William A. Beard

Laboratory of Structural Biology, NIEHS, National Institutes of Health

Affiliated withNIEHS, National Institutes of Health

Research Area

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 26	2013

Other Publications

Article	Year
Loss of DNA polymerase beta stacking interactions with templating purines, but not pyrimidines, alters catalytic efficiency and fidelity. The Journal of biological chemistry\| PubMed ID: 11756435	2002
Polymerase beta simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se. Journal of molecular biology\| PubMed ID: 11955015	2002
Efficiency of correct nucleotide insertion governs DNA polymerase fidelity. The Journal of biological chemistry\| PubMed ID: 12370169	2002
Rapid segmental and subdomain motions of DNA polymerase beta. The Journal of biological chemistry\| PubMed ID: 12458221	2003
Structure of DNA polymerase beta with the mutagenic DNA lesion 8-oxodeoxyguanine reveals structural insights into its coding potential. Structure (London, England : 1993)\| PubMed ID: 12517346	2003
Structural insights into the origins of DNA polymerase fidelity. Structure (London, England : 1993)\| PubMed ID: 12737815	2003
Localization of the deoxyribose phosphate lyase active site in human DNA polymerase iota by controlled proteolysis. The Journal of biological chemistry\| PubMed ID: 12777390	2003
High-level expression and purification of untagged and histidine-tagged HIV-1 reverse transcriptase. Protein expression and purification\| PubMed ID: 14766302	2004
Influence of DNA structure on DNA polymerase beta active site function: extension of mutagenic DNA intermediates. The Journal of biological chemistry\| PubMed ID: 15145936	2004
Highly organized but pliant active site of DNA polymerase beta: compensatory mechanisms in mutant enzymes revealed by dynamics simulations and energy analyses. Biophysical journal\| PubMed ID: 15189842	2004
Critical role of magnesium ions in DNA polymerase beta's closing and active site assembly. Journal of the American Chemical Society\| PubMed ID: 15238001	2004
Dynamic characterization of a DNA repair enzyme: NMR studies of [methyl-13C]methionine-labeled DNA polymerase beta. Biochemistry\| PubMed ID: 15248749	2004
Structural insights into DNA polymerase beta deterrents for misincorporation support an induced-fit mechanism for fidelity. Structure (London, England : 1993)\| PubMed ID: 15458631	2004
DNA polymerase beta and flap endonuclease 1 enzymatic specificities sustain DNA synthesis for long patch base excision repair. The Journal of biological chemistry\| PubMed ID: 15561706	2005
DNA polymerase lambda mediates a back-up base excision repair activity in extracts of mouse embryonic fibroblasts. The Journal of biological chemistry\| PubMed ID: 15749700	2005
Nucleotide-induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate. Structure (London, England : 1993)\| PubMed ID: 16084394	2005
Structural insight into the DNA polymerase beta deoxyribose phosphate lyase mechanism. DNA repair\| PubMed ID: 16172026	2005
Mismatch-induced conformational distortions in polymerase beta support an induced-fit mechanism for fidelity. Biochemistry\| PubMed ID: 16201758	2005
Syn-full behavior by T7 DNA polymerase. Structure (London, England : 1993)\| PubMed ID: 16271879	2005
A thymine isostere in the templating position disrupts assembly of the closed DNA polymerase beta ternary complex. Biochemistry\| PubMed ID: 16285726	2005
Structure and mechanism of DNA polymerase Beta. Chemical reviews\| PubMed ID: 16464010	2006
Magnesium-induced assembly of a complete DNA polymerase catalytic complex. Structure (London, England : 1993)\| PubMed ID: 16615916	2006
Determination of lysine pK values using [5-13C]lysine: application to the lyase domain of DNA Pol beta. Journal of the American Chemical Society\| PubMed ID: 16787052	2006
Activities and mechanism of DNA polymerase beta. Methods in enzymology\| PubMed ID: 16793365	2006
Energy analysis of chemistry for correct insertion by DNA polymerase beta. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 16938895	2006
Structure of DNA polymerase beta with a benzo[c]phenanthrene diol epoxide-adducted template exhibits mutagenic features. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 17079493	2006
Magnesium-cationic dummy atom molecules enhance representation of DNA polymerase beta in molecular dynamics simulations: improved accuracy in studies of structural features and mutational ef... Journal of molecular biology\| PubMed ID: 17174326	2007
Regulation of DNA repair fidelity by molecular checkpoints: "gates" in DNA polymerase beta's substrate selection. Biochemistry\| PubMed ID: 17176036	2006
Modifying the beta,gamma leaving-group bridging oxygen alters nucleotide incorporation efficiency, fidelity, and the catalytic mechanism of DNA polymerase beta. Biochemistry\| PubMed ID: 17209556	2007
Differing conformational pathways before and after chemistry for insertion of dATP versus dCTP opposite 8-oxoG in DNA polymerase beta. Biophysical journal\| PubMed ID: 17293403	2007
Coordination of steps in single-nucleotide base excision repair mediated by apurinic/apyrimidinic endonuclease 1 and DNA polymerase beta. The Journal of biological chemistry\| PubMed ID: 17355977	2007
The X family portrait: structural insights into biological functions of X family polymerases. DNA repair\| PubMed ID: 17631059	2007
Exploring the role of large conformational changes in the fidelity of DNA polymerase beta. Proteins\| PubMed ID: 17671961	2008
(R)-beta,gamma-fluoromethylene-dGTP-DNA ternary complex with DNA polymerase beta. Journal of the American Chemical Society\| PubMed ID: 18031037	2007
DNA polymerase beta fidelity: halomethylene-modified leaving groups in pre-steady-state kinetic analysis reveal differences at the chemical transition state. Biochemistry\| PubMed ID: 18161950	2008
Incorrect nucleotide insertion at the active site of a G:A mismatch catalyzed by DNA polymerase beta. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 18391201	2008
Negligible impact of pol iota expression on the alkylation sensitivity of pol beta-deficient mouse fibroblast cells. DNA repair\| PubMed ID: 18434259	2008
Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation. Molecular cell\| PubMed ID: 18471977	2008
Alpha,beta-methylene-2'-deoxynucleoside 5'-triphosphates as noncleavable substrates for DNA polymerases: isolation, characterization, and stability studies of novel 2'-deoxycyclonucleosides,... Journal of medicinal chemistry\| PubMed ID: 18811136	2008
Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates: a convenient synthesis of useful probes for DNA polymerase beta structure and function. Organic letters\| PubMed ID: 19351147	2009
Coordination between polymerase beta and FEN1 can modulate CAG repeat expansion. The Journal of biological chemistry\| PubMed ID: 19674974	2009
A real-time fluorescence method for enzymatic characterization of specialized human DNA polymerases. Nucleic acids research\| PubMed ID: 19684079	2009
DNA polymerase beta and PARP activities in base excision repair in living cells. DNA repair\| PubMed ID: 19748837	2009
DNA polymerase beta substrate specificity: side chain modulation of the "A-rule". The Journal of biological chemistry\| PubMed ID: 19759017	2009
Halogenated beta,gamma-methylene- and ethylidene-dGTP-DNA ternary complexes with DNA polymerase beta: structural evidence for stereospecific binding of the fluoromethylene analogues. Journal of the American Chemical Society\| PubMed ID: 20465217	2010
DNA polymerase beta ribonucleotide discrimination: insertion, misinsertion, extension, and coding. The Journal of biological chemistry\| PubMed ID: 20519499	2010
Mutagenic conformation of 8-oxo-7,8-dihydro-2'-dGTP in the confines of a DNA polymerase active site. Nature structural & molecular biology\| PubMed ID: 20526335	2010
DNA polymerase structure-based insight on the mutagenic properties of 8-oxoguanine. Mutation research\| PubMed ID: 20696268	2010
Synthesis and biological evaluation of fluorinated deoxynucleotide analogs based on bis-(difluoromethylene)triphosphoric acid. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 20724659	2010
Base excision repair and design of small molecule inhibitors of human DNA polymerase Î². Cellular and molecular life sciences : CMLS\| PubMed ID: 20844920	2010
Substrate channeling in mammalian base excision repair pathways: passing the baton. The Journal of biological chemistry\| PubMed ID: 20952393	2010
Molecular insights into DNA polymerase deterrents for ribonucleotide insertion. The Journal of biological chemistry\| PubMed ID: 21733843	2011
Metal-induced DNA translocation leads to DNA polymerase conformational activation. Nucleic acids research\| PubMed ID: 22169953	2012
Binary complex crystal structure of DNA polymerase Î² reveals multiple conformations of the templating 8-oxoguanine lesion. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 22178760	2012
Stereospecific formation of a ternary complex of (S)-Î±,Î²-fluoromethylene-dATP with DNA pol Î². Chembiochem : a European journal of chemical biology\| PubMed ID: 22315190	2012
Structures of dNTP intermediate states during DNA polymerase active site assembly. Structure (London, England : 1993)\| PubMed ID: 22959623	2012
DNA sequence context effects on the glycosylase activity of human 8-oxoguanine DNA glycosylase. The Journal of biological chemistry\| PubMed ID: 22989888	2012
Effect of Î²,Î³-CHF- and Î²,Î³-CHCl-dGTP halogen atom stereochemistry on the transition state of DNA polymerase Î². Biochemistry\| PubMed ID: 23043620	2012
DNA polymerase Î² gap-filling translesion DNA synthesis. Chemical research in toxicology\| PubMed ID: 23121263	2012
DNA polymerase minor groove interactions modulate mutagenic bypass of a templating 8-oxoguanine lesion. Nucleic acids research\| PubMed ID: 23267011	2013
Perspective: pre-chemistry conformational changes in DNA polymerase mechanisms. Theoretical chemistry accounts\| PubMed ID: 23459563	2012
Amino acid substitution in the active site of DNA polymerase Î² explains the energy barrier of the nucleotidyl transfer reaction. Journal of the American Chemical Society\| PubMed ID: 23647366	2013
Insights into the conformation of aminofluorene-deoxyguanine adduct in a DNA polymerase active site. The Journal of biological chemistry\| PubMed ID: 23798703	2013
Observing a DNA polymerase choose right from wrong. Cell\| PubMed ID: 23827680	2013
Understanding the loss-of-function in a triple missense mutant of DNA polymerase Î² found in prostate cancer. International journal of oncology\| PubMed ID: 23877444	2013