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

Cerutti, D.S., Baker, N.A. and McCammon, J.A. Solvent reaction field potential inside an uncharged globular protein: A bridge between implicit and explicit solvent sodels? J Chem Phys. 127:155101-155113 (2007).
Dolinsky, T.J., Czodrowski, P., Li, H., Nielson, J.E., Jensen, J.H., Klebe, G. and Baker, N.A. PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res. 35:W522-W525 (2007).
Cheng, Y., Suen, J.K., Zhang, D., Bond, S.D., Zhang, Y., Song, Y., Baker, N.A., Bajaj, C.L., Holst, M.J. and McCammon, J.A. Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations. Biophysical Journal 92:3397-3406 (2007).
Schnieders, M.J., Baker, N.A., Ren, P., and Ponder, J.W. Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum. J. Chem Phys 126:124114-12135 (2007).

Peter M. Burgers

Chilkova, O., Stenlund, P., Isoz, I., Stith, C,M., Grabowski, P., Lundstrom, E.B., Burgers, P.M. and Johansson, E. The eukaryotic leading and lagging strand DNA polymerases are loaded onto primer-ends via separate mechanisms but have comparable processivity in the presence of PCNA. Nucleic Acids Research 35:6588-6597 (2007).
McCulloch, S.D., Wood, A., Garg, P., Burgers, P.M. and Kunkel, T.A. Effects of accessory proteins on the bypass of a cis-syn thymine-thymine dimer by Saccharomyces cerevisiae DNA polymerase eta. Biochemistry 46:8888-8896 (2007).
Wood, A. Garg, P. and Burgers, P.M. A Ubiguitin-binding motif in the translesion DNA polymerase rev1 mediates its essential functional interaction with ubiquitinated PCNA in response to DNA damage. J Biol Chem 282:20256-20263 (2007).
Majka, J. and Burgers, P.M. Clamping the Mec1/ATR checkpoint kinase into action. Cell Cycle 6:1157-1160 (2007).
McElhinny, S.A., Stith, C.M., Burgers, P.M. and Kunkel, T.A. Inefficient proofreading and biased error rates during inaccurate DNA synthesis by a mutant derivative of Saccharomyces cerevisiae DNA polymerase delta. J Biol Chem 282:2324-2332 (2007).

Peter Chivers

Benanti, E.L. and Chivers, P.T. The N-terminal arm of the Helicobacter pylori Ni2+-dependent transcription factor NikR is required for specific DNA-binding. J Biochem 282:20365-20375 (2007).
Leitch, S., Bradley, M.J., Rowe, J.L., Chivers, P.T. and Maroney, M.J. Nickel-specific response in the transcriptional regulator, Escherichia coli NikR. J Am Chem Soc 129:5085-5095 (2007).
Kennedy, D.C., Herbst, R.W., Iwig, J.S., Chivers, P.T. and Maroney, M.J. A dynamic Zn site in Helocobacter pylori HypA: A potential mechnism for metal-specific protein activity. J Am Chem Soc 129:16-17 (2007).
Chivers, P.T. A galvanizing story — Protein stability and zinc homeostasis. J Bacteriol. 189:2953–2954 (2007).

Enrico Di Cera

Gianni S, Ivarsson, Y, Bah A., Bush-Pelc, L.A. and Di Cera E. Mechanism of Na(+) binding to thrombin resolved by ultra-rapid kinetics. Biophys Chem. 131:111-114 (2007).
Di Cera, E. Thrombin as procoagulant and anticoagulant. J Thromb Haemost 5:196-202 (2007).
Bush-Pelc, L.A., Marino, F., Chen, Z., Pineda, A.O. Mathews, F.S. and Di Cera, E. Important role of the Cys-191: Cys-220 disulfide bond in thrombin function and allostery. J Biol Chem 282:27165-27170 (2007).
Page, M.J. and Di Cera E. Is it possible to transform trypsin to thrombin? IUBMB Life 59:413-414 (2007).
Bah, A., Chen, Z., Bush-Pelc, L.A., Mathews, F.S. and Di Cera, E. Crystal structures of murine thrombin in complex with the extracellular fragments of murine protease-activated receptors PAR3 and PAR4. Proc Natl Acad Sci U S A. 104:11603-11608 (2007).
Marino, F., Chen, Z., Ergenekan, C.E., Bush-Pelc, L.A., Mathews, F.S. and Di Cera, E. Structural basis of Na+ activation mimicry in murine thrombin. J Biol Chem. 282:16355-16361 (2007).
Silva-Junior, F.P., Guedes, H.L., Garvey, L.C., Aguiar, A.S., Bourguignon, S.C., Di Cera, E. and Giovanni-De Simone, S. BJ-48, a novel thrombin-like enzyme from the Bothrops jararacussu venom with high selectivity for Arg over Lys in P1: Role of N-glycosylation in thermostability and active site accessibility. Toxicon 50:18-31 (2007).
Greco, M.N. Hawkins, M.J., Powell, E.T., Almond Jr, H.R., Garavilla, L.D., Hall, J., Minor, L.K., Wang, Y., Corcoran, T.W., Di Cera, E., Cantwell, A.M., Savvides, S.N., Damiano, B.P. and Maryanoff, B.E. Discovery of potent, selectirve, orally active, nonpeptide inhibitors of human mast cell chymase. J Med Chem 50:1527-1530 (2007).
Di Cera, E., Page, M.J., Bah, A., Bush-Pelc, L.A. and Garvey, L.C. Thrombin allostery. Phys Chem Chem Phys 9:1291-1306 (2007).
Pineda, A.O., Chen, Z.W., Marino, F., Mathews, F.S., Mosesson, M.W. and Di Cera, E. Crystal structure of thrombin in complex with fibrinogen gamma' peptide. Biophys Chem 125:556-559 (2007).
Gruber, A., Marzec, U.M., Bush, L., Di Cera, E., Fernandez, J.A., Berny, M.A., Tucker, E.L. McCarty, O.J., Griffin, J.H. and Hanson, S.R. Relative antithrombotic and antihemostatic effects of protein C activator versus low molecular weight heparin in primates. Blood 109:3733-3740 (2007).

Tom Ellenberger

Tsodikov, O.V., Ivanov, D., Orelli, B., Staresincic, L, Shoshani, I., Oberman, R., Scharer, O.D., Wagner, G. and Ellenberger, T. Structural basis for the recruitment of ERCC1-XPF to nucleotide excision repair complexes by XPA. EMBO J. 26:4768-4776 (2007).
Aihara, H., Huang, W.M. and Ellenberger, T. An interlocked dimer of the Protelomerase TelK Distorts DNA Structure for the Formation of Hairpin Telemeres. Mol Cell. 27:901-913 (2007).
Ivanov, D., Tsodikov, O.V., Kasanov, J., Ellenberger, T., Wagner, G. and Colins, T. Domain-swapped dimerization of the HIV-1 capsid C-terminal domain. Proc Natl Acad Sci USA 104:4353-4358 (2007).
Wang, X., Kennedy, R., Ray, K., Stuckert, P., Ellenberger, T. and D' Andrea, A.D. Chk1-mediated phosphorylation of FANCE is required for the Fanconi anemia/BRCA pathway. Mol Cell Biol 27:3098-3108 (2007).
Kowal, P., Gurtan, A.M., Stuckert, P., D'Andrea, A.D. and Ellenberger, T. Structural determinants of human FANCF protein that function in the assembly of DNA damage signaling complex. J. Biol Chem 282:2047-2055 (2007).

Elliot Elson

Saffarian, S., Li, Y., Elson, E.L. and Pike, L.J. Oligomerization of the EGF receptor investigated by live cell fluorescence intensity distribution analysis. Biophys J 93:1021-1031 (2007).
Nekouzadeh, A., Pryse, K.M., Elson, E.L. and Genin, G.M. A simplified approach to quasi-linear viscoelastic modeling. J Biomech 40:3070-3078 (2007).

William A. Frazier

Isenberg, J.S., Hyodo, F., Pappan, L.K., Abu-Asab, M., Tsokos, M., Krishna, M.C., Frazier, W.A. and Roberts, D.D. Blocking thrombosopondin-1/CD47 signaling alleviates deleterious effects of aging on tissue responses to ischemia. Arterioscler Thromb Vasc Biol 27:2585-2588 (2007).
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 anti-thrombotic activity of nitric oxide/cGMP signaling. Blood 109:1945-1952 (2007).
Isenberg, J.S., Romeo, M.J., Abu-Asab, M., Tsokos, M., Oldenborg, A., Pappan, L., Wink, D.A., Frazier, W.A. and Roberts, D.D. Increasing survival of ischemic tissue by targeting CD47. Circ. Res.100:712-720. (2007).

Carl Frieden

Frieden, C. Protein aggregation Processes: In search of the mechanism. Protein Science16:2334-2344 (2007).
Li, H. and Frieden, C. Observation of sequential steps in the folding of intestinal fatty acid binding protein using a slow folding mutant and 19F NMR. Proc Natl Acad Sci USA 104:11993-11998 (2007).
Li, H. and Frieden, C. Comparison of C40/82A and P27A C40/82A Barstar mutants using (19)F NMR. Biochemistry 46:4337-4347 (2007).

Roberto Galletto

Galletto, R. and Kowalczykowski, S.C. RecA. Curr Biol 17:R395-397 (2007).

Kathleen B. Hall

Coppins, R.L., Hall, K.B. and Groisman, E.A. The intricate world of riboswitches. Curr Opin Microbiol. 10:176-181 (2007).

Katherine Henzler-Wildman

Henzler-Wildman K.A. and Kern D. Dynamic personalities of proteins. Nature 450:964-972 (2007).
Henzler-Wildman K.A., Lei M., Thai V., Kerns S.J., Karplus M., and Kern D. A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 450:913-916 (2007).
Henzler-Wildman K.A., Thai V., Lei M., Ott M., Wolf-Watz M., Fenn T., Pozharski E., Wilson M.A., Petsko G.A., Karplus M., Hübner C.G., and Kern, D. Intrinsic motions along an enzymatic reaction trajectory. Nature 450:838-844 (2007).

Timothy M. Lohman

Niedziela-Majka, A., Chesnik, M.A., Tomko, E.J. and Lohman, T.M. B\. Stearothermophilus PCRA monomer is a single stranded DNA translocase but not a processive helicase in vitro. J Biol Chem 282:27076-27085 (2007).
Tomko, E.J., Fischer, C.J., Niedziela-Majka, A. and Lohman, T.M. A nonuniform stepping mechanism for E. coli UvrD monomer translocation along single-stranded DNA. Mol Cell 26:335-347 (2007).
Roy, R., Kozlov, A.G., Lohman, T.M. and Ha, T. Dynamic structural rearrangements between DNA binding modes of E. coli SSB protein. J Mol Biol 369:1244-1257 (2007).

Garland R. Marshall

Schweitzer-Stenner, R., Gonzales, W., Feng, J.A. and Marshall, G.R. Conformational manifold of alpha-aminoisobutyric acid (Aib) containing alanine-based tripeptides in aqueous solution explored by vibrational spectroscopy, electronic circular dichroism spectroscopy, and molecular dynamics simulations. J Am Chem Soc. 129:13095-13109 (2007).
Zhang, X., Nikiforovich, G.V. and Marshall, G.R. Conformational templates for rational drug design: Flexibility of cyclo (d-Pro(1)-Ala(2)-Ala(3)-Ala(4)-Ala(5)) in DMSO solution. J Med Chem 50:2921-2925 (2007).
Nikiforovich, G.V., Marshall, G.R. and Achilefu, S. Molecular modeling suggests conformational scaffolds specifically targeting five subtypes of somatostatin receptors. Chem Biol Drug Des 69:163-169. (2007).
Che, Y., Brooks, B.R. and Marshall, G.R. Protein recognition motifs: Design of peptidomimetics of helix surfaces. Biopolymers 86:288-297 (2007).
Nikiforovich, G.V., Taylor, C.M. and Marshall, G.R. Modeling of the complex betweeen transducin and photoactivated rhodopsin, a prototypical G-protein-coupled receptor. Biochemistry 46:4734-4744 (2007).
Taylor, C.M.,Nikiforovich, G.V. and Marshall, G.R. Defining the interface between the C-terminal fragment of alpha-transducin and photoactivated rhodopsin. Biophys J 92:4325-4334 (2007).
Che, Y, Brooks, B.R., Riley, D.P., Reaka, A.J. and Marshall, G.R. Engineering metal complexes of chiral pentaazacrowns as privileged reverse-turn scaffolds. Chem Biol Drug Des 69:99-110 (2007).

F. Scott Mathews

Ma, J.K., Wang, Y., Carrell, C.J., Mathews, F.S. and Davidson, V.L. A single methionine residue dictates the kinetic mechanism of interprotein electron transfer from methylamine dehydrogenase to amicyanin(,). Biochemistry 46:11137-11146 (2007).
Bush-Pelc, L.A., Marino, F., Chen, Z., Pineda, A.O. Mathews, F.S. and Di Cera, E. Important role of the Cys-191: Cys-220 disulfide bond in thrombin function and allostery. J Biol Chem 282:27165-27170 (2007).
Bah, A., Chen, Z., Bush-Pelc, L.A., Mathews, F.S. and Di Cera, E. Crystal structures of murine thrombin in complex with the extracellular fragments of murine protease-activated receptors PAR3 and PAR4. Proc Natl Acad Sci U S A. 104:11603-11608 (2007).
Ma, J.K., Mathews, F.S. and Davidson, V.L. Correlation of rhombic distortion of the type 1 copper site of M98Q amicyanin with increased electron transfer reorganization energy. Biochemistry 46:8561-8568 (2007).
Marino, F., Chen, Z., Ergenekan, C.E., Bush-Pelc, L.A., Mathews, F.S. and Di Cera, E. Structural basis of Na+ activation mimicry in murine thrombin. J Biol Chem. 282:16355-16361 (2007).
Pineda, A.O., Chen, Z.W., Marino, F., Mathews, F.S., Mosesson, M.W. and Di Cera, E. Crystal structure of thrombin in complex with fibrinogen gamma' peptide. Biophys Chem 125:556-559 (2007).

Linda J. Pike

Saffarian, S., Li, Y., Elson, E.L. and Pike, L.J. Oligomerization of the EGF receptor investigated by live cell fluorescence intensity distribution analysis. Biophys J 93:1021-1031 (2007).

Jay W. Ponder

Schnieders, M.J., Baker, N.A., Ren, P., and Ponder, J.W. Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum. J. Chem Phys 126:124114-12135 (2007).
Rasmussen, T.D., Ren, P., Ponder, J.W. and Jensen, F. Force field modeling of conformational energies: Importance of multipole moments and intramolecular polarization. Int J Quantum Chem B 107:1390-1395 (2007).

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.

Cerutti, D.S., Baker, N.A. and McCammon, J.A. Solvent reaction field potential inside an uncharged globular protein: A bridge between implicit and explicit solvent sodels? J Chem Phys. 127:155101-155113 (2007).

Dolinsky, T.J., Czodrowski, P., Li, H., Nielson, J.E., Jensen, J.H., Klebe, G. and Baker, N.A. PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res. 35:W522-W525 (2007).

Cheng, Y., Suen, J.K., Zhang, D., Bond, S.D., Zhang, Y., Song, Y., Baker, N.A., Bajaj, C.L., Holst, M.J. and McCammon, J.A. Finite element analysis of the time-dependent Smoluchowski equation for acetylcholinesterase reaction rate calculations. Biophysical Journal 92:3397-3406 (2007).

Schnieders, M.J., Baker, N.A., Ren, P., and Ponder, J.W. Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum. J. Chem Phys 126:124114-12135 (2007).

McCulloch, S.D., Wood, A., Garg, P., Burgers, P.M. and Kunkel, T.A. Effects of accessory proteins on the bypass of a cis-syn thymine-thymine dimer by Saccharomyces cerevisiae DNA polymerase eta. Biochemistry 46:8888-8896 (2007).

Wood, A. Garg, P. and Burgers, P.M. A Ubiguitin-binding motif in the translesion DNA polymerase rev1 mediates its essential functional interaction with ubiquitinated PCNA in response to DNA damage. J Biol Chem 282:20256-20263 (2007).

Majka, J. and Burgers, P.M. Clamping the Mec1/ATR checkpoint kinase into action. Cell Cycle 6:1157-1160 (2007).

McElhinny, S.A., Stith, C.M., Burgers, P.M. and Kunkel, T.A. Inefficient proofreading and biased error rates during inaccurate DNA synthesis by a mutant derivative of Saccharomyces cerevisiae DNA polymerase delta. J Biol Chem 282:2324-2332 (2007).

Benanti, E.L. and Chivers, P.T. The N-terminal arm of the Helicobacter pylori Ni2+-dependent transcription factor NikR is required for specific DNA-binding. J Biochem 282:20365-20375 (2007).

Leitch, S., Bradley, M.J., Rowe, J.L., Chivers, P.T. and Maroney, M.J. Nickel-specific response in the transcriptional regulator, Escherichia coli NikR. J Am Chem Soc 129:5085-5095 (2007).

Kennedy, D.C., Herbst, R.W., Iwig, J.S., Chivers, P.T. and Maroney, M.J. A dynamic Zn site in Helocobacter pylori HypA: A potential mechnism for metal-specific protein activity. J Am Chem Soc 129:16-17 (2007).

Chivers, P.T. A galvanizing story — Protein stability and zinc homeostasis. J Bacteriol. 189:2953–2954 (2007).

Gianni S, Ivarsson, Y, Bah A., Bush-Pelc, L.A. and Di Cera E. Mechanism of Na(+) binding to thrombin resolved by ultra-rapid kinetics. Biophys Chem. 131:111-114 (2007).

Di Cera, E. Thrombin as procoagulant and anticoagulant. J Thromb Haemost 5:196-202 (2007).

Bush-Pelc, L.A., Marino, F., Chen, Z., Pineda, A.O. Mathews, F.S. and Di Cera, E. Important role of the Cys-191: Cys-220 disulfide bond in thrombin function and allostery. J Biol Chem 282:27165-27170 (2007).

Page, M.J. and Di Cera E. Is it possible to transform trypsin to thrombin? IUBMB Life 59:413-414 (2007).

Bah, A., Chen, Z., Bush-Pelc, L.A., Mathews, F.S. and Di Cera, E. Crystal structures of murine thrombin in complex with the extracellular fragments of murine protease-activated receptors PAR3 and PAR4. Proc Natl Acad Sci U S A. 104:11603-11608 (2007).

Marino, F., Chen, Z., Ergenekan, C.E., Bush-Pelc, L.A., Mathews, F.S. and Di Cera, E. Structural basis of Na+ activation mimicry in murine thrombin. J Biol Chem. 282:16355-16361 (2007).

Di Cera, E., Page, M.J., Bah, A., Bush-Pelc, L.A. and Garvey, L.C. Thrombin allostery. Phys Chem Chem Phys 9:1291-1306 (2007).

Pineda, A.O., Chen, Z.W., Marino, F., Mathews, F.S., Mosesson, M.W. and Di Cera, E. Crystal structure of thrombin in complex with fibrinogen gamma' peptide. Biophys Chem 125:556-559 (2007).

Gruber, A., Marzec, U.M., Bush, L., Di Cera, E., Fernandez, J.A., Berny, M.A., Tucker, E.L. McCarty, O.J., Griffin, J.H. and Hanson, S.R. Relative antithrombotic and antihemostatic effects of protein C activator versus low molecular weight heparin in primates. Blood 109:3733-3740 (2007).

Tsodikov, O.V., Ivanov, D., Orelli, B., Staresincic, L, Shoshani, I., Oberman, R., Scharer, O.D., Wagner, G. and Ellenberger, T. Structural basis for the recruitment of ERCC1-XPF to nucleotide excision repair complexes by XPA. EMBO J. 26:4768-4776 (2007).

Aihara, H., Huang, W.M. and Ellenberger, T. An interlocked dimer of the Protelomerase TelK Distorts DNA Structure for the Formation of Hairpin Telemeres. Mol Cell. 27:901-913 (2007).

Ivanov, D., Tsodikov, O.V., Kasanov, J., Ellenberger, T., Wagner, G. and Colins, T. Domain-swapped dimerization of the HIV-1 capsid C-terminal domain. Proc Natl Acad Sci USA 104:4353-4358 (2007).

Wang, X., Kennedy, R., Ray, K., Stuckert, P., Ellenberger, T. and D' Andrea, A.D. Chk1-mediated phosphorylation of FANCE is required for the Fanconi anemia/BRCA pathway. Mol Cell Biol 27:3098-3108 (2007).

Kowal, P., Gurtan, A.M., Stuckert, P., D'Andrea, A.D. and Ellenberger, T. Structural determinants of human FANCF protein that function in the assembly of DNA damage signaling complex. J. Biol Chem 282:2047-2055 (2007).

Saffarian, S., Li, Y., Elson, E.L. and Pike, L.J. Oligomerization of the EGF receptor investigated by live cell fluorescence intensity distribution analysis. Biophys J 93:1021-1031 (2007).

Nekouzadeh, A., Pryse, K.M., Elson, E.L. and Genin, G.M. A simplified approach to quasi-linear viscoelastic modeling. J Biomech 40:3070-3078 (2007).

Isenberg, J.S., Hyodo, F., Pappan, L.K., Abu-Asab, M., Tsokos, M., Krishna, M.C., Frazier, W.A. and Roberts, D.D. Blocking thrombosopondin-1/CD47 signaling alleviates deleterious effects of aging on tissue responses to ischemia. Arterioscler Thromb Vasc Biol 27:2585-2588 (2007).

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 anti-thrombotic activity of nitric oxide/cGMP signaling. Blood 109:1945-1952 (2007).

Isenberg, J.S., Romeo, M.J., Abu-Asab, M., Tsokos, M., Oldenborg, A., Pappan, L., Wink, D.A., Frazier, W.A. and Roberts, D.D. Increasing survival of ischemic tissue by targeting CD47. Circ. Res.100:712-720. (2007).

Frieden, C. Protein aggregation Processes: In search of the mechanism. Protein Science16:2334-2344 (2007).

Li, H. and Frieden, C. Observation of sequential steps in the folding of intestinal fatty acid binding protein using a slow folding mutant and 19F NMR. Proc Natl Acad Sci USA 104:11993-11998 (2007).

Li, H. and Frieden, C. Comparison of C40/82A and P27A C40/82A Barstar mutants using (19)F NMR. Biochemistry 46:4337-4347 (2007).

Galletto, R. and Kowalczykowski, S.C. RecA. Curr Biol 17:R395-397 (2007).

Coppins, R.L., Hall, K.B. and Groisman, E.A. The intricate world of riboswitches. Curr Opin Microbiol. 10:176-181 (2007).

Henzler-Wildman K.A. and Kern D. Dynamic personalities of proteins. Nature 450:964-972 (2007).

Henzler-Wildman K.A., Lei M., Thai V., Kerns S.J., Karplus M., and Kern D. A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 450:913-916 (2007).

Henzler-Wildman K.A., Thai V., Lei M., Ott M., Wolf-Watz M., Fenn T., Pozharski E., Wilson M.A., Petsko G.A., Karplus M., Hübner C.G., and Kern, D. Intrinsic motions along an enzymatic reaction trajectory. Nature 450:838-844 (2007).

Niedziela-Majka, A., Chesnik, M.A., Tomko, E.J. and Lohman, T.M. B\. Stearothermophilus PCRA monomer is a single stranded DNA translocase but not a processive helicase in vitro. J Biol Chem 282:27076-27085 (2007).

Tomko, E.J., Fischer, C.J., Niedziela-Majka, A. and Lohman, T.M. A nonuniform stepping mechanism for E. coli UvrD monomer translocation along single-stranded DNA. Mol Cell 26:335-347 (2007).

Roy, R., Kozlov, A.G., Lohman, T.M. and Ha, T. Dynamic structural rearrangements between DNA binding modes of E. coli SSB protein. J Mol Biol 369:1244-1257 (2007).

Zhang, X., Nikiforovich, G.V. and Marshall, G.R. Conformational templates for rational drug design: Flexibility of cyclo (d-Pro(1)-Ala(2)-Ala(3)-Ala(4)-Ala(5)) in DMSO solution. J Med Chem 50:2921-2925 (2007).

Nikiforovich, G.V., Marshall, G.R. and Achilefu, S. Molecular modeling suggests conformational scaffolds specifically targeting five subtypes of somatostatin receptors. Chem Biol Drug Des 69:163-169. (2007).

Che, Y., Brooks, B.R. and Marshall, G.R. Protein recognition motifs: Design of peptidomimetics of helix surfaces. Biopolymers 86:288-297 (2007).

Nikiforovich, G.V., Taylor, C.M. and Marshall, G.R. Modeling of the complex betweeen transducin and photoactivated rhodopsin, a prototypical G-protein-coupled receptor. Biochemistry 46:4734-4744 (2007).

Taylor, C.M.,Nikiforovich, G.V. and Marshall, G.R. Defining the interface between the C-terminal fragment of alpha-transducin and photoactivated rhodopsin. Biophys J 92:4325-4334 (2007).

Che, Y, Brooks, B.R., Riley, D.P., Reaka, A.J. and Marshall, G.R. Engineering metal complexes of chiral pentaazacrowns as privileged reverse-turn scaffolds. Chem Biol Drug Des 69:99-110 (2007).

Ma, J.K., Wang, Y., Carrell, C.J., Mathews, F.S. and Davidson, V.L. A single methionine residue dictates the kinetic mechanism of interprotein electron transfer from methylamine dehydrogenase to amicyanin(,). Biochemistry 46:11137-11146 (2007).

Bush-Pelc, L.A., Marino, F., Chen, Z., Pineda, A.O. Mathews, F.S. and Di Cera, E. Important role of the Cys-191: Cys-220 disulfide bond in thrombin function and allostery. J Biol Chem 282:27165-27170 (2007).

Bah, A., Chen, Z., Bush-Pelc, L.A., Mathews, F.S. and Di Cera, E. Crystal structures of murine thrombin in complex with the extracellular fragments of murine protease-activated receptors PAR3 and PAR4. Proc Natl Acad Sci U S A. 104:11603-11608 (2007).

Ma, J.K., Mathews, F.S. and Davidson, V.L. Correlation of rhombic distortion of the type 1 copper site of M98Q amicyanin with increased electron transfer reorganization energy. Biochemistry 46:8561-8568 (2007).

Marino, F., Chen, Z., Ergenekan, C.E., Bush-Pelc, L.A., Mathews, F.S. and Di Cera, E. Structural basis of Na+ activation mimicry in murine thrombin. J Biol Chem. 282:16355-16361 (2007).

Pineda, A.O., Chen, Z.W., Marino, F., Mathews, F.S., Mosesson, M.W. and Di Cera, E. Crystal structure of thrombin in complex with fibrinogen gamma' peptide. Biophys Chem 125:556-559 (2007).

Saffarian, S., Li, Y., Elson, E.L. and Pike, L.J. Oligomerization of the EGF receptor investigated by live cell fluorescence intensity distribution analysis. Biophys J 93:1021-1031 (2007).

Schnieders, M.J., Baker, N.A., Ren, P., and Ponder, J.W. Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum. J. Chem Phys 126:124114-12135 (2007).

Rasmussen, T.D., Ren, P., Ponder, J.W. and Jensen, F. Force field modeling of conformational energies: Importance of multipole moments and intramolecular polarization. Int J Quantum Chem B 107:1390-1395 (2007).

PUBLICATIONS

2008 | 2007 | 2006 | 2005 | 2004 | 2003