On the functional significance of soft modes predicted by coarse-grained models for membrane proteins (Q41172407)

27 September 2017

On the functional significance of soft modes predicted by coarse-grained models for membrane proteins (English)

1 reference

27 September 2017

1 reference

Ivet Bahar

0 references

language of work or name

1 reference

1 June 2010

1 reference

The Journal of General Physiology

27 September 2017

1 reference

27 September 2017

135

1 reference

27 September 2017

1 reference

27 September 2017

563-573

1 reference

Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

A flexible docking scheme to explore the binding selectivity of PDZ domains

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Global dynamics of proteins: bridging between structure and function

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Hierarchical coarse-graining strategy for protein-membrane systems to access mesoscopic scales

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Inward-facing conformation of glutamate transporters as revealed by their inverted-topology structural repeats.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Transport mechanism of a bacterial homologue of glutamate transporters.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

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

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Molecular simulations elucidate the substrate translocation pathway in a glutamate transporter

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Structural analysis of ion selectivity in the NaK channel

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Structure of a potentially open state of a proton-activated pentameric ligand-gated ion channel

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Time-resolved mechanism of extracellular gate opening and substrate binding in a glutamate transporter

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Principles of flexible protein-protein docking

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

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

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Recognition dynamics up to microseconds revealed from an RDC-derived ubiquitin ensemble in solution

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Mechanism of signal propagation upon retinal isomerization: insights from molecular dynamics simulations of rhodopsin restrained by normal modes

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Signal propagation in proteins and relation to equilibrium fluctuations

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Coarse-grained biomolecular simulation with REACH: realistic extension algorithm via covariance Hessian.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Determination of conformationally heterogeneous states of proteins

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Coupling substrate and ion binding to extracellular gate of a sodium-dependent aspartate transporter

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Association of putative concave protein-binding sites with the fluctuation behavior of residues

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Relation between native ensembles and experimental structures of proteins

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Common mechanism of pore opening shared by five different potassium channels

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Can conformational change be described by only a few normal modes?

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Normal mode analysis suggests a quaternary twist model for the nicotinic receptor gating mechanism

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Molecular dynamics simulation of the M2 helices within the nicotinic acetylcholine receptor transmembrane domain: structure and collective motions

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

An analysis of core deformations in protein superfamilies

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Sulfhydryl modification of V449C in the glutamate transporter EAAT1 abolishes substrate transport but not the substrate-gated anion conductance

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Structural models of the MscL gating mechanism

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Anisotropy of fluctuation dynamics of proteins with an elastic network model

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Structural rearrangements underlying K+-channel activation gating

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

The normal modes of the gramicidin-A dimer channel

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

oGNM: online computation of structural dynamics using the Gaussian Network Model

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Dynamical properties of the MscL of Escherichia coli: a normal mode analysis

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Conformational change of proteins arising from normal mode calculations

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Activation of the ghrelin receptor is described by a privileged collective motion: a model for constitutive and agonist-induced activation of a sub-class A G-protein coupled receptor (GPCR).

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Protein-ligand docking accounting for receptor side chain and global flexibility in normal modes: evaluation on kinase inhibitor cross docking

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Normal mode partitioning of Langevin dynamics for biomolecules

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Langevin dynamics of molecules with internal rigid fragments in the harmonic regime.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Predisposition of the dark state of rhodopsin to functional changes in structure

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Anisotropic network model: systematic evaluation and a new web interface

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

The open state gating mechanism of gramicidin a requires relative opposed monomer rotation and simultaneous lateral displacement

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Channel opening motion of alpha7 nicotinic acetylcholine receptor as suggested by normal mode analysis

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

Representing receptor flexibility in ligand docking through relevant normal modes.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2888054

How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis

19 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1085%2FJGP.200910368

Normal mode analysis as a prerequisite for drug design: Application to matrix metalloproteinases inhibitors

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1085%2FJGP.200910368

Functional modes of proteins are among the most robust

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20513758

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Comparisons of protein family dynamics

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20513758

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Dynamics of heteropentameric nicotinic acetylcholine receptor: implications of the gating mechanism

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20513758

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1085/JGP.200910368

1 reference

27 September 2017

1 reference

PMC publication ID

2888054

27 September 2017

PubMed publication ID

20513758

1 reference

PMC publication ID

2888054