NMR chemical shifts of the rhodopsin chromophore in the dark state and in bathorhodopsin: a hybrid QM/MM molecular dynamics study.

Details

Serval ID
serval:BIB_1F88880CCC9D
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
NMR chemical shifts of the rhodopsin chromophore in the dark state and in bathorhodopsin: a hybrid QM/MM molecular dynamics study.
Journal
Journal of Physical Chemistry. B
Author(s)
Röhrig U.F., Sebastiani D.
ISSN
1520-6106 (Print)
ISSN-L
1520-5207
Publication state
Published
Issued date
2008
Peer-reviewed
Oui
Volume
112
Number
4
Pages
1267-1274
Language
english
Abstract
We investigate nuclear magnetic resonance (NMR) parameters of the rhodopsin chromophore in the dark state of the protein and in the early photointermediate bathorhodopsin via first-principles molecular dynamics simulations and NMR chemical shift calculations in a hybrid quantum/classical (QM/MM) framework. NMR parameters are particularly sensitive to structural properties and to the chemical environment, which allows us to address different questions about the retinal chromophore in situ. Our calculations show that both the 13C and the 1H NMR chemical shifts are rather insensitive to the protonation state of Glu181, an ionizable amino acid side chain located in the vicinity of the isomerizing 11-cis bond. Thus, other techniques should be better suited to establish its protonation state. The calculated chemical shifts for bathorhodopsin further support our previously published theoretical structure, which is in very good agreement with more recent X-ray data.
Keywords
Carbon/chemistry, Darkness, Magnetic Resonance Spectroscopy, Models, Molecular, Molecular Structure, Protons, Rhodopsin/chemistry
Pubmed
Web of science
Create date
30/10/2015 9:18
Last modification date
20/08/2019 12:55
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