Computation of conformational coupling in allosteric proteins (Q30872872)

13 October 2017

Computation of conformational coupling in allosteric proteins (English)

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13 October 2017

computational biology

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Wendy E Thomas

3

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David Baker

object named as

David Baker

series ordinal

2

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author name string

Brian A Kidd

series ordinal

1

1 reference

13 October 2017

28 August 2009

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PLOS Computational Biology

13 October 2017

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13 October 2017

5

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13 October 2017

8

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13 October 2017

e1000484

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Creative Commons Attribution 4.0 International

13 October 2017

start time

28 August 2009

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

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Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms

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Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis

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Allostery and cooperativity revisited

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Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR

21 June 2018

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Contact rearrangements form coupled networks from local motions in allosteric proteins

21 June 2018

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High-resolution structure prediction and the crystallographic phase problem

21 June 2018

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Functional residues serve a dominant role in mediating the cooperativity of the protein ensemble

21 June 2018

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B-RAF and N-RAS mutations are preserved during short time in vitro propagation and differentially impact prognosis

21 June 2018

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Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues

21 June 2018

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

21 June 2018

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Directed evolution to probe protein allostery and integrin I domains of 200,000-fold higher affinity.

21 June 2018

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Determination of network of residues that regulate allostery in protein families using sequence analysis

21 June 2018

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21 June 2018

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Allosteric mechanisms of signal transduction

21 June 2018

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21 June 2018

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Thrombin: a paradigm for enzymes allosterically activated by monovalent cations

21 June 2018

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Conversion between three conformational states of integrin I domains with a C-terminal pull spring studied with molecular dynamics

21 June 2018

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Protein structure prediction using Rosetta

21 June 2018

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

21 June 2018

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Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T<-->R2 transition.

21 June 2018

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ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL

21 June 2018

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Cyclic coordinate descent: A robotics algorithm for protein loop closure.

21 June 2018

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CheZ-Mediated Dephosphorylation of the Escherichia coli Chemotaxis Response Regulator CheY: Role for CheY Glutamate 89

21 June 2018

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Structures of the alpha L I domain and its complex with ICAM-1 reveal a shape-shifting pathway for integrin regulation

21 June 2018

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Genetic analysis of response regulator activation in bacterial chemotaxis suggests an intermolecular mechanism

21 June 2018

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Integrin activation and structural rearrangement

21 June 2018

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Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations

21 June 2018

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The structure of apo human glutamate dehydrogenase details subunit communication and allostery

21 June 2018

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Crystal structure of activated CheY. Comparison with other activated receiver domains

21 June 2018

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Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation.

21 June 2018

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Modeling the cAMP-induced allosteric transition using the crystal structure of CAP-cAMP at 2.1 A resolution

21 June 2018

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21 June 2018

The Protein Data Bank

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Evolutionarily conserved pathways of energetic connectivity in protein families

21 June 2018

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Mapping the intercellular adhesion molecule-1 and -2 binding site on the inserted domain of leukocyte function-associated antigen-1.

21 June 2018

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The structural distribution of cooperative interactions in proteins: analysis of the native state ensemble

21 June 2018

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Bayesian statistical analysis of protein side-chain rotamer preferences

21 June 2018

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Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions

21 June 2018

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The three-dimensional structure of two mutants of the signal transduction protein CheY suggest its molecular activation mechanism

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2720451

Identification of residues of the H-ras protein critical for functional interaction with guanine nucleotide exchange factors

21 June 2018

1 reference

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SCOP: a structural classification of proteins database for the investigation of sequences and structures

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2720451

Comparison of Experimental Binding Data and Theoretical Models in Proteins Containing Subunits*

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2720451

Molecular switch for signal transduction: structural differences between active and inactive forms of protooncogenic ras proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2720451

ras oncogenes: their role in neoplasia

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2720451

Communication modules in bacterial signaling proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2720451

Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion

21 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000484

Reconciling the "old" and "new" views of protein allostery: a molecular simulation study of chemotaxis Y protein (CheY).

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000484

Mutations leading to altered CheA binding cluster on a face of CheY.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000484

Flagellar motor-switch binding face of CheY and the biochemical basis of suppression by CheY mutants that compensate for motor-switch defects in Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000484

Biochemical and functional characterization of germ line KRAS mutations

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000484

Structure of the constitutively active double mutant CheYD13K Y106W alone and in complex with a FliM peptide

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000484

Amide hydrogen exchange and internal dynamics in the chemotactic protein CheY from Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000484

Local motions in a benchmark of allosteric proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000484

Stereochemistry of Cooperative Effects in Haemoglobin: Haem–Haem Interaction and the Problem of Allostery

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000484

Allostery in a coarse-grained model of protein dynamics

21 January 2018

1 reference

12 December 2020

Structure/function studies of the ras protein

1 reference

12 December 2020

Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model

1 reference

12 December 2020

Two-state allosteric behavior in a single-domain signaling protein

1 reference

12 December 2020

10.1371/JOURNAL.PCBI.1000484

Identifiers

DOI

1 reference

13 October 2017

journals/ploscb/KiddBT09

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

13 October 2017

1 reference

PMCID

2720451