A MODEL FOR THE MECHANISM OF POLYMERASE TRANSLOCATION

A general mechanism for polymerase translocation is elaborated. The ce ntral feature of this mechanism is that a rapid translocational equili brium is established after each cycle of nucleoside monophosphate inco rporation such that the polymerase distributes itself by diffusional s liding 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 cou pled to conformational transitions in the polymerase. For example, a r ecent study of force generation by Escherichia coli RNA polymerase dur ing transcription suggests that it is a mechanoenzyme analogous to kin esin of myosin motor proteins. While the proposed mechanism does not r ule out conformational transitions during polymerase translocation, it suggests that they may be unnecessary and that translocation can be e xplained in terms of the affinity of the active site for nucleoside tr iphosphate and the relative free energies of the polymerase bound at d ifferent positions on the template. This mechanism makes specific pred ictions which are borne out experimentally with polymerases as distinc t as E. coli DNAP I, phage T7 RNAP, and E. coli RNAP. (C) 1997 Academi c Press Limited