Beyond standard molecular dynamics: Investigating the molecular mechanisms of G protein-coupled receptors with enhanced molecular dynamics methods

Jennifer M. Johnston, Marta Filizola

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

21 Scopus citations

Abstract

The majority of biological processes mediated by G Protein-Coupled Receptors (GPCRs) take place on timescales that are not conveniently accessible to standard molecular dynamics (MD) approaches, notwithstanding the current availability of specialized parallel computer architectures, and efficient simulation algorithms. Enhanced MD-based methods have started to assume an important role in the study of the rugged energy landscape of GPCRs by providing mechanistic details of complex receptor processes such as ligand recognition, activation, and oligomerization. We provide here an overview of these methods in their most recent application to the field.

Original languageEnglish
Title of host publicationG Protein-Coupled Receptors - Modeling and Simulation
PublisherSpringer New York LLC
Pages95-125
Number of pages31
ISBN (Print)9789400774223
DOIs
StatePublished - 2014

Publication series

NameAdvances in Experimental Medicine and Biology
Volume796
ISSN (Print)0065-2598

Keywords

  • Biased simulations
  • Coarse-graining
  • Dimers
  • Enhanced methods
  • Free-energy calculations
  • GPCR activation
  • GPCR dynamics
  • GPCR function
  • GPCR structure
  • Ligand recognition
  • Metadynamics
  • Molecular mechanisms
  • Oligomerization
  • Umbrella sampling

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