On the conservation of the slow conformational dynamics within the amino acid kinase family: NAGK the paradigm.
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.
Marcos
Enrique
E
Department of Biological Chemistry and Molecular Modelling, IQAC-CSIC, Barcelona, Spain.
Crehuet
Ramon
R
Bahar
Ivet
I
D000494:Allosteric Regulation; D016880:Anisotropy; D020134:Catalytic Domain; D019295:Computational Biology / Q000379:methods*; D008390:Markov Chains; D056004:Molecular Dynamics Simulation; D016011:Normal Distribution; D017851:Phosphotransferases (Carboxyl Group Acceptor) / Q000737:chemistry* / Q000378:metabolism; D015398:Signal Transduction; D013329:Structure-Activity Relationship
D017851:Phosphotransferases (Carboxyl Group Acceptor); C018721:acetylglutamate kinase
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