Abstract
Hepatitis C Virus (HCV) NS5B protein is a RNA-dependent RNA polymerase essential for replication of the viral RNA genome. Genome of HCV is an RNA molecule of approximately 9600 nucleotides, structured in a coding region that contains one large open reading frame (ORF), flanked by non-translated regions (NTR) at the 5’ and 3’ ends encoding a polyprotein precursor of about 3,000 amino acids. High concentrations of GTP (guanosine 5’-triphosphate) have been shown to stimulate de novo RNA synthesis by HCV NS5B. Molecular dynamics (MD) simulations have been performed on NS5B complex to investigate the stability and conformational changes with GTP. It is observed that the backbone atom of NS5B attains stability after 50ns. In vitro, NS5B has been shown to be capable of template-directed RNA synthesis on its own, requiring only divalent metals (magnesium or manganese) as cofactors. In addition, the MM-GBSA approach was introduced to analyze the interactions between inhibitors and NS5B.
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