PUBLICATIONS

2008 | 2007 | 2006 | 2005 | 2004 | 2003

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

Nathan A. Baker

Bradley, M.J., Chivers, P.T. and Baker, N.A. Molecular dynamics simulation of the Escherichia coli NikR protein: Equilibrium conformational fluctuations reveal interdomain allosteric communication pathways. J Mol Biol. 378:1155-1173 (2008).
Lee, S.J., Song, Y. and Baker, N.A. Molecular dynamics simulations of asymmetric NaCl and KCl solutions separated by phosphatidylcholine bilayers: Potential drops and structural changes induced by strong Na+-lipid interactions and finite size effects. Biophys J. 94:3565-3576 (2008).
Dong, F., Olsen, B. and Baker, N.A. Computational methods for biomolecular electrostatics. Methods Cell Biol. 84:843-870 (2008).

Peter M. Burgers

Nick McElhinny, S.A., Gordenin, D.A., Stith, C.M., Burgers, P.M. and Kunkel, T.A. Division of labor at the eukaryotic replication fork. Mol Cell. 30:137-144 (2008).
Wardle, J., Burgers, P.M., Cann, I.K., Darley, K., Darley, K., Heslop, P., Johansson, E., Lin, L.J., McGlynn, P., Sanvoisin, J., Stith, C.M. and Connolly, B.A. Uracil recognition by replicative DNA polymerases is limited to the archaea, not occurring with bacteria and eukarya. Nucleic Acids Res 36:705-711 (2008).

Peter T. Chivers

Iwig, J.S., Leitch, S., Herbst, R.W., Maroney, M.J. and Chivers, P.T. Ni(II) and Co(II) sensing by Escherichia coli RcnR. J Am Chem Soc. 130:7592-7606 (2008).
Bradley, M.J., Chivers, P.T. and Baker, N.A. Molecular dynamics simulation of the Escherichia coli NikR protein: Equilibrium conformational fluctuations reveal interdomain allosteric communication pathways. J Mol Biol. 378:1155-1173 (2008).

Enrico Di Cera

Tanaka, K.A., Gruber, A., Szlam, F., Bush, L.A., Hanson, S.R. and Di Cera, E. Interaction between thrombin mutant W215A/E217A and direct thrombin I\inhibitor. Blood Coagul Fibrinolysis 19:465-468 (2008).
Papaconstantinou, M.E., Bah, A. and Di Cera, E. Role of the A chain in thrombin function. Cell Mol Life Sci. [Epub ahead of print] (2008)
Di Cera, E. Engineering protease specificity made simple, but not simpler. Nat Chem Biol 4:270-271 (2008).
Page, M.J., Carrell, C.J. and Di Cera, E. Engineering protein allostery: 1.05 A resolution structure and enzymatic properties of a Na(+)-activated trypsin. J Mol Biol. 378:666-672. (2008).
Di Cera, E. Thrombin. Mol Aspects Med. (Epub ahead of print) (2008).
Nieman, M.T., Burke, F., Warnock, M., Zhou, Y., Sweigart, J., Chen, A., Ricketts, D., Lucchesi, B.R., Chen, Z., Di Cera, E., Hilfinger, J., Kim, J.S., Mosberg, H.I. and Schmaier, A.H. Thrombostatin FM compounds: Direct thrombin inhibitors - Mechanism of action in vitro and in vivo. J Thromb Haemost. 6:837-845 (2008).
Page, M.J. and Di Cera, E. Serine peptidases: Classification, structure and function. Cell Mol Life Sci. 65:1220-1236 (2008).
Gandhi, P.S., Chen, Z., Mathews, F.S. and Di Cera, E. Structural identification of the pathway of long-range communication in an allosteric enzyme. Proc Natl Acad Sci U S A. 105:1832-1837 (2008).
Berny, M.A., White, T.C., Tucker, E.I., Bush-Pelc, L.A., Di Cera, E., Gruber, A. and McCarty, O.J. Thrombin mutant W215A/E217A acts as a platelet GPIb antagonist. Arterioscler Thromb Vasc Biol. 28:329-334 (2008).

Tom Ellenberger

Ellenberger, T. and Tomkinson, A.E. Eukaryotic DNA ligases: Structural and functional insights. Annu Rev Biochem 77:313-338 (2008).
Chen, X., Zhong, S., Zhu, X., Dziegielewska, B., Ellenberger, T., Wilson, G.M., MacKerell, A.D. Jr and Tomkinson, A.E. Rational design of human DNA ligase inhibitors that target cellular DNA replication and repair. Cancer Res. 68:3169-3177 (2008).
Cotner-Gohara, E., Kim, I.K., Tomkinson, A.E. and Ellenberger, T. Two DNA binding and nick recognition modules in human DNA ligase III. J. Biol. Chem. 283:10764-10772 (2008).

Elliot Elson

Tan, Y.C., Shen, A.Q., Li, Y., Elson, E. and Ma, L. Engineering lipid tubules using nano-sized building blocks: The combinatorial self-assembly of vesicles. Lab on a Chip 8:339-345 (2008).

William A. Frazier

Isenberg, J.S., Romeo, M.J., Maxhimer, J.B., Smedley, J., Frazier, W.A. and Roberts, D.D. Gene silencing of CD47 and antibody ligation of Thrombospondin-1 enhance ischemic tissue survival in a porcine model: Implications for human disease. Ann Surg. 247:860-868 (2008).
Isenberg, J.S., Romeo, M.J, Yu, C., Yu, C.K., Nghiem, K., Monsale, J., Rick, M.E., Wink, D.A., Frazier, W.A. and Roberts, D.D. Thrombospondin-1 stimulates platelet aggregation by blocking the antithrombotic activity of nitric oxide/cGMP signaling. Blood 111:613-623 (2008).
Isenberg, J.S., Roberts, D.D. and Frazier, W.A. CD47. A new target in cardiovascular therapy. Arterioscler Thromb Vasc Biol. 28:615-621 (2008).
Isenberg, J.S., Pappan, L.K., Romeo, M.J., Abu-Asab, M., Tsokos, M., Wink, D.A., Frazier, W.A. and Roberts, D.D. Blockade of thrombospondin-1-CD47 interactions prevents necrosis of full thickness skin grafts. Ann Surg. 247:180-190 (2008).

Timothy M. Lohman

Lohman, T.M., Tomko, E.J. and Wu, C.G. Non-hexameric DNA helicases and translocases: Mechanisms and regulation. Nat Rev Mol Cell Biol. 9:391-401 (2008).
Wong, C.J. and Lohman, T.M. Kinetic control of Mg(2+)-dependent melting of duplex DNA ends by Escherichia coli RecBC. J Mol Biol. 378:759-775 (2008).

Garland R. Marshall

Nikiforovich, G.V., Marshall, G.R. and Baranski, T.J. Modeling molecular mechanisms of binding of the anaphylatoxin C5a to the C5a receptor. Biochemistry 47:3117-3130 (2008).
Cegelski, L, Marshall, G.R., Eldridge, G.R. and Hultgren, S.J. The biology and future prospects of antivirulence therapies. Nature Rev Microbiol. 6:17-27 (2008).
Che, Y. and Marshall, G.R. Privileged scaffolds targeting reverse-turn and helix recognition. Expert Opin Ther Targets 12:101-114 (2008).
Ye, Y., Liu, M., Kao, J.L. and Marshall, G.R. Design, synthesis, and metal binding of novel pseudo-oligopeptides containing two phosphinic acid groups. Biopolymers 89:72-85 (2008).
Berg-Cross, S., Kao, J., Wu, Y. and Marshall, G.R. c[D-pro-Pro-D-pro-N-Methyl-Ala] Adopts a rigid conformation that serves as a scaffold to mimic reverse-turn. Biopolymers 90:384-393 (2008).
Marshall, G.R., Feng, J.A. and Kuster, D.J. Back to the future: Ribonuclease A. Biopolymers 90:259-277 (2008).

F. Scott Mathews

Hassan-Abadallah, A., Zhao, G., Chen, Z., Mathews, F.S. and Schuman Jorns, M. Arginine 49 is a bifunctional residue important in catalysis and biosynthesis of monomeric sarcosine oxidase: A context-sensitive model for the electrostatic impact of arginine to lysine mutations. Biochemistry 47:2913-2922 (2008).
Gandhi, P.S., Chen, Z., Mathews, F.S. and Di Cera, E. Structural identification of the pathway of long-range communication in an allosteric enzyme. Proc Natl Acad Sci U S A. 105:1832-1837 (2008).

Gregory V. Nikiforovich

Sen, S., Baranski, T.J. and Nikiforovich, G.V. Conformational movement of F251 contributes to the molecular mechanism of constitutive activation in the C5a receptor. Chemical Biology & Drug Design 71:197-204 (2008).
Hagemann, I.S., Miller, D.L., Klco, J.M., Nikiforovich, G.V., and Baranski, T.J. Structure of the complement factor 5a receptor-ligand complex studied by disulfide trapping and molecular modelings. J. Biol. Chem. 283:7763-7775 (2008).
Nikiforovich, G.V., Marshall, G.R. and Baranski, T.J. Modeling molecular mechanisms of binding of the anaphylatoxin C5a to the C5a receptor. Biochemistry 47:3117-3130 (2008).

Linda J. Pike

Macdonald, J.L. and Pike, L.J. Heterogeneity in EGF-binding affinities arises from negative cooperativity in an aggregating system. PNAS 105:112-117 (2008).

PUBLICATIONS 2008 | 2007 | 2006 | 2005 | 2004 | 2003

2008 | 2007 | 2006 | 2005 | 2004 | 2003

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

Bradley, M.J., Chivers, P.T. and Baker, N.A. Molecular dynamics simulation of the Escherichia coli NikR protein: Equilibrium conformational fluctuations reveal interdomain allosteric communication pathways. J Mol Biol. 378:1155-1173 (2008).

Lee, S.J., Song, Y. and Baker, N.A. Molecular dynamics simulations of asymmetric NaCl and KCl solutions separated by phosphatidylcholine bilayers: Potential drops and structural changes induced by strong Na+-lipid interactions and finite size effects. Biophys J. 94:3565-3576 (2008).

Dong, F., Olsen, B. and Baker, N.A. Computational methods for biomolecular electrostatics. Methods Cell Biol. 84:843-870 (2008).

Nick McElhinny, S.A., Gordenin, D.A., Stith, C.M., Burgers, P.M. and Kunkel, T.A. Division of labor at the eukaryotic replication fork. Mol Cell. 30:137-144 (2008).

Iwig, J.S., Leitch, S., Herbst, R.W., Maroney, M.J. and Chivers, P.T. Ni(II) and Co(II) sensing by Escherichia coli RcnR. J Am Chem Soc. 130:7592-7606 (2008).

Bradley, M.J., Chivers, P.T. and Baker, N.A. Molecular dynamics simulation of the Escherichia coli NikR protein: Equilibrium conformational fluctuations reveal interdomain allosteric communication pathways. J Mol Biol. 378:1155-1173 (2008).

Tanaka, K.A., Gruber, A., Szlam, F., Bush, L.A., Hanson, S.R. and Di Cera, E. Interaction between thrombin mutant W215A/E217A and direct thrombin I\inhibitor. Blood Coagul Fibrinolysis 19:465-468 (2008).

Papaconstantinou, M.E., Bah, A. and Di Cera, E. Role of the A chain in thrombin function. Cell Mol Life Sci. [Epub ahead of print] (2008)

Di Cera, E. Engineering protease specificity made simple, but not simpler. Nat Chem Biol 4:270-271 (2008).

Page, M.J., Carrell, C.J. and Di Cera, E. Engineering protein allostery: 1.05 A resolution structure and enzymatic properties of a Na(+)-activated trypsin. J Mol Biol. 378:666-672. (2008).

Di Cera, E. Thrombin. Mol Aspects Med. (Epub ahead of print) (2008).

Page, M.J. and Di Cera, E. Serine peptidases: Classification, structure and function. Cell Mol Life Sci. 65:1220-1236 (2008).

Gandhi, P.S., Chen, Z., Mathews, F.S. and Di Cera, E. Structural identification of the pathway of long-range communication in an allosteric enzyme. Proc Natl Acad Sci U S A. 105:1832-1837 (2008).

Berny, M.A., White, T.C., Tucker, E.I., Bush-Pelc, L.A., Di Cera, E., Gruber, A. and McCarty, O.J. Thrombin mutant W215A/E217A acts as a platelet GPIb antagonist. Arterioscler Thromb Vasc Biol. 28:329-334 (2008).

Ellenberger, T. and Tomkinson, A.E. Eukaryotic DNA ligases: Structural and functional insights. Annu Rev Biochem 77:313-338 (2008).

Chen, X., Zhong, S., Zhu, X., Dziegielewska, B., Ellenberger, T., Wilson, G.M., MacKerell, A.D. Jr and Tomkinson, A.E. Rational design of human DNA ligase inhibitors that target cellular DNA replication and repair. Cancer Res. 68:3169-3177 (2008).

Cotner-Gohara, E., Kim, I.K., Tomkinson, A.E. and Ellenberger, T. Two DNA binding and nick recognition modules in human DNA ligase III. J. Biol. Chem. 283:10764-10772 (2008).

Tan, Y.C., Shen, A.Q., Li, Y., Elson, E. and Ma, L. Engineering lipid tubules using nano-sized building blocks: The combinatorial self-assembly of vesicles. Lab on a Chip 8:339-345 (2008).

Isenberg, J.S., Romeo, M.J., Maxhimer, J.B., Smedley, J., Frazier, W.A. and Roberts, D.D. Gene silencing of CD47 and antibody ligation of Thrombospondin-1 enhance ischemic tissue survival in a porcine model: Implications for human disease. Ann Surg. 247:860-868 (2008).

Isenberg, J.S., Romeo, M.J, Yu, C., Yu, C.K., Nghiem, K., Monsale, J., Rick, M.E., Wink, D.A., Frazier, W.A. and Roberts, D.D. Thrombospondin-1 stimulates platelet aggregation by blocking the antithrombotic activity of nitric oxide/cGMP signaling. Blood 111:613-623 (2008).

Isenberg, J.S., Roberts, D.D. and Frazier, W.A. CD47. A new target in cardiovascular therapy. Arterioscler Thromb Vasc Biol. 28:615-621 (2008).

Isenberg, J.S., Pappan, L.K., Romeo, M.J., Abu-Asab, M., Tsokos, M., Wink, D.A., Frazier, W.A. and Roberts, D.D. Blockade of thrombospondin-1-CD47 interactions prevents necrosis of full thickness skin grafts. Ann Surg. 247:180-190 (2008).

Lohman, T.M., Tomko, E.J. and Wu, C.G. Non-hexameric DNA helicases and translocases: Mechanisms and regulation. Nat Rev Mol Cell Biol. 9:391-401 (2008).

Wong, C.J. and Lohman, T.M. Kinetic control of Mg(2+)-dependent melting of duplex DNA ends by Escherichia coli RecBC. J Mol Biol. 378:759-775 (2008).

Nikiforovich, G.V., Marshall, G.R. and Baranski, T.J. Modeling molecular mechanisms of binding of the anaphylatoxin C5a to the C5a receptor. Biochemistry 47:3117-3130 (2008).

Cegelski, L, Marshall, G.R., Eldridge, G.R. and Hultgren, S.J. The biology and future prospects of antivirulence therapies. Nature Rev Microbiol. 6:17-27 (2008).

Che, Y. and Marshall, G.R. Privileged scaffolds targeting reverse-turn and helix recognition. Expert Opin Ther Targets 12:101-114 (2008).

Ye, Y., Liu, M., Kao, J.L. and Marshall, G.R. Design, synthesis, and metal binding of novel pseudo-oligopeptides containing two phosphinic acid groups. Biopolymers 89:72-85 (2008).

Berg-Cross, S., Kao, J., Wu, Y. and Marshall, G.R. c[D-pro-Pro-D-pro-N-Methyl-Ala] Adopts a rigid conformation that serves as a scaffold to mimic reverse-turn. Biopolymers 90:384-393 (2008).

Marshall, G.R., Feng, J.A. and Kuster, D.J. Back to the future: Ribonuclease A. Biopolymers 90:259-277 (2008).

Gandhi, P.S., Chen, Z., Mathews, F.S. and Di Cera, E. Structural identification of the pathway of long-range communication in an allosteric enzyme. Proc Natl Acad Sci U S A. 105:1832-1837 (2008).

Sen, S., Baranski, T.J. and Nikiforovich, G.V. Conformational movement of F251 contributes to the molecular mechanism of constitutive activation in the C5a receptor. Chemical Biology & Drug Design 71:197-204 (2008).

Hagemann, I.S., Miller, D.L., Klco, J.M., Nikiforovich, G.V., and Baranski, T.J. Structure of the complement factor 5a receptor-ligand complex studied by disulfide trapping and molecular modelings. J. Biol. Chem. 283:7763-7775 (2008).

Nikiforovich, G.V., Marshall, G.R. and Baranski, T.J. Modeling molecular mechanisms of binding of the anaphylatoxin C5a to the C5a receptor. Biochemistry 47:3117-3130 (2008).

Macdonald, J.L. and Pike, L.J. Heterogeneity in EGF-binding affinities arises from negative cooperativity in an aggregating system. PNAS 105:112-117 (2008).

PUBLICATIONS

2008 | 2007 | 2006 | 2005 | 2004 | 2003