title: Computational prediction of residues involved in fidelity checking for DNA synthesis in DNA polymerase I.
abstract: Recent single-molecule Förster resonance energy transfer studies of DNA polymerase I have led to the proposal of a postinsertion fidelity-checking site. This site is hypothesized to ensure proper base pairing of the newly inserted nucleotide. To help test this hypothesis, we have used energy decomposition, electrostatic free energy response, and noncovalent interaction analysis analyses to identify residues involved in this putative checking site. We have used structures of DNA polymerase I from two different organisms, the Klenow fragment from Escherichia coli and the Bacillus fragment from Bacillus stearothermophilus. Our results point to several residues that show altered interactions for three mispairs compared to the correctly paired DNA dimer. Furthermore, many of these residues are conserved among A family polymerases. The identified residues provide potential targets for mutagenesis studies for investigation of the fidelity-checking site hypothesis.
authors.affiliation: Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States.
authors.forename: Sarah E
authors.initials: SE
authors.lastname: Graham
authors.forename: FatimaSultana
authors.initials: F
authors.lastname: Syeda
authors.forename: G Andrés
authors.initials: GA
authors.lastname: Cisneros
mesh_terms: D000595:Amino Acid Sequence; D020029:Base Pairing; D004247:DNA / Q000096:biosynthesis* / Q000737:chemistry; D004256:DNA Polymerase I / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D004926:Escherichia coli / Q000201:enzymology; D001411:Geobacillus stearothermophilus / Q000201:enzymology; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D016296:Mutagenesis; D011487:Protein Conformation; D013816:Thermodynamics
chemical_list: D004247:DNA; D004256:DNA Polymerase I