ArticlePLoS computational biology2010
On the conservation of the slow conformational dynamics within the amino acid kinase family: NAGK the paradigm.
Article in PLoS computational biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 42 citations in OpenAlex.
- The crystal structure of Thermus thermophilus UMP kinase complexed with a phosphoryl group acceptor and donor.PloS one · 2025Article
- Structural dynamics of human deoxyuridine 5'-triphosphate nucleotidohydrolase (dUTPase).Scientific reports · 2024Article
- Statistical learning of protein elastic network from positional covariance matrix.Computational and structural biotechnology journal · 2023Article
- Characterization of Differential Dynamics, Specificity, and Allostery of Lipoxygenase Family Members.Journal of chemical information and modeling · 2019Article
- FindTargetsWEB: A User-Friendly Tool for Identification of Potential Therapeutic Targets in Metabolic Networks of Bacteria.Frontiers in genetics · 2019Article
- An integrative, multi-omics approach towards the prioritization of Klebsiella pneumoniae drug targets.Scientific reports · 2018Article
- Two distinct sites of client protein interaction with the chaperone cpSRP43.The Journal of biological chemistry · 2018Article
- Selection on protein structure, interaction, and sequence.Protein science : a publication of the Protein Society · 2016Review
- Comparison of the Internal Dynamics of Metalloproteases Provides New Insights on Their Function and Evolution.PloS one · 2015Article
- An allosteric signaling pathway of human 3-phosphoglycerate kinase from force distribution analysis.PLoS computational biology · 2014Article
- The underappreciated role of allostery in the cellular network.Annual review of biophysics · 2013Review
- Conformational response to solvent interaction and temperature of a protein (Histone h3.1) by a multi-grained monte carlo simulation.PloS one · 2013Article
- Conservation of flexible residue clusters among structural and functional enzyme homologues.The Journal of biological chemistry · 2012Article
- A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function.Journal of molecular biology · 2012Article
- The interface of protein structure, protein biophysics, and molecular evolution.Protein science : a publication of the Protein Society · 2012Review
- Mechanisms of intramolecular communication in a hyperthermophilic acylaminoacyl peptidase: a molecular dynamics investigation.PloS one · 2012Article
- Changes in dynamics upon oligomerization regulate substrate binding and allostery in amino acid kinase family members.PLoS computational biology · 2011Article
- ProDy: protein dynamics inferred from theory and experiments.Bioinformatics (Oxford, England) · 2011Article
- Structural and functional characterization of the Mycobacterium tuberculosis uridine monophosphate kinase: insights into the allosteric regulation.Nucleic acids research · 2011Article
- Molecular dynamics of mesophilic-like mutants of a cold-adapted enzyme: insights into distal effects induced by the mutations.PloS one · 2011Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
N-acetyl-L-glutamate kinase (NAGK) is the structural paradigm for examining the catalytic mechanisms and dynamics of amino acid kinase family members. Given that the slow conformational dynamics of the NAGK (at the microseconds time scale or slower) may be rate-limiting, it is of importance to assess the mechanisms of the most cooperative modes of motion intrinsically accessible to this enzyme. Here, we present the results from normal mode analysis using an elastic network model representation, which shows that the conformational mechanisms for substrate binding by NAGK strongly correlate with the intrinsic dynamics of the enzyme in the unbound form. We further analyzed the potential mechanisms of allosteric signalling within NAGK using a Markov model for network communication. Comparative analysis of the dynamics of family members strongly suggests that the low-frequency modes of motion and the associated intramolecular couplings that establish signal transduction are highly conserved among family members, in support of the paradigm sequence-->structure-->dynamics-->function.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.