A model for the mechanism of polymerase translocation

Richard Guajardo, Rui J Sousa

Research output: Contribution to journalArticle

153 Citations (Scopus)

Abstract

A general mechanism for polymerase translocation is elaborated. The central feature of this mechanism is that a rapid translocational equilibrium is established after each cycle of nucleoside monophosphate incorporation such that the polymerase distributes itself by diffusional sliding between all accessible positions on the template with relative occupancy determined by relative free energy. While alternative models for translocation have not been fully developed, much of the language currently used to describe this step suggests an active mechanism coupled to conformational transitions in the polymerase. For example, a recent study of force generation by Escherichia coli RNA polymerase during transcription suggests that it is a mechanoenzyme analogous to kinesin of myosin motor proteins. While the proposed mechanism does not rule out conformational transitions during polymerase translocation, it suggests that they may be unnecessary and that translocation can be explained in terms of the affinity of the active site for nucleoside triphosphate and the relative free energies of the polymerase bound at different positions on the template. This mechanism makes specific predictions which are borne out experimentally with polymerases as distinct as E. coli DNAP I, phage T7 RNAP, and E. coli RNAP.

Original languageEnglish (US)
Pages (from-to)8-19
Number of pages12
JournalJournal of Molecular Biology
Volume265
Issue number1
DOIs
StatePublished - Jan 10 1997

Fingerprint

Escherichia coli
Nucleosides
Bacteriophage T7
Kinesin
DNA-Directed RNA Polymerases
Myosins
Catalytic Domain
Language
Proteins
dinitroaminophenol
triphosphoric acid

Keywords

  • Mechanism
  • Polymerase kinetics
  • Polymerases
  • Processivity
  • Translocation

ASJC Scopus subject areas

  • Virology

Cite this

A model for the mechanism of polymerase translocation. / Guajardo, Richard; Sousa, Rui J.

In: Journal of Molecular Biology, Vol. 265, No. 1, 10.01.1997, p. 8-19.

Research output: Contribution to journalArticle

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