Department of Biochemistry and Molecular Biophysics

2009 Publications

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

Gary K. Ackers
  • Holt, J.M. and Ackers, G.K. The Hill coefficient: Inadequate resolution of cooperativity in human hemoglobin. Methods Enzymol 455:193-212 (2009).
Wayne M. Barnes
  • Kermekchiev, M.B., Kirilova, L.I., Vail, E.E. and Barnes, W. Mutants of Taq DNA polymerase resistant to PCR inhibitors allow DNA amplification from whole blood and crude soil samples. Nucleic Acids Res. 37:e40 (2009).
Peter M. Burgers
  • Navadgi-Patil, V.M. and Burgers, P.M. The unstructured C-terminal tail of the 9-1-1 clamp subunit Ddc1 activates Mec1/ATR via two distinct mechanisms p743. Mol Cell 36:743-753 (2009).
  • Li, X., Stith, C.M., Burgers, P.M. and Heyer, W.D. PCNA is required for initiation of recombination-associated DNA synthesis by DNA polymerase delta. Mol Cell 36:704-713 (2009).
  • Pike, J.E., Burgers, P.M., Campbell, J.L. and Bambara, R.A. Pif1 helicase lengthens some Okazaki fragment flaps necessitating Dna2 nuclease/helicase action in the two-nuclease processing pathway. J Biol Chem 284:25170-25180 (2009).
  • Navadgi-Patil, V.M. and Burgers, P.M. A tale of two tails: Activation of DNA damage checkpoint kinase Mec1/ATR by the 9-1-1 clamp and by Dpb11/TopBP1. DNA Repair 8:996-1003 (2009).
  • Stone, J.E., Kissling, G.E., Lujan, S.A., Rogozin, I.B., Stith, C.M., Burgers, P.M. and Kunkel, T.A. Low-fidelity DNA synthesis by the L979F mutator derivative of Saccharomyces cerevisiae DNA polymerase {zeta}. Nucleic Acids Res. 37:3774-3787 (2009).
  • McCulloch, S.D., Kokoska, R.J., Garg, P., Burgers, P.M. and Kunkel, T.A. The efficiency and fidelity of 8-oxo-guanine bypass by DNA polymerases {delta} and {eta}. Nucleic Acids Res 37:2830-2840 (2009).
  • Chon, H., Vassilev, A., Depamphilis, M.L., Zhao, Y., Zhang, J., Burgers, P.M., Crouch, R.J. and Cerritelli, S.M. Contributions of the two Accessory subunits, RNASEH2B and RNASEH2C, to the activity and properties of the human RNase H2 complex. Nucleic Acids Res. 37:96-110 (2009).
  • Burgers, P.M. Polymerase dynamics at the eukaryotic DNA replication fork. J Biol Chem 284:4041-4045 (2009).
John A. Cooper
  • Butler, B. and Cooper, J.A. Distinct roles for the actin nucleators Arp2/3 and hDia1 during NK-mediated cytoxicity. Curr Biol 19:1886-1896 (2009).
  • Pollard, T.D. and Cooper, J.A. Actin, a central player in cell shape and movement. Science 326:1208-1212 (2009).
  • Moore, J.K., Magidson, V., Khodjakov, A. and Cooper, J.A. The spindle position checkpoint requires positional feedback from cytoplasmic microtubules. Curr Biol 19:2026-2030 (2009).
  • Liang, Y., Niederstrasser, H., Edwards, M., Jackson, C.E. and Cooper, J.A. Distinct roles for CARMIL isoforms in cell migration. Mol Biol Cell 20:5290-5305 (2009).
  • Moore, J.K., Stuchell-Brereton, M.D. and Cooper, J.A. Function of dynein in budding yeast: Mitotic spindle positioning in a polarized cell. Cell Motil Cytoskeleton 66:546-555 (2009).
  • Zaichick, S.V., Metodiev, M.V., Nelson, S.A., Durbrovskyi, O., Draper, E., Cooper, J.A. and Stone, D.E. The mating-specific Galpha interacts with a kinesin-14 and regulates pheromone induced nuclear migration in budding yeast. Mol Biol Cell 20:2820-2830 (2009).
  • Moore, J.K., Sept, D. and Cooper, J.A. Neurodegeneration mutations in dynactin impair dynein-dependent nuclear migration. Proc Natl Acad Sci USA 106:5147-5152 (2009).
Tom Ellenberger
  • Antony, E., Tomko, E.J., Xiao, Q., Krejci, L, Lohman, T.M. and Ellenberger, T. Srs2 disassembles Rad51 filaments by a protein-protein interaction triggering ATP turnover and dissociation of Rad51 from DNA. Molecular Cell 35:105-115 (2009).
  • Etzion, Y., Hackett, A., Proctor, B.M., Ren, J., Nolan, B., Ellenberger, T. and Muslin, A.J. An unbiased chemical biology screen identifies agents that modulate uptake of oxidized LDL by macrophages. Circ Res 105:148-157 (2009).
  • Song, W., Pascal, J.M. and Ellenberger, T. and Tomkinson, A.E. The DNA binding domain of human DNA ligase I interacts with both nicked DNA and the DNA sliding clamps. DNA Repair 8:912-919 (2009).
Elliot Elson
  • Marquez, J.P., Legant, W., Lam, V., Cayemberg, A., Elson, E. and Wakatsuki, T. High-throughput measurements of hydrogel tissue construct mechanics. Tissue Eng Part C Methods 15:181-190 (2009).
William A. Frazier
  • Lawrence, D.W., King, S.B., Frazier, W.A. and Koenig, J.M. Decreased CD47 expression during spontaneous apoptosis targets neutrophils for phagocytosis by monocyte-derived macrophages. Early Human Dev. 85:659-663 (2009).
  • Isenberg, J.S., Qin, Y., Maxhimer, J.B., Sipes, J.M., Despres, D., Schnermann, J., Frazier, W.A. and Roberts, D.D. Thrombospondin-1 and CD47 regulate blood pressure and cardiac responses to vasoactive stress. Matrix Biology 28:110-119 (2009).
  • Uluçkan, O., Becker, S.N., Deng, H., Zou, W., Prior, J.L., Piwnica-Worms, D., Frazier, W.A. and Weilbaecher, K.N. CD47 regulates bone mass and tumor metastasis to bone. Cancer Res 69:3196-3204 (2009).
  • Isenberg, J.S. Annis, D.S., Pendrak, M.L., Ptaszynska, M., Frazier, W.A., Mosher, D.F. and Roberts, D.D. Differential interactions of thrombospondins-1, -2 and -4 with CD47 and effects on cGMP signaling and ischemic injury responses. J Biol Chem 284:1116-1125 (2009).
  • Kohyama, M., Ise, W., Edelson, B.T., Wilker, P.R., Hildner, K., Mejia, C., Frazier, W.A., Murphy, T.L. and Murphy, K.M. Role for Spi-C in the development of red pulp macrophages and splenic iron homeostasis. Nature 457:318-321 (2009).
Carl Frieden
  • Hu, X., Crick, S.L., Bu, G., Frieden, C., Pappu, R.V. and Lee, J.M. Amyloid seeds formed by cellular uptake, concentration, and aggregation of the amyloid-beta peptide. Proc Natl Acad Sci USA 106:20324-20329 (2009).
  • Garai, K., Mustafi, S.M., Baban, B. and Frieden, C. Structural differences between apoli proprotein E3 and E4 as measured by (19)F- NMR. Protein Sci 19:66-74 (2009).
  • Zhang, R., Hu, X., Khant, H., Ludtke, S.J., Chiu, W., Schmeid, M.F., Frieden, C. and Lee, J.M. Interprotofiliment interactions between Alzheimer’s A{beta}1-42 peptides in amyloid fibrils revealed by cryoEM. PNAS 106:4653-4658 (2009).
  • Garai, K., Crick, S.L., Mustafi, S.M. and Frieden, C. Expression and purification of amyloid-beta peptides from Escherichia coli. Protein Expr Purif. 66:107-112 (2009).
Eric A. Galburt
  • Galburt, E.A., Grill, S.W. and Bustamante, C. Single molecule transcription elongation. Methods 48:323-332 (2009).
  • Depken, M, Galburt, E.A. and Grill, S.W. The origin of short transcriptional pauses. Biophys J 96:2189-2193 (2009).
Roberto Galletto
  • Andreeva, I.E., Szymanski, M.R., Jezewska, M.J., Galletto, R. and Bujalowski, W. Dynamics of the ssDNA recognition by the RepA hexameric helicase of plasmid RSF 1010: Analyses using fluorescence stopped-flow intensity and anisotropy methods. J Mol Biol 38:751-775 (2009).
Kathleen B. Hall
  • Melnykov, A.V. and Hall, K.B. Revival of high-order fluorescence correlation analysis: Generalized theory and biochemical applications. J Phys Chem B 113:15629-15638 (2009).
  • Clerte, C. and Hall, K.B. The domains of polypyrimidine tract binding protein have distinct RNA structural preferences. Biochemistry 48:2063-2074 (2009).
James W. Janetka
  • Aronov, A.A., Tang, Q., Martinez-Botella,G., Bemis, G.W., Cao, J., Chen, G., Ewing, N.P., Ford, P.J., Germann, U.A., Green, J., Hale, M.R., Jacobs, M., Janetka, J.W., Maltais, F., Markland, W., Namchuk M.N., Nanthakumar, S., Poondru, S., Straub, J., ter Haar, E. and Xie, X. Structure-guided design of potent and selective pyrimidylpyrrole inhibitors of extracellular signal-regulated kinase (ERK) using conformational control. J Medicinal Chemistry 52:6362-6368 (2009).
  • Janetka, J.W. and Ashwell, S. Checkpoint kinase inhibitors: A review of the patent literature. Expert Opinion on Therapeutic Patents 19:165-197 (2009).
Andrzej M. Krezel
  • Gupta, S.S., Borin, B.N., Cover, T.L. and Krezel, A.M. Structural analysis of the DNA-binding domain of the Helicobacter pylori response regulator ArsR. J Biol Chem. 284:6536-6545 (2009).
Linda Kurz
  • Kurz, L.C., Constantine, C.Z., Jiang, H. and Kappock, T.J. The partial substrate dethiaacetyl-coenzyme A mimics all critical carbon acid reactions in the condensation half-reaction catalyzed by thermoplasma acidophilum citrate synthase. Biochemistry 48:7878-7891 (2009).
Weikai Li
  • Crystal structure of NL63 respiratory coronavirus receptor-binding domain complexed with its human receptor. Proc Natl Acad of Sci USA 106:19970-19974 (2009).
Timothy M. Lohman
  • Roy, R., Kozlov, A.G., Lohman, T.M. and Ha, T. SSB protein diffusion on single-stranded DNA stimulates RecA filament formation. Nature 461:1092-1097 (2009).
  • Antony, E., Tomko, E.J., Xiao, Q., Krejci, L, Lohman, T.M. and Ellenberger, T. Srs2 disassembles Rad51 filaments by a protein-protein interaction triggering ATP turnover and dissociation of Rad51 from DNA. Molecular Cell 35:105-115 (2009).
Garland R. Marshall
  • Feng, J.A., Kao, J. and Marshall, G.R. A second look at mini-protein stability: Analysis of FSD-1 using circular dichroism, differential scanning calorimetry, and simulations. Biophys J 97:2803-2810 (2009).
  • Marshall, G.R., Kuster, D.J. and Che, Y. Chemogenomics with protein secondary-structure mimetics. Methods Mol Biol. 575:123-158 (2009).
  • Oprea, T.I., Bologa, C.G., Boyer, S., Curpan, R.F., Glen, R.C., Hopkins, A.L., Lipinski, C.A., Marshall, G.R., Martin, Y.C., Ostopovici-Halip, L., Rishton, G., Ursu, O., Vaz, R.J., Waller, C., Waldmann, H. and Sklar, L.A. A Crowdsourcing evaluation of the NIH chemical probes. Nat Chem Biol 5:441-447 (2009).
  • Arbor, S. and Marshall, G.R. A virtual library of constrained cyclic tetrapeptides that mimics all four side-chain orientations for over half the reverse turns in the protein data bank. J Comput Aided Mol Des. 23:87-95 (2009).
F. Scott Mathews
  • Sukumar, N., Mathews, F.S., Gordon, M.M., Ealik, S.E. and Alpers, D.H. Postcrystallization analysis of the irreproducibility of the human intrinsic factor-cobalamin complex crystals. Cryst Growth Des. 9:348-351 (2009).
  • Kommoju, P.R., Bruckner, R.C., Ferreira, P., Carrell, C.J., Mathews, F.S., and Jorns, M.S. Factors that affect oxygen activation and coupling of the two redox cycles in the aromatization reaction catalyzed by NikD, an unusual amino acid oxidase. Biochemistry 48:9542-9555 (2009).
  • Sukumar, N., Dewanti, A., Merli, A., Rossi, G.L., Mitra, B. and Mathews, F.S. Structures of the G81A mutant form of the active chimera of (S)-mandelate dehydrogenase and its complex with two of its substrates. Acta Crystallogr D Biol Crystallogr 65:543-552 (2009).
Linda J. Pike
  • Macdonald-Obermann, J.L. and Pike, L.J. The intracellular juxtamembrane domain of the EGF receptor is responsible for the allosteric regulation of EGF binding. J Biol Chem 284:13570-13576 (2009).
  • Macdonald-Obermann, J.L. and Pike, L.J. Palmitoylation of the EGF receptor impairs signal transduction and abolishes
    high-affinity ligand binding. Biochemistry 48:2505-2513 (2009).
  • Yang, K.S., Ilagan, MX., Pinica-Worms, D. and Pike, L.J. Luciferase fragment complementation imaging of conformational changes in the EGF receptor. J Biol Chem 284:7474-7482 (2009).
  • Pike, L.J. The challenge of lipid rafts. J. Lipid Res. 50:S323-S328 (2009).