Coarse-grained modeling of the actin filament derived from atomistic-scale simulations (Q34354242)

1 August 2017

Coarse-grained modeling of the actin filament derived from atomistic-scale simulations (English)

1 reference

1 August 2017

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2

Gregory A Voth

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1 August 2017

Jhih-Wei Chu

1

1 reference

PubMed ID

16361345

1 August 2017

language of work or name

English

0 references

publication date

16 December 2005

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1 August 2017

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1 August 2017

90

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1 August 2017

5

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1 August 2017

1572-1582

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All-atom empirical potential for molecular modeling and dynamics studies of proteins

1 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

Models of the collective behavior of proteins in cells: tubulin, actin and motor proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

Actin-destabilizing factors disrupt filaments by means of a time reversal of polymerization

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

Normal mode-based fitting of atomic structure into electron density maps: application to sarcoplasmic reticulum Ca-ATPase

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

Mechanical processes in biochemistry

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

Refinement of F-actin model against fiber diffraction data by long-range normal modes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

A comparative study of motor-protein motions by using a simple elastic-network model

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

Simulation of F-actin filaments of several microns

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

Crystal structure of monomeric actin in the ATP state. Structural basis of nucleotide-dependent actin dynamics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

Bridging microscopic and mesoscopic simulations of lipid bilayers

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

The crystal structure of uncomplexed actin in the ADP state

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

Annealing accounts for the length of actin filaments formed by spontaneous polymerization

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

Single-molecule biomechanics with optical methods

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

Manipulation of single molecules in biology

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

Vibrational dynamics of transfer RNAs: comparison of the free and synthetase-bound forms

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

Direct measurement of the torsional rigidity of single actin filaments

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

VMD: visual molecular dynamics

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

The elasticity of a single supercoiled DNA molecule

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

A conformational change in the actin subunit can change the flexibility of the actin filament

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

Direct measurement of stiffness of single actin filaments with and without tropomyosin by in vitro nanomanipulation

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

Dynamic and elastic properties of F-actin: a normal-modes analysis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

Normal modes as refinement parameters for the F-actin model

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

Actin polymerization and its regulation by proteins from nonmuscle cells

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

Atomic model of the actin filament

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

Atomic structure of the actin:DNase I complex

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

Structural basis for the destabilization of F-actin by phosphate release following ATP hydrolysis

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

Kinetic mechanism of end-to-end annealing of actin filaments

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

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

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367308

Molecular dynamics simulation of the formation, structure, and dynamics of small phospholipid vesicles

9 December 2018

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

A multiscale coarse-graining method for biomolecular systems

1 reference

12 December 2020

F-actin is a helix with a random variable twist

1 reference

12 December 2020

Flexibility of actin filaments derived from thermal fluctuations. Effect of bound nucleotide, phalloidin, and muscle regulatory proteins

1 reference

12 December 2020

Fluctuating filaments: statistical mechanics of helices

1 reference

12 December 2020

Thermal fluctuations of elastic filaments with spontaneous curvature and torsion

1 reference

12 December 2020

A theorem on amplitudes of thermal atomic fluctuations in large molecules assuming specific conformations calculated by normal mode analysis

1 reference

12 December 2020

10.1529/BIOPHYSJ.105.073924

Identifiers

DOI

1 reference

1 August 2017

1 reference

1 August 2017

1 reference

PubMed ID

16361345