Understanding Structural and Dynamic Effects Induced by Key Components of the HCV Polymerase Replication Complex

Abstract

Hepatitis C virus (HCV) is a wide spread health concern for which there is no vaccine available. HCV contains a single-stranded RNA genome and replicates with the aid of an RNA-dependent RNA polymerase known as non-structural protein 5B (NS5B). NS5B adopts at least two different conformations to replicate viral RNA. The closed conformation is thought to be necessary for initiation of replication while the open conformation is required for elongation of the newly synthesized RNA strand. Transitions between these two conformations play a crucial role in NS5B function. Our goal is to understand how the distribution of conformations sampled by the enzyme is altered during different stages of replication. In previous studies we observed that the free enzyme is able to occupy conformational states that are expected to be relevant for the different stages of RNA replication. Our current studies examine the impact of specific components of the replication complex in shifting the ratio of conformational states adopted by the enzyme. To accomplish this goal we performed Molecular Dynamics simulations of the enzyme bound to various combinations of nucleotides and RNA template. We anticipate that the binding of these components will change the relative population of the different conformations in a way that facilitates enzyme function.