(Q35042768)

6 August 2017

title

Molecular dynamics simulations of viral RNA polymerases link conserved and correlated motions of functional elements to fidelity (English)

1 reference

6 August 2017

5

Craig E Cameron

1 reference

6 August 2017

Ibrahim M Moustafa

1

1 reference

6 August 2017

Hujun Shen

series ordinal

2

1 reference

6 August 2017

Brandon Morton

series ordinal

3

1 reference

6 August 2017

Coray M Colina

series ordinal

4

1 reference

6 August 2017

language of work or name

English

0 references

publication date

7 May 2011

1 reference

Journal of Molecular Biology

6 August 2017

published in

1 reference

6 August 2017

volume

410

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6 August 2017

issue

1

1 reference

6 August 2017

page(s)

159-181

1 reference

Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms

6 August 2017

cites work

1 reference

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Structural basis for active site closure by the poliovirus RNA-dependent RNA polymerase

8 July 2018

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Long-Range Interaction Networks in the Function and Fidelity of Poliovirus RNA-Dependent RNA Polymerase Studied by Nuclear Magnetic Resonance

8 July 2018

1 reference

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Dynamics on multiple timescales in the RNA-directed RNA polymerase from the cystovirus phi6

8 July 2018

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Features and development of Coot

8 July 2018

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Structural insights into replication initiation and elongation processes by the FMDV RNA-dependent RNA polymerase

8 July 2018

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Dynamics: the missing link between structure and function of the viral RNA-dependent RNA polymerase?

8 July 2018

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Therapeutically targeting RNA viruses via lethal mutagenesis

8 July 2018

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Recombination between polioviruses and co-circulating Coxsackie A viruses: role in the emergence of pathogenic vaccine-derived polioviruses

8 July 2018

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Determinants of RNA-dependent RNA polymerase (in)fidelity revealed by kinetic analysis of the polymerase encoded by a foot-and-mouth disease virus mutant with reduced sensitivity to ribavirin

8 July 2018

1 reference

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The crystal structure of coxsackievirus B3 RNA-dependent RNA polymerase in complex with its protein primer VPg confirms the existence of a second VPg binding site on Picornaviridae polymerases

8 July 2018

1 reference

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Molecular simulations of protein dynamics: new windows on mechanisms in biology

8 July 2018

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Dynamic personalities of proteins

8 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

The design of drugs for HIV and HCV

8 July 2018

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A hierarchy of timescales in protein dynamics is linked to enzyme catalysis

8 July 2018

1 reference

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Intrinsic motions along an enzymatic reaction trajectory

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

Picornavirus genome replication. Identification of the surface of the poliovirus (PV) 3C dimer that interacts with PV 3Dpol during VPg uridylylation and construction of a structural model for the PV 3C2-3Dpol complex

8 July 2018

1 reference

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Sequential structures provide insights into the fidelity of RNA replication

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

Crystal Structure of Poliovirus 3CD Protein: Virally Encoded Protease and Precursor to the RNA-Dependent RNA Polymerase

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

Stabilization of Poliovirus Polymerase by NTP Binding and Fingers–Thumb Interactions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

Foot-and-mouth disease virus mutant with decreased sensitivity to ribavirin: implications for error catastrophe

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

Relating protein motion to catalysis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

An antiviral mechanism investigated with ribavirin as an RNA virus mutagen for foot-and-mouth disease virus

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

Recombinant viral RdRps can initiate RNA synthesis from circular templates

8 July 2018

1 reference

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Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

The Amber biomolecular simulation programs

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

Remote site control of an active site fidelity checkpoint in a viral RNA-dependent RNA polymerase

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

Molecular dynamics and protein function

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

Ribavirin and lethal mutagenesis of poliovirus: molecular mechanisms, resistance and biological implications

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

Incorporation fidelity of the viral RNA-dependent RNA polymerase: a kinetic, thermodynamic and structural perspective

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

Structural basis for proteolysis-dependent activation of the poliovirus RNA-dependent RNA polymerase

8 July 2018

1 reference

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UCSF Chimera--a visualization system for exploratory research and analysis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

Poliovirus RNA-dependent RNA polymerase (3Dpol): kinetic, thermodynamic, and structural analysis of ribonucleotide selection

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

Poliovirus RNA-dependent RNA polymerase (3Dpol): pre-steady-state kinetic analysis of ribonucleotide incorporation in the presence of Mg2+.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

Challenges for the development of ribonucleoside analogues as inducers of error catastrophe

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

A perspective on enzyme catalysis.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

A single mutation in poliovirus RNA-dependent RNA polymerase confers resistance to mutagenic nucleotide analogs via increased fidelity

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

The Protein Data Bank: unifying the archive

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

Crystal structures of active and inactive conformations of a caliciviral RNA-dependent RNA polymerase

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

Analysis of RNA-dependent RNA polymerase structure and function as guided by known polymerase structures and computer predictions of secondary structure

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

Clustered charged-to-alanine mutagenesis of poliovirus RNA-dependent RNA polymerase yields multiple temperature-sensitive mutants defective in RNA synthesis

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

Essential dynamics of proteins

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

Broad-spectrum antiviral activity of Virazole: 1-beta-D-ribofuranosyl-1,2,4-triazole-3-carboxamide

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

Identification of four conserved motifs among the RNA-dependent polymerase encoding elements

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

Relationships among the positive strand and double-strand RNA viruses as viewed through their RNA-dependent RNA polymerases

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

Dynamics of folded proteins

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

Nucleic acid polymerases use a general acid for nucleotidyl transfer

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

Engineering attenuated virus vaccines by controlling replication fidelity

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

The crystal structure of the RNA-dependent RNA polymerase from human rhinovirus: a dual function target for common cold antiviral therapy

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

Structure of foot-and-mouth disease virus RNA-dependent RNA polymerase and its complex with a template-primer RNA.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

A Ratchet Mechanism of Transcription Elongation and Its Control

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3114172

Molecular dynamics simulations of biomolecules

25 October 2018

1 reference

12 December 2020

Poliovirus RNA-dependent RNA polymerase (3D(pol)). Assembly of stable, elongation-competent complexes by using a symmetrical primer-template substrate (sym/sub)

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12 December 2020

Large-amplitude nonlinear motions in proteins

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12 December 2020

Laboratory surveillance for wild and vaccine-derived polioviruses, January 2007-June 2008

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12 December 2020

10.1016/J.JMB.2011.04.078

Identifiers

DOI

1 reference

6 August 2017

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6 August 2017

1 reference