Department of Biochemistry and Molecular Biophysics

2012 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
  • Holt, J.M. and Ackers, G.K. Kinetic trapping of a key hemoglobin intermediate. Methods Mol Biol 796:19-29 (2012).
Gregory R. Bowman
  • Bowman, G.R. and Geissler, P.L. Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites. Proc Natl Acad Sci U S A 29:11681-11686 (2012)
  • Bowman, G.R. Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty. J Chem Phys 137:134111 (2012).
  • Levin, A.M., Bates, D.L., Ring, A.M., Krieg, C., Lin, J.T., Su, L., Moraga, I., Raeber, M.E., Bowman, G.R., Novick, P., Pande, V.S., Fathman, C.G., Boyman, O. and Garcia, K.C. Exploiting a natural conformational switch to engineer an interleukin-2 ‘superkine’. Nature 484:529-533 (2012).
  • Ring, A.M., Lin, J., Feng, D., Mitra, S., Rickert, M., Bowman, G.R., Pande, V.S., Li, P., Moraga, I., Spolski, R., Özkan, E., Leonard, W.J. and Garcia, K.C. Mechanistic and structural insight into the functional dichotomy between IL-2 and IL-15. Nature Immunology 13:1187-1195 (2012).
  • Cui, R.Z., Silva, D.A., Song, J., Bowman, G.R., Zhuang, W. and Huang, X. Bridging the gap between optical spectroscopic experiments and computer simulations for fast protein folding dynamics. Curr Phys Chem 2:45-58 (2012).
  • Voelz, V.A., Jager, M., Yao, S., Chen, Y., Zhu, L., Waldauer, S.A., Bowman, G.R., Friedrichs, M., Bakajin, O., Lapidus, L.J., Weiss, S. and Pande, V.S. Slow unfolded-state structuring in ACBP folding revealed by theory and experiment. J Am Chem Soc 134:12565-12577 (2012).
Peter M. Burgers
  • Sparks, J.L., Kumar, R., Singh, M., Wold, M.S., Pandita, T.K. and Burgers, P.M. Human Exonuclease 5 is a Novel Sliding Exonuclease Required for Genome Stability. J Biol Chem 287:42773-42783 (2012).
  • Makarova, A.V., Stodola, J.L. and Burgers, P.M. A four-unit DNA polymerase ζ complex containing Pol δ accessory subunits is essential for PCNA-mediated mutagenesis. Nucleic Acids Res. 40:11618-11626 (2012).
  • Sparks, J.L., Chon, H., Cerritelli, S.M., Kunkel, T.A., Johansson, E., Crouch, R.J. and Burgers, P.M. RNase H2-initiated ribonucleotide excision repair. Mol Cell. 47:980-986 (2012).
  • Lazzaro, F., Novarina, D., Amara, F., Watt, D.L., Stone, J.E., Costanzo, V., Burgers, P.M., Kunkel, T.A., Plevani, P. and Mulzi-Falconi, M. RNase H and postreplication repair protect cells from ribonucleotides incorporated in DNA. Mol Cell. 45:99-110 (2012).
Tom Ellenberger
  • Della-Maria, J., Hegde, M.L., McNeill, D.R., Matsumoto, Y., Tsai, M.S., Ellenberger, T., Wilson, D.M., Mitra, S. and Tomkinson, A.E. The interaction between polynucleotide kinase phosphatase and the DNA repair alkylation damage and stable association at DNA damage sites. J Mol Biol 287:39233-39244 (2012).
  • Ellenberger, T. An Arresting Development in Transcription. Mol Cell. 46:3-4 (2012).
  • Kim, I.K., Kiefer, J.R., Ho, C.M., Stegeman, R.A., Classen, S., Tainer, J.A. and Ellenberger, T. Structure of mammalian poly(ADP-ribose) glycohydrolase reveals a flexible tyrosine clasp as a substrate-binding element. Nat Struct Mol Biol 19:653-656 (2012).
Elliot L. Elson
  • Lee, S.L., Nekouzadeh, A., Butler, B., Pryse, K.M., McDonnaughey, W.B., Nathan, A.C., Legant, W.B., Schaefer, P.M., Pless, R.B., Elson, E.L. and Genin, G.M. Physically-induced cytoskeleton remodeling of cells in three-dimensional culture. PLoS One 7:e45512 (2012).
  • Pryse, K.M., Rong, X., Whisler, J.A., McConnaughey, W.B., Jiang, Y.F., Melnykov, A.V., Elson, E.L. and Genin, G.M. Confidence intervals for concentration and brightness from fluorescence fluctuation measurements. Biophys J 103:898-906 (2012).
William A. Frazier
  • Soto-Pantoja, D.R., Miller, T.W., Frazier, W.A. and Roberts, D.D. Inhibitory signaling through signal regulatory protein-alpha is not sufficient to explain the antitumor activities of CD47 antibodies. PNAS 109:E2842 (2012).
Carl Frieden
  • Shu, Q., Crick, S.L., Pinkner, J.S., Ford, B., Hultgren, S.J. and Frieden, C. The E. coli CsgB nucleator of Curli assembles to beta-sheet oligomers that alter the CsgA fibrillization mechanism. PNAS 109:6502-6507 (2012).
  • Frieden, C. and Garai, K. Structural differences between apoE3 and apoE4 may be useful in developing therapeutic agents for Alzheimer’s disease. PNAS 109:8913-8918 (2012).
Roberto Galletto
  • Kozlov, A.G., Galletto, R. and Lohman, T.M. SSB-DNA binding monitored by fluorescence intensity and anisotropy. Methods Mol Biol 922:55-83 (2012).
Kathleen B. Hall
  • Rau, M., Stump, W.T. and Hall, K.B. Intrinsic flexibility of snRNA hairpin loops facilitates protein binding. RNA 18:1984-1985 (2012).
  • Hall, K.B. Spectroscopic probes of RNA structure and dynamics. Methods Mol Biol 875:67-84 (2012).
  • Nayak, R.K., Peersen, O.B., Hall, K.B. and Van Orden, A.K. Millisecond time scale folding and unfolding of DNA hairpins using rapid-mixing stopped-flow kinetics. J Am Chem Soc 134:2453-2456 (2012).
James J. Havranek
  • Tang, Y.T., Gao, R., Havranek, J.J., Groisman, E.A., Stock, Marshall, G.R. Inhibition of bacterial virulence: Drug-like molecules targeting the Salmonella enterica PhoP response regulator Chem Biol Drug Des 79:1007-1017 (2012).
  • Borgo, B. and Havranek, J.J. Automated selection of stabilizing mutations in designed and natural proteins. Proc Natl Acad Sci, USA 109:1949-1499 (2012).
James W. Janetka
  • Guiton, P.S., Cusumano, C.K., Kline, K.A., Dodson, D.W., Han, Z., Janetka, J.W., Henderson, J.P., Caparon, M.G. and Hultgren, S.J. Combination small molecular therapy prevents uropathogenic Escherichia coli cather-associated urinary tract infections in mice. Antimicrob Agents Chemother. 56:4738-4745 (2012).
  • Kostakioti, M., Hadjifrangiskou, M., Cusumano, C.K., Hannan, T.J., Janetka, J.W. and Hultgren, S.J. Distinguishing the contribution of type 1 pili from that of other QseB-misregulated factors when QseC is absent during urinary tract infection. Infect Immun 80:2826-2834 (2012).
  • Oza, V.B., Ashwell, S., Almeida, L., Brassil, P., Bree, J., Deng, C., Gero, T., Grondine, M., Horn, C., Ioannidis, S., Liu, D., Lyne, P.D., Newcombe, N., Pass, M., Read, J., Ready, S., Rowsell, S., Su, M., Toader, D., Vasbinder, M., Yu, D., Yu, Y., Xue, Y., Zabludoff, S. and Janetka, J.W. Discovery of checkpoint kinase inhibitor (S)-5-(3-fluorophenyl)-N-(piperidin-3-yl)-3-ureidothiophene-2-carboxamide (AZD7762) by structure based design and optimization of thiophene carboxamide ureas. Journal of Medicinal Chemistry 55:5130-5142 (2012).
  • Han, Z., Pinkner, J.S., Ford, B., Chorell, E., Crowley, J.M., Cusumano, C.K., Campbell, S., Henderson, J.P., Hultgren, S.J. and Janetka, J.W. Lead optimization studies on FimH antagonists: Discovery of potent and orally bioavailable ortho-substituted biphenyl mannosides. Journal of Medicinal Chemistry 55:3945-3959 (2012).
  • Yang, B., Hird, A.W., Russell, D.J., Fauber, B.P., Dakin, L.A., Zheng, X., Su, Q., Godin, R., Brassil, P., Devereaux, E. and Janetka, J.W. Discovery of novel hedgehog antagonists from cell-based screening: Isosteric modification of p38 bisamides as potent inhibitors of SMO. Bioorganic & Medicinal Chemistry Letters 22:4907-4911 (2012).
Timothy M. Lohman
  • Kozlov, A.G., Galletto, R. and Lohman, T.M. SSB-DNA binding monitored by fluorescence intensity and anisotropy. Methods Mol Biol 922:55-83 (2012).
  • Kozlov, A.G. and Lohman, T.M. SSB binding to ssDNA using isothermal titration calorimetry. Methods Mol Biol 922:37-54 (2012).
  • Wu, C.G., Xie, F. and Lohman, T.M. The primary and secondary translocase activities within E. coli RecBC helicase are tightly coupled to ATP hydrolysis by the RecB motor. J Mol Biol 423:303-314 (2012).
  • Fischer, C.J., Tomko, E.J, Wu, C.G. and Lohman, T.M. Fluorescence methods to study DNA translocation and unwinding kinetics by nucleic acid motors. Methods Mol Biol 875:85-104 (2012).
  • Tomko, E.J., Fischer, C.J. and Lohman, T.M. Single stranded DNA translocation of E. coli uvrD monomer is tightly coupled to ATP hydrolysis. J Mol Biol 418:32-46 (2012).
  • Antony, E., Korolev, S., Weiland, E.A. and Lohman, T.M. Plasmodium falciparum SSB tetramer wraps single stranded DNA with similar topology but opposite polarity to E. coli SSB. J Mol Biol 420:269-283 (2012).
  • Antony, E., Kozlov, A.G., Nguyen, B. and Lohman, T.M. Plasmodium falciparum SSB tetramer binds single stranded DNA only in a fully wrapped mode. J Mol Biol 420:284-295 (2012).
  • Ha, T., Kozlov, A.G. and Lohman, T.M. Single molecule views of protein movement on single-stranded DNA. Annual Review of Biophysics 41:295-319 (2012).
Garland R. Marshall
  • Zheng, X., Wu, C., Ponder, J.W. and Marshall, G.R. Molecular dynamics of highly stabilized beta-hairpin models of epigenetic recognition motifs. J Am Chem Soc 134:15970-15978 (2012).
  • Ballante, F., Musmuca, I., Marshall, G.R. and Ragno, R. Comprehensive Models of Wild-Type and Mutant HIV-1 Reverse Transcriptases. J Comput Aided Mol Des 26:907-919 (2012).
  • Silvestri, L., Ballante, F., Marshall, G.R. and Ragno, R. Histone Deacetylase Inhibitors: Structure-Based Modeling and Isoform-Selectivity Prediction. J Chem Info Model 52:2215-2235 (2012).
  • Tang, Y.T., Gao, R., Havranek, J.J., Groisman, E.A., Stock, A.M. and Marshall, G.R. Inhibition of bacterial virulence: Drug-like molecules targeting the Salmonella enterica PhoP response regulator. Chem Biol Drug Des 79:1007-1017 (2012).
  • Marshall, G.R. Limiting assumptions in structure-based design: Binding entropy. J Comput Aided Mol Des 26:3-8 (2012).
F. Scott Mathews
  • Chen, Z.W., Vignaud, C., Jaafar, A., Levy, B., Gueritte, F., Guenard, D., Lederer, F. and Mathews, F.S. High resolution crystal structure of rat long chain hydroxy acid oxidase in complex with the inhibitor 4-carboxy-5-[(4-chlorophenyl)sulfanyl]-1, 2, 3-thiadiazole. Implications for inhibitor specificity and drug design. Biochimie 94:1172-1179 (2012).
Linda J. Pike
  • Li, Y., Macdonald-Obermann, J., Westfall, C., Piwnica-Worms, D. and Pike, L.J. Quantitation of the effect of ErbB2 on EGF receptor binding and dimerization. J Biol Chem 287:31116-31125 (2012).
  • Pike, L.J. Negative co-operativity in the EGF receptor. Biochem Soc Trans 40:15-19 (2012).
  • Macdonald-Obermann, J.L., Piwnica-Worms, D. and Pike, L.J. Mechanics of EGF receptor/ErbB2 kinase activation evealed by luciferase fragment complementation imaging. Proc Natl Acad Sci USA 109:137-142 (2012).
  • Adak, S., Deandrade, D. and Pike, L.J. The tethering arm of the EGF receptor is required for negative cooperativity and signal transduction. J Biol Chem 286:1545-1555 (2012).