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Visual pigment rhodopsin : a computer simulation of the molecular dynamics of 11-cis-retinal chromophore and amino-acid residues in the chromophore centre

Kholmirzo Tagoikulovich Kholmurodov 1
Kholmirzo Tagoikulovich Kholmurodov
, 
Tatyana Borisovna Feldman 2
Tatyana Borisovna Feldman
, 
Mikhail Arkad'evich Ostrovsky 2
Mikhail Arkad'evich Ostrovsky
10.1070/MC2006v016n01ABEH002255
Published 2006-01-31
Focus article , Volume 16, Issue 1, 1-8
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Kholmurodov K. T., Feldman T. B., Ostrovsky M. A. Visual pigment rhodopsin : a computer simulation of the molecular dynamics of 11-cis-retinal chromophore and amino-acid residues in the chromophore centre // Mendeleev Communications. 2006. Vol. 16. No. 1. pp. 1-8.
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Kholmurodov K. T., Feldman T. B., Ostrovsky M. A. Visual pigment rhodopsin : a computer simulation of the molecular dynamics of 11-cis-retinal chromophore and amino-acid residues in the chromophore centre // Mendeleev Communications. 2006. Vol. 16. No. 1. pp. 1-8.
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TY - JOUR
DO - 10.1070/MC2006v016n01ABEH002255
UR - https://mendcomm.colab.ws/publications/10.1070/MC2006v016n01ABEH002255
TI - Visual pigment rhodopsin : a computer simulation of the molecular dynamics of 11-cis-retinal chromophore and amino-acid residues in the chromophore centre
T2 - Mendeleev Communications
AU - Kholmurodov, Kholmirzo Tagoikulovich
AU - Feldman, Tatyana Borisovna
AU - Ostrovsky, Mikhail Arkad'evich
PY - 2006
DA - 2006/01/31
PB - Mendeleev Communications
SP - 1-8
IS - 1
VL - 16
ER -
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@article{2006_Kholmurodov,
author = {Kholmirzo Tagoikulovich Kholmurodov and Tatyana Borisovna Feldman and Mikhail Arkad'evich Ostrovsky},
title = {Visual pigment rhodopsin : a computer simulation of the molecular dynamics of 11-cis-retinal chromophore and amino-acid residues in the chromophore centre},
journal = {Mendeleev Communications},
year = {2006},
volume = {16},
publisher = {Mendeleev Communications},
month = {Jan},
url = {https://mendcomm.colab.ws/publications/10.1070/MC2006v016n01ABEH002255},
number = {1},
pages = {1--8},
doi = {10.1070/MC2006v016n01ABEH002255}
}
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Kholmurodov, Kholmirzo Tagoikulovich, et al. “Visual pigment rhodopsin : a computer simulation of the molecular dynamics of 11-cis-retinal chromophore and amino-acid residues in the chromophore centre.” Mendeleev Communications, vol. 16, no. 1, Jan. 2006, pp. 1-8. https://mendcomm.colab.ws/publications/10.1070/MC2006v016n01ABEH002255.
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Abstract

Based on a computer molecular simulation, we have investigated the conformational dynamics of rhodopsin and its free opsin. A special emphasis was made on the behaviour of the chromophore group – 11-cis-retinal within the rhodopsin molecule in its dark-adapted state. The molecular dynamics trajectories were traced in the time range of 3000 ps. We have generated 3×106 discrete states of free opsin and rhodopsin in order to compare the rhodopsin and opsin structural conformation changes. Analysis of the 11-cis-retinal adjustment process in the chromophore site of opsin in correlation with the behaviour of the nearest surrounding amino acid residues has been carried out. The possible molecular mechanisms of the conformational adaptation of 11-cis-retinal in the protein binding pocket, which occur during the physiological regeneration of the visual pigment rhodopsin, are discussed.

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