A1 Journal article (refereed)
Protonation of the Biliverdin IXα Chromophore in the Red and Far-Red Photoactive States of Bacteriophytochrome (2019)
Modi, V., Donnini, S., Groenhof, G., & Morozov, D. (2019). Protonation of the Biliverdin IXα Chromophore in the Red and Far-Red Photoactive States of Bacteriophytochrome. Journal of Physical Chemistry B, 123(10), 2325-2334. https://doi.org/10.1021/acs.jpcb.9b01117
JYU authors or editors
Publication details
All authors or editors: Modi, Vaibhav; Donnini, Serena; Groenhof, Gerrit; Morozov, Dmitry
Journal or series: Journal of Physical Chemistry B
ISSN: 1520-6106
eISSN: 1520-5207
Publication year: 2019
Volume: 123
Issue number: 10
Pages range: 2325-2334
Publisher: American Chemical Society
Publication country: United States
Publication language: English
DOI: https://doi.org/10.1021/acs.jpcb.9b01117
Publication open access: Openly available
Publication channel open access: Partially open access channel
Publication is parallel published (JYX): https://jyx.jyu.fi/handle/123456789/63174
Abstract
The tetrapyrrole chromophore biliverdin IXα (BV) in the bacteriophytochrome from Deinococcus radiodurans (DrBphP) is usually assumed to be fully protonated, but this assumption has not been systematically validated by experiments or extensive computations. Here, we use force field molecular dynamics simulations and quantum mechanics/molecular mechanics calculations with density functional theory and XMCQDPT2 methods to investigate the effect of the five most probable protonation forms of BV on structural stability, binding pocket interactions, and absorption spectra in the two photochromic states of DrBphP. While agreement with X-ray structural data and measured UV/vis spectra suggest that in both states the protonated form of the chromophore dominates, we also find that a minor population with a deprotonated D-ring could contribute to the red-shifted tail in the absorption spectra.
Keywords: photochemistry; proteins; molecular dynamics; quantum chemistry
Free keywords: phytochrome; excited states
Contributing organizations
Related projects
- FluProCad: a software package for computer aided disign of fluorescent proteins
- Groenhof, Gerrit
- Research Council of Finland
- Excitation energy transfer in chemical and biological systems
- Morozov, Dmitry
- Research Council of Finland
- Rakenne-dynamiikka-toiminnan suhteet phy
- Donnini, Serena
- Research Council of Finland
Ministry reporting: Yes
Reporting Year: 2019
JUFO rating: 1