PUBLICATIONS

2009 | 2008 | 2007 | 2006 | 2005 | 2004

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

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).

Nathan A. Baker

Silva, J.R., Pan, H., Wu, D., Nekouzadeh, A., Decker, K.F., Cui, J., Baker, N.A., Sept, D. and Rudy, Y.A. A multiscale model linking ion-channel molecular dynamics and electrostatics to the cardiac action potential. Proc Natl Acad Sci USA 106:11102-11106 (2009).
Olsen, B.N., Schlesinger, P.H. and Baker, N.A. Perturbations of membrane structure by cholesterol and cholesterol derivatives are determined by sterol orientation. J Am Chem Soc 131:4854-4865 (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

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 (E-pub ahead of print.) (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).

Peter T. Chivers

Iwig, J.S. and Chivers, P.T. DNA recognition and wrapping by Escherichia coli RcnR. J Mol Biol 393:514-526 (2009).
Benanti, E.L. and Chivers, P.T. An intact urease assembly pathway is required to compete with NikR for nickel ions in Helicobacter pylori. J Bacteriol 191:2405-2408 (2009).

Enrico Di Cera

Niu, W., Chen, Z., Busch-Pelc, L.A., Bah, A., Gandhi, P.S. and Di Cera, E. The mutant N143P reveals how Na+ activates thrombin. J Biol Chem (E-pub ahead of print.) (2009).
Gandhi, P.S., Page, M.J., Chen, Z., Bush-Pelc, L.A. and Di Cera, E. Mechanism of the anticoagulant activity of the thrombin mutant W215A/E217A. J Biol Chem 284:24098-24105 (2009).
Di Cera, E. Know your APC. Blood 113:5970-5978 (2009).
Bah, A., Carrell, C.J., Chen, Z., Gandhi, P.S. and Di Cera, E. Stabilization of the E* form turns thrombin into an anticoagulant. J Biol Chem (E-pub ahead of print.) (2009).
Di Cera, E. Serine proteases. IUBMB Life 61:510-515 (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 (E-pub ahead of print.) (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 (E-pub ahead of print.) (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 (E-pub ahead of print.) (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).

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).

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

Marshall, G.R., Kuster, D.J. and Che, Y. Chemogenomics with protein secondary-structure mimetics. Methods Mol Biol. 575:123-158 (2009).
Nikiforovich, G.V., Taylor, C.M., Marshall, G.R. and Baranski, T.J. Modeling the possible conformations of the extracellular loops in G-protein-coupled receptors. Proteins (E-pub ahead of print.) (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

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 (E-pub ahead of print.) (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).

PUBLICATIONS

2009 | 2008 | 2007 | 2006 | 2005 | 2004

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

Holt, J.M. and Ackers, G.K. The Hill coefficient: Inadequate resolution of cooperativity in human hemoglobin. Methods Enzymol 455:193-212 (2009).

Silva, J.R., Pan, H., Wu, D., Nekouzadeh, A., Decker, K.F., Cui, J., Baker, N.A., Sept, D. and Rudy, Y.A. A multiscale model linking ion-channel molecular dynamics and electrostatics to the cardiac action potential. Proc Natl Acad Sci USA 106:11102-11106 (2009).

Olsen, B.N., Schlesinger, P.H. and Baker, N.A. Perturbations of membrane structure by cholesterol and cholesterol derivatives are determined by sterol orientation. J Am Chem Soc 131:4854-4865 (2009).

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).

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 (E-pub ahead of print.) (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).

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).

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 (E-pub ahead of print.) (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 (E-pub ahead of print.) (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).

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).

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).

Melnykov, A.V. and Hall, K.B. Revival of high-order fluorescence correlation analysis: Generalized theory and biochemical applications. J Phys Chem B (E-pub ahead of print.) (2009).

Clerte, C. and Hall, K.B. The domains of polypyrimidine tract binding protein have distinct RNA structural preferences. Biochemistry 48:2063-2074 (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).

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).

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).

Marshall, G.R., Kuster, D.J. and Che, Y. Chemogenomics with protein secondary-structure mimetics. Methods Mol Biol. 575:123-158 (2009).

Nikiforovich, G.V., Taylor, C.M., Marshall, G.R. and Baranski, T.J. Modeling the possible conformations of the extracellular loops in G-protein-coupled receptors. Proteins (E-pub ahead of print.) (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).

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 (E-pub ahead of print.) (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).

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).