Quantum Mechanical and Molecular Mechanics Modeling of Membrane-Embedded Rhodopsins

Mikhail N. Ryazantsev, Dmitrii M. Nikolaev, Andrey V. Struts, Michael F. Brown

Research output: Contribution to journalReview articlepeer-review

2 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)425-449
Number of pages25
JournalJournal of Membrane Biology
Volume252
Issue number4-5
DOIs
StatePublished - Oct 1 2019

Keywords

  • GPCR
  • Membrane
  • Molecular dynamics
  • Protein dynamics
  • Quantum mechanics
  • Retinal

ASJC Scopus subject areas

  • Biophysics
  • Physiology
  • Cell Biology

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