title: Computational study of putative residues involved in DNA synthesis fidelity checking in Thermus aquaticus DNA polymerase I.
abstract: A fidelity-checking site for DNA polymerase I has been proposed based on recent single-molecule Förster resonance energy transfer studies. The checking site is believed to ensure proper base pairing of the newly inserted nucleotide. Computational studies have been utilized to predict residues involved in this putative checking site on the Klenow and Bacillus fragments. Here, we employ energy decomposition analysis, electrostatic free energy response, and noncovalent interaction plots to identify the residues involved in the hypothesized checking site in the homologous Klenow fragment from Thermus aquaticus (Klentaq). Our results indicate multiple protein residues that show altered interactions for three mispairs compared to the correctly paired DNA dimer. Many of these residues are also conserved along A family polymerases.
authors.affiliation: Department of Chemistry, Wayne State University, Detroit, Michigan, USA.
authors.forename: Angela A
authors.initials: AA
authors.lastname: Elias
authors.affiliation: Department of Chemistry, Wayne State University, Detroit, Michigan, USA. Electronic address: andres@chem.wayne.edu.
authors.forename: G Andrés
authors.initials: GA
authors.lastname: Cisneros
mesh_terms: D019295:Computational Biology / Q000379:methods*; D004256:DNA Polymerase I / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D004269:DNA, Bacterial / Q000096:biosynthesis* / Q000737:chemistry; D008958:Models, Molecular; D011487:Protein Conformation; D013816:Thermodynamics; D013824:Thermus / Q000201:enzymology* / Q000235:genetics
chemical_list: D004269:DNA, Bacterial; D004256:DNA Polymerase I
keywords: DNA synthesis fidelity; Electrostatic free energy response; Energy decomposition analysis; Klentaq; Molecular dynamics; Noncovalent interaction analysis; Postinsertion fidelity checking