ArticleJournal of molecular biology2011
Molecular dynamics simulations of viral RNA polymerases link conserved and correlated motions of functional elements to fidelity.
Article in Journal of molecular biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed, 86 citations in OpenAlex.
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- Induced intra- and intermolecular template switching as a therapeutic mechanism against RNA viruses.Molecular cell · 2021Article
- Natural plant products as potential inhibitors of RNA dependent RNA polymerase of Severe Acute Respiratory Syndrome Coronavirus-2.PloS one · 2021Article
- Dissecting nucleotide selectivity in viral RNA polymerases.Computational and structural biotechnology journal · 2021Review
- Residues within the Foot-and-Mouth Disease Virus 3DJournal of virology · 2020Article
- 2'-C-methylated nucleotides terminate virus RNA synthesis by preventing active site closure of the viral RNA-dependent RNA polymerase.The Journal of biological chemistry · 2019Article
- Rational Control of Poliovirus RNA-Dependent RNA Polymerase Fidelity by Modulating Motif-D Loop Conformational Dynamics.Biochemistry · 2019Article
- Determining selection free energetics from nucleotide pre-insertion to insertion in viral T7 RNA polymerase transcription fidelity control.Nucleic acids research · 2019Article
- Computational Simulations of DNA Polymerases: Detailed Insights on Structure/Function/Mechanism from Native Proteins to Cancer Variants.Chemical research in toxicology · 2017Article
- Picornaviral polymerase structure, function, and fidelity modulation.Virus research · 2017Review
- Cystoviral RNA-directed RNA polymerases: Regulation of RNA synthesis on multiple time and length scales.Virus research · 2017Review
- Triphosphate Reorientation of the Incoming Nucleotide as a Fidelity Checkpoint in Viral RNA-dependent RNA Polymerases.The Journal of biological chemistry · 2017Article
- Computational predictions suggest that structural similarity in viral polymerases may lead to comparable allosteric binding sites.Virus research · 2016Article
- ATP Is an Allosteric Inhibitor of Coxsackievirus B3 Polymerase.Biochemistry · 2016Article
- Design of a Genetically Stable High Fidelity Coxsackievirus B3 Polymerase That Attenuates Virus Growth in Vivo.The Journal of biological chemistry · 2016Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
The viral RNA-dependent RNA polymerase (RdRp) is essential for multiplication of all RNA viruses. The sequence diversity of an RNA virus population contributes to its ability to infect the host. This diversity emanates from errors made by the RdRp during RNA synthesis. The physical basis for RdRp fidelity is unclear but is linked to conformational changes occurring during the nucleotide-addition cycle. To understand RdRp dynamics that might influence RdRp function, we have analyzed all-atom molecular dynamics simulations on the nanosecond timescale of four RdRps from the picornavirus family that exhibit 30-74% sequence identity. Principal component analysis showed that the major motions observed during the simulations derived from conserved structural motifs and regions of known function. The dynamics of residues participating in the same biochemical property, for example, RNA binding, nucleotide binding or catalysis, were correlated even when spatially distant on the RdRp structure. The conserved and correlated dynamics of functional structural elements suggest coevolution of dynamics with structure and function of the RdRp. Crystal structures of all picornavirus RdRps exhibit a template-nascent RNA duplex channel too small to fully accommodate duplex RNA. Simulations revealed opening and closing motions of the RNA and nucleoside triphosphate channels, which might be relevant to nucleoside triphosphate entry, inorganic pyrophosphate exit and translocation. A role for nanosecond timescale dynamics in RdRp fidelity is supported by the altered dynamics of the high-fidelity G64S derivative of PV RdRp relative to wild-type enzyme.
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Registered trials
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