1. Dissecting nucleotide selectivity in viral RNA polymerases
- Author
-
Moises Ernesto Romero, Chunhong Long, Jin Yu, and Daniel La Rocco
- Subjects
Kinetic modeling ,Molecular dynamics (MD) simulation ,DNA polymerase ,viruses ,Biophysics ,RNA/DNA polymerase (RNAP/DNAP) ,RNA-dependent RNA polymerase ,Computational biology ,Biochemistry ,Article ,Vaccine Related ,03 medical and health sciences ,0302 clinical medicine ,Structural Biology ,Transcription (biology) ,Biodefense ,Genetics ,medicine ,T7 RNA polymerase ,Polymerase ,030304 developmental biology ,0303 health sciences ,Numerical and Computational Mathematics ,biology ,Prevention ,Helicase ,Computation Theory and Mathematics ,Fidelity control ,RNA dependent RNA polymerase ,Computer Science Applications ,Infectious Diseases ,Emerging Infectious Diseases ,Good Health and Well Being ,RNA dependent RNA polymerase (RdRp) ,RNA/DNA polymerase ,Viral replication ,Nucleotide selection ,030220 oncology & carcinogenesis ,biology.protein ,Proofreading ,Generic health relevance ,Infection ,TP248.13-248.65 ,Biotechnology ,medicine.drug - Abstract
Designing antiviral therapeutics is of great concern per current pandemics caused by novel coronavirus or SARS-CoV-2. The core polymerase enzyme in the viral replication/transcription machinery is generally conserved and serves well for drug target. In this work we briefly review structural biology and computational clues on representative single-subunit viral polymerases that are more or less connected with SARS-CoV-2 RNA dependent RNA polymerase (RdRp), in particular, to elucidate how nucleotide substrates and potential drug analogs are selected in the viral genome synthesis. To do that, we first survey two well studied RdRps from Polio virus and hepatitis C virus in regard to structural motifs and key residues that have been identified for the nucleotide selectivity. Then we focus on related structural and biochemical characteristics discovered for the SARS-CoV-2 RdRp. To further compare, we summarize what we have learned computationally from phage T7 RNA polymerase (RNAP) on its stepwise nucleotide selectivity, and extend discussion to a structurally similar human mitochondria RNAP, which deserves special attention as it cannot be adversely affected by antiviral treatments. We also include viral phi29 DNA polymerase for comparison, which has both helicase and proofreading activities on top of nucleotide selectivity for replication fidelity control. The helicase and proofreading functions are achieved by protein components in addition to RdRp in the coronavirus replication-transcription machine, with the proofreading strategy important for the fidelity control in synthesizing a comparatively large viral genome.
- Published
- 2021
- Full Text
- View/download PDF