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Red-light absorption and fluorescence of phytochrome chromophores: a comparative theoretical study
Linköpings universitet, Institutionen för fysik, kemi och biologi, Beräkningsfysik. Linköpings universitet, Tekniska högskolan.
Linköpings universitet, Institutionen för fysik, kemi och biologi, Beräkningsfysik. Linköpings universitet, Tekniska högskolan.
2013 (Engelska)Ingår i: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 425, s. 19-28Artikel i tidskrift (Refereegranskat) Published
Abstract [en]

Currently, much experimental effort is being invested in the engineering of phytochromes, a large superfamily of photoreceptor proteins, into fluorescent proteins suitable for bioimaging in the near-infrared regime. In this work, we gain insight into the potential of computational methods to contribute to this development by investigating how well representative quantum chemical methods reproduce recently recorded red-light absorption and emission maxima of synthetic derivatives of the bilin chromophores of phytochromes. Focusing on the performance of time-dependent density functional theory but using also the ab initio CIS(D), CC2 and CASPT2 methods, we explore how various methodological considerations influence computed spectra and find, somewhat surprisingly, that density functionals lacking exact exchange reproduce the experimental measurements with smaller errors than functionals that include exact exchange. Thus, for the important class of chromophores that bilins constitute, the widely established trend that hybrid functionals give more accurate excitation energies than pure functionals does not apply.

Ort, förlag, år, upplaga, sidor
Elsevier, 2013. Vol. 425, s. 19-28
Nyckelord [en]
bilin chromophores, photoreceptor proteins, fluorescent proteins, excited states, quantum chemistry
Nationell ämneskategori
Naturvetenskap
Identifikatorer
URN: urn:nbn:se:liu:diva-96694DOI: 10.1016/j.chemphys.2013.07.018ISI: 000327443700003OAI: oai:DiVA.org:liu-96694DiVA, id: diva2:642899
Anmärkning

Funding agencies|Linkoping University||Swedish Research Council||Olle Engkvist Foundation||Wenner-Gren Foundations||

Tillgänglig från: 2013-08-23 Skapad: 2013-08-23 Senast uppdaterad: 2017-12-06Bibliografiskt granskad
Ingår i avhandling
1. Photochemical properties of phytochrome and firefly luciferase chromophores: A theoretical study
Öppna denna publikation i ny flik eller fönster >>Photochemical properties of phytochrome and firefly luciferase chromophores: A theoretical study
2014 (Engelska)Licentiatavhandling, sammanläggning (Övrigt vetenskapligt)
Abstract [en]

This licentiate thesis presents computational chemistry studies on photochemical properties of phytochrome and firefly luciferase chromophores.

Phytochromes are bilin-containing proteins that based on the ambient light environment regulate a number of physiological and developmental processes in bacteria, cyanobacteria, fungi and plants. From the viewpoint of computational modeling, however, only a few studies have been devoted to these systems. In this thesis, two systematic studies comparing calculated and experimental UV-vis spectra of bilin chromophores in protein and solution environments are presented. The rst study focuses on how hybrid quantum mechanics/molecular mechanics methods are best applied to calculate absorption spectra of a bacteriophytochrome. The second study, in turn, investigates the performance of a number of quantum chemical methods in calculating absorption and emission spectra of sterically locked bilin chromophores.

Firefly luciferase catalyzes a chemical reaction in which the electronically excited oxyluciferin is formed and subsequently emits light. Depending on the conditions, oxyluciferin can exist in a number of dierent chemical forms. To date, there is no consensus regarding which of these that most signicantly contributes to the light emission. In this thesis, the most probable form of the light emitter is predicted by calculating excited-state pKE and pKa values, in aqueous solution, of the various equilibrium reactions relevant for the oxyluciferin system.

Ort, förlag, år, upplaga, sidor
Linköping: Linköping University Electronic Press, 2014. s. 43
Serie
Linköping Studies in Science and Technology. Thesis, ISSN 0280-7971 ; 1640
Nationell ämneskategori
Naturvetenskap
Identifikatorer
urn:nbn:se:liu:diva-103338 (URN)10.3384/lic.diva-103338 (DOI)978-91-7519-427-1 (ISBN)
Presentation
2014-02-07, Archimedes, B-huset, Campus Valla, Linköpings universitet, Linköping, 13:15 (Engelska)
Opponent
Handledare
Tillgänglig från: 2014-01-17 Skapad: 2014-01-17 Senast uppdaterad: 2014-01-22Bibliografiskt granskad
2. Computational Studies of Photobiological Keto-Enol Reactions and Chromophores
Öppna denna publikation i ny flik eller fönster >>Computational Studies of Photobiological Keto-Enol Reactions and Chromophores
2015 (Engelska)Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
Abstract [en]

This thesis presents computational chemistry studies of keto-enol reactions and chromophores of photobiological signicance.

The rst part of the thesis is concerned with two protein-bound chromophores that, depending on the chemical conditions, can exist in a number of dierent ketonic and enolic forms. The rst chromophore is astaxanthin, which occurs in the protein complex responsible for the deep-blue color of lobster carapace. By investigating how dierent forms of astaxanthin absorb UV-vis radiation of dierent wavelengths, a model is presented that explains the origin of the dramatic color change from deep-blue to red upon cooking of live lobsters.

The second chromophore is the oxyluciferin light emitter of fireflies, which is formed in the catalytic center of the enzyme firefly luciferase. To date, there is no consensus regarding which of the possible ketonic and enolic forms is the key contributor to the light emission. In the thesis, the intrinsic tendency of oxyluciferin to prefer one particular form over other possible forms is established through calculation of keto-enol and acid-base excited-state equilibrium constants in aqueous solution.

The second part of the thesis is concerned with two families of biological photoreceptors: the blue-light-absorbing LOV-domain proteins and the red-light-absorbing phytochromes. Based on the ambient light environment, these proteins regulate physiological and developmental processes by switching between inactive and active conformations. In both families, the conversion of the inactive into the active conformation is triggered by a chemical reaction of the respective chromophore.

The LOV-domain proteins bind a LOV-domain proteins bidn in flavin chromophore and regulate processes such as chloroplast relocation and phototropism in plants. An important step in the activation of these photoreceptors is a singlet-triplet transition between two electronically excited states of the flavin chromophore. In the thesis, this transition is used as a prototype example for illustrating, for the rst time, the ability of rst-principles methods to calculate rate constants of inter-excited state phosphorescence events.

Phytochromes, in turn, bind bilin chromophores and are active in the regulation of processes like seed germination and  flowering time in plants. Following two systematic studies identifying the best way to model the UV-vis absorption and fluorescence spectra of these photoreceptors, it is demonstrated that steric interactions between the chromophore and the apoprotein play a decisive role for how phytochromes are activated by light.

Ort, förlag, år, upplaga, sidor
Linköping: Linköping University Electronic Press, 2015. s. 76
Serie
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 1713
Nationell ämneskategori
Teoretisk kemi
Identifikatorer
urn:nbn:se:liu:diva-122614 (URN)10.3384/diss.diva-122614 (DOI)978-91-7685-922-3 (ISBN)
Disputation
2015-12-18, Nobel (BL32), B-huset, Campus Valla, Linköping, 13:15 (Engelska)
Opponent
Handledare
Tillgänglig från: 2015-11-19 Skapad: 2015-11-11 Senast uppdaterad: 2017-01-03Bibliografiskt granskad

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