Regular Article

Theoretical Chemistry Accounts

, 131:1287

Perspective: pre-chemistry conformational changes in DNA polymerase mechanisms

  • Tamar SchlickAffiliated withDepartment of Chemistry, New York UniversityCourant Institute of Mathematical Sciences, New York University Email author 
  • , Karunesh AroraAffiliated withDepartments of Chemistry and Biophysics, University of Michigan
  • , William A. BeardAffiliated withLaboratory of Structural Biology, National Institute of Environmental Sciences, National Institutes of Health
  • , Samuel H. WilsonAffiliated withLaboratory of Structural Biology, National Institute of Environmental Sciences, National Institutes of Health

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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 polymerase β representing 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.

Keywords

Enzyme catalysis Intrinsic protein dynamics Pre-chemistry conformational adjustments Nucleotidyl transfer DNA polymerase β Catalytic cycle chemical step