(Q30588355)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24889093%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

title

Structure-based simulations reveal concerted dynamics of GPCR activation (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24889093%20AND%20SRC:MED&resulttype=core&format=json

G protein-coupled receptor

19 March 2020

main subject

0 references

author

Nicholas Leioatts

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24889093%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

Alan Grossfield

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24889093%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

author name string

Pooja Suresh

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24889093%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

Tod D Romo

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24889093%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

language of work or name

English

0 references

publication date

9 June 2014

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24889093%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24889093%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

volume

82

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24889093%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

issue

10

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24889093%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

page(s)

2538-2551

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24889093%20AND%20SRC:MED&resulttype=core&format=json

Statistical Convergence of Equilibrium Properties in Simulations of Molecular Solutes Embedded in Lipid Bilayers.

19 March 2020

cites work

1 reference

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

20 June 2018

1 reference

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Retinal ligand mobility explains internal hydration and reconciles active rhodopsin structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Emerging paradigms in GPCR allostery: implications for drug discovery

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Activation and dynamic network of the M2 muscarinic receptor

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

The interplay of structure and dynamics: insights from a survey of HIV-1 reverse transcriptase crystal structures.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Ligand-dependent activation and deactivation of the human adenosine A(2A) receptor.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Substrate-specific reorganization of the conformational ensemble of CSK implicates novel modes of kinase function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Elastic Network Models are Robust to Variations in Formalism

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Agonist dynamics and conformational selection during microsecond simulations of the A(2A) adenosine receptor

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Biomolecular dynamics: order-disorder transitions and energy landscapes

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

The shadow map: a general contact definition for capturing the dynamics of biomolecular folding and function

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Ligand-dependent conformations and dynamics of the serotonin 5-HT(2A) receptor determine its activation and membrane-driven oligomerization properties

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Action of molecular switches in GPCRs--theoretical and experimental studies.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Activation mechanism of the β2-adrenergic receptor

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Ligand-induced modulation of the free-energy landscape of G protein-coupled receptors explored by adaptive biasing techniques

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Molecular simulations and solid-state NMR investigate dynamical structure in rhodopsin activation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Crystal structure of the β2 adrenergic receptor-Gs protein complex

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Showcasing modern molecular dynamics simulations of membrane proteins through G protein-coupled receptors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Structural insights into agonist-induced activation of G-protein-coupled receptors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Recent progress in the study of G protein-coupled receptors with molecular dynamics computer simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Crystal structure of metarhodopsin II

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

The structural basis of agonist-induced activation in constitutively active rhodopsin

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Retinal dynamics underlie its switch from inverse agonist to agonist during rhodopsin activation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Structure of a nanobody-stabilized active state of the β(2) adrenoceptor

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Conserved Binding Mode of Human β 2 Adrenergic Receptor Inverse Agonists and Antagonist Revealed by X-ray Crystallography

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

SMOG@ctbp: simplified deployment of structure-based models in GROMACS

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Concerted interconversion between ionic lock substates of the beta(2) adrenergic receptor revealed by microsecond timescale molecular dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

LOOS: an extensible platform for the structural analysis of simulations.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

A G protein-coupled receptor at work: the rhodopsin model.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

The structure and function of G-protein-coupled receptors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Ligand binding and micro-switches in 7TM receptor structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Comparative analysis of GPCR crystal structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Helix movement is coupled to displacement of the second extracellular loop in rhodopsin activation.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

An all-atom structure-based potential for proteins: bridging minimal models with all-atom empirical forcefields

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Extracting function from a beta-trefoil folding motif

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Crystal structure of the ligand-free G-protein-coupled receptor opsin

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

High-resolution distance mapping in rhodopsin reveals the pattern of helix movement due to activation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

New G-protein-coupled receptor crystal structures: insights and limitations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Coarse-grained free energy functions for studying protein conformational changes: a double-well network model

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Conformational complexity of G-protein-coupled receptors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Conformational transitions of adenylate kinase: switching by cracking

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

How many drug targets are there?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Crystal structure of a photoactivated deprotonated intermediate of rhodopsin

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Folding-based molecular simulations reveal mechanisms of the rotary motor F1-ATPase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Molecular mechanism of 7TM receptor activation--a global toggle switch model

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Comparative molecular dynamics--similar folds and similar motions?

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Role of the conserved NPxxY(x)5,6F motif in the rhodopsin ground state and during activation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Escaping free-energy minima

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Beta2 adrenergic receptor activation. Modulation of the proline kink in transmembrane 6 by a rotamer toggle switch

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Activation of the beta 2-adrenergic receptor involves disruption of an ionic lock between the cytoplasmic ends of transmembrane segments 3 and 6.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Crystal structure of rhodopsin: A G protein-coupled receptor

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Essential dynamics of proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Projection of Monte Carlo and molecular dynamics trajectories onto the normal mode axes: human lysozyme

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

Respective roles of short- and long-range interactions in protein folding

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4177312

The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure

20 June 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24617

Replica Monte Carlo simulation of spin glasses.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24617

Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24617

Simple energy landscape model for the kinetics of functional transitions in proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24617

Convergence of sampling in protein simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24617

Accurate and efficient description of protein vibrational dynamics: comparing molecular dynamics and Gaussian models

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24617

Functional role of the "ionic lock"--an interhelical hydrogen-bond network in family A heptahelical receptors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24617

Topological frustration and the folding of interleukin-1 beta

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24617

Slow Protein Conformational Dynamics from Multiple Experimental Structures: The Helix/Sheet Transition of Arc Repressor

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FPROT.24617

Block Covariance Overlap Method and Convergence in Molecular Dynamics Simulation

21 January 2018

1 reference

12 December 2020

Requirement of rigid-body motion of transmembrane helices for light activation of rhodopsin

1 reference

12 December 2020

Structure and function in rhodopsin: effects of disulfide cross-links in the cytoplasmic face of rhodopsin on transducin activation and phosphorylation by rhodopsin kinase

1 reference

12 December 2020

Convergence of molecular dynamics simulations of membrane proteins

1 reference

12 December 2020

Identifiers

DOI

10.1002/PROT.24617

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24889093%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24889093%20AND%20SRC:MED&resulttype=core&format=json

19 March 2020

PubMed publication ID

24889093

1 reference