Department of Biochemistry and Molecular Biophysics

2010 Publications

The following is a partial list of publications by faculty, post-doctoral associates, students, and staff of Biochemistry and Molecular Biophysics.

Wayne M. Barnes
  • Zhang, Z., Kermekchiev, M.B. and Barnes, W.M. Direct DNA amplification from crude clinical samples using a PCR enhancer cocktail and novel mutants of Taq. J Mol Diagn. 12:152-161 (2010).
Peter M. Burgers
  • Brown, J.A., Zhang, L., Sherrer, S.M., Taylor, J.S., Burgers, P.M. and Suo, Z. Pre-steady-state kinetic analysis of truncated and full-length Saccharomyces cerevisiae DNA polymerase eta. J Nucleic Acids 2010:1-11 (2010).
  • Pike,J.E., Henry, R.A., Burgers, P.M., Campbell, J.L. and Bambara, R.A. An alternative pathway for Okazaki fragment processing: Resolution of fold-back flaps by Pif1 helicase. J Biol Chem 285:41712-41723 (2010).
  • Lydeard, J.R., Lipkin-Moore, Z., Sheu, Y.J., Stillman, B., Burgers, P.M. and Haber, J.E. Break-induced replication requires all essential DNA replication factors except those specific for pre-RC assembly. Genes Dev 24:1133-1144 (2010).
  • Nick McElhinny, S.A., Watts, B.E., Kumar, D, Watt, D.L., Lundstrom, E.B., Burgers, P.M., Johansson, E., Chabes, A. and Kunkel, T.A. Abundant ribonucleotide incorporation into DNA by yeast replicative polymerases. Proc Natl Acad Sci USA 107:4949-4954 (2010).
  • Dallmann, H.G., Fackelmayer, O.J., Tomer, G., Chen, J., Wiktor-Becker, A., Ferrara, T., Pope, C., Oliveira, M.T., Burgers, P.M., Kaguni, L.S. and McHenry, C.S. Parallel multiplicative target screening against divergent bacterial replicases: Identification of specific inhibitors with broad spectrum potential. Biochemistry 49:2551-2562 (2010).
  • Burgers, P.M., Stith, C.M., Yoder, B.L. and Sparks, J.L. Yeast Exonuclease 5 is essential for mitochondrial genome maintenance. Mol Cell Biol 30:1457-1466 (2010).
John A. Cooper
  • Moore, J.K., Chudalayandi, P., Heil-Chapdelaine, R.A. and Cooper, J.A. The spindle position checkpoint is coordinated by the Elm1 kinase. J Cell Biol 191:493-503 (2010).
  • Kim,T., Cooper, J.A. and Sept, D. The interaction of capping protein with the barbed end of the actin filament. J Mol Biol 404:794-802 (2010).
  • Hernandez-Valladares, M., Kim, T., Kannan, B., Tung, A., Aguda, A.H., Larsson, M., Cooper, J.A. and Robinson, R.C. Structural characterization of a capping protein interaction motif defines a family of actin filament regulators. Nat Struct Mol Biol 17:497-503 (2010).
  • Lin, M.C., Galletta, B.J., Sept, D. and Cooper, J.A. Overlapping and distinct functions for cofilin, coronin and Aip1 in actin dynamics in vivo. J Cell Sci 123:1329-1342 (2010).
  • Moore, J.K. and Cooper, J.A. Coordinating mitosis with cell polarity: Molecular motors at the cell cortex. Semin Cell Dev Biol 21:283-289 (2010).
Tom Ellenberger
  • Cotner-Gohara, E., Kim, I.K., Tainer, J.A., Tomkinson, A.E. and Ellenberger, T. Human DNA ligase III recognizes DNA ends by dynamic switching between two DNA bound states. Biochemistry 49:6165-6176 (2010).
  • Han, Z., Pinkner, J.S., Ford, B., Obermann, R., Nolan, W., Wildman, S.A., Hobbs, D., Ellenberger, T., Cusumano, C.K., Hultgren, S.J. and Janetka, J.W. Structure-based drug design and optimization of mannoside bacterial FimH antagonists. J Med Chem 53:4779-4792 (2010).
  • Perry, J.J. and Cotner-Gohara, E., Ellenberger, T. and Tainer, J.A. Structural dynamics in DNA damage signaling and repair. Curr Opin Struct Biol 20:283-294 (2010).
  • Orelli, B., McClendon, T.B., Tsodikov, O.V., Ellenberger, T., Niedernhofer, L.J. and Scharer, O.D. The XPA-binding domain of ERCC1 is required for nucleotide excision repair but not other DNA repair pathways. J Biol Chem 285:3705-3712 (2010).
Elliot L. Elson
  • Qui, H., Zhu, Y., Sun, Z., Trzeciakowski, J.P., Gansner, M., Depre, C., Resuello, R.R., Natividad, F.F., Hunter, W.C., Genin, G.M., Elson, E.L., Vatner, D.E., Meininger, G.A. and Vatner, S.F. Vascular smooth muscle cell stiffness as a mechanism for increased aortic stiffness with aging. Circ Res 107:615-619 (2010).
  • Elson, E.L., Fried, E., Dolbow, J.E. and Genin, G.M. Phase separation in biological membranes: Integration of theory and experiment. Annu Rev Biophys 9:207-226 (2010).
  • Marquez, J.P., Elson, E.L. and Genin, G.M. Whole cell mechanics of contractile fibroblasts: Relations between effective cellular and extracellular matrix moduli. Philos Transact A Math Phys Eng Sci 368:635-654 (2010).
William A. Frazier
  • Stewart, C.R., Stuart, L.M., Wilkinson, K., van Gils, J.M., Deng, J., Halle, A., Rayner, K.J., Boyer, L., Zhong, R., Frazier, W.A., Lacy-Hulbert, A., Khoury, J.E. Golenbock, D.T. and Moore, K.J. CD36 ligands promote sterile inflammation through assembly of a toll-like receptor 4 and 6 heterodimer. Nat Immunol 11:155-161 (2010).
  • Stewart, C.R., Stuart, L.M., Wilkinson, K., van Gils, J.M., Deng, J., Halle, A., Rayner, K.J., Boyer, L., Zhong, R., Frazier, W.A., Lacy-Hulbert, A., Khoury, J.E. Golenbock, D.T. and Moore, K.J. CD36 ligands promote sterile inflammation through assembly of a toll-like receptor 4 and 6 heterodimer. Nat Immunol 11:155-161 (2010).
Carl Frieden
  • Frieden, C. Sidney Frederick Velick. Biogr Mem Natl Acad Sci (2010).
  • Garai, K. and Frieden, C. The association-dissociation behavior of the ApoE proteins: Kinetic and equilibrium studies. Biochemistry 49:9533-9541 (2010).
  • Niu, W., Shu, Q., Chen, Z., Mathews, S., Di Cera, E. and Frieden, C. The role of Zn(2+) on the structure and stability of murine adenosine deaminase. J Phys Chem B 114:16156-16165 (2010).
  • Baldwin, R.L., Frieden, C. and Rose, G.D. Dry molten globule intermediates and the mechanism of protein unfolding. Proteins 78:2725-2737(2010).
  • Mustafi, S.M., Garai, K., Crick, S.L., Baban, B. and Frieden, C. Substoichiometric inhibition of Abeta(1-40) aggregation by a tandem Abeta(40-1-Gly8-1-40) peptide. Biochem Biophys Res Commun 397:509-512 (2010).
  • Garai, K., Mustafi, S.M., Baban, B. and Frieden, C. Structural differences between apolipoprotein E3 and E4 as measured by (19)F NMR. Protein Sci. 19:66-74. (2010).
Roberto Galletto
  • Barranco-Medina, S. and Galletto, R. DNA binding induces dimerization of S. cerevisiae Pif1. Biochemistry 49:8445-8454 (2010).
  • Updegrove, T.B., Correia, J.J., Galletto, R., Bujalowski, W. and Wartell, R.M. E. coli DNA associated with isolated Hfq interacts with Hfq’s distal surface and C-terminal domain. Biochim Biophys Acta 1799:588-596 (2010).
Kathleen B. Hall
  • Williams, S.G. and Hall, K.B. Coevolution of Drosophila snf protein and its snRNA targets. Biochemistry 49:4571-4582 (2010).
  • Liu, F., Maynard, C., Scott, G., Melnykov, A., Hall, K.B. and Gruebele, M. A natural missing link between activated and downhill protein folding scenarios. Phys Chem Chem Phys. 12:3542-3549 (2010).
  • Maynard, C.M. and Hall, K.B. Interactions between PTB RRMs induce slow motions and increase RNA binding affinity. Mol Cell Biol 397:260-277 (2010).
Jim W. Janetka
  • Oza, V., Ashwell, S., Brassil, P., Breed, J., Deng, C., Ezhuthachan, J., Haye, H., Horn, C., Janetka, J., Lyne, P., Newcombe, N., Otterbien, L., Pass, M., Read, J., Roswell, S., Su, M. Toader, D.,Yu, D., Yu, Y., Valentine, A., Webborn, P., White, A., Zabludoff, S. and Zheng, X. Discovery of a novel class of triazolones as checkpoint kinase inhibitors – Hit to lead exploration. Bioorganic & Medicinal Chemistry Letters 20:5133-5138 (2010).
  • Han, Z., Pinkner, J.S., Ford, B., Obermann, R., Nolan, W., Wildman, S.A., Hobbs, D., Ellenberger, T., Cusumano, C.K., Hultgren, S.J. and Janetka, J.W. Structure-based drug design and optimization of mannoside bacterial FimH antagonists. J Med Chem 53:4779-4792 (2010).
Andrzej M. Krezel
  • Loh, J.T., Gupta, S.S., Friedman, D.B., Krezel, A.M. and Cover, T.L. Analysis of protein expression regulated by the Helicobacter pylori ArsRS two-component signal transduction system. J Bacteriol. 192:2034-2043. (2010).
Weikai Li
  • Li. W., Schulman, S., Dutton, R., Boyd, D., Beckwith, J. and Rapoport, T.A. Structure of a bacterial homolog of vitamin K epoxide reductase. Nature 463:501-512 (2010).
  • Schulman, S., Wang, B., Li, W. and Rapport, T.A. Vitamin K epoxide reductase prefers ER membrane-anchored thioredoxin-like redox partners. Proc Natl Acad Sci USA 107:15027-15032 (2010).
Timothy M. Lohman
  • Tomko, E.J., Jia, H., Park, J., Maluf, N.K., Ha, T. and Lohman, T.M. 5′-Single-stranded/duplex DNA junctions are loading sites for E. coli UvrD translocase. EMBO J 29:3826-3839 (2010).
  • Antony, E. and Lohman, T.M. “Non-hexameric SF1 DNA helicases and translocases”. Encyclopedia of Biological Chemistry, (2nd edition) W.J. Lennarz and M.D. Lane, eds. Elsevier Science (2010).
  • Wu, C.G., Bradford, C. and Lohman, T.M. Escherichia coli RecBC helicase has two translocase activities controlled by a single ATPase motor. Nat Struct Mol Biol 17:1210-1217 (2010).
  • Kozlov, A.G., Eggington, J.M., Cox, M.M. and Lohman, T.M. Binding of the Dimeric Deinococcus radiodurans SSB protein to single-stranded DNA. Biochemistry 49:8266-8275 (2010).
  • Park, J., Myong, S., Niedziela-Majka, A., Lee, K.S., Yu, J., Lohman, T.M. and Ha, Taekjip, T. PcrA helicase dismantles RecA filaments by reeling in DNA in uniform steps. Cell 142:544-555 (2010).
  • Lohman, T.M. Clipping along. J Mol Biol 399:663-664 (2010).
  • Tomko, E.J., Fischer, C.J. and Lohman, T.M. Ensemble methods for monitoring enzyme translocation along single stranded nucleic acids. Methods 51:269-276 (2010).
  • Kozlov, A.G., Cox, M.M. and Lohman, T.M. Regulation of single stranded DNA binding by the C-termini of E. coli SSB protein. J Biol Chem 285:17246-17252 (2010).
  • Kozlov, A.G., Jezewska, M.J., Bujalowski, W. and Lohman, T.M. Binding specificity of E. coli SSB protein for the chi subunit of DNA pol III holoenzyme and PriA helicase. Biochemistry 49:3555-3566 (2010).
  • Fischer, C.J., Wooten, L., Tomko, E.J. and Lohman, T.M. Kinetics of motor protein translocation on single-stranded DNA. Methods Mol Biol 587:45-56 (2010).
Garland R. Marshall
  • Feng, J.A. and Marshall, G.R. SKATE: A docking program that decouples systematic sampling from scoring. J Comp Chem 31:2540-2554 (2010).
  • Van Eps, N., Anderson, L.L., Kisselev, O.G., Baranski, T.J., Hubbell, W.L. and Marshall, G.R. Electron paramagnetic resonance studies of functionally active, nitroxide spin-labeled peptide analogues of the C-terminus of a G-protein alpha subunit. Biochemistry 49:6877-6886 (2010).
  • Bourne, G.T., Kuster, D.J. and Marshall, G.R. Synthesis of the phenylpyridal scaffold as a helical peptide mimetic. Chemistry16:8439-8445 (2010).
  • Yang, R.Y., Yang, K.S.,Pike, L.J. and Marshall, G.R. Targeting the dimerization of epidermal growth factor receptors with small-molecule inhibitors. Chem Biol Drug Des 76:1-9 (2010).
  • Nikiforovich, G.V., Taylor, C.M., Marshall, G.R. and Baranski, T.J. Modeling the possible conformations of the extracellular loops in G-protein-coupled receptors. Proteins 78:271-285 (2010).
  • Taylor, C.M., Rockweiler, N.B., Liu, C., Rikimaru, L., Tunemalm, A.K., Kisselev, O.G. and Marshall, G.R. Using ligand-based virtual screening to allosterically stabalize the activated state of a GPCR. Chem Biol Drug Des 75:325-332 (2010).
F. Scott Mathews
  • Niu, W., Shu, Q., Chen, Z., Mathews, S., Di Cera, E. and Frieden, C. The role of Zn(2+) on the structure and stability of murine adenosine deaminase. J Phys Chem B 114:16156-16165 (2010).
  • Chen, Z., Datta, S., Dubois, J.L., Klinman, J.P. and Mathews, F.S. Mutation at a strictly conserved, active site tyrosine in the copper amine oxidase leads to uncontrolled oxygenase activity. Biochemistry 49:7393-7402 (2010).
  • Jorns, M.S., Chen, Z.W. and Mathews, F.S. Structural characterization of mutations at the oxygen activation site in monomeric sarcosine oxidase. Biochemistry 49:3631-3639 (2010).
Linda J. Pike
  • Yang, K.S., Macdonald-Obermann, J., Piwnica-Worms, D. and Pike, L.J. Asp-960/Glu-961 control the movement of the C-terminal tail of the EGF receptor to regulate asymmetric dimer formation. J Biol Chem 285:24014-24022 (2010).
  • Yang, R.Y., Yang, K.S.,Pike, L.J. and Marshall, G.R. Targeting the dimerization of epidermal growth factor receptors with small-molecule inhibitors. Chem Biol Drug Des 76:1-9 (2010).
Ana Ruiz-Manzano
  • Schulze, J.M., Kane, C.M. and Ruiz-Manzano, A. The YEATS domain of Taf14 in Saccharomyces cerevisiae has a negative impact on cell growth. Mol Genet Genomics. 283:365-380 (2010).