(Q30498314)

19 October 2017

Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins (English)

1 reference

19 October 2017

2

Peter G Wolynes

1 reference

19 October 2017

Wenfei Li

1

1 reference

19 October 2017

Shoji Takada

series ordinal

3

1 reference

19 October 2017

language of work or name

English

0 references

publication date

9 February 2011

1 reference

Proceedings of the National Academy of Sciences of the United States of America

19 October 2017

1 reference

19 October 2017

108

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19 October 2017

9

1 reference

19 October 2017

3504-3509

1 reference

On the role of frustration in the energy landscapes of allosteric proteins

19 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048140

Characterizing protein energy landscape by self-learning multiscale simulations: application to a designed β-hairpin

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048140

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048140

Many local motions cooperate to produce the adenylate kinase conformational transition

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048140

Multiscale methods for protein folding simulations

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048140

Functional versus folding landscapes: the same yet different

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048140

Large conformational changes in proteins: signaling and other functions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048140

Rational modulation of conformational fluctuations in adenylate kinase reveals a local unfolding mechanism for allostery and functional adaptation in proteins

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048140

Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048140

Protein elastic network models and the ranges of cooperativity

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048140

Single molecule conformational dynamics of adenylate kinase: energy landscape, structural correlations, and transition state ensembles

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048140

Localizing frustration in native proteins and protein assemblies

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048140

A hierarchy of timescales in protein dynamics is linked to enzyme catalysis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048140

Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048140

Conformational transitions of adenylate kinase: switching by cracking

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048140

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048140

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048140

Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048140

Exploring protein native states and large-scale conformational changes with a modified generalized born model

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048140

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048140

Conformational change of proteins arising from normal mode calculations

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048140

Anisotropy of fluctuation dynamics of proteins with an elastic network model

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048140

Theory of protein folding: the energy landscape perspective

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048140

Structure at 2.8 A resolution of F1-ATPase from bovine heart mitochondria

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048140

Theoretical Studies of Protein Folding

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048140

Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 A resolution. A model for a catalytic transition state

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3048140

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

28 July 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018983108

Gaussian Dynamics of Folded Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018983108

Dynamic activation of an allosteric regulatory protein.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018983108

Roles of static and dynamic domains in stability and catalysis of adenylate kinase

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018983108

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/10.1073%2FPNAS.1018983108

Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like model.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018983108

Energy landscape along an enzymatic reaction trajectory: hinges or cracks?

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018983108

Kinetics and statistical distributions of single-molecule conformational dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018983108

Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.1018983108

21 January 2018

Identifiers

DOI

10.1073/PNAS.1018983108

1 reference

19 October 2017

0 references

1 reference

19 October 2017

PubMed publication ID

21307307

1 reference