Thumb inhibitor binding eliminates functionally important dynamics in the hepatitis C virus RNA polymerase

Authors

  • Brittny C. Davis,

    1. Department of Chemistry and Biochemistry, University of Maryland–Baltimore County, Baltimore, Maryland 21250
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  • Ian F. Thorpe

    Corresponding author
    1. Department of Chemistry and Biochemistry, University of Maryland–Baltimore County, Baltimore, Maryland 21250
    • Department of Chemistry and Biochemistry, University of Maryland–Baltimore County, Baltimore, MD 21250
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  • After this manuscript was accepted for publication, the authors discovered that an error was made in the calculation of the solvent accessible surface area (SASA) values reported in the manuscript. As a result, figure 4 and table I of the original manuscript contained incorrect data. The main impact of this error was to shift the magnitude of the computed values, while leaving the overall trends in the data unaffected. This change does not alter any of the conclusions made in the article and does not impact the text of the document. However, revised versions of figure 4 and table I containing the correct data have been included in this version of the article.

Abstract

Hepatitis C virus (HCV) has infected almost 200 million people worldwide, typically causing chronic liver damage and severe complications such as liver failure. Currently, there are few approved treatments for viral infection. Thus, the HCV RNA-dependent RNA polymerase (gene product NS5B) has emerged as an important target for small molecule therapeutics. Potential therapeutic agents include allosteric inhibitors that bind distal to the enzyme active site. While their mechanism of action is not conclusively known, it has been suggested that certain inhibitors prevent a conformational change in NS5B that is crucial for RNA replication. To gain insight into the molecular origin of long-range allosteric inhibition of NS5B, we employed molecular dynamics simulations of the enzyme with and without an inhibitor bound to the thumb domain. These studies indicate that the presence of an inhibitor in the thumb domain alters both the structure and internal motions of NS5B. Principal components analysis identified motions that are severely attenuated by inhibitor binding. These motions may have functional relevance by facilitating interactions between NS5B and RNA template or nascent RNA duplex, with presence of the ligand leading to enzyme conformations with narrower and thus less accessible RNA binding channels. This study provides the first evidence for a mechanistic basis of allosteric inhibition in NS5B. Moreover, we present evidence that allosteric inhibition of NS5B results from intrinsic features of the enzyme free energy landscape, suggesting a common mechanism for the action of diverse allosteric ligands. Proteins 2013. © 2012 Wiley Periodicals, Inc.

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