Coarse-grained description of protein internal dynamics: an optimal strategy for decomposing proteins in rigid subunits.
The possibility of accurately describing the internal dynamics of proteins, in terms of movements of a few approximately-rigid subparts, is an appealing biophysical problem with important implications for the analysis and interpretation of data from experiments or numerical simulations. The problem is tackled here by means of a novel variational approach that exploits information about equilibrium fluctuations of interresidues distances, provided, e.g., by atomistic molecular dynamics simulations or coarse-grained models. No contiguity in primary sequence or in space is enforced a priori for amino acids grouped in the same rigid unit. The identification of the rigid protein moduli, or dynamical domains, provides valuable insight into functionally oriented aspects of protein internal dynamics. To illustrate this point, we first discuss the decomposition of adenylate kinase and HIV-1 protease and then extend the investigation to several representatives of the hydrolase enzymatic class. The known catalytic site of these enzymes is found to be preferentially located close to the boundary separating the two primary dynamical subdomains.
Potestio
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R
Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy.
Pontiggia
F
F
Micheletti
C
C
D000263:Adenylate Kinase / Q000737:chemistry*; D020134:Catalytic Domain; D004926:Escherichia coli / Q000201:enzymology*; D016333:HIV Protease / Q000737:chemistry*; D015497:HIV-1 / Q000201:enzymology*; D008958:Models, Molecular; D020836:Protein Structure, Quaternary; D021122:Protein Subunits / Q000737:chemistry
D021122:Protein Subunits; D000263:Adenylate Kinase; D016333:HIV Protease; C514803:p16 protease, Human immunodeficiency virus 1