Activation of the West Nile virus NS3 protease: Molecular dynamics evidence for a conformational selection mechanism

TitleActivation of the West Nile virus NS3 protease: Molecular dynamics evidence for a conformational selection mechanism
Publication TypeJournal Article
Year of Publication2009
AuthorsEkonomiuk D., Caflisch A.
JournalProtein Science
Volume18
Issue5
Pagination1003-1111
Date Published2009 May
Type of ArticleResearch Article
ISSN1469-896X
KeywordsCatalytic Domain, Computer Simulation, Enzyme Stability, Models, Molecular, Protein Binding, Protein Conformation, RNA Helicases, Serine Endopeptidases, Substrate Specificity, Viral Nonstructural Proteins, Water, West Nile virus
Abstract

The flaviviral nonstructural 3 protease (NS3pro) is essential for virus replication and is therefore a pharmaceutically relevant target to fight Dengue and West Nile virus (WNV). NS3pro is a chymotrypsin-like serine protease which requires a polypeptide cofactor (NS2B) for activation. Recent X-ray crystallography studies have led to the suggestion that the substrate binds to the two-component NS2B-NS3pro enzyme by an induced-fit mechanism. Here, multiple explicit water molecular dynamics simulations of the WNV NS2B-NS3pro enzyme show that the active conformation of the NS2B cofactor (in which its β-loop is part of the substrate binding site) is stable over a 50-ns time scale even in the absence of the inhibitor. The partial and reversible opening of the NSB2 β-loop and its correlated motion with an adjacent NS3pro loop, both observed in the simulations started from the active conformation, are likely to facilitate substrate binding and product release. Moreover, in five of eight simulations without inhibitor (started from two X-ray structures both with improperly formed oxyanion hole) the Thr132-Gly133 peptide bond flips spontaneously thereby promoting the formation of the catalytically competent oxyanion hole, which then stays stable until the end of the runs. The simulation results provide evidence at atomic level of detail that the substrate binds to the NS2B-NS3pro enzyme by conformational selection, rather than induced-fit mechanism.

DOI10.1002/pro.110
pubindex

0114

Alternate JournalProtein Sci.
PubMed ID19388022
PubMed Central IDPMC2771302
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