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The Journal of Membrane Biology

, Volume 252, Issue 4–5, pp 425–449 | Cite as

Quantum Mechanical and Molecular Mechanics Modeling of Membrane-Embedded Rhodopsins

  • Mikhail N. Ryazantsev
  • Dmitrii M. Nikolaev
  • Andrey V. Struts
  • Michael F. BrownEmail author
Article
  • 139 Downloads
Part of the following topical collections:
  1. Membrane and Receptor Dynamics

Abstract

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.

Keywords

GPCR Membrane Molecular dynamics Protein dynamics Quantum mechanics Retinal 

Notes

Funding

This work was supported by the US National Institutes of Health (EY012049 and EY02604) and by the US National Science Foundation (MCB 1817862 and CHE 1904125) (to M.F.B.). A.V.S. was supported by the Russian Foundation for Basic Research (Grant 16-04-00494A). M.N.R. was supported by the Skolkovo Foundation (Grant agreement for Russian educational and scientific organization No. 7 dd 19.12.2017) and the Skolkovo Institute of Science and Technology (General agreement No. 3663-MRA dd 25.12.2017).

Compliance with Ethical Standards

Conflict of interest

The authors declare that they have no conflicts of interest.

Research Involving Human and Animal Participants

This article does not contain any studies with human participants or animals performed by any of the authors.

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© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Institute of ChemistrySaint Petersburg State UniversitySaint PetersburgRussia
  2. 2.Saint-Petersburg Academic University – Nanotechnology Research and Education Centre RASSaint PetersburgRussia
  3. 3.Department of Chemistry and BiochemistryUniversity of ArizonaTucsonUSA
  4. 4.Laboratory of Biomolecular NMRSaint Petersburg State UniversitySaint PetersburgRussia
  5. 5.Department of PhysicsUniversity of ArizonaTucsonUSA

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