title: Perspective: pre-chemistry conformational changes in DNA polymerase mechanisms.
abstract: In recent papers, there has been a lively exchange concerning theories for enzyme catalysis, especially the role of protein dynamics/pre-chemistry conformational changes in the catalytic cycle of enzymes. Of particular interest is the notion that substrate-induced conformational changes that assemble the polymerase active site prior to chemistry are required for DNA synthesis and impact fidelity (i.e., substrate specificity). High-resolution crystal structures of DNA polymeraseβrepresenting intermediates of substrate complexes prior to the chemical step are available. These structures indicate that conformational adjustments in both the protein and substrates must occur to achieve the requisite geometry of the reactive participants for catalysis. We discuss computational and kinetic methods to examine possible conformational change pathways that lead from the observed crystal structure intermediates to the final structures poised for chemistry. The results, as well as kinetic data from site-directed mutagenesis studies, are consistent with models requiring pre-chemistry conformational adjustments in order to achieve high fidelity DNA synthesis. Thus, substrate-induced conformational changes that assemble the polymerase active site prior to chemistry contribute to DNA synthesis even when they do not represent actual rate-determining steps for chemistry.
authors: Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, NY 10003, USA. Courant Institute of Mathematical Sciences, New York, University, 251 Mercer Street, New York, NY 10012, USA.
authors: Tamar
authors: T
authors: Schlick
authors: Karunesh
authors: K
authors: Arora
authors: William A
authors: WA
authors: Beard
authors: Samuel H
authors: SH
authors: Wilson
keywords: Catalytic cycle chemical step; DNA polymerase β; Enzyme catalysis; Intrinsic protein dynamics; Nucleotidyl transfer; Pre-chemistry conformational adjustments