Department of Biochemistry and Molecular Biophysics

2011 Publications

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

Gary K. Ackers
  • Johnson, M.L., Holt, J. and Ackers, G.K. Biothermodynamics, Part D. Preface. Methods Enzymol 492:xii-xiv (2011).
  • Johnson, M.L., Holt, J. and Ackers, G.K. Biothermodynamics, Part C. Preface. Methods Enzymol 488:xv (2011).
Gregory R. Bowman
  • Bowman, G.R., Voelz, V.A. and Pande, V.S. Atomistic folding simulations of the five-helix bundle protein λ6-85. J Am Chem Soc 133:664-667 (2011).
  • Bowman, G.R., Voelz, V.A. and Pande, V.S. Taming the complexity of protein folding. Curr Opin Struct Biol 21:4-11 (2011).
  • Silva, D., Bowman, G.R., Sosa-Peinado, A. and Huang, X. A role for both conformational selection and induced fit in ligand binding by the LAO protein. PLoS Comput Biol 7:e1002054 (2011).
Peter M. Burgers
  • Netz, D.J., Stith, C.M., Stümpfig, M., Köpf, G., Vogel, D., Genau, H.M., Stodola, J.L., Lill, R., Burgers, P.M. and Pierik, A.J. Eukaryotic DNA polymerases require an iron-sulfur cluster for the formation of active complexes. Nat Chem Biol 8:125-132 (2011).
  • Navadgi-Patil, V.M., Kumar, S. and Burgers, P.M. The unstructured C-terminal tail of yeast Dpb11 (human TopBP1) is dispensable for DNA replication and the S phase checkpoint but required for the G2/M checkpoint. J Biol Chem 286:40999-41007 (2011).
  • Burgers, P.M. It’s all about flaps: DNA2 and checkpoint activation. Cell Cycle 10:2417-2418 (2011).
  • Watt, D.L., Johansson, E., Burgers, P.M. and Kunkel, T.A. Replication of ribonucleotide-containing DNA templates by yeast replicative polymerases. DNA Repair 10:897-902 (2011).
  • Stone, J.E., Kumar, D., Binz, S.K., Inase, A., Iwai, S., Chabes, A., Burgers, P.M. and Kunkel, T.A. Lesion Bypass by S. cerevisiae Pol ΞΆ Alone. DNA Repair (Amst). 10:826-834 (2011).
  • Navadgi-Patil, V.M. and Burgers, P.M. Cell-cycle-specific activators of the Mec1/ATR checkpoint. Biochem Soc Trans. 39:600-605 (2011).
John A. Cooper
  • Stuchell-Brereton, M.D., Siglin, A., Li, J., Moore, J.K., Ahmed, S., Williams, J.C. and Cooper, J.A. Functional interaction between dynein light chain and intermediate chain is required for mitotic spindle positioning. Mol Biol Cell 22:2690-2701 (2011).
Tom Ellenberger
  • Sperry, J.B., Smith, C.L., Caparon, M.G., Ellenberger, T. and Gross, M.L. Mapping the protein-protein interface between a toxin and its cognate antitoxin from the bacterial pathogen Streptococcus pyogenes. Biochem 50:4038-4045 (2011).
  • Smith, C.L., Ghosh, J., Elam, J.S., Pinkner, J.S., Hultgren, S.J., Caparon, M.G. and Ellenberger, T. Structural basis of Streptococcus pyogenes immunity to its NAD(+) glycohydrolase toxin. Structure 19:192-202 (2011).
Elliot L. Elson
  • Elson, E. Fluorescence correlation spectroscopy: Past, present, future. Biophys J 101:2855-2870 (2011).
  • Collier, I.E., Legant, W., Marmer, B., Lubman, O., Saffarian, S., Wakatsuki, T., Elson, E. and Goldberg, G.I. Diffusion of MMPs on the surface of collagen fibrils: The mobile cell surface – collagen substratum interface. PLoS One 6:e24029 (2011).
  • Thomopoulos, S., Das, R., Birman, V., Smith, L., Ku, K., Elson, E., Pryse, K.M., Marquez, P. and Genin, G.M. Fibrocartilage tissue engineering: The role of the stress environment on cell morphology and matrix expression. Tissue Eng Part A. 17:1039-1053 (2011).
William A. Frazier
  • Frazier, E.P., Isenberg, J.S., Shiva, S., Zhao, L., Schlesinger, P., Dimitry, J., Abu-Asab, M.S., Tsokoa, M. Roberts, D.D. and Frazier, W.A. Age-dependent regulation of skeletal muscle mitochrondria by the thrombospondin-1 receptor CD47. Matrix Biology 30:154-161 (2011).
Carl Frieden
  • Gau, B.C., Garai, K., Frieden, C. and Gross, M.L. Mass spectrometry-based protein footprinting characterizes the structures of oligomeric apolipoprotein E2, E3 and E4. Biochemistry 50:8117-8126 (2011).
  • Huang, R.Y., Garai, K., Frieden, C. and Gross, M.L. Hydrogen/deuterium exchange and electron-transfer dissociation mass spectrometry determine the interface and dynamics of apolipoprotein E oligomerization. Biochemistry 50:9273-9282 (2011).
  • Garai, K., Baban, B. and Frieden, C. The self-association and stability of the APOE isoforms at low pH: Implications for APOE-lipid interactions. Biochemistry 50:6356-6364 (2011).
  • Garai, K., Baban, B. and Frieden, C. Dissociation of apolipoprotein E oligomers to monomer is required for high-affinity binding to phospholipid vesicles. Biochemistry 50:2550-2558 (2011).
Eric Galburt
  • Galburt, E.A., Parrondo, J.M. and Grill, S.W. RNA polymerase pushing. Biophys Chem 157:43-47 (2011).
Kathleen B. Hall
  • Williams, S.G. and Hall, K.B. Human U2B” protein binding to snRNA stemloops. Biophys Chem 159:82-89 (2011).
James J. Havranek
  • Leaver-Fay, A., Tyka, M., Lewis, S.M., Lange, O.F., Thompson, J., Jacak, R., Kaufman, K., Renfrew, P.D., Smith, C.A., Sheffler, W., Davis, I.W., Cooper, S., Truille, A., Mandell, D.J., Richter, F., Bay, Y.E., Fleishman, S.J., Corn, J.E., Kim, D.E., Lyskov, S., Berrondo, M., Mentzer, S., Popovic, Z., Havranek, J.J., Karanicolas, J., Das, R., Meiler, J., Kortemme, T., Gray, J.J., Kuhlman, B., Baker, D. and Bradley, P. ROSETTA3: An object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol. 487:545-574 (2011).
Jim W. Janetka
  • Cusumano, C.K., Pinkner, J.S., Han, Z., Greene, S.E., Ford, B.A., Crowley, J.R., Henderson, J.P., Janetka, J.W. and Hultgren, S.J. Treatment and prevention of urinary tract infection with orally active FimH inhibitors. Science Translational Medicine 3:1-10 (2011).
  • Ma, C.X., Janetka, J.W. and Piwnica-Worms, H. Death by releasing the breaks: CHK1 inhibitors as cancer therapeutics. Trends in Molecular Medicine 17:88-96 (2011).
Weikai Li
    Li, W. and Li, F. Cross-crystal averaging with search models to improve molecular replacement phases. Structure 19:155-161 (2011).
Timothy M. Lohman
  • Balci, H., Arslan, S., Myong, S., Lohman, T.M. and Ha, T. Single-molecule nanopositioning: Structural transitions of a helicase-DNA complex during ATP hydrolysis. Biophys J 101:976-984 (2011).
  • Niedziela-Majka, A., Maluf, N.K., Antony, E. and Lohman, T.M. Self-assembly of E. coli MutL and its Complexes with DNA. Biochemistry 50:7868-7880 (2011).
  • Zhou, R., Kozlov, A.G., Roy, R., Zhang, J., Korolev, S., Lohman, T.M. and Ha, T. SSB functions as a sliding platform that migrates on DNA via reptation. Cell 146:222-232 (2011).
  • Jia, H., Korolev, S., Niedziela-Majka, A., Maluf, N.K., Gauss, G.H., Myong, S., Ha, T., Waksman, G. and Lohman, T.M. Rotations of the 2B sub-domain of E. coli UvrD helicase/translocase coupled to nucleotide and DNA binding. J Mol Biol 411:633-648 (2011).
  • Kozlov, A.G. and Lohman, T.M. E. coli SSB tetramer binds the first and second molecules of (dT)(35) with heat capacities of opposite sign. Biophys Chem 159:48-57 (2011).
Garland R. Marshall
  • Nikiforovich, G.V., Taylor, C.M., Marshall, G.R. and Baranski, T.J. Difference between restoring and predicting 3D structures of the loops in G-protein-coupled receptors by molecular modeling. Proc Natl Acad Sci USA 108:E341 (2011).
  • Wildman, S.A., Zheng, X., Sept, D., Auletta, J.T., Rosenberry, T.L. and Marshall, G.R. Drug-like leads for steric discrimination between substrate and inhibitors of human acetylcholinesterase. Chem Biol Drug Des. 78:495-504 (2011).
  • Tang, Y.T. and Marshall, G.R. Virtual screening for lead discovery. Methods Mol Biol. 716:1-22 (2011).
  • Feng, J.A. and Marshall, G.R. PHOENIX: A scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements. J Chem Inf Model 79:787-802 (2011).
F. Scott Mathews
  • Kommoju, P.R., Chen, Z.W., Bruckner, R.C., Mathews, F.S. and Jorns, M.S. Probing oxygen sites in two flavoprotein oxidases using chloride as an oxygen surrogate. Biochemistry 50:5521-5534 (2011).
  • Li, J., Gan, J.H., Mathews, F.S. and Xia, Z.X. The enzymatic reaction-induced configuration change of the prosthetic group PQQ of methanol dehydrogenase. Biochem Biophys Res Commun 406:621-626 (2011).
  • Choi, M., Sukumar, N., Mathews, F.S., Liu, A. and Davidson, V.L. Proline 96 of the copper ligand loop of amicyanin regulates electron transfer from methylamine dehydrogenase by positioning other residues at the protein-protein interface. Biochemistry 50:1265-1273 (2011).
Linda J. Pike
  • Adak, S., Yang, K.S., Macdonald-Obermann, J. and Pike, L.J. The membrane proximal intracellular domain of the EGF receptor underlies negative cooperativity in ligand binding. J Biol Chem 286:45146-45155 (2011).