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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...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical
Society
2019
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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 |
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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 |
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