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Carlsson, Jonas
Publications (10 of 18) Show all publications
Carlsson, J. & Persson, B. (2012). Investigating protein variants using structural calculation techniques. In: Andrew J. W. Orry and Ruben Abagyan (Ed.), Homology Modeling: Methods and Protocols (pp. 313-330). Springer, 857
Open this publication in new window or tab >>Investigating protein variants using structural calculation techniques
2012 (English)In: Homology Modeling: Methods and Protocols / [ed] Andrew J. W. Orry and Ruben Abagyan, Springer, 2012, Vol. 857, p. 313-330Chapter in book (Other academic)
Abstract [en]

Knowledge about protein tertiary structure can guide experiments, assist in the understanding of structure-function relationships, and aid the design of new therapeutics for disease. Homology modeling is an in silico method that predicts the tertiary structure of an amino acid sequence based on a homologous experimentally determined structure. In, Homology Modeling: Methods and Protocols experts in the field describe each homology modeling step from first principles, provide case studies for challenging modeling targets and describe methods for the prediction of how other molecules such as drugs can interact with the protein. Written in the highly successful Methods in Molecular Biology series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory. Thorough and intuitive, Homology Modeling: Methods and Protocols guides scientists in the available homology modeling methods.

Place, publisher, year, edition, pages
Springer, 2012
Series
Methods in Molecular Biology, ISSN 1064-3745, E-ISSN 1940-6029 ; 857
Keywords
Sequence alignment (Bioinformatics), Life sciences, Biochemistry, Protein Science, Protein Structure
National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:liu:diva-81961 (URN)10.1007/978-1-61779-588-6_14 (DOI)978-1-61779-587-9 (ISBN)978-1-61779-588-6 (ISBN)
Available from: 2012-09-26 Created: 2012-09-26 Last updated: 2017-04-10Bibliographically approved
Andrésen, C., Helander, S., Lemak, A., Fares, C., Csizmok, V., Carlsson, J., . . . Sunnerhagen, M. (2012). Transient structure and dynamics in the disordered c-Myc transactivation domain affect Bin1 binding. Nucleic Acids Research, 40(13), 6353-6366
Open this publication in new window or tab >>Transient structure and dynamics in the disordered c-Myc transactivation domain affect Bin1 binding
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2012 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 40, no 13, p. 6353-6366Article in journal (Refereed) Published
Abstract [en]

The crucial role of Myc as an oncoprotein and as a key regulator of cell growth makes it essential to understand the molecular basis of Myc function. The N-terminal region of c-Myc coordinates a wealth of protein interactions involved in transformation, differentiation and apoptosis. We have characterized in detail the intrinsically disordered properties of Myc-1-88, where hierarchical phosphorylation of S62 and T58 regulates activation and destruction of the Myc protein. By nuclear magnetic resonance (NMR) chemical shift analysis, relaxation measurements and NOE analysis, we show that although Myc occupies a very heterogeneous conformational space, we find transiently structured regions in residues 22-33 and in the Myc homology box I (MBI; residues 45-65); both these regions are conserved in other members of the Myc family. Binding of Bin1 to Myc-1-88 as assayed by NMR and surface plasmon resonance (SPR) revealed primary binding to the S62 region in a dynamically disordered and multivalent complex, accompanied by population shifts leading to altered intramolecular conformational dynamics. These findings expand the increasingly recognized concept of intrinsically disordered regions mediating transient interactions to Myc, a key transcriptional regulator of major medical importance, and have important implications for further understanding its multifaceted role in gene regulation.

Place, publisher, year, edition, pages
Oxford University Press (OUP): Policy C / Oxford University Press, 2012
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-82076 (URN)10.1093/nar/gks263 (DOI)000306970700051 ()
Note

Funding Agencies|VINNOVA||CIHR||Swedish Research Council||Swedish Cancer Foundation||Swedish Child Cancer Foundation||Canadian Cancer Society||Ontario Research Fund|GL2-01-030|NIH Protein Structure Initiative grant|U54 GM094597|Canada Research Chairs Program||Swedish NMR Centre||Knut and Alice Wallenberg Foundation||Linkoping University||

Available from: 2012-09-28 Created: 2012-09-28 Last updated: 2017-12-07
Tegler, L. T., Fromell, K., Jonsson, B.-H., Viljanen, J., Winander, C., Carlsson, J. & Baltzer, L. (2011). Polypeptide Conjugate Binders that Discriminate between Two Isoforms of Human Carbonic Anhydrase in Human Blood.. ChemBioChem (Print), 12(4), 559-566
Open this publication in new window or tab >>Polypeptide Conjugate Binders that Discriminate between Two Isoforms of Human Carbonic Anhydrase in Human Blood.
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2011 (English)In: ChemBioChem (Print), ISSN 1439-4227, E-ISSN 1439-7633, Vol. 12, no 4, p. 559-566Article in journal (Refereed) Published
Abstract [en]

Two binder candidates 4-C37L34-B and 3-C15L8-B from a 16-membered set of 42-residue polypeptide conjugates designed to bind human carbonic anhydrase II (HCAII), were shown to bind HCAII with high affinity in a fluorescence-based screening assay. Two carbonic anhydrase isoforms with 60 % homology exist in human blood with HCAI being present in five- to sevenfold excess over HCAII. The ability of the binders to discriminate between HCAI and HCAII was evaluated with regard to what selectivity could be achieved by the conjugation of polypeptides from a 16-membered set to a small organic molecule that binds both isoforms with similar affinities. The polypeptide conjugate 4-C37L34-B bound HCAII with a K(D) of 17 nM and HCAI with a K(D) of 470 nM, that is, with a 30-fold difference in affinity. The corresponding dissociation constants for the complexes formed from 3-C15L8-B and the two carbonic anhydrases were 60 and 390 nM, respectively. This demonstration of selectivity between two very similar proteins is striking in view of the fact that the molecular weight of each one of the conjugate molecules is little more than 5000, the fold is unordered, and the polypeptide sequences were designed de novo and have no prior relationship to carbonic anhydrases. The results suggest that synthetic polypeptide conjugates can be prepared from organic molecules that are considered to be weak binders with low selectivity, yielding conjugates with properties that make them attractive alternatives to biologically generated binders in biotechnology and biomedicine.

Place, publisher, year, edition, pages
Wiley, 2011
National Category
Natural Sciences
Identifiers
urn:nbn:se:liu:diva-65765 (URN)10.1002/cbic.201000556 (DOI)000288080700010 ()21264993 (PubMedID)
Available from: 2011-02-20 Created: 2011-02-20 Last updated: 2017-12-11
Fucile, G., Garcia, C., Carlsson, J., Sunnerhagen, M. & Christendat, D. (2011). Structural and biochemical investigation of two Arabidopsis shikimate kinases: The heat-inducible isoform is thermostable. Protein Science, 20(7), 1125-1136
Open this publication in new window or tab >>Structural and biochemical investigation of two Arabidopsis shikimate kinases: The heat-inducible isoform is thermostable
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2011 (English)In: Protein Science, ISSN 0961-8368, E-ISSN 1469-896X, Vol. 20, no 7, p. 1125-1136Article in journal (Refereed) Published
Abstract [en]

The expression of plant shikimate kinase (SK; EC 2.7.1.71), an intermediate step in the shikimate pathway to aromatic amino acid biosynthesis, is induced under specific conditions of environmental stress and developmental requirements in an isoform-specific manner. Despite their important physiological role, experimental structures of plant SKs have not been determined and the biochemical nature of plant SK regulation is unknown. The Arabidopsis thaliana genome encodes two SKs, AtSK1 and AtSK2. We demonstrate that AtSK2 is highly unstable and becomes inactivated at 37 degrees C whereas the heat-induced isoform, AtSK1, is thermostable and fully active under identical conditions at this temperature. We determined the crystal structure of AtSK2, the first SK structure from the plant kingdom, and conducted biophysical characterizations of both AtSK1 and AtSK2 towards understanding this mechanism of thermal regulation. The crystal structure of AtSK2 is generally conserved with bacterial SKs with the addition of a putative regulatory phosphorylation motif forming part of the adenosine triphosphate binding site. The heat-induced isoform, AtSK1, forms a homodimer in solution, the formation of which facilitates its relative thermostability compared to AtSK2. In silico analyses identified AtSK1 site variants that may contribute to AtSK1 stability. Our findings suggest that AtSK1 performs a unique function under heat stress conditions where AtSK2 could become inactivated. We discuss these findings in the context of regulating metabolic flux to competing downstream pathways through SK-mediated control of steady state concentrations of shikimate.

Place, publisher, year, edition, pages
Cold Spring Harbor Laboratory Press, 2011
Keywords
shikimate; heat stress; Arabidopsis thaliana
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-69819 (URN)10.1002/pro.640 (DOI)000292257600006 ()
Available from: 2011-08-10 Created: 2011-08-08 Last updated: 2017-12-08
Hellgren, M., Carlsson, J., Ostberg, L. J., Staab, C. A., Persson, B. & Hoog, J.-O. (2010). Enrichment of ligands with molecular dockings and subsequent characterization for human alcohol dehydrogenase 3. CELLULAR AND MOLECULAR LIFE SCIENCES, 67(17), 3005-3015
Open this publication in new window or tab >>Enrichment of ligands with molecular dockings and subsequent characterization for human alcohol dehydrogenase 3
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2010 (English)In: CELLULAR AND MOLECULAR LIFE SCIENCES, ISSN 1420-682X, Vol. 67, no 17, p. 3005-3015Article in journal (Refereed) Published
Abstract [en]

Alcohol dehydrogenase 3 (ADH3) has been assigned a role in nitric oxide homeostasis due to its function as an S-nitrosoglutathione reductase. As altered S-nitrosoglutathione levels are often associated with disease, compounds that modulate ADH3 activity might be of therapeutic interest. We performed a virtual screening with molecular dockings of more than 40,000 compounds into the active site of human ADH3. A novel knowledge-based scoring method was used to rank compounds, and several compounds that were not known to interact with ADH3 were tested in vitro. Two of these showed substrate activity (9-decen-1-ol and dodecyltetraglycol), where calculated binding scoring energies correlated well with the logarithm of the k (cat)/K (m) values for the substrates. Two compounds showed inhibition capacity (deoxycholic acid and doxorubicin), and with these data three different lines for specific inhibitors for ADH3 are suggested: fatty acids, glutathione analogs, and cholic acids.

Place, publisher, year, edition, pages
Springer Science Business Media, 2010
Keywords
Alcohol dehydrogenase, Enzyme kinetics, Inhibitors, Molecular docking, S-Nitrosoglutathione, Virtual screening
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-58964 (URN)10.1007/s00018-010-0370-2 (DOI)000280917900011 ()
Available from: 2010-09-03 Created: 2010-09-03 Last updated: 2010-09-03
Ruiz Pavón, L., Karlsson, P., Carlsson, J., Samyn, D., Persson, B., Persson, B. L. & Spetea, C. (2010). Functionally Important Amino Acids in the Arabidopsis Thylakoid Phosphate Transporter: Homology Modeling and Site-directed Mutagenesis. Biochemistry, 49(30), 6430-6439
Open this publication in new window or tab >>Functionally Important Amino Acids in the Arabidopsis Thylakoid Phosphate Transporter: Homology Modeling and Site-directed Mutagenesis
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2010 (English)In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 49, no 30, p. 6430-6439Article in journal (Other academic) Published
Abstract [en]

The anion transporter 1 (ANTR1) from Arabidopsis thaliana, homologous to the mammalian SLC17 family, has recently been localized to the chloroplast thylakoid membrane. When expressed heterologously in Escherichia coli, ANTR1 mediates a Na+-dependent active transport of inorganic phosphate (Pi). The aim of this study was to identify amino acids involved in substrate binding/translocation by ANTR1 and in the Na+-dependence of its activity. A threedimensional structural model of ANTR1 was constructed using the crystal structure of glycerol-3-phosphate/phosphate antiporter (GlpT) from E.coli as a template. Based on this model and multiple sequence alignments, five highly conserved residues in plant ANTRs and mammalian SLC17 homologues have been selected for site-directed mutagenesis, namely Arg-120, Ser-124 and Arg-201 inside the putative translocation pathway, Arg-228 and Asp-382 exposed at the cytosolic surface of the protein. The activities of the wild type and mutant proteins have been analyzed using expression in E. coli and radioactive transport assays, and compared with bacterial cells carrying an empty plasmid. Based on Pi- and Na+-dependent kinetics, we propose that Arg-120, Arg-201 and Arg-228 are involved in binding and translocation of the substrate, Ser-124 functions as a periplasmic gate for Na+ ions, and finally Asp-382 participates in the turnover of the transporter via ionic interaction with either Arg-228 or Na+ ions. We also propose that the corresponding residues may have a similar function in other plant and mammalian SLC17 homologous transporters.

National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:liu:diva-51119 (URN)10.1021/bi100239j (DOI)
Note
On the day of the defence day the status of this article was ManuscriptAvailable from: 2009-10-19 Created: 2009-10-19 Last updated: 2017-12-12Bibliographically approved
Ruiz-Pavon, L., Karlsson, P., Carlsson, J., Samyn, D., Persson, B., Persson, B. L. & Spetea Wiklund, C. (2010). Modeling and Mutational analysis of Anion transporter 1 protein of Arabidopsis thaliana. Paper presented at 35th Congress of the Federation-of-European-Biochemical-Societies, Gothenburg, Sweden, June 26-July 01, 2010. The FEBS Journal, 277(Suppl. 1), 231-231
Open this publication in new window or tab >>Modeling and Mutational analysis of Anion transporter 1 protein of Arabidopsis thaliana
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2010 (English)In: The FEBS Journal, ISSN 1742-464X, E-ISSN 1742-4658, Vol. 277, no Suppl. 1, p. 231-231Article in journal, Meeting abstract (Other academic) Published
Abstract [en]

The  thylakoid   anion  transporter 1  (ANTR1)   from  Arabidopsisthaliana,  has been characterized as a Na-dependent Pi transporter when expressed in E. coli (1), but  no data  is yet available  for the protein  structure  and  amino  acids involved in transport of Pi. In this  study  a  three-dimensional structural  model  of  ANTR1  was constructed in silico using the crystal structure  of glycerol-3- phosphate/phosphate antiporter from E. coli as a template.  Based on Multiple  Sequence Alignments (MSAs) with other plant  ANT- Rs  and  mammalian   SLC17  homologues,   five  highly  conserved amino  acids involved in Pi transport have been identified,  namely Arg-120, Ser-124 and Arg-201 inside the putative translocation pathway,  Arg-228  and  Asp-382  exposed  at  the  cytoplasmic  sur- face of the protein.  The activity of the protein  as a Na-dependent Pi transporter in the wild type and mutants  was analyzed  by het- erologous  expression  and  uptake   of  radioactive   Pi  into  E.  coli cells. Substitution of the three Arg (120, 201 and 228) for Glu residues  and  of Asp-382 for  an  Asn residue  resulted  in an  inac- tive ANTR1  transporter. All other  mutants  had sufficient activity to  allow  measurement   of  kinetic  parameters, attesting   that  the mutated  proteins  were functional.  Based on  our  results,  we pro- pose that Arg-201 is a critical residue for substrate  binding and translocation, whereas Ser-124 may function  as periplasmic  gate- way for  Na+   ions.  Residue  Arg-120  plays  an  important role  in Pi  binding  and  associated   conformational  changes,  and  finally that Arg-228 and Asp-382 only weakly participate  in interactions allowing conformational changes to occur at the cytoplasmic  sur-face of the transporter.

Place, publisher, year, edition, pages
Wiley-Blackwell, 2010
National Category
Engineering and Technology
Identifiers
urn:nbn:se:liu:diva-58961 (URN)000278565100804 ()
Conference
35th Congress of the Federation-of-European-Biochemical-Societies, Gothenburg, Sweden, June 26-July 01, 2010
Available from: 2010-09-03 Created: 2010-09-03 Last updated: 2017-12-12Bibliographically approved
Carlsson, J., Wedell, A. & Persson, B. (2009). A structural model of human steroid 11-betahydroxylase,CYP11B1, used to predict consequences of mutations.
Open this publication in new window or tab >>A structural model of human steroid 11-betahydroxylase,CYP11B1, used to predict consequences of mutations
2009 (English)Article in journal (Other academic) Submitted
Abstract [en]

A prediction method has been developed to estimate the severity of amino acid residue exchanges in human steroid 11-beta-hydroxylase, CYP11B1, due to mutations in the corresponding gene. The prediction is based both on structural and on sequence dependent parameters. The method uses two approaches; one with general molecular property weights and one with a consensus voting strategy based upon distribution of molecular properties, which does not require any training. Both methods are tested on known mutations in CYP11B1 and result in 85% prediction accuracy. The consensus voting method is then further evaluated on 9 proteins with an average of 81% prediction accuracy. A server utilizing the results from the consensus voting on CYP11B1 is provided where the user can extract information about new mutants. A similar server is also provided for mutants in human steroid 21-hydroxylase (CYP21).

Keywords
CYP11B1, steroid 11-beta-hydroxylase, molecular modeling, structural prediction, mutations
National Category
Natural Sciences
Identifiers
urn:nbn:se:liu:diva-51118 (URN)
Available from: 2009-10-19 Created: 2009-10-19 Last updated: 2009-10-19Bibliographically approved
Carlsson, J., Soussi, T. & Persson, B. (2009). Investigation and prediction of the severity of p53 mutants using parameters from structural calculations. The FEBS Journal, 276(15), 4142-4155
Open this publication in new window or tab >>Investigation and prediction of the severity of p53 mutants using parameters from structural calculations
2009 (English)In: The FEBS Journal, ISSN 1742-464X, E-ISSN 1742-4658, Vol. 276, no 15, p. 4142-4155Article in journal (Refereed) Published
Abstract [en]

A method has been developed to predict the effects of mutations in the p53 cancer suppressor gene. The new method uses novel parameters combined with previously established parameters. The most important parameter is the stability measure of the mutated structure calculated using molecular modelling. For each mutant, a severity score is reported, which can be used for classification into deleterious and nondeleterious. Both structural features and sequence properties are taken into account. The method has a prediction accuracy of 77% on all mutants and 88% on breast cancer mutations affecting WAF1 promoter binding. When compared with earlier methods, using the same dataset, our method clearly performs better. As a result of the severity score calculated for every mutant, valuable knowledge can be gained regarding p53, a protein that is believed to be involved in over 50% of all human cancers.

Keywords
Cancer; molecular modelling; mutations; p53; structural prediction
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:liu:diva-20141 (URN)10.1111/j.1742-4658.2009.07124.x (DOI)
Available from: 2009-08-31 Created: 2009-08-31 Last updated: 2017-12-13Bibliographically approved
Carlsson, J. (2009). Mutational effects on protein structure and function. (Doctoral dissertation). Linköping: Linköping University Electronic Press
Open this publication in new window or tab >>Mutational effects on protein structure and function
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

In this thesis several important proteins are investigated from a structural perspective. Some of the proteins are disease related while other have important but not completely characterised functions. The techniques used are general as demonstrated by applications on metabolic proteins (CYP21, CYP11B1, IAPP, ADH3), regulatory proteins (p53, GDNF) and a transporter protein (ANTR1).

When the protein CYP21 (steroid 21-hydroxylase) is deficient it causes CAH (congenital adrenal hyperplasia). For this protein, there are about 60 known mutations with characterised clinical phenotypes. Using manual structural analysis we managed to explain the severity of all but one of the mutations. By observing the properties of these mutations we could perform good predictions on, at the time, not classified mutations.

For the cancer suppressor protein p53, there are over thousand mutations with known activity. To be able to analyse such a large number of mutations we developed an automated method for evaluation of the mutation effect called PREDMUT. In this method we include twelve different prediction parameters including two energy parameters calculated using an energy minimization procedure. The method manages to differentiate severe mutations from non-severe mutations with 77% accuracy on all possible single base substitutions and with 88% on mutations found in breast cancer patients.

The automated prediction was further applied to CYP11B1 (steroid 11-beta-hydroxylase), which in a similar way as CYP21 causes CAH when deficient. A generalized method applicable to any kind of globular protein was developed. The method was subsequently evaluated on nine additional proteins for which mutants were known with annotated disease phenotypes. This prediction achieved 84% accuracy on CYP11B1 and 81% accuracy in total on the evaluation proteins while leaving 8% as unclassified. By increasing the number of unclassified mutations the accuracy of the remaining mutations could be increased on the evaluation proteins and substantially increase the classification quality as measured by the Matthews correlation coefficient. Servers with predictions for all possible single based substitutions are provided for p53, CYP21 and CYP11B1.

The amyloid formation of IAPP (islet amyloid polypeptide) is strongly connected to diabetes and has been studied using both molecular dynamics and Monte Carlo energy minimization. The effects of mutations on the amount and speed of amyloid formation were investigated using three approaches. Applying a consensus of the three methods on a number of interesting mutations, 94% of the mutations could be correctly classified as amyloid forming or not, evaluated with in vitro measurements.

In the brain there are many proteins whose functions and interactions are largely unknown. GDNF (glial cell line-derived neurotrophic factor) and NCAM (neural cell adhesion molecule) are two such neuron connected proteins that are known to interact. The form of interaction was studied using protein--protein docking where a docking interface was found mediated by four oppositely charged residues in respective protein. This interface was subsequently confirmed by mutagenesis experiments. The NCAM dimer interface upon binding to the GDNF dimer was also mapped as well as an additional interacting protein, GFRα1, which was successfully added to the protein complex without any clashes.

A large and well studied protein family is the alcohol dehydrogenase family, ADH. A class of this family is ADH3 (alcohol dehydrogenase class III) that has several known substrates and inhibitors. By using virtual screening we tried to characterize new ligands. As some ligands were already known we could incorporate this knowledge when the compound docking simulations were scored and thereby find two new substrates and two new inhibitors which were subsequently successfully tested in vitro.

ANTR1 (anion transporter 1) is a membrane bound transporter important in the photosynthesis in plants. To be able to study the amino acid residues involved in inorganic phosphate transportation a homology model of the protein was created. Important residues were then mapped onto the structure using conservation analysis and we were in this way able to propose roles of amino acid residues involved in the transportation of inorganic phosphate. Key residues were subsequently mutated in vitro and a transportation process could be postulated.

To conclude, we have used several molecular modelling techniques to find functional clues, interaction sites and new ligands. Furthermore, we have investigated the effect of muations on the function and structure of a multitude of disease related proteins.

 

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2009. p. 80
Series
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 1271
Keywords
Mutation, prediction, phenotypes, homology model, virtual screening, molecular dynamics, amyloid, cancer, membrane protein
National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:liu:diva-50491 (URN)978-91-7393-539-9 (ISBN)
Public defence
2009-11-06, Planck, Fysikhuset, Campus Valla, Linköpings universitet, Linköping, 10:00 (English)
Opponent
Supervisors
Available from: 2009-10-19 Created: 2009-10-12 Last updated: 2009-10-19Bibliographically approved
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