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

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Related projects

Ministry reporting: Yes

Reporting Year: 2019

JUFO rating: 1