Cargando…

Protonation of the Biliverdin IXα Chromophore in the Red and Far-Red Photoactive States of a Bacteriophytochrome

[Image: see text] 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...

Descripción completa

Detalles Bibliográficos
Autores principales: Modi, Vaibhav, Donnini, Serena, Groenhof, Gerrit, Morozov, Dmitry
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2019
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6727380/
https://www.ncbi.nlm.nih.gov/pubmed/30762368
http://dx.doi.org/10.1021/acs.jpcb.9b01117
_version_ 1783449238037856256
author Modi, Vaibhav
Donnini, Serena
Groenhof, Gerrit
Morozov, Dmitry
author_facet Modi, Vaibhav
Donnini, Serena
Groenhof, Gerrit
Morozov, Dmitry
author_sort Modi, Vaibhav
collection PubMed
description [Image: see text] 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.
format Online
Article
Text
id pubmed-6727380
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher American Chemical Society
record_format MEDLINE/PubMed
spelling pubmed-67273802019-09-06 Protonation of the Biliverdin IXα Chromophore in the Red and Far-Red Photoactive States of a Bacteriophytochrome Modi, Vaibhav Donnini, Serena Groenhof, Gerrit Morozov, Dmitry J Phys Chem B [Image: see text] 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. American Chemical Society 2019-02-14 2019-03-14 /pmc/articles/PMC6727380/ /pubmed/30762368 http://dx.doi.org/10.1021/acs.jpcb.9b01117 Text en Copyright © 2019 American Chemical Society This is an open access article published under a Creative Commons Attribution (CC-BY) License (http://pubs.acs.org/page/policy/authorchoice_ccby_termsofuse.html) , which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited.
spellingShingle Modi, Vaibhav
Donnini, Serena
Groenhof, Gerrit
Morozov, Dmitry
Protonation of the Biliverdin IXα Chromophore in the Red and Far-Red Photoactive States of a Bacteriophytochrome
title Protonation of the Biliverdin IXα Chromophore in the Red and Far-Red Photoactive States of a Bacteriophytochrome
title_full Protonation of the Biliverdin IXα Chromophore in the Red and Far-Red Photoactive States of a Bacteriophytochrome
title_fullStr Protonation of the Biliverdin IXα Chromophore in the Red and Far-Red Photoactive States of a Bacteriophytochrome
title_full_unstemmed Protonation of the Biliverdin IXα Chromophore in the Red and Far-Red Photoactive States of a Bacteriophytochrome
title_short Protonation of the Biliverdin IXα Chromophore in the Red and Far-Red Photoactive States of a Bacteriophytochrome
title_sort protonation of the biliverdin ixα chromophore in the red and far-red photoactive states of a bacteriophytochrome
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6727380/
https://www.ncbi.nlm.nih.gov/pubmed/30762368
http://dx.doi.org/10.1021/acs.jpcb.9b01117
work_keys_str_mv AT modivaibhav protonationofthebiliverdinixachromophoreintheredandfarredphotoactivestatesofabacteriophytochrome
AT donniniserena protonationofthebiliverdinixachromophoreintheredandfarredphotoactivestatesofabacteriophytochrome
AT groenhofgerrit protonationofthebiliverdinixachromophoreintheredandfarredphotoactivestatesofabacteriophytochrome
AT morozovdmitry protonationofthebiliverdinixachromophoreintheredandfarredphotoactivestatesofabacteriophytochrome