Instantaneous normal modes as an unforced reaction coordinate for protein conformational transitions (Q33858575)

29 July 2017

title

Instantaneous normal modes as an unforced reaction coordinate for protein conformational transitions (English)

1 reference

29 July 2017

Cheng Peng

1

1 reference

29 July 2017

Liqing Zhang

series ordinal

2

1 reference

29 July 2017

Teresa Head-Gordon

series ordinal

3

1 reference

29 July 2017

language of work or name

English

0 references

publication date

1 May 2010

1 reference

29 July 2017

number of pages

9

1 reference

based on heuristic

inferred from page(s)

published in

Biophysical Journal

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29 July 2017

volume

98

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29 July 2017

issue

10

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29 July 2017

page(s)

2356-2364

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

29 July 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

The atomistic mechanism of conformational transition in adenylate kinase: a TEE-REX molecular dynamics study

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

Allosteric regulation and catalysis emerge via a common route.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

Single molecule conformational dynamics of adenylate kinase: energy landscape, structural correlations, and transition state ensembles

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

Multiscale complex network of protein conformational fluctuations in single-molecule time series

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

Dynamic personalities of proteins

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

A hierarchy of timescales in protein dynamics is linked to enzyme catalysis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

Intrinsic motions along an enzymatic reaction trajectory

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

Illuminating the mechanistic roles of enzyme conformational dynamics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

Toxin-induced conformational changes in a potassium channel revealed by solid-state NMR.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

Coarse-grained normal mode analysis in structural biology

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

Using path sampling to build better Markovian state models: predicting the folding rate and mechanism of a tryptophan zipper beta hairpin

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

Molecular dynamics simulations of peptides and proteins with amplified collective motions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

Transition path sampling: throwing ropes over rough mountain passes, in the dark.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

Conformational change of proteins arising from normal mode calculations

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

Structural mechanism of muscle contraction.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 A resolution. A model for a catalytic transition state

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

Conformational transition pathways explored by Monte Carlo simulation integrated with collective modes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

Normal mode partitioning of Langevin dynamics for biomolecules

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

Conformational transitions in adenylate kinase. Allosteric communication reduces misligation

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

An NMA-guided path planning approach for computing large-amplitude conformational changes in proteins.

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

Roles of static and dynamic domains in stability and catalysis of adenylate kinase

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

Local conformational fluctuations can modulate the coupling between proton binding and global structural transitions in proteins

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

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

29 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2872262

Structural biology. Dynamic visions of enzymatic reactions

29 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20483345

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.BPJ.2010.01.044

1 reference

29 July 2017

1 reference

29 July 2017

1 reference