Literature DB >> 31096158

Allostery in G protein-coupled receptors investigated by molecular dynamics simulations.

João Marcelo Lamim Ribeiro1, Marta Filizola2.   

Abstract

G-protein-coupled receptors (GPCRs) are allosteric signaling machines that trigger distinct functional responses depending on the particular conformational state they adopt upon binding. This so-called GPCR functional selectivity is prompted by ligands of different efficacy binding at orthosteric or allosteric sites on the receptor, as well as by interactions with intracellular protein partners or other receptor types. Molecular dynamics (MD) simulations can provide important mechanistic, thermodynamic, and kinetic insights into these interactions at a level of molecular detail that is necessary to rightly inform modern drug discovery. Here, we review the most recent MD contributions to understanding GPCR allostery, with an emphasis on their strengths and limitations.
Copyright © 2019 Elsevier Ltd. All rights reserved.

Entities:  

Year:  2019        PMID: 31096158      PMCID: PMC6692184          DOI: 10.1016/j.sbi.2019.03.016

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  32 in total

1.  On-the-Fly Learning and Sampling of Ligand Binding by High-Throughput Molecular Simulations.

Authors:  S Doerr; G De Fabritiis
Journal:  J Chem Theory Comput       Date:  2014-04-04       Impact factor: 6.006

2.  Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs.

Authors:  Ron O Dror; Hillary F Green; Celine Valant; David W Borhani; James R Valcourt; Albert C Pan; Daniel H Arlow; Meritxell Canals; J Robert Lane; Raphaël Rahmani; Jonathan B Baell; Patrick M Sexton; Arthur Christopoulos; David E Shaw
Journal:  Nature       Date:  2013-10-13       Impact factor: 49.962

Review 3.  GPCR Dynamics: Structures in Motion.

Authors:  Naomi R Latorraca; A J Venkatakrishnan; Ron O Dror
Journal:  Chem Rev       Date:  2016-09-13       Impact factor: 60.622

4.  Induced effects of sodium ions on dopaminergic G-protein coupled receptors.

Authors:  Jana Selent; Ferran Sanz; Manuel Pastor; Gianni De Fabritiis
Journal:  PLoS Comput Biol       Date:  2010-08-12       Impact factor: 4.475

5.  Gi- and Gs-coupled GPCRs show different modes of G-protein binding.

Authors:  Ned Van Eps; Christian Altenbach; Lydia N Caro; Naomi R Latorraca; Scott A Hollingsworth; Ron O Dror; Oliver P Ernst; Wayne L Hubbell
Journal:  Proc Natl Acad Sci U S A       Date:  2018-02-20       Impact factor: 11.205

6.  Structural insights into the subtype-selective antagonist binding to the M2 muscarinic receptor.

Authors:  Ryoji Suno; Sangbae Lee; Shoji Maeda; Satoshi Yasuda; Keitaro Yamashita; Kunio Hirata; Shoichiro Horita; Maki S Tawaramoto; Hirokazu Tsujimoto; Takeshi Murata; Masahiro Kinoshita; Masaki Yamamoto; Brian K Kobilka; Nagarajan Vaidehi; So Iwata; Takuya Kobayashi
Journal:  Nat Chem Biol       Date:  2018-11-12       Impact factor: 15.040

7.  Kinetic and thermodynamic insights into sodium ion translocation through the μ-opioid receptor from molecular dynamics and machine learning analysis.

Authors:  Xiaohu Hu; Yibo Wang; Amanda Hunkele; Davide Provasi; Gavril W Pasternak; Marta Filizola
Journal:  PLoS Comput Biol       Date:  2019-01-24       Impact factor: 4.475

8.  Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways.

Authors:  Kai J Kohlhoff; Diwakar Shukla; Morgan Lawrenz; Gregory R Bowman; David E Konerding; Dan Belov; Russ B Altman; Vijay S Pande
Journal:  Nat Chem       Date:  2013-12-15       Impact factor: 24.427

9.  Proposed Mode of Binding and Action of Positive Allosteric Modulators at Opioid Receptors.

Authors:  Yi Shang; Holly R Yeatman; Davide Provasi; Andrew Alt; Arthur Christopoulos; Meritxell Canals; Marta Filizola
Journal:  ACS Chem Biol       Date:  2016-02-17       Impact factor: 5.100

10.  Catalytic activation of β-arrestin by GPCRs.

Authors:  Kelsie Eichel; Damien Jullié; Benjamin Barsi-Rhyne; Naomi R Latorraca; Matthieu Masureel; Jean-Baptiste Sibarita; Ron O Dror; Mark von Zastrow
Journal:  Nature       Date:  2018-05-02       Impact factor: 49.962

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  6 in total

1.  Current Trends in GPCR Allostery.

Authors:  Khuraijam Dhanachandra Singh; Sadashiva S Karnik
Journal:  J Membr Biol       Date:  2021-01-20       Impact factor: 1.843

2.  Identification of ligand-specific G protein-coupled receptor states and prediction of downstream efficacy via data-driven modeling.

Authors:  Oliver Fleetwood; Jens Carlsson; Lucie Delemotte
Journal:  Elife       Date:  2021-01-28       Impact factor: 8.140

3.  Dynamical Correlations Reveal Allosteric Sites in G Protein-Coupled Receptors.

Authors:  Pedro Renault; Jesús Giraldo
Journal:  Int J Mol Sci       Date:  2020-12-27       Impact factor: 5.923

Review 4.  In Silico Drug Design for Purinergic GPCRs: Overview on Molecular Dynamics Applied to Adenosine and P2Y Receptors.

Authors:  Veronica Salmaso; Kenneth A Jacobson
Journal:  Biomolecules       Date:  2020-05-26

Review 5.  Insights From Molecular Dynamics Simulations of a Number of G-Protein Coupled Receptor Targets for the Treatment of Pain and Opioid Use Disorders.

Authors:  João Marcelo Lamim Ribeiro; Marta Filizola
Journal:  Front Mol Neurosci       Date:  2019-08-23       Impact factor: 5.639

Review 6.  DEER Analysis of GPCR Conformational Heterogeneity.

Authors:  Matthias Elgeti; Wayne L Hubbell
Journal:  Biomolecules       Date:  2021-05-22
  6 in total

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