Direct probing of solvent accessibility and mobility at the binding interface of polymerase (Dpo4)-DNA complex.

ABSTRACT: Water plays essential structural and dynamical roles in protein-DNA recognition through contributing to enthalpic or entropic stabilization of binding complex and by mediating intermolecular interactions and fluctuations for biological function. These interfacial water molecules are confined by the binding partners in nanospace, but in many cases they are highly mobile and exchange with outside bulk solution. Here, we report our studies of the interfacial water dynamics in the binary and ternary complexes of a polymerase (Dpo4) with DNA and an incoming nucleotide using a site-specific tryptophan probe with femtosecond resolution. By systematic comparison of the interfacial water motions and local side chain fluctuations in the apo, binary, and ternary states of Dpo4, we observed that the D

SUBMITTER: Qin Y 

PROVIDER: S-EPMC3903812 | biostudies-literature | 2013 Dec

REPOSITORIES: biostudies-literature