[Investigation of the Dependence of Escherichia coli RNA Polymerase σ70-Subunit Structure on Ionic Strength by Molecular Dynamics Simulation Method]

A P Tolstova; E V Dubrovin; O N Koroleva

[Investigation of the Dependence of Escherichia coli RNA Polymerase σ70-Subunit Structure on Ionic Strength by Molecular Dynamics Simulation Method]

Biofizika. 2015 Nov-Dec;60(6):1045-9.

[Article in Russian]

Authors

A P Tolstova, E V Dubrovin, O N Koroleva

PMID: 26841497

Abstract

The σ70-subunit of E. coli RNA polymerase (a small protein, being a part of RNA holoenzyme, and responsible for initiation of transcription of constitutive genes) is modeled at different ionic strengths. Two variants of the location of C-end domain 4 are obtained. At low ionic strength domain 4 interacts with the region of high negative charge 190-210 AK within NCR domain. At high ionic strength this region was screened and domain 4 was free and set away from domain NCR. We suppose that this leads to the increase in polymerization rate. Simulation data do not confirm any hypothesis about a self-inhibition mechanism.

MeSH terms

Biophysical Phenomena
DNA-Directed RNA Polymerases / chemistry*
Escherichia coli / chemistry*
Escherichia coli / genetics
Models, Molecular*
Molecular Dynamics Simulation*
Osmolar Concentration
Protein Conformation / drug effects
Protein Subunits / chemistry
Salts / chemistry
Sigma Factor / chemistry*
Transcription, Genetic

Substances

Protein Subunits
Salts
Sigma Factor
RNA polymerase sigma 70
DNA-Directed RNA Polymerases