(Q34206064)

31 July 2017

RNA polymerase II with open and closed trigger loops: active site dynamics and nucleic acid translocation (English)

1 reference

31 July 2017

Michael Feig

1

1 reference

PubMed ID

20959099

31 July 2017

Zachary F Burton

series ordinal

2

1 reference

PubMed ID

20959099

31 July 2017

language of work or name

English

0 references

publication date

1 October 2010

1 reference

31 July 2017

10

1 reference

based on heuristic

inferred from page(s)

published in

Biophysical Journal

1 reference

31 July 2017

99

1 reference

31 July 2017

8

1 reference

31 July 2017

2577-2586

1 reference

All-atom empirical potential for molecular modeling and dynamics studies of proteins

31 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

RNA polymerase II flexibility during translocation from normal mode analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

Site-directed mutagenesis, purification and assay of Saccharomyces cerevisiae RNA polymerase II.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

CHARMM: the biomolecular simulation program

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

Rpb9 subunit controls transcription fidelity by delaying NTP sequestration in RNA polymerase II.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

Millisecond phase kinetic analysis of elongation catalyzed by human, yeast, and Escherichia coli RNA polymerase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

A bridge to transcription by RNA polymerase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

Bridge helix and trigger loop perturbations generate superactive RNA polymerases.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

Structure of eukaryotic RNA polymerases

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

Molecular dynamics studies of the energetics of translocation in model T7 RNA polymerase elongation complexes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

Single-molecule studies of RNA polymerase: motoring along

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

RNA polymerase: the vehicle of transcription

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

Structural basis for substrate loading in bacterial RNA polymerase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

Correct and incorrect nucleotide incorporation pathways in DNA polymerase beta

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

Direct observation of base-pair stepping by RNA polymerase

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

Scalable molecular dynamics with NAMD

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

NTP-driven translocation and regulation of downstream template opening by multi-subunit RNA polymerases

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

Simplified normal mode analysis of conformational transitions in DNA-dependent polymerases: the elastic network model

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

Evolution and physics in comparative protein structure modeling.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

Modeling of loops in protein structures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

Architecture of RNA polymerase II and implications for the transcription mechanism

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

Eukaryotic transcriptional control

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

VMD: visual molecular dynamics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

Role of the RNA polymerase trigger loop in catalysis and pausing.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

Dynamic error correction and regulation of downstream bubble opening by human RNA polymerase II.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

Normal-mode analysis suggests protein flexibility modulation throughout RNA polymerase's functional cycle.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

The structural mechanism of translocation and helicase activity in T7 RNA polymerase

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

Improved treatment of the protein backbone in empirical force fields.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

A Ratchet Mechanism of Transcription Elongation and Its Control

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2956212

Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20959099

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Zinc binding in proteins and solution: a simple but accurate nonbonded representation

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20959099

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1016/J.BPJ.2010.08.010

1 reference

31 July 2017

1 reference

31 July 2017

1 reference

PubMed ID

20959099