(Q41153386)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21112297%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

title

Relation between the conformational heterogeneity and reaction cycle of Ras: molecular simulation of Ras (English)

1 reference

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17 January 2020

2

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17 January 2020

author name string

Chigusa Kobayashi

series ordinal

1

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17 January 2020

language of work or name

English

0 references

publication date

1 December 2010

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17 January 2020

1 reference

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17 January 2020

volume

99

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17 January 2020

issue

11

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17 January 2020

page(s)

3726-3734

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GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

17 January 2020

cites work

1 reference

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Structural Basis for Conformational Dynamics of GTP-bound Ras Protein

27 September 2017

1 reference

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Ras membrane orientation and nanodomain localization generate isoform diversity

27 September 2017

1 reference

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Ras conformational switching: simulating nucleotide-dependent conformational transitions with accelerated molecular dynamics

27 September 2017

1 reference

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Solution structure and dynamics of the small GTPase RalB in its active conformation: significance for effector protein binding

27 September 2017

1 reference

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Mechanisms of Ras membrane organization and signalling: Ras on a rocker.

27 September 2017

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Novel type of Ras effector interaction established between tumour suppressor NORE1A and Ras switch II

27 September 2017

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Mapping the nucleotide and isoform-dependent structural and dynamical features of Ras proteins

27 September 2017

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Effector Proteins Exert an Important Influence on the Signaling-active State of the Small GTPase Cdc42

27 September 2017

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A novel switch region regulates H-ras membrane orientation and signal output

27 September 2017

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Ras nanoclusters: molecular structure and assembly

27 September 2017

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Crystal structure of M-Ras reveals a GTP-bound "off" state conformation of Ras family small GTPases.

27 September 2017

1 reference

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Single-molecule imaging analysis of Ras activation in living cells

27 September 2017

1 reference

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A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Structural evidence for feedback activation by Ras.GTP of the Ras-specific nucleotide exchange factor SOS

27 September 2017

1 reference

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Direct visualization of Ras proteins in spatially distinct cell surface microdomains

27 September 2017

1 reference

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Mechanical force generation by G 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=2998596

The guanine nucleotide-binding switch in three dimensions

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Dynamic properties of the Ras switch I region and its importance for binding to effectors

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

GTP-dependent segregation of H-ras from lipid rafts is required for biological activity

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Crystal structure and functional analysis of Ras binding to its effector phosphoinositide 3-kinase gamma

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

The pre-hydrolysis state of p21(ras) in complex with GTP: new insights into the role of water molecules in the GTP hydrolysis reaction of ras-like 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=2998596

The structural basis of the activation of Ras by Sos

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Structural basis for the interaction of Ras with RalGDS

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

The importance of two conserved arginine residues for catalysis by the ras GTPase-activating protein, neurofibromin

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Molecular switch in signal transduction: reaction paths of the conformational changes in ras p21.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Regional polysterism in the GTP-bound form of the human c-Ha-Ras protein

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Role of phosphoinositide 3-OH kinase in cell transformation and control of the actin cytoskeleton by Ras

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Ras/Rap effector specificity determined by charge reversal

27 September 2017

1 reference

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The differential effects of the Gly-60 to Ala mutation on the interaction of H-Ras p21 with different downstream targets

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Function and regulation of ras.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Solution structure and dynamics of ras p21.GDP determined by heteronuclear three- and four-dimensional NMR spectroscopy

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Essential dynamics 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=2998596

Multiple Ras functions can contribute to mammalian cell transformation

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Molecular switch for signal transduction: structural differences between active and inactive forms of protooncogenic ras 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=2998596

Refinement of protein dynamic structure: normal mode refinement

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Refined crystal structure of the triphosphate conformation of H-ras p21 at 1.35 A resolution: implications for the mechanism of GTP hydrolysis

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

The GTPase superfamily: a conserved switch for diverse cell functions

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

The GTPase superfamily: conserved structure and molecular 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=2998596

Mutational and kinetic analyses of the GTPase-activating protein (GAP)-p21 interaction: the C-terminal domain of GAP is not sufficient for full activity

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

A distinct class of dominant negative Ras mutants: cytosolic GTP-bound Ras effector domain mutants that inhibit Ras signaling and transformation and enhance cell adhesion

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Ligand-induced conformational changes in ras p21: a normal mode and energy minimization analysis.

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Calculation of pathways for the conformational transition between the GTP- and GDP-bound states of the Ha-ras-p21 protein: calculations with explicit solvent simulations and comparison with calculations in vacuum.

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Mutagenesis of the H-ras p21 at glycine-60 residue disrupts GTP-induced conformational change

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

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

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Transition Networks for the Comprehensive Characterization of Complex Conformational Change in Proteins.

14 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Fundamental link between folding states and functional states of proteins

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Two conformational states of Ras GTPase exhibit differential GTP-binding kinetics

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Structure and dynamics of the full-length lipid-modified H-Ras protein in a 1,2-dimyristoylglycero-3-phosphocholine bilayer

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Dynamic polymorphism of Ras observed by single molecule FRET is the basis for molecular recognition.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Structure of the G60A mutant of Ras: implications for the dominant negative effect

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Automated computation of low-energy pathways for complex rearrangements in proteins: application to the conformational switch of Ras p21.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Perturbation of the conformational equilibria in Ras by selective mutations as studied by 31P NMR spectroscopy

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Development of polyphosphate parameters for use with the AMBER force field.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Structure-based mutagenesis reveals distinct functions for Ras switch 1 and switch 2 in Sos-catalyzed guanine nucleotide exchange

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Increasing complexity of the Ras signaling pathway

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Conformational transitions in p21ras and in its complexes with the effector protein Raf-RBD and the GTPase activating protein GAP.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

Molecular dynamics simulation of the solution structures of Ha-ras-p21 GDP and GTP complexes: flexibility, possible hinges, and levers of the conformational transition.

19 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2998596

High frequency (139.5 GHz) electron paramagnetic resonance characterization of Mn(II)-H2(17)O interactions in GDP and GTP forms of p21 ras

19 August 2018

1 reference

12 December 2020

Surface Change of Ras Enabling Effector Binding Monitored in Real Time at Atomic Resolution

1 reference

12 December 2020

Transient Kinetic Studies on the Interaction of Ras and the Ras-Binding Domain of c-Raf-1 Reveal Rapid Equilibration of the Complex†

1 reference

12 December 2020

High frequency (139.5 GHz) electron paramagnetic resonance spectroscopy of the GTP form of p21 ras with selective 17O labeling of threonine

1 reference

12 December 2020

Large-amplitude nonlinear motions in proteins

1 reference

12 December 2020

10.1016/J.BPJ.2010.09.063

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21112297%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21112297%20AND%20SRC:MED&resulttype=core&format=json

17 January 2020

1 reference