Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism (Q36276838)

13 August 2017

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

1 reference

13 August 2017

Karunesh Arora

1

1 reference

PMCID

2141805

13 August 2017

Charles L Brooks

series ordinal

2

1 reference

PMCID

2141805

13 August 2017

language of work or name

English

0 references

publication date

13 November 2007

1 reference

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

13 August 2017

1 reference

13 August 2017

104

1 reference

13 August 2017

47

1 reference

13 August 2017

18496-18501

1 reference

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

13 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

Conformational transitions of adenylate kinase: switching by cracking

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

Application of a Theory of Enzyme Specificity to Protein Synthesis

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

The N-terminal end of the catalytic domain of SRC kinase Hck is a conformational switch implicated in long-range allosteric regulation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

Molecular dynamics and protein function

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

Escherichia coli adenylate kinase dynamics: comparison of elastic network model modes with mode-coupling (15)N-NMR relaxation data

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

Molecular dynamics simulations of biomolecules

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

Protein and peptide folding explored with molecular simulations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

Mechanism-based design of a protein kinase inhibitor

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

Crystal structures of two mutants of adenylate kinase from Escherichia coli that modify the Gly-loop

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

Comparison of Experimental Binding Data and Theoretical Models in Proteins Containing Subunits*

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

Mechanism of adenylate kinase. Critical evaluation of the X-ray model and assignment of the AMP site

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

Mechanism of adenylate kinase. Structural and functional roles of the conserved arginine-97 and arginine-132.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

Molecular dynamics of apo-adenylate kinase: a principal component analysis

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

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

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

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

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

Domain closure in adenylate kinase.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

Molecular dynamics of apo-adenylate kinase: a distance replica exchange method for the free energy of conformational fluctuations.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

Harmonic Fourier beads method for studying rare events on rugged energy surfaces.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

Conformational transition pathway of polymerase beta/DNA upon binding correct incoming substrate

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

Simple energy landscape model for the kinetics of functional transitions in proteins

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

Activation energy of catalysis-related domain motion in E. coli adenylate kinase.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

Nudged elastic band calculation of minimal energy paths for the conformational change of a GG non-canonical pair

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

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

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

Improved treatment of the protein backbone in empirical force fields.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

An iso-random Bi Bi mechanism for adenylate kinase.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2141805

Free Energy Landscape of A-DNA to B-DNA Conversion in Aqueous Solution

22 September 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0706443104

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0706443104

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0706443104

Backbone Dynamics ofEscherichia coliAdenylate Kinase at the Extreme Stages of the Catalytic Cycle Studied by15N NMR Relaxation†

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0706443104

Multinuclear magnetic resonance studies of Escherichia coli adenylate kinase in free and bound forms. Resonance assignment, secondary structure and ligand binding

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18000050

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Mechanism of adenylate kinase. Is there a relationship between local substrate dynamics, local binding energy, and the catalytic mechanism?

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18000050

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/18000050

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.0706443104

1 reference

13 August 2017

0 references

1 reference

13 August 2017

1 reference

PMCID

2141805