ArticleJournal of molecular biology2008
Molecular dynamics simulation of the Escherichia coli NikR protein: equilibrium conformational fluctuations reveal interdomain allosteric communication pathways.
Article in Journal of molecular biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 68 citations in OpenAlex.
- Bacterial Metallostasis: Metal Sensing, Metalloproteome Remodeling, and Metal Trafficking.Chemical reviews · 2024Review
- Bacterial Transcriptional Regulators: A Road Map for Functional, Structural, and Biophysical Characterization.International journal of molecular sciences · 2022Review
- Revisiting allostery in CREB-binding protein (CBP) using residue-based interaction energy.Journal of computer-aided molecular design · 2020Article
- A Time-Dependent Quantum Approach to Allostery and a Comparison With Light-Harvesting in Photosynthetic Phenomenon.Frontiers in molecular biosciences · 2020Article
- Dynamic allostery-based molecular workings of kinase:peptide complexes.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- ProSNEx: a web-based application for exploration and analysis of protein structures using network formalism.Nucleic acids research · 2019Article
- Allosteric Communication Networks in Proteins Revealed through Pocket Crosstalk Analysis.ACS central science · 2017Article
- Dynamical persistence of active sites identified in maltose-binding protein.Journal of molecular modeling · 2017Article
- Discovery of Novel Allosteric Eg5 Inhibitors Through Structure-Based Virtual Screening.Chemical biology & drug design · 2016Article
- Emerging Computational Methods for the Rational Discovery of Allosteric Drugs.Chemical reviews · 2016Review
- Evolution of Macromolecular Docking Techniques: The Case Study of Nickel and Iron Metabolism in Pathogenic Bacteria.Molecules (Basel, Switzerland) · 2015Review
- Identification of the binding site of an allosteric ligand using STD-NMR, docking, and CORCEMA-ST calculations.ChemMedChem · 2013Article
- Secondary anionic phospholipid binding site and gating mechanism in Kir2.1 inward rectifier channels.Nature communications · 2013Article
- Dynamics of heme complexed with human serum albumin: a theoretical approach.European biophysics journal : EBJ · 2012Article
- Biomolecular electrostatics and solvation: a computational perspective.Quarterly reviews of biophysics · 2012Review
- Exploring residue component contributions to dynamical network models of allostery.Journal of chemical theory and computation · 2012Article
- Space warping order parameters and symmetry: application to multiscale simulation of macromolecular assemblies.The journal of physical chemistry. B · 2012Article
- Comparing Conformational Ensembles Using the Kullback-Leibler Divergence Expansion.Journal of chemical theory and computation · 2012Article
- Metal site occupancy and allosteric switching in bacterial metal sensor proteins.Archives of biochemistry and biophysics · 2012Review
- Helicobacter pylori NikR protein exhibits distinct conformations when bound to different promoters.The Journal of biological chemistry · 2011Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Escherichia coli NikR is a homotetrameric Ni(2+)- and DNA-binding protein that functions as a transcriptional repressor of the NikABCDE nickel permease. The protein is composed of two distinct domains. The N-terminal 50 amino acids of each chain forms part of the dimeric ribbon-helix-helix (RHH) domains, a well-studied DNA-binding fold. The 83-residue C-terminal nickel-binding domain forms an ACT (aspartokinase, chorismate mutase, and TyrA) fold and contains the tetrameric interface. In this study, we have utilized an equilibrium molecular dynamics simulation in order to explore the conformational dynamics of the NikR tetramer and determine important residue interactions within and between the RHH and ACT domains to gain insight into the effects of Ni(2+) on DNA-binding activity. The molecular simulation data were analyzed using two different correlation measures based on fluctuations in atomic position and noncovalent contacts together with a clustering algorithm to define groups of residues with similar correlation patterns for both types of correlation measure. Based on these analyses, we have defined a series of residue interrelationships that describe an allosteric communication pathway between the Ni(2+)- and DNA-binding sites, which are separated by 40 A. Several of the residues identified by our analyses have been previously shown experimentally to be important for NikR function. An additional subset of the identified residues structurally connects the experimentally implicated residues and may help coordinate the allosteric communication between the ACT and RHH domains.
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Registered trials
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