title: Polymerase beta simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se.
abstract: The large-scale opening motion of mammalian DNA polymerase beta is followed at atomic resolution by dynamic simulations that link crystal "closed" and "open" conformations. The closing/opening conformational change is thought to be key to the ability of polymerases to choose a correct nucleotide (through "induced fit") and hence maintain DNA repair synthesis fidelity. Corroborating available structural and kinetic measurements, our studies bridge static microscopic crystal structures with macroscopic kinetic data by delineating a specific sequence, Phe272 ring flip, large thumb movement, Arg258 rotation with release of catalytic Mg2+, together with estimated time-scales, that suggest the Arg258 rearrangement as a limiting factor of large subdomain motions. If similarly slow in the closing motion, this conformational change might be restricted further when an incorrect nucleotide binds and thus play a role in pol beta's selectivity for the correct nucleotide. These results suggest new lines of experimentation in the study of polymerase mechanisms (e.g. enzyme mutants), which should provide further insights into mechanisms of error discrimination and DNA synthesis fidelity.
authors.affiliation: Department of Chemistry and Courant, Institute of Mathematical Sciences, New York University and the Howard Hughes Medical Institute, 251 Mercer Street, New York, New York 10012, USA.
authors.forename: Linjing
authors.initials: L
authors.lastname: Yang
authors.forename: William A
authors.initials: WA
authors.lastname: Beard
authors.forename: Samuel H
authors.initials: SH
authors.lastname: Wilson
authors.forename: Suse
authors.initials: S
authors.lastname: Broyde
authors.forename: Tamar
authors.initials: T
authors.lastname: Schlick
mesh_terms: D001120:Arginine / Q000737:chemistry* / Q000378:metabolism*; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004247:DNA / Q000378:metabolism; D019951:DNA Polymerase beta / Q000737:chemistry* / Q000378:metabolism*; D006801:Humans; D006860:Hydrogen Bonding; D007700:Kinetics; D008274:Magnesium / Q000378:metabolism; D008958:Models, Molecular; D009038:Motion; D009690:Nucleic Acid Conformation; D017434:Protein Structure, Tertiary; D012399:Rotation; D013329:Structure-Activity Relationship; D014867:Water / Q000378:metabolism
chemical_list: D014867:Water; D004247:DNA; D001120:Arginine; D019951:DNA Polymerase beta; D008274:Magnesium