Department of Biochemistry and Molecular Biophysics

2007 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
  • Chilkova, O., Stenlund, P., Isoz, I., Stith, C,M., Grabowski, P., Lundstrom, E.B., Burgers, P.M. and Johansson, E. The eukaryotic leading and lagging strand DNA polymerases are loaded onto primer-ends via separate mechanisms but have comparable processivity in the presence of PCNA. Nucleic Acids Research 35:6588-6597 (2007).
  • McCulloch, S.D., Wood, A., Garg, P., Burgers, P.M. and Kunkel, T.A. Effects of accessory proteins on the bypass of a cis-syn thymine-thymine dimer by Saccharomyces cerevisiae DNA polymerase eta. Biochemistry 46:8888-8896 (2007).
  • Wood, A. Garg, P. and Burgers, P.M. A Ubiguitin-binding motif in the translesion DNA polymerase rev1 mediates its essential functional interaction with ubiquitinated PCNA in response to DNA damage. J Biol Chem 282:20256-20263 (2007).
  • Majka, J. and Burgers, P.M. Clamping the Mec1/ATR checkpoint kinase into action. Cell Cycle 6:1157-1160 (2007).
  • McElhinny, S.A., Stith, C.M., Burgers, P.M. and Kunkel, T.A. Inefficient proofreading and biased error rates during inaccurate DNA synthesis by a mutant derivative of Saccharomyces cerevisiae DNA polymerase delta. J Biol Chem 282:2324-2332 (2007).
John A. Cooper
  • Nelson, S.A. and Cooper, J.A. A novel pathway that coordinates mitotic exit with spindle position. Mol Biol Cell 18:3440-3450 (2007).
  • Tehrani,S., Tomasevic, N., Weed, S., Sakowicz, R. and Cooper, J.A. Src phosphorylation of cortactin enhances actin assembly. Proc Natl Acad Sci USA 104:11933-11938 (2007).
  • Haarer, B.K., Helfant, A.H., Nelson, S.A., Cooper, J.A. and Amberg, D.C. Stable preanaphase spindle positioning requires Bud6p and an apparent interaction between the spindle pole bodies and the neck. Eukaryot Cell 6:797-807 (2007).
  • Kim,K., McCully, M.E., Bhattacharya, N., Butler, B., Sept, D. and Cooper, J.A. Structure/function analysis of the interaction of phosphatidylinositol 4,5-bisphosphate with actin-capping protein: Implications for how capping protein binds the actin filament. J Biol Chem 282:5871-5879 (2007).
Tom Ellenberger
  • Tsodikov, O.V., Ivanov, D., Orelli, B., Staresincic, L, Shoshani, I., Oberman, R., Scharer, O.D., Wagner, G. and Ellenberger, T. Structural basis for the recruitment of ERCC1-XPF to nucleotide excision repair complexes by XPA. EMBO J. 26:4768-4776 (2007).
  • Aihara, H., Huang, W.M. and Ellenberger, T. An interlocked dimer of the protelomerase TelK distorts DNA structure for the formation of hairpin telemeres. Mol Cell. 27:901-913 (2007).
  • Ivanov, D., Tsodikov, O.V., Kasanov, J., Ellenberger, T., Wagner, G. and Colins, T. Domain-swapped dimerization of the HIV-1 capsid C-terminal domain. Proc Natl Acad Sci USA 104:4353-4358 (2007).
  • Wang, X., Kennedy, R., Ray, K., Stuckert, P., Ellenberger, T. and D’
    Andrea, A.D. Chk1-mediated phosphorylation of FANCE is required for the Fanconi anemia/BRCA pathway. Mol Cell Biol 27:3098-3108 (2007).
  • Kowal, P., Gurtan, A.M., Stuckert, P., D’Andrea, A.D. and Ellenberger, T. Structural determinants of human FANCF protein that function in the assembly of DNA damage signaling complex. J. Biol Chem 282:2047-2055 (2007).
Elliot Elson
  • Saffarian, S., Li, Y., Elson, E.L. and Pike, L.J. Oligomerization of the EGF receptor investigated by live cell fluorescence intensity distribution analysis. Biophys J 93:1021-1031 (2007).
  • Nekouzadeh, A., Pryse, K.M., Elson, E.L. and Genin, G.M. A simplified approach to quasi-linear viscoelastic modeling. J Biomech 40:3070-3078 (2007).
William A. Frazier
  • Isenberg, J.S., Hyodo, F., Pappan, L.K., Abu-Asab, M., Tsokos, M., Krishna, M.C., Frazier, W.A. and Roberts, D.D. Blocking thrombosopondin-1/CD47 signaling alleviates deleterious effects of aging on tissue responses to ischemia. Arterioscler Thromb Vasc Biol 27:2585-2588 (2007).
  • 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 anti-thrombotic activity of nitric oxide/cGMP signaling. Blood 109:1945-1952 (2007).
  • Isenberg, J.S., Romeo, M.J., Abu-Asab, M., Tsokos, M., Oldenborg, A., Pappan, L., Wink, D.A., Frazier, W.A. and Roberts, D.D. Increasing survival of ischemic tissue by targeting CD47. Circ. Res.100:712-720. (2007).
Carl Frieden
  • Frieden, C. Protein aggregation Processes: In search of the mechanism. Protein Science 16:2334-2344 (2007).
  • Li, H. and Frieden, C. Observation of sequential steps in the folding of intestinal fatty acid binding protein using a slow folding mutant and 19F NMR. Proc Natl Acad Sci USA 104:11993-11998 (2007).
  • Li, H. and Frieden, C. Comparison of C40/82A and P27A C40/82A Barstar mutants using (19)F NMR. Biochemistry 46:4337-4347 (2007).
Eric A. Galburt
  • Galburt, E.A., Grill, S.W., Wiedmann, A., Lubkowska, L., Choy, J., Nogales, E., Kashlev, M. and Bustamante, C.J. Backtracking determines the force sensitivity fo RNAP II in a factor-dependent manner. Nature 446:820-823 (2007).
Roberto Galletto
  • Galletto, R. and Kowalczykowski, S.C. RecA. Curr Biol 17:R395-397 (2007).
Kathleen B. Hall
  • Coppins, R.L., Hall, K.B. and Groisman, E.A. The intricate world of riboswitches. Curr Opin Microbiol. 10:176-181 (2007).
James W. Janetka
  • Janetka, J.W., Satyshur, K.A., Rich, D.H. A cyclic side-chain-linked biphenyl ether tripeptide: H3N+-cyclo-[Phe(4-O)-Phe-Phe(3-O)]-OMe.Cl– Acta Crystallographica Section C 52:3112-3114 (2007).
  • Aronov, A.M., Bakers, C., Bemis, G.W., Cao, J., Chen, G., Ford, P.J., Germann, U.A., Green, J., Hale, M.R., Jacobs, M., Janetka, J.W., Maltais, F., Martinez-Botella, G., Namchuk, M.N., Straub, J., Tang, Q. and Xie, X. Flipped out: Structure-guided design of selective pyrazolylpyrrole ERK inhibitors. J Medicinal Chemistry 50:1280-1287 (2007).
Weikai Li
  • Ye, J., Cho, S.H., Fuselier, J., Li, W., Beckwith, J. and Rapoport, T.A. Crystal structure of an unusual thioredoxin protein with a zinc finger domain. J Biol Chem. 282:34945-34951 (2007).
  • Li, W., Schulman, S., Boyd, D., Erlandson, K., Beckwith, J. and Rapoport, T.A. The plug domain of the SecY protein stabilizes the closed state of the translocation channel and maintains a membrane seal. Mol Cell. 26:511-521 (2007).
Timothy M. Lohman
  • Niedziela-Majka, A., Chesnik, M.A., Tomko, E.J. and Lohman, T.M. B. Stearothermophilus PCRA monomer is a single stranded DNA translocase but not a processive helicase in vitro. J Biol Chem 282:27076-27085 (2007).
  • Tomko, E.J., Fischer, C.J., Niedziela-Majka, A. and Lohman, T.M. A nonuniform stepping mechanism for E. coli UvrD monomer translocation along single-stranded DNA. Mol Cell 26:335-347 (2007).
  • Roy, R., Kozlov, A.G., Lohman, T.M. and Ha, T. Dynamic structural rearrangements between DNA binding modes of E. coli SSB protein. J Mol Biol 369:1244-1257 (2007).
Garland R. Marshall
  • Schweitzer-Stenner, R., Gonzales, W., Feng, J.A. and Marshall, G.R. Conformational manifold of alpha-aminoisobutyric acid (Aib) containing alanine-based tripeptides in aqueous solution explored by vibrational spectroscopy, electronic circular dichroism spectroscopy, and molecular dynamics simulations. J Am Chem Soc. 129:13095-13109 (2007).
  • Zhang, X., Nikiforovich, G.V. and Marshall, G.R. Conformational templates for rational drug design: Flexibility of cyclo (d-Pro(1)-Ala(2)-Ala(3)-Ala(4)-Ala(5)) in DMSO solution. J Med Chem 50:2921-2925 (2007).
  • Nikiforovich, G.V., Marshall, G.R. and Achilefu, S. Molecular modeling suggests conformational scaffolds specifically targeting five subtypes of somatostatin receptors. Chem Biol Drug Des 69:163-169. (2007).
  • Che, Y., Brooks, B.R. and Marshall, G.R. Protein recognition motifs: Design of peptidomimetics of helix surfaces. Biopolymers 86:288-297 (2007).
  • Nikiforovich, G.V., Taylor, C.M. and Marshall, G.R. Modeling of the complex betweeen transducin and photoactivated rhodopsin, a prototypical G-protein-coupled receptor. Biochemistry 46:4734-4744 (2007).
  • Taylor, C.M.,Nikiforovich, G.V. and Marshall, G.R. Defining the interface between the C-terminal fragment of alpha-transducin and photoactivated rhodopsin. Biophys J 92:4325-4334 (2007).
  • Che, Y, Brooks, B.R., Riley, D.P., Reaka, A.J. and Marshall, G.R. Engineering metal complexes of chiral pentaazacrowns as privileged reverse-turn scaffolds. Chem Biol Drug Des 69:99-110 (2007).
F. Scott Mathews
  • Ma, J.K., Wang, Y., Carrell, C.J., Mathews, F.S. and Davidson, V.L. A single methionine residue dictates the kinetic mechanism of interprotein electron transfer from methylamine dehydrogenase to amicyanin(,). Biochemistry 46:11137-11146 (2007).
  • Bush-Pelc, L.A., Marino, F., Chen, Z., Pineda, A.O. Mathews, F.S. and Di Cera, E. Important role of the Cys-191: Cys-220 disulfide bond in thrombin function and allostery. J Biol Chem 282:27165-27170 (2007).
  • Bah, A., Chen, Z., Bush-Pelc, L.A., Mathews, F.S. and Di Cera, E. Crystal structures of murine thrombin in complex with the extracellular fragments of murine protease-activated receptors PAR3 and PAR4.
    Proc Natl Acad Sci U S A. 104:11603-11608 (2007).
  • Ma, J.K., Mathews, F.S. and Davidson, V.L. Correlation of rhombic distortion of the type 1 copper site of M98Q amicyanin with increased electron transfer reorganization energy. Biochemistry 46:8561-8568 (2007).
  • Marino, F., Chen, Z., Ergenekan, C.E., Bush-Pelc, L.A., Mathews, F.S. and Di Cera, E. Structural basis of Na+ activation mimicry in murine thrombin.
    J Biol Chem. 282:16355-16361 (2007).
  • Pineda, A.O., Chen, Z.W., Marino, F., Mathews, F.S., Mosesson, M.W. and Di Cera, E. Crystal structure of thrombin in complex with fibrinogen gamma’ peptide. Biophys Chem 125:556-559 (2007).

Linda J. Pike

  • Saffarian S., Li Y., Elson E.L., & Pike L.J. (2007). “Oligomerization of the EGF receptor investigated by live cell fluorescence intensity distribution analysis.” Biophys J. 2007 Aug 1;93(3):1021-31. Epub 2007 May 11. (Abstract)

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