(Q34184754)

31 July 2017

Analysis of functional motions in Brownian molecular machines with an efficient block normal mode approach: myosin-II and Ca2+ -ATPase (English)

1 reference

31 July 2017

0 references

Guohui Li

1

1 reference

PubMed ID

14747312

31 July 2017

Qiang Cui

series ordinal

2

1 reference

PubMed ID

14747312

31 July 2017

language of work or name

English

0 references

publication date

1 February 2004

1 reference

31 July 2017

1 reference

31 July 2017

86

1 reference

31 July 2017

743-763

1 reference

31 July 2017

2

1 reference

The working stroke upon myosin–nucleotide complexes binding to actin

31 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

The missing link between thermodynamics and structure in F1-ATPase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Electron microscopy of functional ribosome complexes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Motors in muscle: the function of conventional myosin II.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Early stages of energy transduction by myosin: roles of Arg in switch I, of Glu in switch II, and of the salt-bridge between them

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca(2+)-ATPase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Molecular dynamics simulations of biomolecules

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Structural changes in the calcium pump accompanying the dissociation of calcium

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

A calcium pump made visible

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Dynamics of proteins in crystals: comparison of experiment with simple models

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Modeling supramolecular assemblages

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Nanoseconds molecular dynamics simulation of primary mechanical energy transfer steps in F1-ATP synthase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

A structural model for the catalytic cycle of Ca(2+)-ATPase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Flexibility and packing in proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Kinetic resolution of a conformational transition and the ATP hydrolysis step using relaxation methods with a Dictyostelium myosin II mutant containing a single tryptophan residue

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

The physics of molecular motors

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

What the structure of a calcium pump tells us about its mechanism

5 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

5 July 2018

https://pubmed.ncbi.nlm.nih.gov/14747312

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Steered molecular dynamics and mechanical functions of proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Conformational change of proteins arising from normal mode calculations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

The role of the M6-M7 loop (L67) in stabilization of the phosphorylation and Ca(2+) binding domains of the sarcoplasmic reticulum Ca(2+)-ATPase (SERCA).

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Anisotropy of fluctuation dynamics of proteins with an elastic network model

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Three conformational states of scallop myosin S1

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

X-ray structures of the apo and MgATP-bound states of Dictyostelium discoideum myosin motor domain

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Structural mechanism of muscle contraction.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 A resolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Effective energy functions for protein structure prediction.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

The way things move: looking under the hood of molecular motor proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Structural bioenergetics and energy transduction mechanisms

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

A study of vibrational relaxation of B-state carbon monoxide in the heme pocket of photolyzed carboxymyoglobin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Investigating protein dynamics in collective coordinate space

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

A database of macromolecular motions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

The allosteric mechanism of the chaperonin GroEL: a dynamic analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Simulating energy flow in biomolecules: application to tuna cytochrome c

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

X-ray structures of the MgADP, MgATPgammaS, and MgAMPPNP complexes of the Dictyostelium discoideum myosin motor domain

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Dissection of the functional domains of the sarcoplasmic reticulum Ca(2+)-ATPase by site-directed mutagenesis.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

The structural basis of the myosin ATPase activity

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

X-ray structure of the magnesium(II).ADP.vanadate complex of the Dictyostelium discoideum myosin motor domain to 1.9 A resolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

The binding change mechanism for ATP synthase--some probabilities and possibilities

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Essential dynamics of proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Interpreting the effects of site-directed mutagenesis on active transport systems

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Structure-function relationships of cation translocation by Ca(2+)- and Na+, K(+)-ATPases studied by site-directed mutagenesis.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Conformational changes of the myosin heads during hydrolysis of ATP as analyzed by x-ray solution scattering.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

X-ray structures of the myosin motor domain of Dictyostelium discoideum complexed with MgADP.BeFx and MgADP.AlF4-

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Can free energy transduction be localized at some crucial part of the enzymatic cycle?

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Dynamics of a small globular protein in terms of low-frequency vibrational modes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

The Utilization of Binding Energy in Coupled Vectorial Processes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Analysis of positional isotope exchange in ATP by cleavage of the beta P-O gamma P bond. Demonstration of negligible positional isotope exchange by myosin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Anatomy of a conformational change: hinged "lid" motion of the triosephosphate isomerase loop.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

The Energy Landscapes and Motions of Proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Definitions of free energy levels in biochemical reactions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Oxygen exchange in the gamma-phosphoryl group of protein-bound ATP during Mg2+-dependent adenosine triphosphatase activity of myosin

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Collective variable description of native protein dynamics.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Mutagenesis of residues involved in control of the Ca2+ entry pathway and conformational changes associated with Ca2+ binding in the SR Ca2+-ATPase.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Requirement of domain-domain interaction for conformational change and functional ATP hydrolysis in myosin

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Dictyostelium myosin II mutations that uncouple the converter swing and ATP hydrolysis cycle

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

The dynamics of the relay loop tryptophan residue in the Dictyostelium myosin motor domain and the origin of spectroscopic signals.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Resolution of conformational states of Dictyostelium myosin II motor domain using tryptophan (W501) mutants: implications for the open-closed transition identified by crystallography.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Building-block approach for determining low-frequency normal modes of macromolecules.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Hinge-bending motion in citrate synthase arising from normal mode calculations.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Effect of solvent on collective motions in globular protein.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

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

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1303924

Site-directed mutagenesis studies of energy coupling in the sarcoplasmic reticulum Ca(2+)-ATPase

28 October 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974152-1

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974152-1

Vibrational Dynamics of Folded Proteins: Significance of Slow and Fast Motions in Relation to Function and Stability

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974152-1

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974152-1

Reaction-rate theory: fifty years after Kramers

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974152-1

Model-free methods of analyzing domain motions in proteins from simulation: a comparison of normal mode analysis and molecular dynamics simulation of lysozyme

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974152-1

Molecular motors and single-molecule enzymology

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974152-1

Modeling molecular motors

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974152-1

An iteration method for the solution of the eigenvalue problem of linear differential and integral operators

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974152-1

A dynamic analysis of the rotation mechanism for conformational change in F(1)-ATPase

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974152-1

Simulation of activation free energies in molecular systems

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974152-1

Molecular dynamics of ferrocytochrome c

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974152-1

Analysis of the low-frequency normal modes of the R state of aspartate transcarbamylase and a comparison with the T state modes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974152-1

Tertiary and quaternary conformational changes in aspartate transcarbamylase: a normal mode study

7 January 2021

2 references

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974152-1

7 January 2021

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974152-1

inferred from DOI database lookup

7 January 2021

based on heuristic

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

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974152-1

Modeling Tricks and Fitting Techniques for Multiresolution Structures

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2804%2974152-1

Energy landscape of a native protein: jumping-among-minima model

7 January 2021

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/14747312

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/S0006-3495(04)74152-1

1 reference

31 July 2017

1 reference

31 July 2017

1 reference

PubMed ID

14747312