Molecular Dynamics Simulation of the Escherichia coli NikR Protein: Equilibrium Conformational Fluctuations Reveal Interdomain Allosteric Communication Pathways
- 14 March 2008
- journal article
- Published by Elsevier in Journal of Molecular Biology
- Vol. 378 (5) , 1155-1173
- https://doi.org/10.1016/j.jmb.2008.03.010
Abstract
No abstract availableKeywords
This publication has 81 references indexed in Scilit:
- Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanismProceedings of the National Academy of Sciences, 2007
- A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysisProceedings of the National Academy of Sciences, 2007
- A solution NMR study showing that active site ligands and nucleotides directly perturb the allosteric equilibrium in aspartate transcarbamoylaseProceedings of the National Academy of Sciences, 2007
- NikR–operator complex structure and the mechanism of repressor activation by metal ionsProceedings of the National Academy of Sciences, 2006
- Residues crucial for maintaining short paths in network communication mediate signaling in proteinsMolecular Systems Biology, 2006
- VMD: Visual molecular dynamicsJournal of Molecular Graphics, 1996
- Essential dynamics of proteinsProteins-Structure Function and Bioinformatics, 1993
- Molecular dynamics with coupling to an external bathThe Journal of Chemical Physics, 1984
- Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical featuresBiopolymers, 1983
- Comparison of simple potential functions for simulating liquid waterThe Journal of Chemical Physics, 1983