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Computational chemistry provides versatile methods for studying the properties and functioning of biological systems at different levels of precision and at different time scales. The aim of this article is to review the computational methodologies that are applicable to rhodopsins as archetypes for photoactive membrane proteins that are of great importance both in nature and in modern technologies. For each class of computational techniques, from methods that use quantum mechanics for simulating rhodopsin photophysics to less-accurate coarse-grained methodologies used for long-scale protein dynamics, we consider possible applications and the main directions for improvement.
| Язык оригинала | Английский |
|---|---|
| Страницы (с-по) | 425-449 |
| Число страниц | 25 |
| Журнал | Journal of Membrane Biology |
| Том | 252 |
| Номер выпуска | 4-5 |
| DOI | |
| Состояние | Опубликовано - окт 2019 |
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Предметные области Scopus
- Биофизика
- Физиология
- Клеточная биология
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Quantum Mechanical and Molecular Mechanics Modeling of Membrane-Embedded Rhodopsins. / Ryazantsev, Mikhail N.; Nikolaev, Dmitrii M.; Struts, Andrey V.; Brown, Michael F.
В: Journal of Membrane Biology, Том 252, № 4-5, 10.2019, стр. 425-449.Результат исследований: Научные публикации в периодических изданиях › Обзорная статья
TY - JOUR
T1 - Quantum Mechanical and Molecular Mechanics Modeling of Membrane-Embedded Rhodopsins
AU - Ryazantsev, Mikhail N.
AU - Nikolaev, Dmitrii M.
AU - Struts, Andrey V.
AU - Brown, Michael F.
PY - 2019/10
Y1 - 2019/10
N2 - Computational chemistry provides versatile methods for studying the properties and functioning of biological systems at different levels of precision and at different time scales. The aim of this article is to review the computational methodologies that are applicable to rhodopsins as archetypes for photoactive membrane proteins that are of great importance both in nature and in modern technologies. For each class of computational techniques, from methods that use quantum mechanics for simulating rhodopsin photophysics to less-accurate coarse-grained methodologies used for long-scale protein dynamics, we consider possible applications and the main directions for improvement.
AB - Computational chemistry provides versatile methods for studying the properties and functioning of biological systems at different levels of precision and at different time scales. The aim of this article is to review the computational methodologies that are applicable to rhodopsins as archetypes for photoactive membrane proteins that are of great importance both in nature and in modern technologies. For each class of computational techniques, from methods that use quantum mechanics for simulating rhodopsin photophysics to less-accurate coarse-grained methodologies used for long-scale protein dynamics, we consider possible applications and the main directions for improvement.
KW - GPCR
KW - Membrane
KW - Molecular dynamics
KW - Protein dynamics
KW - Quantum mechanics
KW - Retinal
KW - PROTEIN-COUPLED RECEPTOR
KW - RESONANCE RAMAN-SPECTROSCOPY
KW - BETA(2) ADRENERGIC-RECEPTOR
KW - EXCITED-STATE RELAXATION
KW - PROTONATED SCHIFF-BASE
KW - FREE-ENERGY LANDSCAPES
KW - COARSE-GRAINED MODEL
KW - SODIUM-ION BINDING
KW - TIME-RESOLVED FTIR
KW - FORCE-FIELD
UR - http://www.scopus.com/inward/record.url?scp=85073556367&partnerID=8YFLogxK
UR - http://www.mendeley.com/research/quantum-mechanical-molecular-mechanics-modeling-membraneembedded-rhodopsins
U2 - 10.1007/s00232-019-00095-0
DO - 10.1007/s00232-019-00095-0
M3 - Обзорная статья
C2 - 31570961
VL - 252
SP - 425
EP - 449
JO - Journal of Membrane Biology
JF - Journal of Membrane Biology
SN - 0022-2631
IS - 4-5
ER -