Fidelity discrimination in DNA polymerase beta: differing closing profiles for a mismatched (G:A) versus matched (G:C) base pair.
Understanding fidelity-the faithful replication or repair of DNA by polymerases-requires tracking of the structural and energetic changes involved, including the elusive transient intermediates, for nucleotide incorporation at the template/primer DNA junction. We report, using path sampling simulations and a reaction network model, strikingly different transition states in DNA polymerase beta's conformational closing for correct dCTP versus incorrect dATP incoming nucleotide opposite a template G. The cascade of transition states leads to differing active-site assembly processes toward the "two-metal-ion catalysis" geometry. We demonstrate that these context-specific pathways imply different selection processes: while active-site assembly occurs more rapidly with the correct nucleotide and leads to primer extension, the enzyme remains open longer, has a more transient closed state, and forms product more slowly when an incorrect nucleotide is present. Our results also suggest that the rate-limiting step in pol beta's conformational closing is not identical to that for overall nucleotide insertion and that the rate-limiting step in the overall nucleotide incorporation process for matched as well as mismatched systems occurs after the closing conformational change.
Radhakrishnan
Ravi
R
Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
Schlick
Tamar
T
D020137:Base Pair Mismatch; D001483:Base Sequence; D003198:Computer Simulation; D019951:DNA Polymerase beta / Q000737:chemistry*; D008958:Models, Molecular; D013997:Time Factors
D019951:DNA Polymerase beta