Understanding G protein-coupled receptor allostery via molecular dynamics simulations: Implications for drug discovery

Shaherin Basith, Yoonji Lee, Sun Choi

Research output: Chapter in Book/Report/Conference proceedingChapter

4 Scopus citations

Abstract

Unraveling the mystery of protein allostery has been one of the greatest challenges in both structural and computational biology. However, recent advances in computational methods, particularly molecular dynamics (MD) simulations, have led to its utility as a powerful and popular tool for the study of protein allostery. By capturing the motions of a protein’s constituent atoms, simulations can enable the discovery of allosteric hot spots and the determination of the mechanistic basis for allostery. These structural and dynamic studies can provide a foundation for a wide range of applications, including rational drug design and protein engineering. In our laboratory, the use of MD simulations and network analysis assisted in the elucidation of the allosteric hotspots and intracellular signal transduction of G protein-coupled receptors (GPCRs), primarily on one of the adenosine receptor subtypes, A 2A adenosine receptor (A 2A AR). In this chapter, we describe a method for calculating the map of allosteric signal flow in different GPCR conformational states and illustrate how these concepts have been utilized in understanding the mechanism of GPCR allostery. These structural studies will provide valuable insights into the allosteric and orthosteric modulations that would be of great help to design novel drugs targeting GPCRs in pathological states.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages455-472
Number of pages18
DOIs
StatePublished - Jan 1 2018
Externally publishedYes

Publication series

NameMethods in Molecular Biology
Volume1762
ISSN (Print)1064-3745

Keywords

  • Allostery
  • G protein-coupled receptor
  • Hotspots
  • Molecular dynamics simulation
  • Network model
  • Structural ensembles

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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    Basith, S., Lee, Y., & Choi, S. (2018). Understanding G protein-coupled receptor allostery via molecular dynamics simulations: Implications for drug discovery. In Methods in Molecular Biology (pp. 455-472). (Methods in Molecular Biology; Vol. 1762). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-7756-7_23