2013 Publications – Department of Biochemistry and Molecular Biophysics

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

Bowman, G.R., Meng, L. and Huang, X. Quantitative comparison of alternative methods for coarse-graining biological networks. J Chem Phys 139:121905 (2013).
Yao, Y., Cui, R.Z., Bowman, G.R., Silva, D.A., Sun, J. and Huang, X. Hierarchical Nystrom methods for constructing Markov state models for conformational dynamics. J Chem Phys 138:174106 (2013).
Qiao, Q., Bowman, G.R. and Huang, X. Dynamics of an intrinsically disordered protein reveal metastable conformations that potentially seed aggregation. J Am Chem Soc 135:16092-16101 (2013).

Chon, H., Sparks, J.L., Rychlik, M., Nowotny, M., Burgers, P.M., Crouch, R.J. and Cerritelli, S.M. RNase H2 roles in genome integrity revealed by unlinking its activities. Nucleic Acids Res. 41:3130-3143 (2013).
Kumar, S. and Burgers, P.M. Lagging strand maturation factor Dna2 is a component of the replication checkpoint initiation machinery. Genes Dev 27:313-321 (2013).
Clausen, A.R., Zhang, S., Burgers, P.M., Lee, M.Y. and Kunkel, T.A. Ribonucleotide incorporation, proofreading and bypass by human DNA polymerase δ. DNA Repair 12:121-127 (2013).

Wallen, J.R., Majka, J. and Ellenberger, T. Discrete interactions between bacteriophage T7 primase-helicase and DNA polymerase drive the formation of a priming complex containing two copies of DNA polymerase. Biochemistry 52:4026-4036 (2013).

Elson, E.L. and Genin, G.M. The role of mechanics in actin stress fiber kinetics. Exp Cell Res. 319:2490-2500 (2013).
Elson, E.L. Brief Introduction to fluorescence correlation spectroscopy. Methods Enzymol. 518:11-41 (2013).
Elson, E.L. 40 years of FCS: How it all began. Methods Enzymol. 518:1-10 (2013).

Zheleznyak, A., Ikotun, O.F., Dimitry, J., Frazier, W.A., Lapi, S.E. Imaging of CD47 expression in xenograft and allograft tumor models. Mol Imaging 12:525-534 (2013).
Azcutia, V., Routledge, M., Williams, M.R., Newton, G., Frazier, W.A., Manica, A., Croce, K.J., Parkos, C.A., Schmider, A.B., Turman, M.V., Soberman, R.J. and Luscinskas, F.W. CD47 plays a critical role in T-cell recruitment by regulation of LFA-1 and VLA-4 integrin adhesive functions. Mol Biol Cell 24:3358-3368 (2013).

Crick, S.L., Ruff, K.M., Garai, K., Frieden, C. and Pappu, R.V. Unmasking the Roles of N- and C-terminal Flanking Sequences from Exon 1 of Huntingtin as Modulators of Polyglutamine Aggregation. PNAS 110:20075-20080 (2013).
Frieden, C. and Garai, K. Concerning the structure of apoE. Protein Sci. 22:1820-1825 (2013).
Verghese, P.B., Castellano, J.M., Garai, K., Wang, Y., Jiang, H., Shah, A., Bu, G., Frieden, C. and Holtzmann, D.M. ApoE influences amyloid-β (Aβ) clearance despite minimal apoE/Aβ association in physiological conditions. PNAS 110:E1807-1816 (2013).
Garai, K. and Frieden, C. Quantitative analysis of the time course of Aβ oligomerization and subsequent growth steps using tetramethylrhodamine-labeled Aβ. Proc Natl Acad Sci USA 110:3321-3326 (2013).

Galletto, R. and Tomko, E.J. Translocation of Saccharomyces cerevisiae Pif1 helicase monomers on single-stranded DNA. Nucleic Acids Res. 41:4613-4627 (2013).

Hall, K.B. RNA does the folding dance of twist, turn, stack. PNAS 110:16706-16707 (2013).
Williams, S.G., Harms, M.J. and Hall, K.B. Resurrection of an urbilaterian U1A/U2B”/SNF protein. J Mol Biol 425:3846-3862 (2013).

Lyskov, S., Chou, F.C., Conchuir, S.O., Der, B.S., Drew, K., Kuroda, D., Xu, J., Weitzner, B.D., Renfrew, P.D., Sripakdeevong, P., Borgo, B., Havranek, J.J., Kuhlman, B., Kortemme, T. Bonneau, R., Gray, J.J. and Das, R. Serverification of molecular modeling applications: The Rosetta Online server that includes everyone (ROSIE). PLoS One 8:e63906 (2013).
Leaver-Fay, A., O’Meara, M.J., tyka, M., Jacak, R., Song, Y., Kellogg, E.H., Thompson, J., Davis, I.W. Paches, R.A., Lyskov, S., Gray, J.J., Kortemme, T., Richardson, J.S., Havranek, J.J., Snoeyink, J., Baker, D. and Kuhlman, B. Scientific benchmarks for guiding macromolecular energy function improvement. Methods Enzymol 523:109-143 (2013).

Totsika, M., Kostakioti, M., Hannan, T.J., Upton, M., Beaton, S.A., Janetka, J.W., Hultgren, S.J. and Schembri, M.A. A FimH inhibitor prevents acute bladder infection and treats chronic cystitis caused by multidrug resistant uropathogenic Escherichia coli ST131. J Infec Dis 208:921-928 (2013).

Borin, B.N., Tang, W., Nice, T.J., McCune, B.T., Virgin, H.W. and Krezel, A.M. Murine norovirus protein NS1/2 aspartate to glutamate mutation, sufficient for persistence, reorients side chain of surface exposed tryptophan within a novel structure domain. Proteins (E-pub ahead of print.) (2013).

Antony, E., Weiland, E., Yuan, Q., Manhart, C. M., Nguyen, B., Kozlov, A. G., McHenry, C. S. and Lohman, T. M. Multiple C-terminal tails within a single E. coli SSB homotetramer coordinate DNA replication and repair. J. Mol. Biol. 425:4802-4819 (2013).
Qiu, Y., Antony, E., Doganay, S., Koh, H., Lohman, T. M. and Myong, S. Srs2 prevents Rad51 filament formation by repetitive motion on DNA. Nature Communications 4 doi:10.1038/ncomms3281 (2013).
Lee, K.S., Balci, H., Jia, H., Lohman, T.M. and Ha, J. Direct imaging in single UvrD helicase dynamics on long single-stranded DNA. Nature Communications 4:1878 (2013).
Xie, F., Wu, C.G., Weiland, E. and Lohman, T.M. Asymmetric regulation of bipolor single-stranded DNA translocation by the two motors within E. coli RecBCD helicase. J Biol Chem 288:1055-1064 (2013).

Marshall, G.R. Limiting assumptions in molecular modeling: Electrostatics. J Comput Aided Mol Des 27:107-114 (2013).

Macdonald-Obermann, J.L., Adak, S., Landgraf, R., Piwnica-Worms, D. and Pike, L.J. Dynamic analysis of the EGF receptor-ErbB2-ErbB3 network by luciferase fragment complementation imaging J. Biol Chem 288:30773-30784 (2013).