Department of Biochemistry and Molecular Biophysics

2008 Publications

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

Peter M. Burgers
  • Stith, C.M., Sterling, J., Resnick, M.A., Gordenin, D.A. and Burgers, P.M. Flexibility of eukaryotic okazaki fragment maturation through regulated strand sisplacement synthesis. J Biol Chem. 283:34129-40 (2008).
  • Navadgi-Patil, V.M. and Burgers, P.M. Yeast DNA replication protein Dpb11 activates the Mec1/ATR checkpoint kinase. J Biol Chem 283:35853-35859 (2008).
  • Kunkel, T.A. and Burgers, P.M. Dividing the workload at a eukaryotic replication fork. Trends Cell Biol 18:521-527 (2008).
  • Rossi, M.L., Pike, J.E., Wang, W., Burgers, P.M., Campbell, J.L. and Bambara, R.A. Pif1 helicase directs eukaryotic Okazaki fragments toward the two-nuclease cleavage pathway for primer removal. J Biol Chem 283:27483-27493 (2008).
  • Sommer, D., Stith, C.M., Burgers, P.M.J. and Lahue, R.S. Partial reconstitution of DNA large loop repair with purified proteins from Saccharomyces cerevisiae. Nuc Acid Res 6:4699-4707 (2008).
  • Nick McElhinny, S.A., Gordenin, D.A., Stith, C.M., Burgers, P.M. and Kunkel, T.A. Division of labor at the eukaryotic replication fork. Mol Cell. 30:137-144 (2008).
  • Wardle, J., Burgers, P.M., Cann, I.K., Darley, K., Darley, K., Heslop, P., Johansson, E., Lin, L.J., McGlynn, P., Sanvoisin, J., Stith, C.M. and Connolly, B.A. Uracil recognition by replicative DNA polymerases is limited to the archaea, not occurring with bacteria and eukarya. Nucleic Acids Res 36:705-711 (2008).
John A. Cooper
  • Butler, B., Kastendieck, D.H. and Cooper, J.A. Differently phosphorylated forms of the coractin homolog HS1 mediate distinct functions in natural killer cells. Nat Immunol 9:887-897. (2008).
  • Cooper, J.A. and Sept, D. New insights into mechanism and regulation of actin capping protein. Int Rev Cell Mol Biol 267:183-206. (2008).
  • Pappas, C.T., Bhattacharya, N., Cooper, J.A. and Gregorio, C.C. Nebulin interacts with CapZ and regulates thin filament architecture within the Z-disc. Mol Biol Cell 1837-1847. (2008).
  • Moore, J.K., Li, J. and Cooper, J.A. Dynactin function in mitotic spindle positioning. Traffic 9:510-527. (2008).
  • Galletta, B.J., Chuang, D.Y. and Cooper, J.A. Distinct roles for Arp2/3 regulators in actin assembly and endocytosis. PLoS Biol 6:e1. (2008).
Tom Ellenberger
  • Raschle, M., Knipsheer, P., Enoiu, M., Angelov, T., Sun, J., Griffith, J.D., Ellenberger, T.E., Scharer, O.D. and Walter, J.C. Mechanism of replication-coupled DNA interstrand crosslink repair. Cell 134:969-980. (2008).
  • Zhong, S., Chen, X., Zhu, X., Dziegielewska, B., Bachman, K.E., Ellenberger, T., Ballin, J.D., Wilson, G.M., Tomkinson, A.E. and MacKerell, Jr., A.D. Identification and validation of human DNA ligase inhibitors using computer-aided drug design. J Med Chem 51:4553-4562 (2008).
  • Ellenberger, T. and Tomkinson, A.E. Eukaryotic DNA ligases: Structural and functional insights. Annu Rev Biochem 77:313-338 (2008).
  • Chen, X., Zhong, S., Zhu, X., Dziegielewska, B., Ellenberger, T., Wilson, G.M., MacKerell, A.D. Jr and Tomkinson, A.E. Rational design of human DNA ligase inhibitors that target cellular DNA replication and repair. Cancer Res. 68:3169-3177 (2008).
  • Cotner-Gohara, E., Kim, I.K., Tomkinson, A.E. and Ellenberger, T. Two DNA binding and nick recognition modules in human DNA ligase III. J. Biol. Chem. 283:10764-10772 (2008).
Elliot Elson
  • Nekouzadeh, A., Pryse, K.M., Elson, E.L. and Genin, G.M. Stretch-activated force shedding, force recovery, and cytoskeletal remodeling in contractile fibroblasts. J Biomech. 41:2964-2971 (2008).
  • Tan, Y.C., Shen, A.Q., Li, Y., Elson, E. and Ma, L. Engineering lipid tubules using nano-sized building blocks: The combinatorial self-assembly of vesicles. Lab on a Chip 8:339-345 (2008).
William A. Frazier
  • Isenberg, J.S. Maxhimer, J.B., Powers, P., Tsokos, M., Frazier, W.A. and Robert, D.D. Treatment of liver ischemia–reperfusion injury by limiting thrombospondin-1/CD47 signaling. Surgery 144:752-761 (2008).
  • Isenberg, J.S., Frazier, W.A., Krishna, M.C., Wink, D.A. and Roberts, D.D. Enhancing cardiovascular dynamics by inhibition of thrombospondin-1/CD47 signaling. Curr Drug Targets 9:833-841 (2008).
  • Vomund, A.N., Stuhlsatz-Krouper, S., Dimitry, J., Song, Y. and Frazier, W.A. A naturally occurring extracellular alpha-beta clasp contributes to stabilization of beta3 Integrins in a bent, resting conformation. Biochemistry 47:11616-11624 (2008).
  • Isenberg, J.S., Romeo, M.J., Maxhimer, J.B., Smedley, J., Frazier, W.A. and Roberts, D.D. Gene silencing of CD47 and antibody ligation of Thrombospondin-1 enhance ischemic tissue survival in a porcine model: Implications for human disease.
    Ann Surg. 247:860-868 (2008).
  • Isenberg, J.S., Romeo, M.J, Yu, C., Yu, C.K., Nghiem, K., Monsale, J., Rick, M.E., Wink, D.A., Frazier, W.A. and Roberts, D.D. Thrombospondin-1 stimulates platelet aggregation by blocking the antithrombotic activity of nitric oxide/cGMP signaling. Blood 111:613-623 (2008).
  • Isenberg, J.S., Roberts, D.D. and Frazier, W.A. CD47. A new target in cardiovascular therapy. Arterioscler Thromb Vasc Biol. 28:615-621 (2008).
  • Isenberg, J.S., Pappan, L.K., Romeo, M.J., Abu-Asab, M., Tsokos, M., Wink, D.A., Frazier, W.A. and Roberts, D.D. Blockade of thrombospondin-1-CD47 interactions prevents necrosis of full thickness skin grafts.
    Ann Surg. 247:180-190 (2008).
Carl Frieden
  • Frieden, C. A lifetime of kinetics. J Biol Chem. 283:19873-19878 (2008).
Kathleen Hall
  • Hall, K.B. RNA in motion. Curr Opin Chem Biol 12:612-618 (2008).
James W. Janetka
  • Zabludoff, S.D., Deng C., Grondine, M.R., Sheehy, A.M., Ashwell, S., Cale, B.L., Green, S., Haye, H.R., Horn, C.L., Janetka, J.W., Liu, D., Mouchet, E., Ready, S., Rosenthal, J.L., Queva, C., Schwartz, G.K., Taylor, K.J., Tse, A.N., Walker, G.E., and White, A.M. AZD7762, a novel checkpoint kinase inhibitor, drives checkpoint abrogation and potentiates DNA-targeted therapies. Molecular Cancer Therapeutics 7:2955-2966 (2008).
  • Ashwell, S., Janetka, J.W. and Zabludoff, S. Keeping checkpoint kinases in line: New selective inhibitors in clinical trials. Expert Opin Investig Drugs 17:1331-1340 (2008).
  • Janetka, J.W., Almeida, L., Ashwella, S., Brassil, P.J., Daly, K., Deng C., Gero, T., Glynn, R.E., Horn, C.L., Ioannidis, S., Lyne, P., Newcombe, N.J., Oza, V.B., Pass, M., Springer, S.K., Su, M., Toader, D., Vasbinder, M.M., Yu, D., Yu, Y. and Zabludoff, S.D. Discovery of a novel class of 2-ureido thiophene carboxamide checkpoint kinase inhibitors. Bioorganic & Medicinal Chemistry Letters 18:4242-4248 (2008).
Andrzej M. Krezel
  • Borin, B.N. and Krezel, A.M. Structure of HP0564 from Helicobacter pylori identifies it as a new transcriptional regulator. Proteins 73:265-268. (2008).
Timothy M. Lohman
  • Shereda, R.D., Kozlov, A.G., Lohman, T.M., Cox, M.M. and Keck, J.L. SSB as an organizer/mobilizer of genome maintenance complexes. CRC Critical Reviews in Biochemistry and Molecular Biology 43:289-318 (2008).
  • Wu, C.G. and Lohman, T.M. Influence of DNA end structure on the mechanism of initiation of DNA unwinding by the Escherichia coli RedBCD and RecBC helicases. J Mol Biol 382:312-326 (2008).
  • Lohman, T.M., Tomko, E.J. and Wu, C.G. Non-hexameric DNA helicases and translocases: Mechanisms and regulation. Nat Rev Mol Cell Biol. 9:391-401 (2008).
  • Wong, C.J. and Lohman, T.M. Kinetic control of Mg(2+)-dependent melting of duplex DNA ends by Escherichia coli RecBC. J Mol Biol. 378:759-775 (2008).
Garland R. Marshall
  • Taylor, C.M., Barda, Y., Kisselev, O.G. and Marshall, G.R. Modulating G-protein coupled receptor/G-protein signal transduction by small molecules suggested by virtual screening. J Med Chem 51:5297-5303 (2008).
  • Nikiforovich, G.V., Marshall, G.R. and Baranski, T.J. Modeling molecular mechanisms of binding of the anaphylatoxin C5a to the C5a receptor. Biochemistry 47:3117-3130 (2008).
  • Cegelski, L, Marshall, G.R., Eldridge, G.R. and Hultgren, S.J. The biology and future prospects of antivirulence therapies.
    Nature Rev Microbiol. 6:17-27 (2008).
  • Che, Y. and Marshall, G.R. Privileged scaffolds targeting reverse-turn and helix recognition.
    Expert Opin Ther Targets 12:101-114 (2008).
  • Ye, Y., Liu, M., Kao, J.L. and Marshall, G.R. Design, synthesis, and metal binding of novel pseudo-oligopeptides containing two phosphinic acid groups. Biopolymers 89:72-85 (2008).
  • Berg-Cross, S., Kao, J., Wu, Y. and Marshall, G.R. c[D-pro-Pro-D-pro-N-Methyl-Ala] Adopts a rigid conformation that serves as a scaffold to mimic reverse-turn. Biopolymers 90:384-393 (2008).
  • Marshall, G.R., Feng, J.A. and Kuster, D.J. Back to the future: Ribonuclease A.
    Biopolymers 90:259-277 (2008).
F. Scott Mathews
  • Hassan-Abadallah, A., Zhao, G., Chen, Z., Mathews, F.S. and Schuman Jorns, M. Arginine 49 is a bifunctional residue important in catalysis and biosynthesis of monomeric sarcosine oxidase: A context-sensitive model for the electrostatic impact of arginine to lysine mutations. Biochemistry 47:2913-2922 (2008).
  • Gandhi, P.S., Chen, Z., Mathews, F.S. and Di Cera, E. Structural identification of the pathway of long-range communication in an allosteric enzyme. Proc Natl Acad Sci U S A. 105:1832-1837 (2008).

Linda J. Pike

  • Eiblmaier M., Meyer L.A., Watson M.A., Fracasso P.M., Pike L.J. & Anderson C.J. (2008). “Correlating EGFR expression with receptor-binding properties and internalization of 64Cu-DOTA-cetuximab in 5 cervical cancer cell lines.” J Nucl Med. 2008 Sep;49(9):1472-9. doi: 10.2967/jnumed.108.052316. Epub 2008 Aug 14. (Abstract)

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  • Macdonald J.L. & Pike L.J. (2008). “Heterogeneity in EGF-binding affinities arises from negative cooperativity in an aggregating system.” Proc Natl Acad Sci U S A. 2008 Jan 8;105(1):112-7. doi: 10.1073/pnas.0707080105. Epub 2007 Dec 28. (Abstract)

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