Conformational Transition Pathway of Polymerase β/DNA upon Binding Correct Incoming Substrate

The closing conformational transition of wild-type polymerase β bound to DNA template/primer before the
chemical step (nucleotidyl transfer reaction) is simulated using the stochastic difference equation (in length
version, “SDEL”) algorithm that approximates long-time dynamics. The order of the events and the intermediate
states during polβ's closing pathway are identified and compared to a separate study of polβ using transition
path sampling (TPS) (Radhakrishnan, R.; Schlick, T. Proc. Natl. Acad. Sci. USA 2004, 101, 5970−5975).
Results highlight the cooperative and subtle conformational changes in the polβ active site upon binding the
correct substrate that may help explain DNA replication and repair fidelity. These changes involve key residues
that differentiate the open from the closed conformation (Asp192, Arg258, Phe272), as well as residues
contacting the DNA template/primer strand near the active site (Tyr271, Arg283, Thr292, Tyr296) and residues
contacting the β and γ phosphates of the incoming nucleotide (Ser180, Arg183, Gly189). This study
compliments experimental observations by providing detailed atomistic views of the intermediates along the
polymerase closing pathway and by suggesting additional key residues that regulate events prior to or during
the chemical reaction. We also show general agreement between two sampling methods (the stochastic
difference equation and transition path sampling) and identify methodological challenges involved in the
former method relevant to large-scale biomolecular applications. Specifically, SDEL is very quick relative to
TPS for obtaining an approximate path of medium resolution and providing qualitative information on the
sequence of events; however, associated free energies are likely very costly to obtain because this will require
both successful further refinement of the path segments close to the bottlenecks and large computational
time.