In Silico Evidence for DNA Polymerase 's Substrate-Induced Conformational Change

Structural information for mammalian DNA polymerase combined with molecular and essential dynamics studies provide atomistically detailed views of functionally important conformational rearrangements that occur during DNA repair and replication. Anchors for our study are available in crystallographic structures of the DNA polymerase in ``open'' (polymerase bound to gapped DNA) and ``closed'' (polymerase bound to gapped DNA and substrate, dCTP) forms; these different states suggest a large-scale conformational change that may help the polymerase choose the correct nucleotide, and hence monitor DNA synthesis fidelity, through an `induced-fit' mechanism. Our dynamics simulations of polymerase /DNA reveal the large-scale closing motions of the thumb and 8-kDa subdomains in the presence of the correct substrate -- leading to nearly perfect rearrangement of residues in the active site for the subsequent chemical step of nucleotidyl transfer -- in contrast to an opening when the substrate is absent, leading to complete disassembly of the active site residues. These studies provide in silico evidence for the substrate induced conformational rearrangements hypothesized experimentally. Further details gleaned from essential dynamics analyses clarify functionally relevant global motions of the polymerase polymerase /DNA complex.

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