liu.seSearch for publications in DiVA
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • oxford
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Modeling of phytochrome absorption spectra
Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
Linköping University, Department of Physics, Chemistry and Biology, Computational Physics. Linköping University, The Institute of Technology.
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. Vol. 34, no 16, 1363-1374 p.
Keyword [en]
photosensory proteins, bilin chromophores, QM/MM methods, time-dependent density functional theory
National Category
Natural Sciences
Identifiers
URN: urn:nbn:se:liu:diva-92393DOI: 10.1002/jcc.23265ISI: 000318696800001OAI: oai:DiVA.org:liu-92393DiVA: diva2:620718
Available from: 2013-05-10 Created: 2013-05-10 Last updated: 2017-12-06Bibliographically approved
In thesis
1. Photochemical properties of phytochrome and firefly luciferase chromophores: A theoretical study
Open this publication in new window or tab >>Photochemical properties of phytochrome and firefly luciferase chromophores: A theoretical study
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: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 (English)
Opponent
Supervisors
Available from: 2014-01-17 Created: 2014-01-17 Last updated: 2014-01-22Bibliographically approved
2. Computational Studies of Photobiological Keto-Enol Reactions and Chromophores
Open this publication in new window or tab >>Computational Studies of Photobiological Keto-Enol Reactions and Chromophores
2015 (English)Doctoral thesis, comprehensive summary (Other academic)
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.

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2015. 76 p.
Series
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 1713
National Category
Theoretical Chemistry
Identifiers
urn:nbn:se:liu:diva-122614 (URN)10.3384/diss.diva-122614 (DOI)978-91-7685-922-3 (ISBN)
Public defence
2015-12-18, Nobel (BL32), B-huset, Campus Valla, Linköping, 13:15 (English)
Opponent
Supervisors
Available from: 2015-11-19 Created: 2015-11-11 Last updated: 2017-01-03Bibliographically approved

Open Access in DiVA

fulltext(616 kB)469 downloads
File information
File name FULLTEXT01.pdfFile size 616 kBChecksum SHA-512
b04ada2023c58ace9b2af1bbd9070c60a105f013c3627ef403da478990f3af11fd07b870b5902ae35c8a7cf4a4e02b092f8248c1a979364ef931f5a4c364fd94
Type fulltextMimetype application/pdf

Other links

Publisher's full text

Authority records BETA

Falklöf, OlleDurbeej, Bo

Search in DiVA

By author/editor
Falklöf, OlleDurbeej, Bo
By organisation
Computational PhysicsThe Institute of Technology
In the same journal
Journal of Computational Chemistry
Natural Sciences

Search outside of DiVA

GoogleGoogle Scholar
Total: 469 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

doi
urn-nbn

Altmetric score

doi
urn-nbn
Total: 175 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • oxford
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf