedID)
    Note

    Funding Agencies|Swedish Research Council; Soderberg foundation [M26/11]; Linkoping University Neurobiology Center

    Available from: 2016-09-19 Created: 2016-09-12 Last updated: 2017-11-21
  • 6.
    Bergqvist, Niclas
    et al.
    Linköping University, Department of Biomedical Engineering. Linköping University, Faculty of Science & Engineering.
    Nyman, Elin
    Linköping University, Department of Biomedical Engineering, Division of Biomedical Engineering. Linköping University, Faculty of Science & Engineering. AstraZeneca RandD, Sweden.
    Cedersund, Gunnar
    Linköping University, Department of Biomedical Engineering, Division of Biomedical Engineering. Linköping University, Faculty of Science & Engineering. Linköping University, Department of Clinical and Experimental Medicine. Linköping University, Faculty of Medicine and Health Sciences.
    Stenkula, Karin G.
    Lund University, Sweden.
    A systems biology analysis connects insulin receptor signaling with glucose transporter translocation in rat adipocytes2017In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 292, no 27, p. 11206-11217Article in journal (Refereed)
    Abstract [en]

    Type 2 diabetes is characterized by insulin resistance, which arises from malfunctions in the intracellular insulin signaling network. Knowledge of the insulin signaling network is fragmented, and because of the complexity of this network, little consensus has emerged for the structure and importance of the different branches of the network. To help overcome this complexity, systems biology mathematical models have been generated for predicting both the activation of the insulin receptor (IR) and the redistribution of glucose transporter 4 (GLUT4) to the plasma membrane. Although the insulin signal transduction between IR and GLUT4 has been thoroughly studied with modeling and time-resolved data in human cells, comparable analyses in cells from commonly used model organisms such as rats and mice are lacking. Here, we combined existing data and models for rat adipocytes with new data collected for the signaling network between IR and GLUT4 to create a model also for their interconnections. To describe all data (amp;gt;140 data points), the model needed three distinct pathways from IR to GLUT4: (i) via protein kinase B (PKB) and Akt substrate of 160 kDa (AS160), (ii) via an AS160-independent pathway from PKB, and (iii) via an additional pathway from IR, e.g. affecting the membrane constitution. The developed combined model could describe data not used for training the model and was used to generate predictions of the relative contributions of the pathways from IR to translocation of GLUT4. The combined model provides a systems-level understanding of insulin signaling in rat adipocytes, which, when combined with corresponding models for human adipocytes, may contribute to model-based drug development for diabetes.

  • 7.
    Birznieks, Ingvars
    et al.
    UNSW Sydney, Australia; Neurosci Res Australia, Australia; Western Sydney Univ, Australia.
    Mcintyre, Sarah
    Linköping University, Department of Clinical and Experimental Medicine, Center for Social and Affective Neuroscience. Linköping University, Faculty of Medicine and Health Sciences. Neurosci Res Australia, Australia; Western Sydney Univ, Australia.
    Nilsson, Hanna Maria
    Linköping University. Sweden; Neurosci Res Australia, Australia.
    Nagi, Saad
    Linköping University, Department of Clinical and Experimental Medicine, Center for Social and Affective Neuroscience. Linköping University, Faculty of Medicine and Health Sciences. Western Sydney Univ, Australia.
    Macefield, Vaughan G.
    Neurosci Res Australia, Australia; Western Sydney Univ, Australia; Baker Heart and Diabet Inst, Australia.
    Mahns, David A.
    Western Sydney Univ, Australia.
    Vickery, Richard M.
    UNSW Sydney, Australia; Neurosci Res Australia, Australia.
    Tactile sensory channels over-ruled by frequency decoding system that utilizes spike pattern regardless of receptor type2019In: eLIFE, E-ISSN 2050-084X, Vol. 8, article id e46510Article in journal (Refereed)
    Abstract [en]

    The established view is that vibrotactile stimuli evoke two qualitatively distinctive cutaneous sensations, flutter (frequencies amp;lt; 60 Hz) and vibratory hum (frequencies amp;gt; 60 Hz), subserved by two distinct receptor types (Meissners and Pacinian corpuscle, respectively), which may engage different neural processing pathways or channels and fulfil quite different biological roles. In psychological and physiological literature, those two systems have been labelled as Pacinian and non-Pacinian channels. However, we present evidence that low-frequency spike trains in Pacinian afferents can readily induce a vibratory percept with the same low frequency attributes as sinusoidal stimuli of the same frequency, thus demonstrating a universal frequency decoding system. We achieved this using brief low-amplitude pulsatile mechanical stimuli to selectively activate Pacinian afferents. This indicates that spiking pattern, regardless of receptor type, determines vibrotactile frequency perception. This mechanism may underlie the constancy of vibrotactile frequency perception across different skin regions innervated by distinct afferent types.

  • 8.
    Brian, Björn
    Linköping University, The Department of Physics, Chemistry and Biology.
    Microarray Technology for Kinetic Analysis of Vesicle Bound Receptor-Ligand Interactions2007Independent thesis Basic level (professional degree), 20 points / 30 hpStudent thesis
    Abstract [en]

    A proof-of-concept for a novel microarray used to study protein-ligand interaction in real-time using label-free detection is presented. Many of todays commercially available instruments lack the ability to immobilize membrane proteins. At the same time, the pharmaceutical industry develops drugs directed towards membrane-bound receptors. The need to study drug-target kinetics and to be able to screen for new medical substances is high. To study the biomolecular interactions in real-time, imaging surface plasmon resonance (iSPR) is used. A patterned sensor surface with hydrophobic barriers assisting in the piezodispensing of NeutrAvidin with complex-bound biotin-ssDNA is created. Histidine-tagged proteins are immobilized at the vesicle surface using divalent nitrilotriacetic acid. The concept of the vesicle immobilization, the protein-binding to vesicles and the protein-ligand interaction is initially studied using a Biacore instrument. The dissociation of the ligand IFNα2 from its receptor ifnar-2 (wt) are in accordance with the literature. In the imaging SPR experiments, it is found that the dissociation of IFNα2 from the ifnar-2 (wt) receptor is slower than expected, probably due to rebinding of the ligand. It is also found that imidazole is needed to avoid vesicle-vesicle interaction. The immobilization of proteins had to be done on-line i.e. when the vesicles were bound to the surface. Depending on the mixture of receptors at the vesicle surface the affinity for the ligand was changed. The results achieved were reproducible.

  • 9.
    del Río, Lía Fernández
    Linköping University, Department of Physics, Chemistry and Biology, Applied Optics . Linköping University, Faculty of Science & Engineering.
    Optical and Structural Characterization of Natural Nanostructures2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The spectacular biodiversity of our planet is the result of millions of years of evolution. Over this time animals and plants have evolved and adapted to different environments, developing specific behavioral and physical adaptations to increase their chances of survival. During the last centuries human's curiosity has pushed us to study and understand the phenomena and mechanisms of the nature that surrounds us. This understanding has even led to the fields of biomimetics where we seek solutions to human challenges by emulating nature.

    Scarab beetles (from the insect family Scarabaeidae) have fascinated humans for centuries due to the brilliant metallic shine of their chitin-rich exoskeletons and more recently for their ability to polarize reflected light. This doctoral thesis focuses on the optical characterization of the polarized reflected light from beetles in the Chrysina genus, although beetles from other genera also have been investigated. All the Chrysina beetles studied here share one characteristic, they all reflect left-handed near-circular polarized light. In some cases we also detect right-handed polarized light.

    We have observed two different main behaviors among the studied Chrysina beetles. Those which are green-colored scatter the reflected polarized light, whereas those with metallic appearance are broadband specular reflectors. We present a detailed analysis of the optical properties with Mueller-matrix spectroscopic ellipsometry combined with optical- and electron-microscopy studies of the exoskeletons. This allow us to create a model that reproduces the optical properties of these structures. The model consists of a chiral (helicoidal) multilayer structure with a gradual change of the pitch and a constant rotation of the optic axis of the layers.

    Beetles are not alone to have polarizing structures in nature and it is known that many birds and insects have the ability to detect linearly polarized light. This raises the question of whether the polarization properties of the beetles are the direct or indirect results of evolution or just pure coincidence. In order to get a better understanding of the possible reasons of this particular ability, we present a simulation study of different possible scenarios in nature where incoming light could be polarized or unpolarized, and where we consider detectors (eyes) sensitive to different states of polarized light. If the beetles are able to use this characteristic for camouflage, to confuse predators or for intraspecific communication is,

    however, still unknown and requires further investigation.

    My research results provide deeper understanding of the properties of light reflected on the beetle's exoskeleton and the nanostructures responsible for the polarization of the reflected light. The developed model could be used as bioinspiration for the fabrication of novel nano-optical devices. My results can also complement biological behavioral experiments aiming to understand the purposes of this specific optical characteristics in nature.

    List of papers
    1. Polarizing properties and structure of the cuticle of scarab beetles from the Chrysina genus
    Open this publication in new window or tab >>Polarizing properties and structure of the cuticle of scarab beetles from the Chrysina genus
    2016 (English)In: PHYSICAL REVIEW E, ISSN 2470-0045, Vol. 94, no 1, p. 012409-Article in journal (Refereed) Published
    Abstract [en]

    The optical properties of several scarab beetles have been previously studied but few attempts have been made to compare beetles in the same genus. To determine whether there is any relation between specimens of the same genus, we have studied and classified seven species from the Chrysina genus. The polarization properties were analyzed with Mueller-matrix spectroscopic ellipsometry and the structural characteristics with optical microscopy and scanning electron microscopy. Most of the Chrysina beetles are green colored or have a metallic look (gold or silver). The results show that the green-colored beetles polarize reflected light mainly at off-specular angles. The gold-colored beetles polarize light left-handed near circular at specular reflection. The structure of the exoskeleton is a stack of layers that form a cusplike structure in the green beetles whereas the layers are parallel to the surface in the case of the gold-colored beetles. The beetle C. gloriosa is green with gold-colored stripes along the elytras and exhibits both types of effects. The results indicate that Chrysina beetles can be classified according to these two major polarization properties.

    Place, publisher, year, edition, pages
    AMER PHYSICAL SOC, 2016
    National Category
    Mathematical Analysis
    Identifiers
    urn:nbn:se:liu:diva-130835 (URN)10.1103/PhysRevE.94.012409 (DOI)000380116500010 ()
    External cooperation:
    Note

    Funding Agencies|Knut and Alice Wallenberg foundation; Swedish Research Council; Centre in Nano Science and Nano Technology (CeNano) at Linkoping University

    Available from: 2016-08-26 Created: 2016-08-26 Last updated: 2016-11-16
    2. Polarizing properties and structural characteristics of the cuticle of the scarab Beetle Chrysina gloriosa
    Open this publication in new window or tab >>Polarizing properties and structural characteristics of the cuticle of the scarab Beetle Chrysina gloriosa
    2014 (English)In: Thin Solid Films, ISSN 0040-6090, E-ISSN 1879-2731, Vol. 571, no 3, p. 410-415Article in journal (Refereed) Published
    Abstract [en]

    The scarab beetle Chrysina gloriosa is green with gold-colored stripes along its elytras. The properties of light reflected on these areas are investigated using Mueller-matrix spectroscopic ellipsometry. Both areas reflect light with high degree of left-handed polarization but this effect occurs for specular reflection for the gold-colored areas and for off-specular angles for the green areas. The colors and polarization phenomena originate from reflection of light in the cuticle and a structural analysis is presented to facilitate understanding of the different behaviors of these two areas. Scanning electron microscopy (SEM) images of the cross section of beetle cuticles show a multilayered structure. On the gold-colored areas the layers are parallel to the surface whereas on the green-colored areas they form cusp-like structures. Optical microscopy images show a rather flat surface in the gold-colored areas compared to the green-colored areas which display a net of polygonal cells with star-shaped cavities in the center. Each of the polygons corresponds to one of the cusps observed in the SEM images. Atomic force microscopy images of the star-shaped cavities are also provided. The roughness of the surface and the cusp-like structure of the green-colored areas are considered to cause scattering on this area.

    Place, publisher, year, edition, pages
    Elsevier, 2014
    Keywords
    Scarab beetle; Near-circular polarization; Mueller-matrix spectroscopic ellipsometry
    National Category
    Atom and Molecular Physics and Optics
    Identifiers
    urn:nbn:se:liu:diva-112885 (URN)10.1016/j.tsf.2013.11.149 (DOI)000346055200013 ()
    Conference
    ICSE-VI International Conference on Spectroscopic Ellipsometry May 2013
    Funder
    Swedish Research CouncilKnut and Alice Wallenberg Foundation
    Available from: 2014-12-18 Created: 2014-12-18 Last updated: 2017-12-05Bibliographically approved
    3. Polarization of light reflected from Chrysina gloriosa under various illuminations
    Open this publication in new window or tab >>Polarization of light reflected from Chrysina gloriosa under various illuminations
    2014 (English)In: Materials Today: Proceedings, Elsevier Ltd , 2014, Vol. 1, p. 172-176Conference paper, Published paper (Refereed)
    Abstract [en]

    When illuminated with unpolarized light, the scarab beetle Chrysina gloriosa, reflects left-handed near-circularly polarized light for a broad range of angles of incidence and wavelengths in the visible. It is, however, known that light scattered from the sky, reflected on water or transmitted through leaves often is linearly polarized. In this study we have analysed the polarization of light reflected on this beetle when illuminated with different polarization states of light. We have also analysed how the response would be with a polarization-sensitive detector. The reflected irradiance is shown to be highest when the incident light is s-polarized or left-handed polarized and the detector is unpolarized (or vice versa). In the case in which both, the source and the detector, are polarized, the irradiance is highest when both are s-polarized. On the contrary the visibility is low when the source is s-polarized and the detector is p-polarized.

    Place, publisher, year, edition, pages
    Elsevier Ltd, 2014
    Series
    Materials Today: Proceedings, ISSN 2214-7853
    Keywords
    Mueller-matrix spectroscopic ellipsometry; Near-circular polarization; Scarab beetle
    National Category
    Physical Sciences
    Identifiers
    urn:nbn:se:liu:diva-116444 (URN)10.1016/j.matpr.2014.09.020 (DOI)2-s2.0-84923048023 (Scopus ID)
    Conference
    Living Light: Uniting biology and photonics - A memorial meeting in honour of Prof Jean-Pol Vigneron
    Available from: 2015-03-27 Created: 2015-03-26 Last updated: 2016-11-16
    4. Comparison and analysis of Mueller-matrix spectra from exoskeletons of blue, green and red Cetonia aurata
    Open this publication in new window or tab >>Comparison and analysis of Mueller-matrix spectra from exoskeletons of blue, green and red Cetonia aurata
    2014 (English)In: Thin Solid Films, ISSN 0040-6090, E-ISSN 1879-2731, Vol. 571, p. 739-743Article in journal (Refereed) Published
    Abstract [en]

    The exoskeleton, also called the cuticle, of specimens of the scarab beetle Cetonia aurata is a narrow-band reflector which exhibits metallic shine. Most specimens of C. aurata have a reflectance maximum in the green part of the spectrum but variations from blue–green to red–green are also found. A few specimens are also more distinct blue or red. Furthermore, the reflected light is highly polarized and at near-normal incidence near-circular left-handed polarization is observed. The polarization and color phenomena are caused by a nanostructure in the cuticle. This nanostructure can be modeled as a multilayered twisted biaxial layer from which reflection properties can be calculated. Specifically we calculate the cuticle Mueller matrix which then is fitted to Mueller matrices determined by dual-rotating compensator ellipsometry in the spectral range 400–800 nm at multiple angles of incidence. This non-linear regression analysis provides structural parameters like pitch of the chiral structure as well as layer refractive index data for the different layers in the cuticle. The objective here is to compare spectra measured on C. aurata with different colors and develop a generic structural model. Generally the degree of polarization is large in the spectral region corresponding to the color of the cuticle which for the blue specimen is 400–600 nm whereas for the red specimen it is 530–730 nm. In these spectral ranges, the Mueller-matrix element m41 is non-zero and negative, in particular for small angles of incidence, implicating that the reflected light becomes near-circularly polarizedwith an ellipticity angle in the range 20°–45°.

    Place, publisher, year, edition, pages
    Elsevier, 2014
    Keywords
    Mueller-matrix ellipsometry; Scarab beetles; Chiral structures; Circular polarization; Natural photonic structures
    National Category
    Condensed Matter Physics
    Identifiers
    urn:nbn:se:liu:diva-112685 (URN)10.1016/j.tsf.2014.02.012 (DOI)000346055200076 ()
    Conference
    6th International Conference on Spectroscopic Ellipsometry (ICSE-VI), May 26–31, 2013, Kyoto, Japan
    Funder
    Knut and Alice Wallenberg FoundationSwedish Research Council
    Available from: 2014-12-08 Created: 2014-12-08 Last updated: 2017-12-05Bibliographically approved
  • 10.
    Feuz, Laurent
    et al.
    Department of Applied Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
    Jonsson, Magnus P.
    Department of Applied Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
    Hook, Fredrik
    Department of Applied Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
    Material-Selective Surface Chemistry for Nanoplasmonic Sensors: Optimizing Sensitivity and Controlling Binding to Local Hot Spots2012In: Nano letters (Print), ISSN 1530-6984, E-ISSN 1530-6992, Vol. 12, no 2, p. 873-879Article in journal (Refereed)
    Abstract [en]

    Optical sensors utilizing the principle of localized surface plasmon resonance (LSPR) offer the advantage of a simple label-free mode of operation, but the sensitivity is typically limited to a very thin region close to the surface. In bioanalytical sensing applications, this can be a significant drawback, in particular since the surface needs to be coated with a recognition layer in order to ensure specific detection of target molecules. We show that the signal upon protein binding decreases dramatically with increasing thickness of the recognition layer, highlighting the need for thin high quality recognition layers compatible with LSPR sensors. The effect is particularly strong for structures that provide local hot spots with highly confined fields, such as in the gap between pairs of gold disks. While our results show a significant improvement in sensor response for pairs over single gold disks upon binding directly to the gold surface, disk pairs did not provide larger signal upon binding of proteins to a recognition layer (already for around 3 nm thin layers) located on the gold. Local plasmonic hot spots are however shown advantageous in combination with directed binding to the hot spots. This was demonstrated using a structure consisting of three surface materials (gold, titanium dioxide, and silicon dioxide) and a new protocol for material-selective surface chemistry of these three materials, which allows for controlled binding only in the gap between pairs of disks. Such a design increased the signal obtained per bound molecule by a factor of around four compared to binding to single disks.

  • 11.
    Feuz, Laurent
    et al.
    Department of Applied Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
    Jonsson, Peter
    Department of Applied Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
    Jonsson, Magnus P.
    Department of Applied Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
    Hook, Fredrik
    Department of Applied Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
    Improving the Limit of Detection of Nanoscale Sensors by Directed Binding to High-Sensitivity Areas2010In: ACS Nano, ISSN 1936-0851, E-ISSN 1936-086X, Vol. 4, no 4, p. 2167-2177Article in journal (Refereed)
    Abstract [en]

    The revelation of protein protein-interactions is one of the main preoccupations in the field of proteomics. Nanoplasmonics has emerged as an attractive surface-based technique because of its ability to sense protein binding under physiological conditions in a label-free manner. Here, we use short-range ordered holes with a diameter of similar to 150 nm and a depth of similar to 50 nm as a nanoplasmonic template. A similar to 40 nm high cylindrical region of Au is exposed on the walls of the holes only, while the rest of the surface consists of TiO(2). Since the sensitivity is confined to the nanometric holes, the use of two different materials for the sensor substrate offers the opportunity to selectively bind proteins to the most sensitive Au regions on the sensor surface. This was realized by applying material-selective poly(ethylene glycol)-based surface chemistry, restricting NeutrAvidin binding to surface-immobilized biotin on the Au areas only. We show that under mass-transport limited conditions (low nM bulk concentrations), the initial time-resolved response of uptake could be increased by a factor of almost 20 compared with the case where proteins were allowed to bind on the entire sensor surface and stress the generic relevance of this concept for nanoscale sensors. In the scope of further optimizing the limit of detection (LOD) of the sensor structure, we present finite-element (FE) simulations to unravel spatially resolved binding rates. These revealed that the binding rates in the holes occur in a highly inhomogeneous manner with highest binding rates observed at the upper rim of the holes and the lowest rates observed at the bottom of the holes. By assuming a plasmonic field distribution with enhanced sensitivity at the Au-TiO(2)interface, the FE simulations reproduced the experimental findings qualitatively.

  • 12.
    Franco-Gonzalez, Juan F.
    et al.
    BIOPHYM, IEM, CSIC, Madrid, Spain.
    Cruz, Victor
    BIOPHYM, IEM, CSIC, Madrid, Spain.
    Ramos, Javier
    BIOPHYM, IEM, CSIC, Madrid, Spain.
    Martinez-Salazar, Javier
    BIOPHYM, IEM, CSIC, Madrid, Spain.
    Protein-Protein and Protein-Membrane Interactions Regarding the Erbb2/Trastuzumab-Fab Complexes. A Coarse-Grained Molecular Dynamics Description2014In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, no 2, p. 666-667Article in journal (Refereed)
    Abstract [en]

    ErbB2 is a member of epidermal growth factor receptor (EGFR) family and is overexpressed in many cancers. Specifically, Trastuzumab, which is a monoclonal antibody, is used against ErbB2, but its action mechanism is still unknown. ErbB2 can exist as both monomers and Homodimers, suggesting that Trastuzumab mechanims may be subtle. On the other hand, the membrane plays a role in the action mechanism of Trastuzumab but generates difficulties for structural studies. Coarse-Grained Molecular Dynamics has been used to study the influence of the Trastuzumab on the protein-protein and protein-membrane interactions of the full ErbB2 receptor. Our simulations start from conformations which both extracelullar and intracelullar domains are extended. The results show in both monomers and homodimers systems a folded conformation on the membrane: several experimental results, mainly obtained on ErbB1 support them. The protein-protein interaction on transmembrane and juxtamembrane domains are disrupted on the dimer and disordered on the monomer by the Trastuzumab effect, therefore, the dimerization-driven activation are unfavourable. We present a detailed description of the type of interactions governing the homodimerization and antobody complexation phenomena and the role that the membrane plays on that.

  • 13.
    Franco-Gonzalez, Juan Felipe
    et al.
    Macromolecular Physics Department, Instituto de Estructura de la Materia, CSIC, Madrid, Spain.
    Cruz, Victor L
    Macromolecular Physics Department, Instituto de Estructura de la Materia, CSIC, Madrid, Spain.
    Ramos, Javier
    Macromolecular Physics Department, Instituto de Estructura de la Materia, CSIC, Madrid, Spain.
    Martínez-Salazar, Javier
    Macromolecular Physics Department, Instituto de Estructura de la Materia, CSIC, Madrid, Spain.
    Conformational flexibility of the ErbB2 ectodomain and trastuzumab antibody complex as revealed by molecular dynamics and principal component analysis.2013In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 19, no 3, p. 1227-1236Article in journal (Refereed)
    Abstract [en]

    Human epidermal growth factor receptor 2 (ErbB2) is a transmembrane oncoprotein that is over expressed in breast cancer. A successful therapeutic treatment is a monoclonal antibody called trastuzumab which interacts with the ErbB2 extracellular domain (ErbB2-ECD). A better understanding of the detailed structure of the receptor-antibody interaction is indeed of prime interest for the design of more effective anticancer therapies. In order to discuss the flexibility of the complex ErbB2-ECD/trastuzumab, we present, in this study, a multi-nanosecond molecular dynamics simulation (MD) together with an analysis of fluctuations, through a principal component analysis (PCA) of this system. Previous to this step and in order to validate the simulations, we have performed a detailed analysis of the variable antibody domain interactions with the extracellular domain IV of ErbB2. This structure has been statically elucidated by x-ray studies. Indeed, the simulation results are in excellent agreement with the available experimental information during the full trajectory. The PCA shows eigenvector fluctuations resulting in a hinge motion in which domain II and C(H) domains approach each other. This move is likely stabilized by the formation of H-bonds and salt bridge interactions between residues of the dimerization arm in the domain II and trastuzumab residues located in the C(H) domain. Finally, we discuss the flexibility of the MD/PCA model in relation with the static x-ray structure. A movement of the antibody toward the dimerization domain of the ErbB2 receptor is reported for the first time. This finding could have important consequences on the biological action of the monoclonal antibody.

  • 14.
    Franco-Gonzalez, Juan Felipe
    et al.
    Biophym, Macromolecular Physics Department, Instituto de Estructura de la Materia, CSIC, Serrano 113-bis, 28006, Madrid, Spain .
    Ramos, Javier
    Biophym, Macromolecular Physics Department, Instituto de Estructura de la Materia, CSIC, Serrano 113-bis, 28006, Madrid, Spain .
    Cruz, Victor L
    Biophym, Macromolecular Physics Department, Instituto de Estructura de la Materia, CSIC, Serrano 113-bis, 28006, Madrid, Spain .
    Martinez-Salazar, Javier
    Biophym, Macromolecular Physics Department, Instituto de Estructura de la Materia, CSIC, Serrano 113-bis, 28006, Madrid, Spain .
    Exploring the dynamics and interaction of a full ErbB2 receptor and Trastuzumab-Fab antibody in a lipid bilayer model using Martini coarse-grained force field.2014In: Journal of Computer-Aided Molecular Design, ISSN 0920-654X, E-ISSN 1573-4951, Vol. 28, no 11, p. 1093-1107Article in journal (Refereed)
    Abstract [en]

    Coarse grained (CG) modeling has been applied to study the influence of the Trastuzumab monoclonal antibody on the structure and dynamics of the full ErbB2 receptor dimer, including the lipid bilayer. The usage of CG models to study such complexes is almost mandatory, at present, due to the large size of the whole system. We will show that the Martini model performs satisfactorily well, giving results well-matched with those obtained by atomistic models as well as with the experimental information existing on homolog receptors. For example, the extra and intracellular domains approach the bilayer surface in both the monomer and dimer cases. The Trastuzumab-Fab hinders the interaction of the receptors with the lipid bilayer. Another interesting effect of the antibody is the disruption of the antiparallel arrangement of the juxtamembrane segments in the dimer case. These findings might help to understand the effect of the antibody on the receptor bioactivity.

  • 15.
    Franco-Gonzalez, Juan Felipe
    et al.
    BIOPHYM, Macromolecular Physics Department, Instituto de Estructura de la Materia, CSIC, Serrano 113 bis, 28006, Madrid, Spain .
    Ramos, Javier
    BIOPHYM, Macromolecular Physics Department, Instituto de Estructura de la Materia, CSIC, Serrano 113 bis, 28006, Madrid, Spain .
    Cruz, Victor L
    BIOPHYM, Macromolecular Physics Department, Instituto de Estructura de la Materia, CSIC, Serrano 113 bis, 28006, Madrid, Spain .
    Martínez-Salazar, Javier
    BIOPHYM, Macromolecular Physics Department, Instituto de Estructura de la Materia, CSIC, Serrano 113 bis, 28006, Madrid, Spain .
    Simulation of homology models for the extracellular domains (ECD) of ErbB3, ErbB4 and the ErbB2-ErbB3 complex in their active conformations.2013In: Journal of Molecular Modeling, ISSN 1610-2940, E-ISSN 0948-5023, Vol. 19, no 2, p. 931-941Article in journal (Refereed)
    Abstract [en]

    Epidermal growth factor receptors (EGFR) are associated with a number of biological processes and are becoming increasingly recognized as important therapeutic targets against cancer. In this work, we provide models based on homology for the extracellular domains (ECD) of ErbB3 and ErbB4 in their active conformations, including a Heregulin ligand, followed by further refinement of the models by molecular dynamics simulations at atomistic scale. We compare the results with a model built for ErbB2 based on crystallographic information and analyze the common features observed among members of the family, namely, the periscope movement of the dimerization arm and the hinge displacement of domain IV. Finally, we refine a model for the interaction of the ECDs corresponding to a ErbB2-ErbB3 heterodimer, which is widely recognized to have a high impact in cancer development.

  • 16.
    Gelmi, Amy
    et al.
    Linköping University, Faculty of Science & Engineering. Linköping University, Department of Physics, Chemistry and Biology, Biosensors and Bioelectronics. Imperial Coll London, England.
    Cieslar-Pobuda, Artur
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences. Silesian Technical University, Poland.
    de Muinck, Ebo
    Linköping University, Department of Medical and Health Sciences, Division of Cardiovascular Medicine. Linköping University, Faculty of Medicine and Health Sciences. Region Östergötland, Heart and Medicine Center, Department of Cardiology in Linköping. Linköping University, Center for Medical Image Science and Visualization (CMIV).
    Los, Marek Jan
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences. Pomeranian Medical University, Poland.
    Rafat, Mehrdad
    Linköping University, Department of Biomedical Engineering, Biomedical Instrumentation. Linköping University, Faculty of Science & Engineering.
    Jager, Edwin
    Linköping University, Department of Physics, Chemistry and Biology, Biosensors and Bioelectronics. Linköping University, Faculty of Science & Engineering.
    Direct Mechanical Stimulation of Stem Cells: A Beating Electromechanically Active Scaffold for Cardiac Tissue Engineering2016In: Advanced Healthcare Materials, ISSN 2192-2640, E-ISSN 2192-2659, Vol. 5, no 12, p. 1471-1480Article in journal (Refereed)
    Abstract [en]

    The combination of stem cell therapy with a supportive scaffold is a promising approach to improving cardiac tissue engineering. Stem cell therapy can be used to repair nonfunctioning heart tissue and achieve myocardial regeneration, and scaffold materials can be utilized in order to successfully deliver and support stem cells in vivo. Current research describes passive scaffold materials; here an electroactive scaffold that provides electrical, mechanical, and topographical cues to induced human pluripotent stem cells (iPS) is presented. The poly(lactic-co-glycolic acid) fiber scaffold coated with conductive polymer polypyrrole (PPy) is capable of delivering direct electrical and mechanical stimulation to the iPS. The electroactive scaffolds demonstrate no cytotoxic effects on the iPS as well as an increased expression of cardiac markers for both stimulated and unstimulated protocols. This study demonstrates the first application of PPy as a supportive electroactive material for iPS and the first development of a fiber scaffold capable of dynamic mechanical actuation.

  • 17.
    Herberthson, Magnus
    et al.
    Linköping University, Department of Mathematics, Mathematics and Applied Mathematics. Linköping University, Faculty of Science & Engineering.
    Yolcu, Cem
    Linköping University, Department of Biomedical Engineering, Division of Biomedical Engineering. Linköping University, Faculty of Science & Engineering.
    Knutsson, Hans
    Linköping University, Department of Biomedical Engineering, Division of Biomedical Engineering. Linköping University, Faculty of Science & Engineering.
    Westin, Carl-Fredrik
    Linköping University, Department of Biomedical Engineering, Division of Biomedical Engineering. Linköping University, Faculty of Science & Engineering. Harvard Med Sch, MA 02115 USA.
    Özarslan, Evren
    Linköping University, Department of Biomedical Engineering, Division of Biomedical Engineering. Linköping University, Faculty of Science & Engineering.
    Orientationally-averaged diffusion-attenuated magnetic resonance signal for locally-anisotropic diffusion2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 4899Article in journal (Refereed)
    Abstract [en]

    Diffusion-attenuated MR signal for heterogeneous media has been represented as a sum of signals from anisotropic Gaussian sub-domains to the extent that this approximation is permissible. Any effect of macroscopic (global or ensemble) anisotropy in the signal can be removed by averaging the signal values obtained by differently oriented experimental schemes. The resulting average signal is identical to what one would get if the micro-domains are isotropically (e.g., randomly) distributed with respect to orientation, which is the case for "powdered" specimens. We provide exact expressions for the orientationally-averaged signal obtained via general gradient waveforms when the microdomains are characterized by a general diffusion tensor possibly featuring three distinct eigenvalues. This extends earlier results which covered only axisymmetric diffusion as well as measurement tensors. Our results are expected to be useful in not only multidimensional diffusion MR but also solid-state NMR spectroscopy due to the mathematical similarities in the two fields.

  • 18.
    Hernandez, Frank Jeyson
    et al.
    Department of Chemical Engineering, Universitat Rovira i Virgili, Tarragona, Spain.
    Dondapati, Srujan Kumar
    Photonics and Optoelectronics Group, Physics Department and Center for Nanoscience CeNS, Ludwig-Maximilians-Universität München, Munich, Germany.
    Ozalp, V Cengiz
    Bioengineering and Bioelectrochemistry Group, Department of Chemical Engineering, Universitat Rovira i Virgili, Tarragona, Spain.
    Pinto, Alessandro
    Bioengineering and Bioelectrochemistry Group, Department of Chemical Engineering, Universitat Rovira i Virgili, Tarragona, Spain.
    O'Sullivan, Ciara K
    Bioengineering and Bioelectrochemistry Group, Department of Chemical Engineering, Universitat Rovira i Virgili, Tarragona, Spain.
    Klar, Thomas A
    Institute of Physics and Institute of Micro and Nanotechnologies, Technical University of Ilmenau, Ilmenau, Germany.
    Katakis, Ioannis
    Bioengineering and Bioelectrochemistry Group, Department of Chemical Engineering, Universitat Rovira i Virgili, Tarragona, Spain.
    Label free optical sensor for Avidin based on single gold nanoparticles functionalized with aptamers2009In: Journal of Biophotonics, ISSN 1864-063X, E-ISSN 1864-0648, Vol. 2, no 4, p. 227-231Article in journal (Refereed)
    Abstract [en]

    Optical spectroscopy of a single gold nanoparticle, functionalized with an aptamer, is used to sense the specific binding of avidin. Herewith, the field of single noble metal nanoparticle biosensors is extended to the important field of aptamer based assays. The sensitivity of this initial, but not yet optimized apta-nano-sensor is in the range of 20 nM. Due to its nanoscopic size, this single nanoparticle based apta-sensor may be used in nanoscopic volumes such as in array type assays or even inside cells.

  • 19.
    Hook, Fredrik
    et al.
    Lund University, Sweden; Chalmers, Sweden.
    Stengel, Gudrun
    Division of Solid State Physics, Lund University, Lund, SE-22100, Sweden .
    Dahlin, Andreas B.
    Lund University, Sweden; Chalmers, Sweden.
    Gunnarsson, Anders
    Division of Solid State Physics, Lund University, Lund, SE-22100, Sweden .
    Jonsson, Magnus P.
    Division of Solid State Physics, Lund University, Lund, SE-22100, Sweden .
    Jonsson, Peter
    Division of Solid State Physics, Lund University, Lund, SE-22100, Sweden .
    Reimhult, Erik
    Department of Applied Physics, Chalmers University of Technology, Göteborg, SE-41296, Sweden .
    Simonsson, Lisa
    Division of Solid State Physics, Lund University, Lund, SE-22100, Sweden .
    Svedhem, Sofia
    Department of Applied Physics, Chalmers University of Technology, Göteborg, SE-41296, Sweden .
    Supported lipid bilayers, tethered lipid vesicles, and vesicle fusion investigated using gravimetric, plasmonic, and microscopy techniques2008In: Biointerphases, ISSN 1934-8630, E-ISSN 1559-4106, Vol. 3, no 2, p. FA108-FA116Article in journal (Refereed)
    Abstract [en]

    This article summarizes our most recent contributions to the rapidly growing field of supported lipid assemblies with emphasis on current studies addressing both fundamental and applied aspects of supported lipid bilayer (SLB) and tethered lipid vesicles (TLVs) to be utilized in sensing applications. The new insights obtained from combining the quartz crystal microbalance with dissipation monitoring technique with surface plasmon resonance are described, and we also present recent studies in which nanoplasmonic sensing has been used in studies of SLBs and TLVs. To gain full control over the spatial arrangement of TLVs in both two and three dimensions, we have developed a method for site-selective and sequence-specific sorting of DNA-tagged vesicles to surfaces modified with complementary DNA. The combination of this method with nanoplasmonic sensing formats is covered as well as the possibility of using DNA-modified vesicles for the detection of unlabeled DNA targets on the single-molecule level. Finally, a new method for membrane fusion induced by hybridization of vesicle-anchored DNA is demonstrated, including new results on content mixing obtained with vesicle populations encapsulating short, complementary DNA strands.

  • 20.
    Janssen, Xander J. A.
    et al.
    Delft University of Technology, Netherlands.
    Jonsson, Magnus P.
    Delft University of Technology, Netherlands.
    Plesa, Calin
    Delft University of Technology, Netherlands.
    Soni, Gautam V.
    Delft University of Technology, Netherlands.
    Dekker, Cees
    Delft University of Technology, Netherlands.
    Dekker, Nynke H.
    Delft University of Technology, Netherlands.
    Rapid manufacturing of low-noise membranes for nanopore sensors by trans-chip illumination lithography2012In: Nanotechnology, ISSN 0957-4484, E-ISSN 1361-6528, Vol. 23, no 47, article id 475302Article in journal (Refereed)
    Abstract [en]

    In recent years, the concept of nanopore sensing has matured from a proof-of-principle method to a widespread, versatile technique for the study of biomolecular properties and interactions. While traditional nanopore devices based on a nanopore in a single layer membrane supported on a silicon chip can be rapidly fabricated using standard microfabrication methods, chips with additional insulating layers beyond the membrane region can provide significantly lower noise levels, but at the expense of requiring more costly and time-consuming fabrication steps. Here we present a novel fabrication protocol that overcomes this issue by enabling rapid and reproducible manufacturing of low-noise membranes for nanopore experiments. The fabrication protocol, termed trans-chip illumination lithography, is based on illuminating a membrane-containing wafer from its backside such that a photoresist (applied on the wafers top side) is exposed exclusively in the membrane regions. Trans-chip illumination lithography permits the local modification of membrane regions and hence the fabrication of nanopore chips containing locally patterned insulating layers. This is achieved while maintaining a well-defined area containing a single thin membrane for nanopore drilling. The trans-chip illumination lithography method achieves this without relying on separate masks, thereby eliminating time-consuming alignment steps as well as the need for a mask aligner. Using the presented approach, we demonstrate rapid and reproducible fabrication of nanopore chips that contain small (12 mu m x 12 mu m) free-standing silicon nitride membranes surrounded by insulating layers. The electrical noise characteristics of these nanopore chips are shown to be superior to those of simpler designs without insulating layers and comparable in quality to more complex designs that are more challenging to fabricate.

  • 21.
    Johansson, Patrik
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, The Institute of Technology.
    Jullesson, David
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, The Institute of Technology.
    Elfwing, Anders
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Liin, Sara
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences.
    Musumeci, Chiara
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Zeglio, Erica
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Elinder, Fredrik
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences.
    Solin, Niclas
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Inganäs, Olle
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Electronic polymers in lipid membranes2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, no 11242Article in journal (Refereed)
    Abstract [en]

    Electrical interfaces between biological cells and man-made electrical devices exist in many forms, but it remains a challenge to bridge the different mechanical and chemical environments of electronic conductors (metals, semiconductors) and biosystems. Here we demonstrate soft electrical interfaces, by integrating the metallic polymer PEDOT-S into lipid membranes. By preparing complexes between alkyl-ammonium salts and PEDOT-S we were able to integrate PEDOT-S into both liposomes and in lipid bilayers on solid surfaces. This is a step towards efficient electronic conduction within lipid membranes. We also demonstrate that the PEDOT-S@alkyl-ammonium: lipid hybrid structures created in this work affect ion channels in the membrane of Xenopus oocytes, which shows the possibility to access and control cell membrane structures with conductive polyelectrolytes.

  • 22.
    Johansson-Åkhe, Isak
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Mirabello, Claudio
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Wallner, Björn
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Predicting protein-peptide interaction sites using distant protein complexes as structural templates2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 4267Article in journal (Refereed)
    Abstract [en]

    Protein-peptide interactions play an important role in major cellular processes, and are associated with several human diseases. To understand and potentially regulate these cellular function and diseases it is important to know the molecular details of the interactions. However, because of peptide flexibility and the transient nature of protein-peptide interactions, peptides are difficult to study experimentally. Thus, computational methods for predicting structural information about protein-peptide interactions are needed. Here we present InterPep, a pipeline for predicting protein-peptide interaction sites. It is a novel pipeline that, given a protein structure and a peptide sequence, utilizes structural template matches, sequence information, random forest machine learning, and hierarchical clustering to predict what region of the protein structure the peptide is most likely to bind. When tested on its ability to predict binding sites, InterPep successfully pinpointed 255 of 502 (50.7%) binding sites in experimentally determined structures at rank 1 and 348 of 502 (69.3%) among the top five predictions using only structures with no significant sequence similarity as templates. InterPep is a powerful tool for identifying peptide-binding sites; with a precision of 80% at a recall of 20% it should be an excellent starting point for docking protocols or experiments investigating peptide interactions. The source code for InterPred is available at http://wallnerlab.org/InterPep/.

  • 23.
    Jonsson, Magnus P.
    et al.
    Department of Applied Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
    Dahlin, Andreas B.
    Department of Applied Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
    Feuz, Laurent
    Department of Applied Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
    Petronis, Sarunas
    Department of Applied Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
    Hook, Fredrik
    Department of Applied Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
    Locally Functionalized Short-Range Ordered Nanoplasmonic Pores for Bioanalytical Sensing2010In: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 82, no 5, p. 2087-2094Article in journal (Refereed)
    Abstract [en]

    Nanoplasmonic sensors based on short-range ordered nano-holes in thin metal films and discrete metal nanoparticles are known to provide similar sensing performance. However, a perforated metal film is unique in the sense that the holes can be designed to penetrate through the substrate, thereby also fulfilling the role of nanofluidic channels. This paper presents a bioanalytical sensing concept based on short-range ordered nanoplasmonic pores (diameter 150 nm) penetrating through a thin (around 250 nm) multilayer membrane composed of gold and silicon nitride (SiN) that is Supported on a Si wafer. Also, a fabrication scheme that enables parallel production of multiple (more than 50) separate sensor chips or more than 1000 separate nanoplasmonic membranes on it single wafer is presented. Together with the localization of the sensitivity to within such short-range ordered nanoholes, the structure provides it two-dimensional nanofluidic network, sized in the order of 100 x 100 mu m(2), with nanoplasmon active regions localized to each individual nanochannel. A material-specific surface-modification scheme was developed to promote specific binding of target molecules on the optically active gold regions only, while suppressing nonspecific adsorption on SiN. Using this protocol, and by monitoring the temporal variation in the plasmon resonance of the structure, we demonstrate flow-through nanoplasmonic sensing of specific biorecognition reactions with a signal-to-noise ratio of around 50 at a temporal resolution below 190 ms. With flow, the uptake was demonstrated to be at least 1 order of magnitude faster than under stagnant conditions, while still keeping the sample consumption at a minimum.

  • 24.
    Jonsson, Magnus P.
    et al.
    DiVision of Solid State Physics, Lund UniVersity, SE-22100 Lund, Sweden.
    Jonsson, Peter
    DiVision of Solid State Physics, Lund UniVersity, SE-22100 Lund, Sweden.
    Dahlin, Andreas B.
    DiVision of Solid State Physics, Lund UniVersity, SE-22100 Lund, Sweden.
    Hook, Fredrik
    DiVision of Solid State Physics, Lund UniVersity, SE-22100 Lund, Sweden.
    Supported lipid bilayer formation and lipid-membrane-mediated biorecognition reactions studied with a new nanoplasmonic sensor template2007In: Nano letters (Print), ISSN 1530-6984, E-ISSN 1530-6992, Vol. 7, no 11, p. 3462-3468Article in journal (Refereed)
    Abstract [en]

    This paper presents the use of the localized surface plasmon resonance (LSPR) sensor concept to probe the formation of macroscopic and laterally mobile supported lipid bilayers (SLBs) on SiO(x)-encapsulated nanohole-containing Au and Ag films. A comparison between Au- and Ag-based sensor templates demonstrates a higher sensitivity for Au-based templates with respect to both bulk and interfacial refractive index (RI) changes in aqueous solution. The lateral mobility of SLBs formed on the SiO(x)-rencapsulated nanohole templates was analyzed using fluorescence recovery after photobleaching (FRAP), demonstrating essentially complete (greater than96%) recovery, but a reduction in diffusivity of about 35% compared with SLBs formed on flat SiO(x) substrates. Furthermore, upon SLB formation, the temporal variation in extinction peak position of the LSPR active templates display a characteristic shape, illustrating what, to the best of our knowledge, is the first example where the nanoplasmonic concept is shown capable of probing biomacromolecular structural changes without the introduction of labels. With a signal-to-noise ratio better than 5 X 10(2) upon protein binding to the cell-membrane mimics, the sensor concept is also proven competitive with state-of-the-art label-free sensors.

  • 25.
    Jonsson, Magnus P.
    et al.
    Division of Solid State Physics, Department of Physics, Lund University, Lund, Sweden..
    Jonsson, Peter
    Division of Solid State Physics, Department of Physics, Lund University, Lund, Sweden..
    Hook, Fredrik
    Division of Solid State Physics, Department of Physics, Lund University, Lund, Sweden..
    Simultaneous Nanoplasmonic and Quartz Crystal Microbalance Sensing: Analysis of Biomolecular Conformational Changes and Quantification of the Bound Molecular Mass2008In: Analytical Chemistry, ISSN 0003-2700, E-ISSN 1520-6882, Vol. 80, no 21, p. 7988-7995Article in journal (Refereed)
    Abstract [en]

    This paper presents a study of supported lipid bilayer (SIB) formation and subsequent protein binding using a sensor that combines localized surface plasmon resonance (LSPR) and quartz crystal microbalance with dissipation (QCM-D) monitoring. The LSPR activity arises from silicon oxide (SiOx) coated nanometric apertures in a thin gold film, which also serves as the active electrode of a QCM-D crystal. Both transducer principles provide signatures for the formation of a SLB upon adsorption and subsequent rupture of adsorbed lipid vesicles. However, the two techniques are sensitive over different regions of the sample: LSPR primarily inside and on the rim of the holes and QCM-D primarily on the planar areas between the holes. Although the dimension of the lipid vesicles is on the same order as the dimension of the nanoholes, it is concluded from the response of the combined system that vesicle rupture in the nanoholes and on the planar region between the holes is synchronized. Furthermore, by determining the thickness of the SLB from the QCM-D response, the characteristic decay length of the LSPR field intensity could be determined. This made it possible not only to determine the mass and refractive index of the homogeneous SLB but also to postulate a generic means to quantify the LSPR response in terms of mass-uptake also for nonhomogeneous films. This is exemplified by measuring the adsorbed lipid mass during vesicle adsorption, yielding the critical lipid vesicle coverage at which spontaneous rupture into a planar bilayer occurs. The generic applicability and versatility of the method is demonstrated from specific protein binding to a functionalized SLB. From the absolute refractive index of the protein, provided from the LSPR data alone, it was possible to determine both the effective thickness of the protein film and the molecular mass (or number) of bound protein.

  • 26.
    Jonsson, Peter
    et al.
    Department of Applied Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
    Jonsson, Magnus P.
    Department of Applied Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
    Hook, Fredrik
    Department of Applied Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
    Sealing of Submicrometer Wells by a Shear-Driven Lipid Bilayer2010In: Nano letters (Print), ISSN 1530-6984, E-ISSN 1530-6992, Vol. 10, no 5, p. 1900-1906Article in journal (Refereed)
    Abstract [en]

    A supported lipid bilayer (SLB) was formed in a microfluidic channel by vesicle fusion. The SLB, formed on a flat part of the surface, was driven by the shear forces of a bulk flow above the SLB to a part of the surface with embedded submicrometer wells. When using a bulk solution with a pH of 9.5 the advancing lipid bilayer sealed the wells, creating free-spanning membranes, whereas at a pH of 8.0 the SLB instead followed the contour of the wells.

  • 27.
    Kiflemariam, Jordanos
    Linköping University, Department of Science and Technology.
    A Biomimetic Manganese Model for Artificial Photosynthesis: Q-band Electron Paramagnetic Resonance Study of a Novel Mn2(II,III) Complex2005Independent thesis Basic level (professional degree), 20 points / 30 hpStudent thesis
    Abstract [en]

    In natural oxygen-producing photosynthesis solar energy is stored as chemical energy, in carbohydrates, fats and amino acids, using water as electron source. The large transmembrane protein complex, PSII, is the key enzyme in the light-driven reactions. Water oxidation is accomplished by a triad in PSII in which the Mn-cluster plays an important role. In the artificial photosynthetic system, nature’s photosynthesis will be mimicked such that hydrogen, a sustainable energy source, can be produced from solar energy and water alone. Since water oxidiation requires the catalytic activity of a Mn-cluster in photosynthesis, different artificially constructed manganese complexes are investigated.

    The dinuclear ([Mn2(II,III)L(µ-OAc)2]ClO4), where L is the X-anion of 2-(N,N-Bis(2-methylpyridyl)aminomethyl)-6-(N-(3,5-ditert-butylbenzyl-2-hydroxy)-N-(pyridylmethyl)aminomethyl)-4-methylphenol, an unsymmetric ligand with two coordinating phenolate groups, has been studied. The two Mn-ions are linked via a mono-µ-oxo bridge and two acetate ligands. Q-band Electron Paramagnetic Resonance was conducted on the Unsymmetric Mn2(II,III) Complex. Aquired results show that the complex has a 2600 Gauss broad signal (11 400-14 000 Gauss) with 14-17 lines at g~2 and hyperfines of 120 Gauss. This is consistent with previous X-band studies. Q-band spectra of the Unsymmetric Mn(II,III) display increased hyperfine resolution compared to Qband spectra of the symmetric complex, Mn2(bpmp)(µ-OAC)2. This is noticeable since Unsymmetric Mn2(II,III) and Mn2 (bpmp)(µ-OAC)2 partly overlap in low-frequency experiments (X-band EPR).

    Further investigations are yet to be expected. Nevertheless, the conducted thesis study provides important knowledge in the futuristic goal of building an artificial super-complex.

  • 28.
    Klenkar, Goran
    Linköping University, Department of Physics, Chemistry and Biology, Sensor Science and Molecular Physics . Linköping University, The Institute of Technology.
    Protein Microarray Chips2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Life is a thing taken for granted by most. However, it is the life-long quest of many to unravel the mysteries of it. Understanding and characterizing the incomprehensively complex molecular interaction networks within a biological organism, which defines that organism, is a vital prerequisite to understand life itself. Already, there has been a lot of research conducted and a large knowledge has been obtained about these pathways over, especially, the last century. We have seen the fruits of these labors in e.g. the development of medicines which have been able to cure or at least arrest many diseases and conditions. However, many diseases are still incurable (e.g. cancer) and a lot more work is still needed for understanding them fully and designing successful treatments. This work describes a generic analytical tool platform for aiding in more efficient (bio)molecular interaction mapping analyses; protein microarray chips. Microarray chips are surfaces with micrometer sized features with the possibility of studying the interactions of many (thousands to tens of thousands) (bio)molecules in parallel. This allows for a higher throughput of analyses to be performed at a reduced time and cost. Protein microarrays have been around for approximately a decade, following in the footsteps of the, so far, more successfully used DNA microarrays (developed in the 1990s). Microarrays of proteins are more difficult to produce because of the more complex nature of proteins as compared to DNA. In our work we have constructed model surfaces which allow for the stable, highly oriented, and functional immobilization of proteins in an array format. Our capture molecules are based on multivalent units of the chelator nitrilotriacetic acid (NTA), which is able to bind histidine-tagged proteins. Furthermore, we have explored an approach for studying lipid membrane bound systems, e.g. receptor-ligand interactions, in a parallelized, microarray format. The approach relies on the addressable, DNA-mediated adsorption of tagged lipid vesicles. In an analogous work we have used the protein microarray concept for the detection of four common narcotics (heroin, amphetamine, ecstasy, and cocaine). The detection is based on the displacement of loosely bound antibodies from surface array positions upon injection of a specific target analyte, i.e. a narcotic substance. The proof-of-concept chip can easily be expanded to monitor many more narcotic substances. In addition, we have also been able to simultaneously detect the explosive trinitrotoluene (TNT) along with the narcotics, showing that the chip is a versatile platform for the detection of virtually any type of harmful or illegal compound. This type of biosensor system is potentially envisaged to be used in the fight against crime, terrorism, drug abuse etc. Infrared reflection absorption spectroscopy together with ellipsometry has been used to characterize molecular layers used in the fabrication processes of the microarray features. Imaging surface plasmon resonance operating in the ellipsometric mode is subsequently used for functional evaluation of the microarrays using a well-defined receptor-ligand model system. This approach allows simultaneous and continuous monitoring of binding events taking place in multiple regions of interest on the microarray chip. A common characteristic of all the instrumentation used is that there is no requirement for labeling of the biomolecules to be detected, e.g. with fluorescent or radioactive probes. This feature allows for a flexible assay design and the use of more native proteins, without any time-consuming pretreatments.

    List of papers
    1. Piezo Dispensed Microarray of Multivalent Chelating Thiols for Dissecting Complex Protein-Protein Interactions
    Open this publication in new window or tab >>Piezo Dispensed Microarray of Multivalent Chelating Thiols for Dissecting Complex Protein-Protein Interactions
    Show others...
    2006 (English)In: Analytical Chemistry, ISSN 0003-2700, Vol. 78, no 11, p. 3643-3650Article in journal (Refereed) Published
    Abstract [en]

    The fabrication of a novel biochip, designed for dissection of multiprotein complex formation, is reported. An array of metal chelators has been produced by piezo dispensing of a bis-nitrilotriacetic acid (bis-NTA) thiol on evaporated gold thin films, prestructured with a microcontact printed grid of eicosanethiols. The bis-NTA thiol is mixed in various proportions with an inert, tri(ethylene glycol) hexadecane thiol, and the thickness and morphological homogeneity of the dispensed layers are characterized by imaging ellipsometry before and after back-filling with the same inert thiol and subsequent rinsing. It is found that the dispensed areas display a monotonic increase in thickness with increasing molar fraction of bis-NTA in the dispensing solution, and they are consistently a few Ångströms thicker than those prepared at the same molar fraction by solution self-assembly under equilibrium-like conditions. The bulkiness of the bis-NTA tail group and the short period of time available for chemisorption and in-plane organization of the dispensed thiols are most likely responsible for the observed difference in thickness. Moreover, the functional properties of this biochip are demonstrated by studying multiple protein−protein interactions using imaging surface plasmon resonance. The subunits of the type I interferon receptor are immobilized as a composition array determined by the surface concentration of bis-NTA in the array elements. Ligand dissociation kinetics depends on the receptor surface concentration, which is ascribed to the formation of a ternary complex by simultaneous interaction of the ligand with the two receptor subunits. Thus, multiplexed monitoring of binding phenomena at various compositions (receptor densities) offers a powerful tool to dissect protein−protein interactions.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-14515 (URN)10.1021/ac060024+ (DOI)
    Available from: 2007-05-22 Created: 2007-05-22 Last updated: 2009-05-22
    2. Differential Protein Assembly on Micropatterned Surfaces with Tailored Molecular and Surface Multivalency
    Open this publication in new window or tab >>Differential Protein Assembly on Micropatterned Surfaces with Tailored Molecular and Surface Multivalency
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    2006 (English)In: ChemBioChem, ISSN 1439-4227, Vol. 7, no 9, p. 1325-1329Article in journal (Refereed) Published
    Keywords
    arrays, multivalent interactions, nitrilotriacetic acid, protein-protein interactions, surface plasmon resonance
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-14516 (URN)10.1002/cbic.200600176 (DOI)
    Available from: 2007-05-22 Created: 2007-05-22 Last updated: 2009-06-08
    3. Multivalent Self-Assembled Monolayers with Terminal Mono-, Bis-, and Tris-nitrilotriacetic Acid Groups: Characterization and Application
    Open this publication in new window or tab >>Multivalent Self-Assembled Monolayers with Terminal Mono-, Bis-, and Tris-nitrilotriacetic Acid Groups: Characterization and Application
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    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:liu:diva-14517 (URN)
    Available from: 2007-05-22 Created: 2007-05-22 Last updated: 2010-01-13
    4. A Microarray for Addressable Adsorption of Lipid Vesicles and Subsequent Protein Interaction Studies
    Open this publication in new window or tab >>A Microarray for Addressable Adsorption of Lipid Vesicles and Subsequent Protein Interaction Studies
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    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:liu:diva-14518 (URN)
    Available from: 2007-05-22 Created: 2007-05-22 Last updated: 2010-01-13
    5. A Microarray Chip for Label-Free Detection of Narcotics
    Open this publication in new window or tab >>A Microarray Chip for Label-Free Detection of Narcotics
    2008 (English)In: Analytical and Bioanalytical Chemistry, ISSN 1618-2642, E-ISSN 1618-2650, Vol. 391, no 5, p. 1679-1688Article in journal (Refereed) Published
    Abstract [en]

    A protein array chip for label-free optical detection of low molecular weight compounds has been developed. As a proof of principle, the chip is proven capable of rapidly (approximately 1 min) determining hits from aqueous cocktails composed of four common narcotics, cocaine, ecstasy, heroin, and amphetamine, using imaging surface plasmon resonance (SPR) as the detection principle. The chip is produced by injecting a mixture of antibodies and letting them self-sort and bind to narcotic analog coupled proteins already present in a predefined pattern on the supporting substrate. An indirect detection method, where antibodies are displaced from the surface upon recognition of their corresponding narcotics, is used to obtain the optical contrast and thus a detectable SPR and/or ellipsometric signal. Two types of readouts are possible from the present setup: intensity SPR images and SPR/ellipsometric sensorgrams. Positive hits were routinely obtained for analyte concentrations of 50 pg/μL and the limit of detection, without any parameter optimizations, seems to fall in the range 0.5 pg/μL (1.4 nM) for heroin, 2.5 pg/μL (8.2 nM) for cocaine, and 5 pg/μL for the other two narcotics (26 nM for ecstasy and 37 nM for amphetamine). With improved readout possibilities (sampling frequency), signal evaluation algorithms, and antibody–antigen design strategies, we believe this limit can be further improved. The chip is shown to work for many measurement cycles with excellent reproducibility. Moreover, with a more advanced fluidic system, excess injected antibodies could be collected and reused for many cycles, which could make the running costs of the system very low. The chip is in no way limited to detection of narcotics. Other low molecular weight compounds could easily be detected on the same chip. For example, trinitrotoluene detection has already been demonstrated using our chip. Possible areas of application for the system are therefore envisaged in airport and underground transport security, customs, drug interdiction, forensics, and as warning alerts on military equipment and personnel.

    Keywords
    Protein microarray, Imaging surface plasmon resonance, Imaging ellipsometry, Narcotics trace detection, Biosensors, Antibody displacement
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:liu:diva-14519 (URN)10.1007/s00216-008-1839-9 (DOI)
    Available from: 2007-05-22 Created: 2007-05-22 Last updated: 2017-12-13
  • 29.
    Liin, Sara
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences. University of Miami, FL, USA.
    Larsson, Johan
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences.
    Berro-Soria, Rene
    University of Miami, FL, USA.
    Hjorth Bentzen, Bo
    The Danish Arrhythmia Research Centre, University of Copenhagen, Copenhagen, Denmark; Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark.
    Larson, H. Peter
    University of Miami, FL, USA.
    Fatty acid analogue N-arachidonoyl taurine restores function of I-Ks channels with diverse long QT mutations2016In: eLIFE, E-ISSN 2050-084X, Vol. 5, article id e20272Article in journal (Refereed)
    Abstract [en]

    About 300 loss-of-function mutations in the I-Ks channel have been identified in patients with Long QT syndrome and cardiac arrhythmia. How specific mutations cause arrhythmia is largely unknown and there are no approved I-Ks channel activators for treatment of these arrhythmias. We find that several Long QT syndrome-associated IKs channel mutations shift channel voltage dependence and accelerate channel closing. Voltage-clamp fluorometry experiments and kinetic modeling suggest that similar mutation-induced alterations in IKs channel currents may be caused by different molecular mechanisms. Finally, we find that the fatty acid analogue N-arachidonoyl taurine restores channel gating of many different mutant channels, even though the mutations are in different domains of the IKs channel and affect the channel by different molecular mechanisms. N-arachidonoyl taurine is therefore an interesting prototype compound that may inspire development of future IKs channel activators to treat Long QT syndrome caused by diverse IKs channel mutations.

  • 30.
    Lindgren, Mikael
    et al.
    Department of Physics, Norwegian University of Science and Technology, 7491 Trondheim, Norway.
    Sörgjerd, Karin
    Linköping University, Department of Physics, Chemistry and Biology, Biochemistry. Linköping University, The Institute of Technology.
    Hammarström, Per
    Linköping University, Department of Physics, Chemistry and Biology, Biochemistry. Linköping University, The Institute of Technology.
    Detection and characterization of aggregates, prefibrillar amyloidogenic oligomers, and protofibrils using fluorescence spectroscopy2005In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 88, no 6, p. 4200-4212Article in journal (Refereed)
    Abstract [en]

    Transthyretin (TTR) is a protein linked to a number of different amyloid diseases including senile systemic amyloidosis and familial amyloidotic polyneuropathy. The transient nature of oligomeric intermediates of misfolded TTR that later mature into fibrillar aggregates makes them hard to study, and methods to study these species are sparse. In this work we explore a novel pathway for generation of prefibrillar aggregates of TTR, which provides important insight into TTR misfolding. Prefibrillar amyloidogenic oligomers and protofibrils of misfolded TTR were generated in vitro through induction of the molten globule type A-state from acid unfolded TTR through the addition of NaCl. The aggregation process produced fairly monodisperse oligomers (300–500 kD) within 2 h that matured after 20 h into larger spherical clusters (30–50 nm in diameter) and protofibrils as shown by transmission electron microscopy. Further maturation of the aggregates showed shrinkage of the spheres as the fibrils grew in length, suggesting a conformational change of the spheres into more rigid structures. The structural and physicochemical characteristics of the aggregates were investigated using fluorescence, circular dichroism, chemical cross-linking, and transmission electron microscopy. The fluorescent dyes 1-anilinonaphthalene-8-sulfonate (ANS), 4-4-bis-1-phenylamino-8-naphthalene sulfonate (Bis-ANS), 4-(dicyanovinyl)-julolidine (DCVJ), and thioflavin T (ThT) were employed in both static and kinetic assays to characterize these oligomeric and protofibrillar states using both steady-state and time-resolved fluorescence techniques. DCVJ, a molecular rotor, was employed for the first time for studies of an amyloidogenic process and is shown useful for detection of the early steps of the oligomerization process. DCVJ bound to the early prefibrillar oligomers (300–500 kD) with an apparent dissociation constant of 1.6 mM, which was slightly better than for ThT (6.8 mM). Time-resolved fluorescence anisotropy decay of ANS was shown to be a useful tool for giving further structural and kinetic information of the oligomeric aggregates. ThT dramatically increases its fluorescence quantum yield when bound to amyloid fibrils; however, the mechanism behind this property is unknown. Data from this work suggest that unbound ThT is also intrinsically quenched and functions similarly to a molecular rotor, which in combination with its environmental dependence provides a blue shift to the characteristic 482nm wavelength when bound to amyloid fibrils.

  • 31.
    Magnusson, Karin
    Linköping University, Department of Physics, Chemistry and Biology.
    DNA chips with conjugated polyelectrolytes as fluorophore in fluorescence amplification mode2008Independent thesis Basic level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The aim of this diploma work is to improve selectivity and sensitivity in DNA-chips by utilizing fluorescence resonance energy transfer (FRET) between conjugated polyelectrolytes (CPEs) and fluorophores.

    Leclerc and co-workers have presented successful results from studies of super FRET between fluorophore tagged DNA and a CPE during hybridisation of the double strand. Orwar and co-workers have constructed a DNA-chip using standard photo lithography creating a pattern of the hydrophobic photoresist SU-8 and cholesterol tagged DNA (chol-DNA). This diploma work will combine and modify these two ideas to fabricate a improved DNA-chip.

    Immobilizing of DNA onto surface has been done by using soft lithography. Hydrophobic pattern arises from the poly(dimethylsiloxane) (PDMS) stamp. The hydrophobic pattern will attract chol-DNA that is adsorbed to the chip. Different sets of fluorophores are covalently bound to the DNA and adding CPEs to the complex will make FRET occur between CPE and bound fluorophore.

    We will here show that the specificity in DNA hybridization by using PDMS patterning was high. FRET clearly occurred, especially with the CPEs as donor to the fluorophore Cy5. The intensity of FRET was higher when the fluorophore and the CPE were conjugated to the same DNA strand. The largest difference in FRET intensity between double stranded and single stranded complexes was observed with the CPE tPOMT. Super FRET has been observed but not yet fully proved. The FRET efficiency was lower with the fluorophore Alexa350 as donor compared to the Cy5/CPE complex. Most of the energy transferred from Alexa350 was extinguished by quenching.

  • 32.
    Mayzel, Maxim
    et al.
    University of Gothenburg, Sweden.
    Ahlner, Alexandra
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Lundström, Patrik
    Linköping University, Department of Physics, Chemistry and Biology, Chemistry. Linköping University, Faculty of Science & Engineering.
    Orekhov, Vladislav Y.
    University of Gothenburg, Sweden.
    Measurement of protein backbone (CO)-C-13 and N-15 relaxation dispersion at high resolution2017In: Journal of Biomolecular NMR, ISSN 0925-2738, E-ISSN 1573-5001, Vol. 69, no 1Article in journal (Refereed)
    Abstract [en]

    Peak overlap in crowded regions of two-dimensional spectra prevents characterization of dynamics for many sites of interest in globular and intrinsically disordered proteins. We present new three-dimensional pulse sequences for measurement of Carr-Purcell-Meiboom-Gill relaxation dispersions at backbone nitrogen and carbonyl positions. To alleviate increase in the measurement time associated with the additional spectral dimension, we use non-uniform sampling in combination with two distinct methods of spectrum reconstruction: compressed sensing and co-processing with multi-dimensional decomposition. The new methodology was validated using disordered protein CD79A from B-cell receptor and an SH3 domain from Abp1p in exchange between its free form and bound to a peptide from the protein Ark1p. We show that, while providing much better resolution, the 3D NUS experiments give the similar accuracy and precision of the dynamic parameters to ones obtained using traditional 2D experiments. Furthermore, we show that jackknife resampling of the spectra yields robust estimates of peak intensities errors, eliminating the need for recording duplicate data points.

  • 33.
    McPhillips, John
    et al.
    Queens University of Belfast, North Ireland.
    Murphy, Antony
    Queens University of Belfast, North Ireland.
    Jonsson, Magnus P.
    Department of Applied Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
    Hendren, William R.
    Queens University of Belfast, North Ireland.
    Atkinson, Ronald
    Queens University of Belfast, North Ireland.
    Hook, Fredrik
    Department of Applied Physics, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.
    Zayats, Anatoly V.
    Queens University of Belfast, North Ireland.
    Pollard, Robert J.
    Queens University of Belfast, North Ireland.
    High-Performance Biosensing Using Arrays of Plasmonic Nanotubes2010In: ACS Nano, ISSN 1936-0851, E-ISSN 1936-086X, Vol. 4, no 4, p. 2210-2216Article in journal (Refereed)
    Abstract [en]

    We show that aligned gold nanotube arrays capable of supporting plasmonic resonances can be used as high performance refractive index sensors in biomolecular binding reactions. A methodology to examine the sensing ability of the inside and outside walls of the nanotube structures is presented. The sensitivity of the plasmonic nanotubes is found to increase as the nanotube walls are exposed, and the sensing characteristic of the inside and outside walls is shown to be different. Finite element simulations showed good qualitative agreement with the observed behavior. Free standing gold nanotubes displayed bulk sensitivities in the region of 250 nm per refractive index unit and a signal-to-noise ratio better than 1000 upon protein binding which is highly competitive with state-of-the-art label-free sensors.

  • 34.
    Melianas, Armantas
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Pranculis, Vytenis
    Center for Physical Sciences and Technology, Vilnius, Lithuania.
    Spoltore, Donato
    Dresden Integrated Center for Applied Physics and Photonic Materials (IAPP) and Institute for Applied Physics, Technische Universität Dresden, Dresden, Germany.
    Benduhn, Johannes
    Dresden Integrated Center for Applied Physics and Photonic Materials (IAPP) and Institute for Applied Physics, Technische Universität Dresden, Dresden, Germany.
    Inganäs, Olle
    Linköping University, Department of Physics, Chemistry and Biology, Biomolecular and Organic Electronics. Linköping University, Faculty of Science & Engineering.
    Gulbinas, Vidmantas
    Center for Physical Sciences and Technology, Vilnius, Lithuania / Department of General Physics and Spectroscopy, Faculty of Physics, Vilnius University, Vilnius, Lithuania.
    Vandewal, Koen
    Dresden Integrated Center for Applied Physics and Photonic Materials (IAPP) and Institute for Applied Physics, Technische Universität Dresden, Dresden, Germany.
    Kemerink, Martijn
    Linköping University, Department of Physics, Chemistry and Biology, Complex Materials and Devices. Linköping University, Faculty of Science & Engineering.
    Charge Transport in Pure and Mixed Phases in Organic Solar Cells2017In: Advanced Energy Materials, ISSN 1614-6840, Vol. 7, no 20Article in journal (Refereed)
    Abstract [en]

    In organic solar cells continuous donor and acceptor networks are considered necessary for charge extraction, whereas discontinuous neat phases and molecularly mixed donor–acceptor phases are generally regarded as detrimental. However, the impact of different levels of domain continuity, purity, and donor–acceptor mixing on charge transport remains only semiquantitatively described. Here, cosublimed donor–acceptor mixtures, where the distance between the donor sites is varied in a controlled manner from homogeneously diluted donor sites to a continuous donor network are studied. Using transient measurements, spanning from sub-picoseconds to microseconds photogenerated charge motion is measured in complete photovoltaic devices, to show that even highly diluted donor sites (5.7%–10% molar) in a buckminsterfullerene matrix enable hole transport. Hopping between isolated donor sites can occur by long-range hole tunneling through several buckminsterfullerene molecules, over distances of up to ≈4 nm. Hence, these results question the relevance of “pristine” phases and whether a continuous interpenetrating donor–acceptor network is the ideal morphology for charge transport.

  • 35.
    Mirabello, Claudio
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Wallner, Björn
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    InterPred: A pipeline to identify and model protein-protein interactions2017In: Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, E-ISSN 1097-0134, Vol. 85, no 6, p. 1159-1170Article in journal (Refereed)
    Abstract [en]

    Protein-protein interactions (PPI) are crucial for protein function. There exist many techniques to identify PPIs experimentally, but to determine the interactions in molecular detail is still difficult and very time-consuming. The fact that the number of PPIs is vastly larger than the number of individual proteins makes it practically impossible to characterize all interactions experimentally. Computational approaches that can bridge this gap and predict PPIs and model the interactions in molecular detail are greatly needed. Here we present InterPred, a fully automated pipeline that predicts and model PPIs from sequence using structural modeling combined with massive structural comparisons and molecular docking. A key component of the method is the use of a novel random forest classifier that integrate several structural features to distinguish correct from incorrect protein-protein interaction models. We show that InterPred represents a major improvement in protein-protein interaction detection with a performance comparable or better than experimental high-throughput techniques. We also show that our full-atom protein-protein complex modeling pipeline performs better than state of the art protein docking methods on a standard benchmark set. In addition, InterPred was also one of the top predictors in the latest CAPRI37 experiment. InterPred source code can be downloaded from http://wallnerlab.org/InterPred (C) 2017 Wiley Periodicals, Inc.

  • 36.
    Mirabello, Claudio
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Wallner, Björn
    Linköping University, Department of Physics, Chemistry and Biology, Bioinformatics. Linköping University, Faculty of Science & Engineering.
    Topology independent structural matching discovers novel templates for protein interfaces2018In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 34, no 17, p. 787-794Article in journal (Refereed)
    Abstract [en]

    Motivation: Protein-protein interactions (PPI) are essential for the function of the cellular machinery. The rapid growth of protein-protein complexes with known 3D structures offers a unique opportunity to study PPI to gain crucial insights into protein function and the causes of many diseases. In particular, it would be extremely useful to compare interaction surfaces of monomers, as this would enable the pinpointing of potential interaction surfaces based solely on the monomer structure, without the need to predict the complete complex structure. While there are many structural alignment algorithms for individual proteins, very few have been developed for protein interfaces, and none that can align only the interface residues to other interfaces or surfaces of interacting monomer subunits in a topology independent (non-sequential) manner. Results: We present InterComp, a method for topology and sequence-order independent structural comparisons. The method is general and can be applied to various structural comparison applications. By representing residues as independent points in space rather than as a sequence of residues, InterComp can be applied to a wide range of problems including interface-surface comparisons and interface-interface comparisons. We demonstrate a use-case by applying InterComp to find similar protein interfaces on the surface of proteins. We show that InterComp pinpoints the correct interface for almost half of the targets (283 of 586) when considering the top 10 hits, and for 24% of the top 1, even when no templates can be found with regular sequence-order dependent structural alignment methods.

  • 37.
    Moy, Austin J.
    et al.
    University of California, Irvine, USA.
    Capulong, Bernard V.
    University of California, Irvine, USA.
    Saager, Rolf B.
    University of California, Irvine, USA.
    Wiersma, Matthew P.
    University of California, Irvine, USA.
    Lo, Patrick C.
    University of California, Irvine, USA.
    Durkin, Anthony J.
    University of California, Irvine, USA.
    Choi, Bernard
    University of California, Irvine, USA.
    Optical properties of mouse brain tissue after optical clearing with FocusClear™2015In: Journal of Biomedical Optics, ISSN 1083-3668, E-ISSN 1560-2281, Vol. 20, no 9, article id 095010Article in journal (Refereed)
    Abstract [en]

    Fluorescence microscopy is commonly used to investigate disease progression in biological tissues. Biological tissues, however, are strongly scattering in the visible wavelengths, limiting the application of fluorescence microscopy to superficial (<200  μm) regions. Optical clearing, which involves incubation of the tissue in a chemical bath, reduces the optical scattering in tissue, resulting in increased tissue transparency and optical imaging depth. The goal of this study was to determine the time- and wavelength-resolved dynamics of the optical scattering properties of rodent brain after optical clearing with FocusClear™. Light transmittance and reflectance of 1-mm mouse brain sections were measured using an integrating sphere before and after optical clearing and the inverse adding doubling algorithm used to determine tissue optical scattering. The degree of optical clearing was quantified by calculating the optical clearing potential (OCP), and the effects of differing OCP were demonstrated using the optical histology method, which combines tissue optical clearing with optical imaging to visualize the microvasculature. We observed increased tissue transparency with longer optical clearing time and an analogous increase in OCP. Furthermore, OCP did not vary substantially between 400 and 1000 nm for increasing optical clearing durations, suggesting that optical histology can improve ex vivo visualization of several fluorescent probes.

  • 38.
    Nadhom, Hama
    Linköping University, Department of Physics, Chemistry and Biology, Biosensors and Bioelectronics. Linköping University, Faculty of Science & Engineering.
    Protein Microparticles for Printable Bioelectronics2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In biosensors, printing involves the transfer of materials, proteins or cells to a substrate. It offers many capabilities thatcan be utilized in many applications, including rapid deposition and patterning of proteins or other biomolecules.However, issues such as stability when using biomaterials are very common. Using proteins, enzymes, as biomaterialink require immobilizations and modifications due to changing in the structural conformation of the enzymes, whichleads to changes in the properties of the enzyme such as enzymatic activity, during the printing procedures andrequirements such as solvent solutions. In this project, an innovative approach for the fabrication of proteinmicroparticles based on cross-linking interchange reaction is presented to increase the stability in different solvents.The idea is to decrease the contact area between the enzymes and the surrounding environment and also preventconformation changes by using protein microparticles as an immobilization technique for the enzymes. The theory isbased on using a cross-linking reagent trigging the formation of intermolecular bonds between adjacent proteinmolecules leading to assembly of protein molecules within a CaCO3 template into a microparticle structure. TheCaCO3 template is removed by changing the solution pH to 5.0, leaving behind pure highly homogenous proteinmicroparticles with a size of 2.4 ± 0.2 μm, according to SEM images, regardless of the incubation solvents. Theenzyme model used is Horse Radish Peroxidase (HRP) with Bovine Serum Albumin (BSA) and Glutaraldehyde (GL)as a cross-linking reagent. Furthermore, a comparison between the enzymatic activity of the free HRP and the BSAHRPprotein microparticles in buffer and different solvents are obtained using Michaelis-Menten Kinetics bymeasuring the absorption of the blue product produced by the enzyme-substrate interaction using a multichannelspectrophotometer with a wavelength of 355 nm. 3,3’,5,5’-tetramethylbenzidine (TMB) was used as substrate. As aresult, the free HRP show an enzymatic activity variation up to ± 50 % after the incubation in the different solventswhile the protein microparticles show much less variation which indicate a stability improvement. Moreover, printingthe microparticles require high microparticle concentration due to contact area decreasing. However, usingmicroparticles as a bioink material prevent leakage/diffusion problem that occurs when using free protein instead.

  • 39.
    Nyman, Elin
    et al.
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Faculty of Science & Engineering. CVMD iMed DMPK AstraZeneca R&D, Gothenburg, Sweden.
    Rozendaal, Yvonne J W
    Eindhoven University of Technology, Eindhoven, The Netherlands.
    Helmlinger, Gabriel
    AstraZeneca, Pharmaceuticals LP, Waltham, MA, USA.
    Hamrén, Bengt
    AstraZeneca, Gothenburg, Sweden.
    Kjellsson, Maria C
    Uppsala University, Uppsala, Sweden.
    Strålfors, Peter
    Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology. Linköping University, Faculty of Medicine and Health Sciences.
    van Riel, Natal A W
    Eindhoven University of Technology, Eindhoven, The Netherlands.
    Gennemark, Peter
    AstraZeneca R&D, Gothenburg, Sweden.
    Cedersund, Gunnar
    Linköping University, Department of Biomedical Engineering. Linköping University, Faculty of Science & Engineering. Linköping University, Faculty of Medicine and Health Sciences. Linköping University, Department of Clinical and Experimental Medicine, Division of Cell Biology.
    Requirements for multi-level systems pharmacology models to reach end-usage: the case of type 2 diabetes2016In: Interface Focus, ISSN 2042-8898, E-ISSN 2042-8901, Vol. 6, no 2, p. 1-14Article, review/survey (Refereed)
    Abstract [en]

    We are currently in the middle of a major shift in biomedical research: unprecedented and rapidly growing amounts of data may be obtained today, from in vitro, in vivo and clinical studies, at molecular, physiological and clinical levels. To make use of these large-scale, multi-level datasets, corresponding multi-level mathematical models are needed, i.e. models that simultaneously capture multiple layers of the biological, physiological and disease-level organization (also referred to as quantitative systems pharmacology-QSP-models). However, today's multi-level models are not yet embedded in end-usage applications, neither in drug research and development nor in the clinic. Given the expectations and claims made historically, this seemingly slow adoption may seem surprising. Therefore, we herein consider a specific example-type 2 diabetes-and critically review the current status and identify key remaining steps for these models to become mainstream in the future. This overview reveals how, today, we may use models to ask scientific questions concerning, e.g., the cellular origin of insulin resistance, and how this translates to the whole-body level and short-term meal responses. However, before these multi-level models can become truly useful, they need to be linked with the capabilities of other important existing models, in order to make them 'personalized' (e.g. specific to certain patient phenotypes) and capable of describing long-term disease progression. To be useful in drug development, it is also critical that the developed models and their underlying data and assumptions are easily accessible. For clinical end-usage, in addition, model links to decision-support systems combined with the engagement of other disciplines are needed to create user-friendly and cost-efficient software packages.

  • 40.
    Olsson, Annakarin
    Linköping University, The Department of Physics, Chemistry and Biology.
    Piezoelectric Coatings on Implants: Sample preparation and construction of test-equipment for in vitro experiments2005Independent thesis Basic level (professional degree), 20 points / 30 hpStudent thesis
    Abstract [en]

    Implants are commonly used for orthopaedic and dental applications. There is however a problem with implants; they have a tendency to get loose after 10-15 years of usage. Bone that is not used will get weaker; this can be concluded from studies of people being immobilised or in microgravity. When an implant is put into bone, the surrounding bone does not experience any deformation and it will resorb. This is called stress shielding. Finally the implant will get loose. To avoid this problem we want to give electrical stimulation to the bone surrounding the implant. Electricity has been used before to stimulate bone, and it has been shown that immobilised bone can almost be maintained by using electric stimulation.

    Piezoelectricity is a property of certain materials that make them generate electricity when they are deformed. When an implant is coated with a piezoelectric material, electrical stimulation can be achieved for the surrounding bone that is stress shielded.

    In this diploma work, a test-equipment is built to stimulate cells. Cells will be grown on a piezoelectric plate that is bent by the test-equipment. Thus, the cells will be stimulated by both mechanical stress and electric potential since the piezoelectric material generates electricity when it is deformed. Piezoelectric samples and culture wells suitable for bending applications are prepared and tested in the equipment.

    Some initial cell growth experiments have been performed to see that the material is suitable for cell growth.

  • 41.
    Pantazis, Antonios
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Divison of Neurobiology. Linköping University, Faculty of Medicine and Health Sciences. Univ Calif Los Angeles, CA 90095 USA.
    Westerberg, Karin
    Amgen Inc, CA 91320 USA.
    Althoff, Thorsten
    Univ Calif Los Angeles, CA 90095 USA.
    Abramson, Jeff
    Univ Calif Los Angeles, CA 90095 USA.
    Olcese, Riccardo
    Univ Calif Los Angeles, CA 90095 USA.
    Harnessing photoinduced electron transfer to optically determine protein sub-nanoscale atomic distances2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, article id 4738Article in journal (Refereed)
    Abstract [en]

    Proteins possess a complex and dynamic structure, which is influenced by external signals and may change as they perform their biological functions. We present an optical approach, distance-encoding photoinduced electron transfer (DEPET), capable of the simultaneous study of protein structure and function. An alternative to FRET-based methods, DEPET is based on the quenching of small conjugated fluorophores by photoinduced electron transfer: a reaction that requires contact of the excited fluorophore with a suitable electron donor. This property allows DEPET to exhibit exceptional spatial and temporal resolution capabilities in the range pertinent to protein conformational change. We report the first implementation of DEPET on human large-conductance K+ (BK) channels under voltage clamp. We describe conformational rearrangements underpinning BK channel sensitivity to electrical excitation, in conducting channels expressed in living cells. Finally, we validate DEPET in synthetic peptide length standards, to evaluate its accuracy in measuring sub-and near-nanometer intramolecular distances.

  • 42.
    Prasad, Sonal
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Divison of Neurobiology. Linköping University, Faculty of Medicine and Health Sciences.
    Fridberger, Anders
    Linköping University, Department of Clinical and Experimental Medicine, Divison of Neurobiology. Linköping University, Faculty of Medicine and Health Sciences.
    Investigating the Role of Radixin in Modulation of Stereocilia Length and Stiffness2018In: TO THE EAR AND BACK AGAIN - ADVANCES IN AUDITORY BIOPHYSICS, AMER INST PHYSICS , 2018, Vol. 1965, article id UNSP 060007Conference paper (Refereed)
    Abstract [en]

    Mammalian hearing depends on deflection of stereocilia on the sensory outer hair cells of the inner ear. Previous data indicate that the stiffness of outer hair cell stereocilia are actively regulated. The molecular mechanism that regulate the deflection of stereocilia are presently less known. The aim of the study is to investigate the mechanistic pathway that underlie the stiffness modulation of outer hair cell stereocilia. Our hypothesis is that the membrane-cytoskeleton linker protein radixin, which is present at high concentration in stereocilia, could contribute to stiffness regulation. To test this hypothesis, we use the radixin blocker DX-52-1 which binds strongly and specifically to radixin. Time-resolved confocal imaging was used to visualize the sound-evoked motion of stereocilia in a semi-intact preparation of the guinea pig temporal bone. Cochlear microphonic potentials were also measured, using electrodes positioned in scala media. We found that the DX-52-1 inhibitor leads to an increase in stereocilia movements and decline in the amplitude of the cochlear microphonic potential. However, DX-52-1 caused a paradoxical increase in electromotility. These results suggest that radixin has a functionally important regulatory role in the mature inner ear.

  • 43.
    Rehn, Emelie
    Linköping University, Department of Medical and Health Sciences, Division of Radiological Sciences. Linköping University, Faculty of Medicine and Health Sciences.
    Modeling of scatter radiation during interventional X-ray procedures2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    During catheterized x-ray interventions the patient and medical staff is exposed to scatter radiation, as a consequence of tissue interactions. Ionizing radiation for medical purpose is potentially dangerous and can cause malignancy, skin damage and more. Studies have suggested an increase in the prevalence of eye lens cataract, thyroid cancer and left sided brain tumors in doctors. Therefore, it is mandatory to reduce the radiation dose in medicine, a principle known as ALARA (as low as Reasonably Achievable). Lead aprons, collars and shieldings are safety precautions to protect the team in the operating room. The x-ray equipment and surgical techniques are constantly evolving and the interventions become more complex which may increase the x-ray dose. Although x-ray imaging is required in interventional procedures endeavors of reducing radiation exposure to staff is of high interest. There is a need to increase the awareness about scatter radiation and radiation protection efforts are gaining momentum. Initiative to train a dose reducing behavior by education and awareness are key documents within the European Union’s guidelines on Radiation protection.

    The aims of this thesis were to create a 3D model for representation of real-time exposure and accumulated scatter radiation to staff performing interventional x-ray procedures and identify parameters that affect the scatter radiation.

    Extensive measurements were made with real time dosimeters while irradiating an anthropomorphic phantom. For five lateral C-arm projections, 68 - 80 data points each were used to measure scatter dose distribution around the patient. In the typical operator position, the effect of craniocaudal projection angle, patient size, field size, image detector height and pulse rate on scatter radiation dose was also investigated.

    It was possible to create a 3D model from interpolated measurement data that can generate dose rate with promising results. Six out of eight modelled doses deviated +/- 26.6 % from the validation cases. A model that delivers relative dose is an intuitive approach in education for interventional x-ray radiation safety. The staff position in relation to the x-ray source and the patient size have a significant correlation to the dose rate. Additional measurements are needed to ensure the reliability of the model. This work completes the effect of scatter radiation distribution around the patient table, which is not yet evaluated as thoroughly by other authors.

  • 44.
    Saager, Rolf B.
    et al.
    University of California, Irvine, USA.
    Quach, Alan
    University of California, Irvine, USA.
    Rowland, Rebecca A.
    University of California, Irvine, USA.
    Baldado, Melissa L.
    University of California, Irvine, USA.
    Durkin, Anthony J.
    University of California, Irvine, USA.
    Low-cost tissue simulating phantoms with adjustable wavelength-dependent scattering properties in the visible and infrared ranges2016In: Journal of Biomedical Optics, ISSN 1083-3668, E-ISSN 1560-2281, Vol. 21, no 6, article id 067001Article in journal (Refereed)
    Abstract [en]

    We present a method for low-cost fabrication of polydimethylsiloxane (PDMS) tissue simulating phantoms with tunable scattering spectra, spanning visible, and near-infrared regimes. These phantoms use optical polishing agents (aluminum oxide powders) at various grit sizes to approximate in vivo tissue scattering particles across multiple size distributions (range: 17 to 3  μm). This class of tunable scattering phantoms is used to mimic distinct changes in wavelength-dependent scattering properties observed in tissue pathologies such as partial thickness burns. Described by a power-law dependence on wavelength, the scattering magnitude of these phantoms scale linearly with particle concentration over a physiologic range [μ's=(0.5 to 2.0  mm−1)] whereas the scattering spectra, specific to each particle size distribution, correlate to distinct exponential coefficients (range: 0.007 to 0.32). Aluminum oxide powders used in this investigation did not detectably contribute to the absorption properties of these phantoms. The optical properties of these phantoms are verified through inverse adding-doubling methods and the tolerances of this fabrication method are discussed.

  • 45.
    Saager, Rolf B.
    et al.
    University of California, Irvine, USA.
    Sharif, Ata
    University of California, Irvine, USA.
    Kelly, Kristen M.
    Beckman Laser Institute and Medical Clinic, USA.
    Durkin, Anthony J.
    University of California, Irvine, USA.
    In vivo isolation of the effects of melanin from underlying hemodynamics across skin types using spatial frequency domain spectroscopy2016In: Journal of Biomedical Optics, ISSN 1083-3668, E-ISSN 1560-2281, Vol. 21, no 5, article id 057001Article in journal (Refereed)
    Abstract [en]

    Skin is a highly structured tissue, raising concerns as to whether skin pigmentation due to epidermal melanin may confound accurate measurements of underlying hemodynamics. Using both venous and arterial cuff occlusions as a means of inducing differential hemodynamic perturbations, we present analyses of spectra limited to the visible or near-infrared regime, in addition to a layered model approach. The influence of melanin, spanning Fitzpatrick skin types I to V, on underlying estimations of hemodynamics in skin as interpreted by these spectral regions are assessed. The layered model provides minimal cross-talk between melanin and hemodynamics and enables removal of problematic correlations between measured tissue oxygenation estimates and skin phototype.

  • 46.
    Silverå Ejneby, Malin
    Linköping University, Department of Clinical and Experimental Medicine, Divison of Neurobiology. Linköping University, Faculty of Medicine and Health Sciences.
    Site and Mechanism of Action of Resin Acids on Voltage-Gated Ion Channels2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Voltage-gated ion channels are pore-forming membrane proteins that open or close their gates when the voltage across the membrane is changed. They underlie the electrical activity that enables the heart to pump blood and the brain to receive and send signals. Changes in expression, distribution, and functional properties of voltage-gated ion channels can lead to diseases, such as epilepsy, cardiac arrhythmia, and pain-related disorders. Drugs that modulate the function of voltage-gated ion channels control these diseases in some patients, but the existing drugs do not adequately help all patients, and some also have severe side effects.

    Resin acids are common components of pine resins, with a hydrophobic three-ringed motif and a negatively charged carboxyl group. They open big-conductance Ca2+-activated K+ (BK) channels and voltage-gated potassium (KV) channels. We aimed to characterize the binding site and mechanism of action of resin acids on a KV channel and explore the effect of a resin acid by modifying the position and valence of charge of the carboxyl group. We tested the effect on several voltage-gated ion channels, including two KV channels expressed in Xenopus laevis oocytes and several voltage-gated ion channels expressed in cardiomyocytes. For this endeavour different electrophysiological techniques, ion channels, and cell types were used together with chemical synthesis of about 140 resin-acid derivatives, mathematical models, and computer simulations.

    We found that resin acids bind between the lipid bilayer and the Shaker KV channel, in the cleft between transmembrane segment S3 and S4, on the extracellular side of the voltage-sensor domain. This is a fundamentally new interaction site for small-molecule compounds that otherwise usually bind to ion channels in pockets surrounded by water. We also showed that the resin acids open the Shaker KV channel via an electrostatic mechanism, exerted on the positively charged voltage sensor S4. The effect of a resin acid increased when the negatively charged carboxyl group (the effector) and the hydrophobic three-ringed motif (anchor in lipid bilayer) were separated by three atoms: longer stalks decreased the effect. The length rule, in combination with modifications of the anchor, was used to design new resin-acid derivatives that open the human M-type (Kv7.2/7.3) channel. A naturally occurring resin acid also reduced the excitability of cardiomyocytes by affecting the voltage-dependence of several voltage-gated ion channels. The major finding was that the resin acid inactivated sodium and calcium channels, while it activated KV channels at more negative membrane voltages. Computer simulations confirmed that the combined effect on different ion channels reduced the excitability of a cardiomyocyte. Finally, the resin acid reversed induced arrhythmic firing of the cardiomyocytes.

    In conclusion, resin acids are potential drug candidates for diseases such as epilepsy and cardiac arrhythmia: knowing the binding site and mechanism of action can help to fine tune the resin acid to increase the effect, as well as the selectivity.

    List of papers
    1. A drug pocket at the lipid bilayer-potassium channel interface
    Open this publication in new window or tab >>A drug pocket at the lipid bilayer-potassium channel interface
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    2017 (English)In: Science Advances, ISSN 0036-8156, E-ISSN 2375-2548, Vol. 3, no 10, article id e1701099Article in journal (Refereed) Published
    Abstract [en]

    Many pharmaceutical drugs against neurological and cardiovascular disorders exert their therapeutic effects by binding to specific sites on voltage-gated ion channels of neurons or cardiomyocytes. To date, all molecules targeting known ion channel sites bind to protein pockets that are mainly surrounded by water. We describe a lipid-protein drug-binding pocket of a potassium channel. We synthesized and electrophysiologically tested 125 derivatives, analogs, and related compounds to dehydroabietic acid. Functional data in combination with docking and molecular dynamics simulations mapped a binding site for small-molecule compounds at the interface between the lipid bilayer and the transmembrane segments S3 and S4 of the voltage-sensor domain. This fundamentally new binding site for small-molecule compounds paves the way for the design of new types of drugs against diseases caused by altered excitability.

    Place, publisher, year, edition, pages
    AMER ASSOC ADVANCEMENT SCIENCE, 2017
    National Category
    Cell and Molecular Biology
    Identifiers
    urn:nbn:se:liu:diva-144164 (URN)10.1126/sciadv.1701099 (DOI)000417998700021 ()29075666 (PubMedID)
    Note

    Funding Agencies|Swedish Research Council; Swedish Brain Foundation; Swedish Heart-Lung Foundation; Swedish National Infrastructure for Computing

    Available from: 2018-01-08 Created: 2018-01-08 Last updated: 2018-05-15
    2. Atom-by-atom tuning of the electrostatic potassium-channel modulator dehydroabietic acid
    Open this publication in new window or tab >>Atom-by-atom tuning of the electrostatic potassium-channel modulator dehydroabietic acid
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    2018 (English)In: The Journal of General Physiology, ISSN 0022-1295, E-ISSN 1540-7748, Vol. 150, no 5, p. 731-750Article in journal (Refereed) Published
    Abstract [en]

    Dehydroabietic acid (DHAA) is a naturally occurring component of pine resin that was recently shown to open voltage-gated potassium (KV) channels. The hydrophobic part of DHAA anchors the compound near the channel’s positively charged voltage sensor in a pocket between the channel and the lipid membrane. The negatively charged carboxyl group exerts an electrostatic effect on the channel’s voltage sensor, leading to the channel opening. In this study, we show that the channel-opening effect increases as the length of the carboxyl-group stalk is extended until a critical length of three atoms is reached. Longer stalks render the compounds noneffective. This critical distance is consistent with a simple electrostatic model in which the charge location depends on the stalk length. By combining an effective anchor with the optimal stalk length, we create a compound that opens the human KV7.2/7.3 (M type) potassium channel at a concentration of 1 µM. These results suggest that a stalk between the anchor and the effector group is a powerful way of increasing the potency of a channel-opening drug.

    Place, publisher, year, edition, pages
    New York, United States: Rockefeller Institute for Medical Research, 2018
    National Category
    Physiology
    Identifiers
    urn:nbn:se:liu:diva-147837 (URN)10.1085/jgp.201711965 (DOI)000434417800008 ()2-s2.0-85046705149 (Scopus ID)
    Note

    Funding agencies: Swedish Research Council [2016-02615]; Swedish Heart-Lung Foundation [20150672]; Swedish Brain Foundation [2016-0326]

    Available from: 2018-05-15 Created: 2018-05-15 Last updated: 2018-06-28Bibliographically approved
    3. Isopimaric acid - a multi-targeting ion channel modulator reducing excitability and arrhythmicity in a spontaneously beating mouse atrial cell line
    Open this publication in new window or tab >>Isopimaric acid - a multi-targeting ion channel modulator reducing excitability and arrhythmicity in a spontaneously beating mouse atrial cell line
    2018 (English)In: Acta Physiologica, ISSN 1748-1708, E-ISSN 1748-1716, Vol. 222, no 1, article id e12895Article in journal (Refereed) Published
    Abstract [en]

    AimAtrial fibrillation is the most common persistent cardiac arrhythmia, and it is not well controlled by present drugs. Because some resin acids open voltage-gated potassium channels and reduce neuronal excitability, we explored the effects of the resin acid isopimaric acid (IPA) on action potentials and ion currents in cardiomyocytes. MethodsSpontaneously beating mouse atrial HL-1 cells were investigated with the whole-cell patch-clamp technique. Results1-25 mol L-1 IPA reduced the action potential frequency by up to 50%. The effect of IPA on six different voltage-gated ion channels was investigated; most voltage-dependent parameters of ion channel gating were shifted in the negative direction along the voltage axis, consistent with a hypothesis that a lipophilic and negatively charged compound binds to the lipid membrane close to the positively charged voltage sensor of the ion channels. The major finding was that IPA inactivated sodium channels and L- and T-type calcium channels and activated the rapidly activating potassium channel and the transient outward potassium channel. Computer simulations of IPA effects on all of the ion currents were consistent with a reduced excitability, and they also showed that effects on the Na channel played the largest role to reduce the action potential frequency. Finally, induced arrhythmia in the HL-1 cells was reversed by IPA. ConclusionLow concentrations of IPA reduced the action potential frequency and restored regular firing by altering the voltage dependencies of several voltage-gated ion channels. These findings can form the basis for a new pharmacological strategy to treat atrial fibrillation.

    Place, publisher, year, edition, pages
    Wiley-VCH Verlagsgesellschaft, 2018
    Keywords
    arrhythmia; atrial fibrillation; ion channels; isopimaric acid; patch clamp; resin acid
    National Category
    Cell and Molecular Biology
    Identifiers
    urn:nbn:se:liu:diva-144564 (URN)10.1111/apha.12895 (DOI)000419864000009 ()28514017 (PubMedID)
    Note

    Funding Agencies|Swedish Research Council; Swedish Heart-Lung Foundation; Swedish Brain Foundation; ALF

    Available from: 2018-01-29 Created: 2018-01-29 Last updated: 2018-05-15
  • 47.
    Skyttner, Camilla
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering.
    Peptide-Liposome Model Systems for Triggered Release2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Liposomes are widely used in drug delivery to improve drug efficacy and to reduce side effects. For liposome-encapsulated drugs to become bioavailable and provide a therapeutic effect they must be released, which typically is a slow process that primarily relies on passive diffusion, liposome rupture or endocytotic uptake. Achieving drug concentrations within the therapeutic window can thus be challenging, resulting in poor efficacy and higher risks drug resistance. Finding means to modulate lipid membrane integrity and to trigger rapid and efficient release of liposomal cargo is thus critical to improve current and future liposomal drug delivery systems. The possibilities to tailor lipid composition and surface functionalization is vital for drug delivery applications but also make liposomes attractive model systems for studies of membrane active biomolecules.

    The overall aim of this thesis work has been to develop new strategies for triggering and controlling changes in lipid membrane integrity and to study the interactions of membrane active peptides with model lipid membranes using both de novo designed and biologically derived synthetic amphipathic cationic peptides. Two different sets of designed peptides have been explored that can fold and heterodimerize into a coiled coil and helix-loop-helix fourhelix bundle, respectively. Conjugation of the cationic lysine rich peptides to liposomes triggered a rapid and concentration dependent release. The additions of their corresponding glutamic acid-rich complementary peptides inhibited the release of liposomal cargo. Possibilities to reduce the inhibitory effect by both proteolytic digestion of the inhibitory peptide and by means of heterodimer exchange have been investigated. Moreover, the effects of peptide size and composition and ability to fold have been studied in order to elucidate the factors that influence the membrane permeabilizing effects of the peptides.

    In addition, the membrane activity of a the two-peptide bacteriocin PLNC8α and PLNC8β has been explored using liposomes as a model system. PLNC8αβ are expressed by Lactobacillus plantarum and were shown to display pronounced membrane-partition folding coupling, leading to rapid release of liposome encapsulated carboxyfluorescein. PLNC8αβ also kill and suppressed growth of the gram-negative bacteria Porphyromonas gingivalis by efficiently damaging the bacterial membrane.

    Although membrane active peptides are highly efficient in perturbing lipid membrane integrity, possibilities to trigger release using external stimuli are also of large interest for therapeutic applications. Light-induced heating of liposome encapsulated gold nanoparticles (AuNPs) has been shown by others as a potential strategy to trigger drug release. To facilitate fabrication of thermoplasmonic liposome systems we developed a simple method for synthesis of small AuNPs inside liposomes, using the liposomes as nanoscale reaction vessels.

    The work presented in this thesis provides new knowledge and techniques for future development of liposome-based drug delivery systems, peptide-based therapeutics and increase our understanding of peptide-lipid interactions.

    List of papers
    1. Tuning Liposome Membrane Permeability by Competitive Peptide Dimerization and Partitioning-Folding Interactions Regulated by Proteolytic Activity
    Open this publication in new window or tab >>Tuning Liposome Membrane Permeability by Competitive Peptide Dimerization and Partitioning-Folding Interactions Regulated by Proteolytic Activity
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    2016 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, no 21123, p. 1-9Article in journal (Refereed) Published
    Abstract [en]

    Membrane active peptides are of large interest for development of drug delivery vehicles and therapeutics for treatment of multiple drug resistant infections. Lack of specificity can be detrimental and finding routes to tune specificity and activity of membrane active peptides is vital for improving their therapeutic efficacy and minimize harmful side effects. We describe a de novo designed membrane active peptide that partition into lipid membranes only when specifically and covalently anchored to the membrane, resulting in pore-formation. Dimerization with a complementary peptide efficiently inhibits formation of pores. The effect can be regulated by proteolytic digestion of the inhibitory peptide by the matrix metalloproteinase MMP-7, an enzyme upregulated in many malignant tumors. This system thus provides a precise and specific route for tuning the permeability of lipid membranes and a novel strategy for development of recognition based membrane active peptides and indirect enzymatically controlled release of liposomal cargo.

    Place, publisher, year, edition, pages
    NATURE PUBLISHING GROUP, 2016
    National Category
    Physical Sciences Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:liu:diva-126131 (URN)10.1038/srep21123 (DOI)000370532500002 ()26892926 (PubMedID)
    Note

    Funding Agencies|Linkoping University; Swedish Research Council (VR); Swedish Foundation for Strategic Research (SSF); Knut and Alice Wallenberg Foundation (KAW); Centre in Nanoscience and Technology (CeNano); Provost Office, NTU

    Available from: 2016-03-15 Created: 2016-03-15 Last updated: 2019-01-22
    2. Antibacterial effects of Lactobacillus and bacteriocin PLNC8 alpha beta on the periodontal pathogen Porphyromonas gingivalis
    Open this publication in new window or tab >>Antibacterial effects of Lactobacillus and bacteriocin PLNC8 alpha beta on the periodontal pathogen Porphyromonas gingivalis
    Show others...
    2016 (English)In: BMC Microbiology, ISSN 1471-2180, E-ISSN 1471-2180, Vol. 16, no 188Article in journal (Refereed) Published
    Abstract [en]

    Background: The complications in healthcare systems associated with antibiotic-resistant microorganisms have resulted in an intense search for new effective antimicrobials. Attractive substances from which novel antibiotics may be developed are the bacteriocins. These naturally occurring peptides are generally considered to be safe and efficient at eliminating pathogenic bacteria. Among specific keystone pathogens in periodontitis, Porphyromonas gingivalis is considered to be the most important pathogen in the development and progression of chronic inflammatory disease. The aim of the present study was to investigate the antimicrobial effects of different Lactobacillus species and the two-peptide bacteriocin PLNC8 alpha beta on P. gingivalis. Results: Growth inhibition of P. gingivalis was obtained by viable Lactobacillus and culture media from L. plantarum NC8 and 44048, but not L. brevis 30670. The two-peptide bacteriocin from L. plantarum NC8 (PLNC8 alpha beta) was found to be efficient against P. gingivalis through binding followed by permeabilization of the membranes, using Surface plasmon resonance analysis and DNA staining with Sytox Green. Liposomal systems were acquired to verify membrane permeabilization by PLNC8 alpha beta. The antimicrobial activity of PLNC8 alpha beta was found to be rapid (1 min) and visualized by TEM to cause cellular distortion through detachment of the outer membrane and bacterial lysis. Conclusion: Soluble or immobilized PLNC8 alpha beta bacteriocins may be used to prevent P. gingivalis colonization and subsequent pathogenicity, and thus supplement the host immune system against invading pathogens associated with periodontitis.

    Place, publisher, year, edition, pages
    BIOMED CENTRAL LTD, 2016
    Keywords
    Periodontitis; P. gingivalis; Lactobacillus; Bacteriocin; PLNC8
    National Category
    Microbiology
    Identifiers
    urn:nbn:se:liu:diva-131904 (URN)10.1186/s12866-016-0810-8 (DOI)000383422500001 ()27538539 (PubMedID)
    Note

    Funding Agencies|Swedish Heart-Lung Foundation; Foundation of Magnus Bergvall; Foundation of Olle Engkvist; Knowledge Foundation, Sweden

    Available from: 2016-10-13 Created: 2016-10-11 Last updated: 2018-08-22
    3. Liposomes as nanoreactors for the photochemical synthesis of gold nanoparticles
    Open this publication in new window or tab >>Liposomes as nanoreactors for the photochemical synthesis of gold nanoparticles
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    2015 (English)In: Journal of Colloid and Interface Science, ISSN 0021-9797, E-ISSN 1095-7103, Vol. 456, p. 206-209Article in journal (Refereed) Published
    Abstract [en]

    A simple and novel method for the photochemical synthesis of AuNPs in liposomes is described. Gold salt is co-encapsulated with the photoinitiator Irgacure-2959 in POPC liposomes prepared via traditional thin-film hydration technique. UVA irradiation for 15 min results in encapsulated AuNPs of 2.8 +/- 1.6 nm in diameter that are primarily dispersed in the aqueous interior of the liposomes. (C) 2015 Elsevier Inc. All rights reserved.

    Place, publisher, year, edition, pages
    Elsevier, 2015
    Keywords
    Liposomes; AuNPs; Nanoreactors
    National Category
    Clinical Medicine Physical Sciences
    Identifiers
    urn:nbn:se:liu:diva-120718 (URN)10.1016/j.jcis.2015.06.033 (DOI)000358458500027 ()26125517 (PubMedID)
    Note

    Funding Agencies|Swedish Foundation for Strategic Research (SSF); Center for Integrative Regenerative Medicine (IGEN) at Linkoping University

    Available from: 2015-08-24 Created: 2015-08-24 Last updated: 2018-08-22
    4. Tuning Liposome Membrane Permeability by Competitive Coiled Coil Heterodimerization and Heterodimer Exchange
    Open this publication in new window or tab >>Tuning Liposome Membrane Permeability by Competitive Coiled Coil Heterodimerization and Heterodimer Exchange
    2018 (English)In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 34, no 22, p. 6529-6537Article in journal (Refereed) Published
    Abstract [en]

    Membrane-active peptides that enable the triggered release of liposomal cargo are of great interest for the development of liposome-based drug delivery systems but require peptide-lipid membrane interactions that are highly defined and tunable. To this end, we have explored the possibility to use the competing interactions between membrane partitioning and heterodimenzation and the folding of a set of four different de novo designed coiled coil peptides Covalent conjugation of the cationic peptides triggered rapid destabilization of membrane mtegrity and the release of encapsulated species. The release was inhibited when introducing complementary peptides as a result of heterodimenzation and folding into coiled mils The degree of inhibition was shown to be dictated by the coiled coil peptide heterodimer dissociation constants, and liposomal release could be reactivated by a heterodimer exchange to render the membrane bound peptide free and thus membrane-active. The possibility to tune the permeability of lipid membranes using highly specific peptide-folding-dependent interactions delineates a new possible approach for the further development of responsive liposome-based drug delivery systems.

    Place, publisher, year, edition, pages
    AMER CHEMICAL SOC, 2018
    National Category
    Biophysics
    Identifiers
    urn:nbn:se:liu:diva-149349 (URN)10.1021/acs.langmuir.8b00592 (DOI)000434893600023 ()29758162 (PubMedID)
    Note

    Funding Agencies|Swedish Research Council (VR) [2017-04475]; Swedish Cancer Foundation [CAN 2017/430]; Swedish Government Strategic Research Area in Materials Science on Functional Materials at Linkoping University [2009-00971]

    Available from: 2018-07-02 Created: 2018-07-02 Last updated: 2019-01-22
  • 48.
    Skyttner, Camilla
    et al.
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering.
    Enander, Karin
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering.
    Aronsson, Christopher
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering.
    Aili, Daniel
    Linköping University, Department of Physics, Chemistry and Biology, Molecular Physics. Linköping University, Faculty of Science & Engineering.
    Tuning Liposome Membrane Permeability by Competitive Coiled Coil Heterodimerization and Heterodimer Exchange2018In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 34, no 22, p. 6529-6537Article in journal (Refereed)
    Abstract [en]

    Membrane-active peptides that enable the triggered release of liposomal cargo are of great interest for the development of liposome-based drug delivery systems but require peptide-lipid membrane interactions that are highly defined and tunable. To this end, we have explored the possibility to use the competing interactions between membrane partitioning and heterodimenzation and the folding of a set of four different de novo designed coiled coil peptides Covalent conjugation of the cationic peptides triggered rapid destabilization of membrane mtegrity and the release of encapsulated species. The release was inhibited when introducing complementary peptides as a result of heterodimenzation and folding into coiled mils The degree of inhibition was shown to be dictated by the coiled coil peptide heterodimer dissociation constants, and liposomal release could be reactivated by a heterodimer exchange to render the membrane bound peptide free and thus membrane-active. The possibility to tune the permeability of lipid membranes using highly specific peptide-folding-dependent interactions delineates a new possible approach for the further development of responsive liposome-based drug delivery systems.

  • 49.
    Strimbu, C. Elliott
    et al.
    Columbia Univ, NY 10027 USA.
    Fridberger, Anders
    Linköping University, Department of Clinical and Experimental Medicine, Divison of Neurobiology. Linköping University, Faculty of Medicine and Health Sciences.
    Imaging Extracellular Calcium in Endolymph2018In: TO THE EAR AND BACK AGAIN - ADVANCES IN AUDITORY BIOPHYSICS, AMER INST PHYSICS , 2018, Vol. 1965, article id UNSP 080005Conference paper (Refereed)
    Abstract [en]

    Hair cell mechanoelectrical transduction and adaptation are believed to be regulated by extracellular calcium. However, the majority of experiments addressing calciums role have been performed on reduced preparations in conditions that do not mimic those present in vivo. We used confocal microscopy and a low affinity (k(d) similar to 11 mu M) ratiometric fluorescent indicator to measure the extracellular calcium concentration in scala media in an in vitro preparation of the guinea pig cochlea. Microelectrodes were used to measure the cochlear microphonic potential during acoustic stimulation. The mean calcium concentration is significantly higher in the tectorial membrane (TM) than the surrounding endolymph, suggesting that the membrane acts as a calcium sink. We also observe calcium hot spots along the underside of the TM, near the outer hair cell bundles and near Hensens stripe close to the inner hair cell bundle. This suggests that the local calcium concentration near the hair bundles exceeds 100 mu M, significantly higher than the bulk endolymph. These results were corroborated with fluorescence correlation spectroscopy using a second calcium sensitive dye, Oregon Green 488-BAPTA. Following a brief exposure to loud sound, TM calcium drops dramatically and shows recovery on a similar timescale as the microphonic potential. Our results suggest that the extracellular calcium concentration near the hair bundles is much higher than previously believed and may also serve as a partial control parameter for temporary threshold shifts.

  • 50.
    Strimbu, Clark Elliott
    et al.
    Linköping University, Department of Clinical and Experimental Medicine, Divison of Neurobiology. Linköping University, Faculty of Medicine and Health Sciences. Columbia Univ, NY 10032 USA.
    Prasad, Sonal
    Linköping University, Department of Clinical and Experimental Medicine, Divison of Neurobiology. Linköping University, Faculty of Medicine and Health Sciences.
    Hakizimana, Pierre
    Linköping University, Department of Clinical and Experimental Medicine, Divison of Neurobiology. Linköping University, Faculty of Medicine and Health Sciences.
    Fridberger, Anders
    Linköping University, Department of Clinical and Experimental Medicine, Divison of Neurobiology. Linköping University, Faculty of Medicine and Health Sciences.
    Control of hearing sensitivity by tectorial membrane calcium2019In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 116, no 12, p. 5756-5764Article in journal (Refereed)
    Abstract [en]

    When sound stimulates the stereocilia on the sensory cells in the hearing organ, Ca2+ ions flow through mechanically gated ion channels. This Ca2+ influx is thought to be important for ensuring that the mechanically gated channels operate within their most sensitive response region, setting the fraction of channels open at rest, and possibly for the continued maintenance of stereocilia. Since the extracellular Ca2+ concentration will affect the amount of Ca2+ entering during stimulation, it is important to determine the level of the ion close to the sensory cells. Using fluorescence imaging and fluorescence correlation spectroscopy, we measured the Ca2+ concentration near guinea pig stereocilia in situ. Surprisingly, we found that an acellular accessory structure close to the stereocilia, the tectorial membrane, had much higher Ca2+ than the surrounding fluid. Loud sounds depleted Ca2+ from the tectorial membrane, and Ca2+ manipulations had large effects on hair cell function. Hence, the tectorial membrane contributes to control of hearing sensitivity by influencing the ionic environment around the stereocilia.

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