2014 Publications

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

Gregory R. Bowman

Peter M. Burgers

• Dovrat, D., Stodola, J.L., Burgers, P.M. and Ahoroni, A. Sequential switching of binding partners on PCNA during in vitro Okazaki fragment maturation. PNAS 111:14118-14123 (2014).
• Kunkel, T.A. and Burgers, P.M. Delivering nonidentical twins. Nat Struct Mol Biol 21:649-651 (2014).
• Lin, Y.C., Li, L., Makarova, A.V., Burgers, P.M. and Lloyd, R.S. Error-prone replication bypass of the primary aflatoxin B1 DNA adduct, AFB1-N7-Gua. J Biol Chem 289:18497-18506 (2014).
• Makarova, A.V., McElhinny, S.A., Watts, B.E., Kunkel, T.A. and Burgers, P.M. Ribonucleotide incorporation by yeast DNA polymerases ζ. DNA Repair 18:63-67 (2014).
• Lin, Y.C., Li, L., Makarova, A.V., Burgers, P.M., Stone, M.P. and Lloyd, R.S. Molecular Basis of Aflatoxin-induced Mutagenesis – Role of the Aflatoxin B1-formamidopyrimidine Adduct. Carcinogenesis 35:1461-1468 (2014).
• Northam, M.R., Moore, E.A., Mertz, T.M., Binz, S.K., Stith, C.M., Stepchenkova, E.I., Wendt, K.L., Burgers, P.M., and Shcherbakova, P.V. DNA polymerases ζ and Rev1 mediate error-prone bypass of non-B DNA structures. Nucleic Acids Res. 42:290-306 (2014).

Elliot L. Elson

• Nguyen, B., Sokoloski, J.E., Galletto, R., Elson, E.L., Wold, M.S. and Lohman, T.M. Diffusion of human replication protein A along single stranded DNA. J Mol Biol 426:3246-3261 (2014)
• Genin, G.M. and Elson, E.L. Mechanically guided cell migration: Less of a stretch than ever. Biophys J 106:776-777 (2014).

William A. Frazier

• Lin, Y., Manning, P.T., Jia, J., Gaut, J.P., Xiao, Z., Capoccia, B.J., Chen, C.C., Hiebsch, R.R., Upadhya, G., Mohanakumar, T., Frazier, W.A. and Chapman, W.C. CD47 blockade reduces ischemia-reperfusion injury and improves outcomes in a rat kidney transplant model. Transplantation 98:394-401 (2014).

Carl Frieden

• Garai, K., Verghese, P.B., Baban, B., Holtzman, D.M. and Frieden, C. The binding of apoE to oligomers and fibrils of amyloid-beta alters the kinetics of amyloid aggregation. Biochemistry 53:6323-6331 (2014).
• Hammes, G. and Frieden, C. “Robert A. Alberty”. Biographical Memoirs Natl Acad Sci. (2014)

Eric A. Galburt

• Garner, A.L., Weiss, L.A., Manzano, A.R., Galburt, E.A. and Stallings, C.L. CarD Integrates Three Functional Modules to Promote Efficient Transcription, Antibiotic Tolerance, and Pathogenesis in Mycobacteria. Mol Microbiol 93:682-697 (2014).
• Galburt, E.A., Tomko, E.J., Stump, W.T. and Ruiz Manzano, A. Force-dependent melting of supercoiled DNA at thermophilic temperatures. Biophysical Chemistry 187-188:23-28 (2014).
• Galburt, E.A. Magnetic tweezers force spectroscopy. Handbook of Imaging in Biological Mechanics. Chapter 38, 481-490. CRC Press (2014)

Roberto Galletto

• Feldmann, E.A. and Galletto, R. The DNA-binding domain of yeast Rap1 interacts with dsDNA in multiple binding modes. Biochemistry 53:7471-7483 (2014)
• Nguyen, B., Sokoloski, J.E., Galletto, R., Elson, E.L., Wold, M.S. and Lohman, T.M. Diffusion of human replication protein A along single stranded DNA. J Mol Biol 426:3246-3261 (2014)

Kathleen B. Hall

• DeKoster, G.T., Delaney, K.J. and Hall, K.B. A compare-and-contrast NMR dynamics study of two related RRMs: U1A and SNF. Biophys J 107:208-219 (2014).
• Williams, S.G. and Hall, K.B. Binding affinity and cooperativity control U2B"/snRNA/U2A' RNP formation. Biochemistry 53:3727-3737 (2014).
• Williams, S.G. and Hall, K.B. Linkage and allostery in snRNP protein:RNA complexes. Biochemistry 53:3529-3539 (2014).
• Delaney, K.J., Williams, S.G., Lawler, M. and Hall, K.B. Climbing the vertebrate branch of U1A/U2B" protein evolution. RNA 20:1035-1045 (2014).
• Hall, K.B. Molecular Biology: Protein Binding Cannot Subdue a Lively RNA. Nature 506:303-304 (2014).

James J. Havranek

• Borgo, B. and Havranek, J.J. Motif-directed redesign of enzyme specificity. Protein Science 23:312-320 (2014).

James W. Janetka

• Han, Z., Harris, P.K.W., Jones, D.E., Chugani, R., Kim, T., Agarwal, M., Shen, W., Wildman, S.A. and Janetka, J.W. Inhibitors of HGFA, matriptase and hepsin serine proteases: A non-kinase strategy to block cell signaling in cancer. ACS Med. Chem. Lett. 5:1219-1224 (2014).

Andrzej M. Krezel

• Borin, B.N., Tang, W. and Krezel, A.M. Helicobacter pylori RNA polymerase α-subunit D-terminal domain shows features unique to ε-proteobacteria and binds NikR/DNA complexes. Protein Science 23:454-463 (2014).

Weikai Li

• Cheng, W. and Li, W. Structural insights into ubiquinone biosynthesis in membranes. Science 343:878-881 (2014).
• Liu, S., Cheng, W., Fowle Grider, R., Shen, G. and Li, W. Structures of an intramembrane vitamin K epoxide reductase homolog reveal control mechanisms for electron transfer. Nature Communications 5:3110 (2014).
• Park, E., Mènètret, J.F., Gumbart, J.C., Ludtke, S.J., Li, W., Whynot, A., Rapoport, T.A. and Akey, C.W. Structure of the SecY channel during initiation of protein translocation. Nature 506:102-106 (2014).

Timothy M. Lohman

• Nguyen, B., Sokoloski, J.E., Galletto, R., Elson, E.L., Wold, M.S. and Lohman, T.M. Diffusion of human replication protein A along single stranded DNA. J Mol Biol 426:3246-3261 (2014)
• Lee, K.S., Marciel, A.B., Kozlov, A.G., Schroeder, C.M., Lohman, T.M. and Ha, T. Ultrafast redistribution of E. coli SSB along long single-stranded DNA via intersegment transfer. J Mol Biol 426:2413-2421 (2014).

Garland R. Marshall

• Liu, C., Ponder, J.W. and Marshall, G.R. Helix stability of oligoglycine, oligoalanine and oligo-beta-alanine dodecamers reflected by hydrogen-bond persistence. Proteins 82:3043-3061 (2014)

Linda J. Pike

• MacDonald-Obermann, J.L. and Pike, L.J. Different EGF receptor ligands show distinct kinetics and biased or partial agonism for homodimer and heterodimer formation. J Biol Chem. 289:26178-26188 (2014).