(Q30652050)

28 September 2017

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

1 reference

molecular dynamics simulation

28 September 2017

0 references

author name string

Hyung-June Woo

series ordinal

1

1 reference

28 September 2017

Yuemin Liu

series ordinal

2

1 reference

28 September 2017

Rui Sousa

series ordinal

3

1 reference

28 September 2017

language of work or name

English

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publication date

1 December 2008

1 reference

28 September 2017

1 reference

28 September 2017

73

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28 September 2017

4

1 reference

28 September 2017

1021-1036

1 reference

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

Dissociation of halted T7 RNA polymerase elongation complexes proceeds via a forward-translocation mechanism

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

Visualizing polynucleotide polymerase machines at work

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

Sequence-resolved detection of pausing by single RNA polymerase molecules.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

Single-molecule analysis of RNA polymerase transcription

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

Thermodynamic and kinetic modeling of transcriptional pausing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

Tracking RNA polymerase, one step at a time.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

Direct observation of base-pair stepping by RNA polymerase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

The N-terminal end of the catalytic domain of SRC kinase Hck is a conformational switch implicated in long-range allosteric regulation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

Backtracking by single RNA polymerase molecules observed at near-base-pair resolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

A microscopic view of ion conduction through the K+ channel.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

Structure of a T7 RNA polymerase elongation complex at 2.9 A resolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

Structure of a transcribing T7 RNA polymerase initiation complex

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

RNA polymerase as a molecular motor

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

A model for the mechanism of polymerase translocation

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

Crystal structure of bacteriophage T7 RNA polymerase at 3.3 A resolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

Structure of a B-DNA dodecamer: conformation and dynamics

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

Optimized atomic radii for protein continuum electrostatics solvation forces.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

Analytical theory of the nonequilibrium spatial distribution of RNA polymerase translocations

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

A Ratchet Mechanism of Transcription Elongation and Its Control

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

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

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

Structural basis for substrate selection by t7 RNA polymerase.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

Structural transitions mediating transcription initiation by T7 RNA polymerase

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

An integrated model of the transcription complex in elongation, termination, and editing

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

The thumb's knuckle. Flexibility in the thumb subdomain of T7 RNA polymerase is revealed by the structure of a chimeric T7/T3 RNA polymerase

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

Free Energy Landscape of A-DNA to B-DNA Conversion in Aqueous Solution

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4447105

Translocation by T7 RNA polymerase: a sensitively poised Brownian ratchet

25 November 2018

1 reference

12 December 2020

Mechanism of intrinsic transcription termination and antitermination

1 reference

12 December 2020

Sequence-dependent kinetic model for transcription elongation by RNA polymerase

1 reference

12 December 2020

Unravelling the mechanism of RNA-polymerase forward motion by using mechanical force

1 reference

12 December 2020

Topological and conformational analysis of the initiation and elongation complex of t7 RNA polymerase suggests a new twist

1 reference

12 December 2020

Identifiers

DOI

10.1002/PROT.22134

1 reference

28 September 2017

1 reference

28 September 2017

PubMed publication ID

18536012

1 reference