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Photochemical properties of phytochrome and firefly luciferase chromophores: A theoretical study
Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
2014 (English)Licentiate thesis, comprehensive summary (Other academic)
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.

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2014. , 43 p.
Series
Linköping Studies in Science and Technology. Thesis, ISSN 0280-7971 ; 1640
National Category
Natural Sciences
Identifiers
URN: urn:nbn:se:liu:diva-103338DOI: 10.3384/lic.diva-103338ISBN: 978-91-7519-427-1 (print)OAI: oai:DiVA.org:liu-103338DiVA: diva2:688529
Presentation
2014-02-07, Archimedes, B-huset, Campus Valla, Linköpings universitet, Linköping, 13:15 (English)
Opponent
Supervisors
Available from: 2014-01-17 Created: 2014-01-17 Last updated: 2014-01-22Bibliographically approved
List of papers
1. Modeling of phytochrome absorption spectra
Open this publication in new window or tab >>Modeling of phytochrome absorption spectra
2013 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 34, no 16, 1363-1374 p.Article in journal (Refereed) Published
Abstract [en]

Phytochromes constitute one of the six well-characterized families of photosensory proteins in Nature. From the viewpoint of computational modeling, however, phytochromes have been the subject of much fewer studies than most other families of photosensory proteins, which is likely a consequence of relevant high-resolution structural data becoming available only in recent years. In this work, hybrid quantum mechanics/molecular mechanics (QM/MM) methods are used to calculate UV-vis absorption spectra of Deinococcus radiodurans bacteriophytochrome. We investigate how the choice of QM/MM methodology affects the resulting spectra and demonstrate that QM/MM methods can reproduce the experimental absorption maxima of both the Q and Soret bands with an accuracy of about 0.15 eV. Furthermore, we assess how the protein environment influences the intrinsic absorption of the bilin chromophore, with particular focus on the Q band underlying the primary photochemistry of phytochromes.

Place, publisher, year, edition, pages
John Wiley & Sons, 2013
Keyword
photosensory proteins, bilin chromophores, QM/MM methods, time-dependent density functional theory
National Category
Natural Sciences
Identifiers
urn:nbn:se:liu:diva-92393 (URN)10.1002/jcc.23265 (DOI)000318696800001 ()
Available from: 2013-05-10 Created: 2013-05-10 Last updated: 2017-12-06Bibliographically approved
2. Red-light absorption and fluorescence of phytochrome chromophores: a comparative theoretical study
Open this publication in new window or tab >>Red-light absorption and fluorescence of phytochrome chromophores: a comparative theoretical study
2013 (English)In: Chemical Physics, ISSN 0301-0104, E-ISSN 1873-4421, Vol. 425, 19-28 p.Article in journal (Refereed) 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.

Place, publisher, year, edition, pages
Elsevier, 2013
Keyword
bilin chromophores, photoreceptor proteins, fluorescent proteins, excited states, quantum chemistry
National Category
Natural Sciences
Identifiers
urn:nbn:se:liu:diva-96694 (URN)10.1016/j.chemphys.2013.07.018 (DOI)000327443700003 ()
Note

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

Available from: 2013-08-23 Created: 2013-08-23 Last updated: 2017-12-06Bibliographically approved
3. Deciphering Excited-State Protonation and Tautomeric States of Oxyluciferin through Calculation of Excited-State Equilibrium Constants
Open this publication in new window or tab >>Deciphering Excited-State Protonation and Tautomeric States of Oxyluciferin through Calculation of Excited-State Equilibrium Constants
2013 (English)Manuscript (preprint) (Other academic)
Abstract [en]

This study investigates the excited-state equilibria of the chemiexcited oxyluciferin light emitter responsible for the emission of light in firefly bioluminescence. To date, there is no consensus regarding which of the possible chemical forms connected by excited-state keto-enol and acid-base equilibrium reactions that is the main contributor to the light emission. Using a hybrid cluster-continuum approach, we perform quantum chemical calculations to obtain the relevant excited-state pKE and pKa values in aqueous solution. As such, we gain insight into the intrinsic tendency of the chemiexcited oxyluciferin light emitter to prefer a particular form.

National Category
Natural Sciences
Identifiers
urn:nbn:se:liu:diva-103337 (URN)
Available from: 2014-01-17 Created: 2014-01-17 Last updated: 2014-01-17Bibliographically approved

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Falklöf, Olle

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