Identification of potential allosteric binding sites in cathepsin K based on intramolecular communication.

Autor: Rocha GV; Programa de Computação Científica, Vice-Presidência de Educação, Informação e Comunicação, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.; Laboratoire de Biologie et de Pharmacologie Appliquée, Ecole Normale Supérieure Paris Saclay, Centre National de la Recherche Scientifique, Cachan, France., Bastos LS; Programa de Computação Científica, Vice-Presidência de Educação, Informação e Comunicação, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.; Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, UK., Costa MGS; Programa de Computação Científica, Vice-Presidência de Educação, Informação e Comunicação, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.; Laboratoire de Biologie et de Pharmacologie Appliquée, Ecole Normale Supérieure Paris Saclay, Centre National de la Recherche Scientifique, Cachan, France.
Jazyk: angličtina
Zdroj: Proteins [Proteins] 2020 Dec; Vol. 88 (12), pp. 1675-1687. Date of Electronic Publication: 2020 Aug 21.
DOI: 10.1002/prot.25985
Abstrakt: Network theory methods and molecular dynamics (MD) simulations are accepted tools to study allosteric regulation. Indeed, dynamic networks built upon correlation analysis of MD trajectories provide detailed information about communication paths between distant sites. In this context, we aimed to understand whether the efficiency of intramolecular communication could be used to predict the allosteric potential of a given site. To this end, we performed MD simulations and network theory analyses in cathepsin K (catK), whose allosteric sites are well defined. To obtain a quantitative measure of the efficiency of communication, we designed a new protocol that enables the comparison between properties related to ensembles of communication paths obtained from different sites. Further, we applied our strategy to evaluate the allosteric potential of different catK cavities not yet considered for drug design. Our predictions of the allosteric potential based on intramolecular communication correlate well with previous catK experimental and theoretical data. We also discuss the possibility of applying our approach to other proteins from the same family.
(© 2020 Wiley Periodicals LLC.)
Databáze: MEDLINE
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