(Q30375578)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19289039%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

title

Coupling between normal modes drives protein conformational dynamics: illustrations using allosteric transitions in myosin II (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19289039%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19289039%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

2

D Thirumalai

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19289039%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

language of work or name

English

0 references

publication date

1 March 2009

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19289039%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19289039%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

volume

96

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19289039%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

page(s)

2128-2137

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19289039%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

issue

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19289039%20AND%20SRC:MED&resulttype=core&format=json

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

23 January 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

MinActionPath: maximum likelihood trajectory for large-scale structural transitions in a coarse-grained locally harmonic energy landscape

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

Toward the mechanism of dynamical couplings and translocation in hepatitis C virus NS3 helicase using elastic 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=2717279

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

Modeling protein conformational changes by iterative fitting of distance constraints using reoriented normal modes.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

A connection rule for alpha-carbon coarse-grained elastic network models using chemical bond information.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

Coarse-grained normal mode analysis in structural biology

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

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=2717279

Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

Coarse-grained models for 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=2717279

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB 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=2717279

Three myosin V structures delineate essential features of chemo-mechanical transduction

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

Relating biochemistry and function in the myosin superfamily

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

Analysis of functional motions in Brownian molecular machines with an efficient block normal mode approach: myosin-II and Ca2+ -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=2717279

A comparative study of motor-protein motions by using a simple elastic-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=2717279

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=2717279

A structural state of the myosin V motor without bound nucleotide

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic 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=2717279

A millennial myosin census

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

Conformational change of proteins arising from normal mode calculations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

Anisotropy of fluctuation dynamics of proteins with an elastic 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=2717279

Structural mechanism of muscle contraction.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

Atomic structure of scallop myosin subfragment S1 complexed with MgADP: a novel conformation of the myosin head

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

Investigating protein dynamics in collective coordinate space

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

Protein conformational transitions explored by mixed elastic network models.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

Anisotropic network model: systematic evaluation and a new web interface.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

Global ribosome motions revealed with elastic network model.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

Myosin flexibility: structural domains and collective vibrations.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

A structural model for actin-induced nucleotide release in myosin

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

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

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

Analysis of domain motions by approximate normal mode calculations.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2717279

Functional modes of proteins are among the most robust

26 November 2018

1 reference

12 December 2020

Elastic models of conformational transitions in macromolecules

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

The requirement for mechanical coupling between head and S2 domains in smooth muscle myosin ATPase regulation and its implications for dimeric motor function

1 reference

12 December 2020

10.1016/J.BPJ.2008.12.3897

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19289039%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:19289039%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

1 reference