(Q36837448)

16 August 2017

Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms (English)

1 reference

16 August 2017

1 reference

Kei-Ichi Okazaki

1

0 references

author name string

Shoji Takada

series ordinal

2

1 reference

PMCID

2516237

16 August 2017

language of work or name

English

0 references

publication date

4 August 2008

1 reference

Proceedings of the National Academy of Sciences of the United States of America

16 August 2017

1 reference

16 August 2017

105

1 reference

16 August 2017

11182-11187

1 reference

16 August 2017

32

1 reference

Intrinsic motions along an enzymatic reaction trajectory

16 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

Illuminating the mechanistic roles of enzyme conformational dynamics

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

Mechanical control of the directional stepping dynamics of the kinesin motor

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

Mechanism of coupled folding and binding of an intrinsically disordered protein

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

Conformational transitions of adenylate kinase: switching by cracking

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

Protein complex formation by acetylcholinesterase and the neurotoxin fasciculin-2 appears to involve an induced-fit mechanism

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

Application of a Theory of Enzyme Specificity to Protein Synthesis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

Folding-based molecular simulations reveal mechanisms of the rotary motor F1-ATPase

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

The Database of Macromolecular Motions: new features added at the decade mark

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

Direct discrimination between models of protein activation by single-molecule force measurements

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

Antibody multispecificity mediated by conformational diversity

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

Molecular recognition by induced fit: how fit is the concept?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

Folding and binding cascades: dynamic landscapes and population shifts

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

Folding and binding cascades: shifts in energy landscapes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

Theory of protein folding: the energy landscape perspective

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

Statistical mechanics of kinetic proofreading in protein folding in vivo

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

Diffusion-controlled bimolecular reaction rates. The effect of rotational diffusion and orientation constraints

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

The Energy Landscapes and Motions of Proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

Observing an induced-fit mechanism during sequence-specific DNA methylation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

Molecular dynamics simulations of NAD+-induced domain closure in horse liver alcohol dehydrogenase

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

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

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

Fly-casting in protein-DNA binding: frustration between protein folding and electrostatics facilitates target recognition

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

Reconciling the "old" and "new" views of protein allostery: a molecular simulation study of chemotaxis Y protein (CheY).

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

A comprehensive and non-redundant database of protein domain movements.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

eF-site and PDBjViewer: database and viewer for protein functional sites.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2516237

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

5 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.0802524105

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.0802524105

Slow Protein Conformational Dynamics from Multiple Experimental Structures: The Helix/Sheet Transition of Arc Repressor

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.0802524105

Protein structural change upon ligand binding: linear response theory

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18678900

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18678900

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Conformational diversity and protein evolution--a 60-year-old hypothesis revisited

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18678900

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.0802524105

1 reference

16 August 2017

0 references

1 reference

16 August 2017

1 reference

PMCID

2516237