ArticlePLoS computational biology2012
What is the role of motif D in the nucleotide incorporation catalyzed by the RNA-dependent RNA polymerase from poliovirus?
Article in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed, 50 citations in OpenAlex.
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- Application of Molecular Dynamics Simulations to the Design of Nucleotide Inhibitors Binding to Norovirus Polymerase.Journal of chemical information and modeling · 2020Article
- Picornaviral polymerase domain exchanges reveal a modular basis for distinct biochemical activities of viral RNA-dependent RNA polymerases.The Journal of biological chemistry · 2020Article
- Rational Control of Poliovirus RNA-Dependent RNA Polymerase Fidelity by Modulating Motif-D Loop Conformational Dynamics.Biochemistry · 2019Article
- Viral Discovery in the Invasive Australian Cane Toad (Rhinella marina) Using Metatranscriptomic and Genomic Approaches.Journal of virology · 2018Article
- A computational approach for predicting off-target toxicity of antiviral ribonucleoside analogues to mitochondrial RNA polymerase.The Journal of biological chemistry · 2018Article
- Structural investigations on mechanism of lapatinib resistance caused by HER-2 mutants.PloS one · 2018Article
- Picornaviral polymerase structure, function, and fidelity modulation.Virus research · 2017Review
- 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
- Methyl Relaxation Measurements Reveal Patterns of Fast Dynamics in a Viral RNA-Directed RNA Polymerase.Biochemistry · 2015Article
- RNA-Dependent RNA Polymerases of Picornaviruses: From the Structure to Regulatory Mechanisms.Viruses · 2015Review
- Mechanistic insight into the functional transition of the enzyme guanylate kinase induced by a single mutation.Scientific reports · 2015Article
- Structure-function relationships underlying the replication fidelity of viral RNA-dependent RNA polymerases.Journal of virology · 2015Article
- Structural dynamics as a contributor to error-prone replication by an RNA-dependent RNA polymerase.The Journal of biological chemistry · 2014Article
- Common and unique features of viral RNA-dependent polymerases.Cellular and molecular life sciences : CMLS · 2014Review
- The crystal structure of a cardiovirus RNA-dependent RNA polymerase reveals an unusual conformation of the polymerase active site.Journal of virology · 2014Article
- Vaccine-derived mutation in motif D of poliovirus RNA-dependent RNA polymerase lowers nucleotide incorporation fidelity.The Journal of biological chemistry · 2013Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Poliovirus (PV) is a well-characterized RNA virus, and the RNA-dependent RNA polymerase (RdRp) from PV (3D(pol)) has been widely employed as an important model for understanding the structure-function relationships of RNA and DNA polymerases. Many experimental studies of the kinetics of nucleotide incorporation by RNA and DNA polymerases suggest that each nucleotide incorporation cycle basically consists of six sequential steps: (1) an incoming nucleotide binds to the polymerase-primer/template complex; (2) the ternary complex (nucleotide-polymerase-primer/template) undergoes a conformational change; (3) phosphoryl transfer occurs (the chemistry step); (4) a post-chemistry conformational change occurs; (5) pyrophosphate is released; (6) RNA or DNA translocation. Recently, the importance of structural motif D in nucleotide incorporation has been recognized, but the functions of motif D are less well explored so far. In this work, we used two computational techniques, molecular dynamics (MD) simulation and quantum mechanics (QM) method, to explore the roles of motif D in nucleotide incorporation catalyzed by PV 3D(pol). We discovered that the motif D, exhibiting high flexibility in either the presence or the absence of RNA primer/template, might facilitate the transportation of incoming nucleotide or outgoing pyrophosphate. We observed that the dynamic behavior of motif A, which should be essential to the polymerase function, was greatly affected by the motions of motif D. In the end, through QM calculations, we attempted to investigate the proton transfer in enzyme catalysis associated with a few amino acid residues of motifs F and D.
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