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

Ackers, G.K. and Holt, J.M. Asymmetric cooperativity in a symmetric tetramer: Human hemoglobin. J Biol Chem 281:11441-11443 (2006).

Nathan A. Baker

Wong, C.J., Rice, R.L., Baker, N.A., Ju, T. and Lohman, T.M. Probing 3'-ssDNA loop formation in E. coli RecBCD/RecBC-DNA complexes using non-natural DNA: A model for "chi" recognition complexes. J Mol Biol 362:26-43 (2006).
Wagoner, J.A. and Baker, N.A. Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms. PNAS, USA 103:8331-8336 (2006).
Konecny, R., Trylska, J, Tama, F., Zhang, D., Baker, N.A., Brooks, C.L. III and McCammon, J.A. Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids. Biopolymers 82:106-120 (2006).

Peter M. Burgers

Majka, J. Niedziela-Majka, A. and Burgers, P.M.J. The checkpoint clamp activated Mec1 kinase during initiation of the DNA damage checkpoint. Mol Cell 24:891-901 (2006).
Northam, M. R., Garg, P., Baitin, D. M., Burgers, P. M. and Shcherbakova, P. V. A novel function of DNA polymerase zeta regulated by PCNA. Embo J 25:4316-4325 (2006).
Zhong, X., Garg, P., Stith, C. M., McElhinny, S. A., Kissling, G. E., Burgers, P. M. and Kunkel, T. A.The fidelity of DNA synthesis by yeast DNA polymerase zeta alone and with accessory proteins. Nucleic Acids Res 34:4736-4742 (2006).
Fortune, J.M., Stith, C.M., Kissling, G.E., Burgers, P.M. and Kunkel, T.A. RPA and PCNA suppress formation of large deletion errors by yeast DNA polymrease (delta). Nucleic Acids Res 34:4335-4341 (2006).
Majka, J., Binz, S.K., Wold, M.S. and Burgers, P.M. RPA directs loading of the DNA damage checkpoint clamp to 5'-DNA junctions. J Biol Chem 281:27855-27861 (2006).
Bylund, G.O. Majka, J. and Burgers, P.M. Overproduction and purification of RFC-related clamp loaders and PCNA-related clamps from Saccharomyces cerevisiae. Methods in Enzymology 409:1-11 (2006).
Zhuang, Z., Yoder, B.L., Burgers, P.M. and Benkovic, S.J. The structure of a ring-opened proliferating cell nuclear antigen-replication factor C complex revealed by fluorescence energy transfer. PNAS, USA 103:2546-2451 (2006).

Peter T. Chivers

Iwig, J.S., Rowe, J.L. and Chivers, P.T. Nickel homeostasis in Escherichia coli - the rcnR-rcnA efflux pathway and its linkage to NikR function. Molecular Microbiology 62:252-262 (2006).

Enrico Di Cera

Bah, A., Garvey, L.C., Ge, J. and Di Cera, E. Rapid kinetics of Na+ binding to thrombin. J Biol Chem 281:40049-40056 (2006).
Page, M.J. and Di Cera, E. Role of Na+ and K+ in enzyme function. Physiol. Rev. 86: 1049-1092 (2006).
Pineda, A.O., Chen, Z.W., Bah, A., Garvey, L.C., Mathews, F.S. and Di Cera, E. Crystal structure of thrombin in a self-inhibited conformation J Biol Chem 281:32922-32928 (2006).
Page, M.J. and Di Cera, E. Is Na(+) a coagulation factor?.Thromb Haemost 95:920-921 (2006).
Feistritzer, C., Schuepbach, R.A., Mosnier, L.O., Bush, L.A., Di Cera, E., Griffin, J.H. and Riewald, M. Protective signaling by activated protein C is mechanistically linked to protein C activation on endothelial cells. J Biol Chem 281:20077-20084 (2006).
Page, M.J., Bleackley, M.R.,Wong, S., Macgillivray, R.T. and Di Cera, E. Conversion of trypsin into a Na(+)-activated enzyme. Biochemistry 45:2987-2993 (2006).
Carrell, C.J., Bush, L.A., Mathews, F.S. and Di Cera, E. High resolution crystal structures of free thrombin in the presence of K(+) reveal the molecular basis of monovalent cation selectivity and an inactive slow form. Biophys Chem 121:177-184 (2006).
Di Cera, E. A structural perspective on enzymes activated by monovalent cations. J Biol Chem 281:1305-1308 (2006).
Gruber, A., Fernandez, J.A., Bush, L., Marzec, U., Griffin, J.H., Hanson, S.R. and Di Cera, E. Limited generation of activated protein C during infusion of the protein C activator thrombin analog W215A/E217A in primates. J Thromb Haemost 4:392-397 (2006).
Bush, L.A., Nelson, R.W. and Di Cera, E. Murine thrombin lacks Na+ activation but retains high catalytic activity. J Biol Chem 281:7183-7188 (2006).

Tom Ellenberger

Pascal, J.M. and Ellenberger, T. RNA ligase does the AMP shuffle. Nat Struct Mol Biol 13:950-951 (2006).
Pascal, J.M., Tsodikov, O.V., Hura, G.L., Song, W., Cotner, E.A., Classen, S., Tomkinson, A.E., Tainer, J.A. and Ellenberger, T. A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA. Mol Cell 24:279-291 (2006).
Chen, X., Pascal, J., Vijayakumar, S., Wilson, G.M., Ellenberger, T. and Tomkinson, A.E. Human DNA ligases I, III, and IV--Purification and new specific assays for these enzymes. Methods in Enzymology 409:39-52 (2006).
King, D.A., Hall, B.E., Iwamoto, M.A., Win, K.Z., Chang, J.F. and Ellenberger, T. Domain structure and protein interactions of the silent information regulator SIR3 revealed by screening a nested deletion library of protein fragments. J Biol Chem 281:20107-20119 (2006).
Radman-Livaja, M., Biswas, T., Ellenberger, T., Landy, A. and Aihara, H. DNA arms do the legwork to ensure the directionality of lambda site-specific recombination. Curr Opin Struct Biol 16:42-50 (2006).
Tomkinson, A.E., Vijayakumar, S., Pascal, J.M. and Ellenberger, T. DNA ligases: Structure, reaction mechanism and function. Chem Rev 106:687-699 (2006).
Kim, T.W., Brieba, L.G., Ellenberger, T. and Kool, E.T. Functional evidence for a small and rigid active site in a high fidelity DNA polymerase: Probing T7 DNA polymerase with variably sized base pairs. J Biol Chem 281:2289-2295 (2006).

Elliot Elson

Wille, J.J., Elson, E.L. and Okamoto, R.J. Cellular and matrix mechanics of bioartificial tissues during continuous cyclic stretch. Ann Biomed Eng 34:1678-1690 (2006).
Marquez, J.P., Genin, G.M., Pryse, K.M. and Elson, E.L. Cellular and matrix contributions to tissue construct stiffness increase with cellular concentration. Ann Biomed Eng 39:2145-2151 (2006).
Asnes, C.F., Marguez, J.P., Elson, E. and Wakatsuki, T. Reconstitution of Frank-Starling mechanism in engineered heart tissues. Biophys J 91:1811-1810 (2006).
Saffarian, S., Qian, H., Collier, I., Elson, E. and Goldberg, G. Powering a burnt bridges Brownian ratchet: A model for an extracellular motor driven by proteolysis of collagen. Phys Rev E Stat Nonlin Soft Matter Phys.73 (4 Pt 1):041909 (2006).
Remond, M.C., Fee, J.A., Elson, E.L. and Taber, L.A. Myosin-based contraction is not necessary for cardiac c-looping in the chick embryo. Anat Embryol 211:443-454 (2006).

William Frazier

Isenberg, J.S., Ridnour, L.A., Dimitry, J., Frazier, W.A., Wink, D.A. and Roberts, D.D. CD47 is necessary for inhibition of nitric oxide-stimulated vascular cell responses by thrombospondin-1. J Biol Chem 281:26069-26080 (2006)
Hagnerud, S., Manna, P.P., Cella, M., Stenberg, A., Frazier, W.A., Colonna, M. and Oldenborg, P.A. Deficit of CD47 results in a defect of marginal zone dendritic cells, blunted immune response to particulate antigen and impairment of skin dendritic cell migration. J Immunol 176:5772-5778. (2006).

Carl Frieden

Crick, S.L, Jayaraman, M., Frieden, C., Wetzel, R. and Pappu, R.V. Fluorescence correlation spectroscopy shows that monomeric polyglutamine molecules form collapsed structures in aqueous solutions. Proc Natl Acad Sci USA 103:16764-16769 (2006).
Li, H . and Frieden, C. Fluorine-19 NMR studies on the acid state of the intestinal fatty acid binding protein. Biochemistry 45:6272-6278 (2006).
Chattopadhyay, K. and Frieden, C. Steady-state and time-resolved fluorescence studies of the intestinal fatty acid binding protein. Proteins 63:327-335 (2006).

Roberto Galletto

Galletto, R., Amitani, I., Baskin, R.J., Kowalczykowski, S.C. Direct observation of individual RecA filaments assembling on single DNA molecules. Nature 443:875-878 (2006).

Kathleen B. Hall

Clerte, C. and Hall, K.B. Characterization of multimeric complexes formed by the human PTB1 protein on RNA. RNA 12:457-475 (2006).

Timothy M. Lohman

Eggington, J.M., Kozlov, A.G., Cox, M.M. and Lohman, T.M. Polar destabilization of DNA duplexes with single-stranded overhangs by the Deinococcus radiodurans SSB protein. Biochemistry 45:14490-14502 (2006).
Kumaran, S., Kozlov, A. G. and Lohman, T. M. Saccharomyces cerevisiae replication protein A binds to single-stranded DNA in multiple salt-dependent modes. Biochemistry 45:11958-11973 (2006).
Wong, C.J., Rice, R.L., Baker, N.A., Ju, T. and Lohman, T.M. Probing 3'-ssDNA loop formation in E. coli RecBCD/RecBC-DNA complexes using non-natural DNA: A model for "chi" recognition complexes. J Mol Biol 362:26-43 (2006).
Kozlov, A.G. and Lohman, T.M. Effects of monovalent anions on a temperature-dependent heat capacity change for excherichia coli SSB tetramer binding to single-stranded DNA. Biochemistry 45:5190-5205 (2006).
Kuznetsov, S. V., Kozlov, A. G., Lohman, T. M. and Ansari, A. Microsecond dynamics of protein-DNA interactions: Direct observation of the wrapping/unwrapping kinetics of single-stranded DNA around the E.coli SSB tetramer. J Mol Biol 359:55-65 (2006).

Garland R. Marshall

Downs, M.A., Arimoto, R., Marshall, G.R. and Kisselev, O.G. G-protein alpha and beta-gamma subunits interact with conformationally distinct signaling states of rhodopsin. Vision Res 446:4442-4448 (2006).
Marshall, G.R. and Riley, D.P. Design of protein and enzyme mimetics. In Handbook of Theoretical and Computational Nanotechnology. M. Rieth and W. Sommers, eds., American Scientific Publishers, Vol. 1, Chapter 137, pp. 1-37 (2006).
Anderson, M.A., Ogbay, B., Kisselev, O.G., Cistola, D.P. and Marshall, G.R. Alternative binding mode of des-carboxylate analogs of G_talpha(340-350) to photoactivated rhodopsin. Chem Biol Drug Des 68:295-307 (2006).
Hata, M. and Marshall, G.R. Do benzodiazepines really mimic beta-turn structures? J Comp-Aided Mol Des 20:321-331 (2006).
Marshall, G.R. and Taylor, C.M. Introduction to Computer-Assisted Drug Design: CADD - Overview & perspective for the future. In Comprehensive Medicinal Chemistry II, Volume 4. J.B. Taylor and D.J. Triggle, eds. Elsevier, Oxford, England, pp. 13-41 (2006).
Vabenoe, J., Nikiforovich, G.V. and Marshall, G.R. A minimalist 3D pharmacophore model for cyclopentapeptide CXCR4 antagonists. Biopolymers (Peptide Sci) 84:459-471 (2006).
Che, Y. and Marshall, G.R. Impact of proline analogs on amide cis-trans isomerism. Biopolymers 81:392-406 (2006).
Nikiforovich, G.V., Zhang, M., Yang, Q., Jagadeesh, G., Chen, H.C. Hunyady, L., Marshall, G.R. and Catt, K.J. Interactions between conserved residues in transmembrane helices 2 and 7 during angiotensin AT(1) receptor activation. Chem Biol Drug Des 68:239-249 (2006).
Vabenoe, J., Nikiforovich, G.V.. and Marshall, G.R. Insight into the binding mode for cyclopentapeptide antogonists of CXCR4 receptor. Chem Biol Drug Des 67:346-354 (2006).
Nikiforovich, G.V.. and Marshall, G.R. 3D modeling of the activated states of constitutively active mutants of rhodopsin. Biochem Biophys Res Commun 345:430-437 (2006).
Ye, Y., Liu, M., Kao, J.L . and Marshall, G.R. Novel trihydroxamate-containing peptides: Design, synthesis, and metal coordination. Biopolymers 84:472-489 (2006).
Anderson, M.A., Ogbay, B., Arimoto, R., Sha, W., Kisselev, O.G. Cistola, D.P. and Marshall, G.R. Relative strength of cation-pi vs salt bridge interactions: The G_Talpha(340-350) peptide/rhodopsin system. JACS 128:7531-7541 (2006).
Che, Y., Brooks, B.R. and Marshall, G.R. Development of small molecules designed to modulate protein-protein interactions. J Comput Aided Mol Des 20:109-130 (2006).

F. Scott Mathews

Sukumar, N., Chen, Z.W., Ferrari, D., Merli, A., Rossi, G.L., Bellamy, H.D., Chistoserdov, A., Davidson, V.L. and Mathews, F.S. Crystal structure of an electron transfer complex between aromatic amine dehydrogenase and azurin from Alcaligenes faecalis. Biochemistry 45:13500-13510 (2006).
Pineda, A.O., Chen, Z.W., Bah, A., Garvey, L.C., Mathews, F.S. and Di Cera, E. Crystal structure of thrombin in a self-inhibited conformation J Biol Chem 281:32922-32928 (2006).
Hynson, R.M., Mathews, F.S. and Schuman Jorns, M. Identification of a stable flavin-thiolate adduct in heterotetrameric sarcosine oxidase J Mol Biol 362:656-663 (2006).
Ma, J.K., Carrell, C.J., Mathews, F.S. and Davidson, V.L. Site-directed mutagenesis of proline 52 to glycine in amicyanin converts a true electron transfer reaction into one that is conformationally gated. Biochemistry 45:8284-8293 (2006).
Chen, Z.W., Hassan-Abdulah, A., Zhao, G., Jorns, M.S. and Mathews, F.S. Heterotetrameric sarcosine oxidase: Structure of a diflavin metalloenzyme at 1.85 Anstrom resolution. J Mol Biol 360:1000-1018 (2006).
Carrell, C.J., Bush, L.A., Mathews, F.S. and Di Cera, E. High resolution crystal structures of free thrombin in the presence of K(+) reveal the molecular basis of monovalent cation selectivity and an inactive slow form. Biophys Chem 121:177-184 (2006).

Linda J. Pike

Macdonald, J., Li, Z., Su, W. and Pike, L.J. The membrane proximal disulfides of the EGF receptor extracellular domain are required for high affinity binding and signal transduction but do not play a role in localization of the receptor to lipid rafts. Biochim Biophys Acta 1763:870-878 (2006).
Pike, L.J. Rafts defined. J Lipid Res 47:1597-1598 (2006).

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.

Ackers, G.K. and Holt, J.M. Asymmetric cooperativity in a symmetric tetramer: Human hemoglobin. J Biol Chem 281:11441-11443 (2006).

Wong, C.J., Rice, R.L., Baker, N.A., Ju, T. and Lohman, T.M. Probing 3'-ssDNA loop formation in E. coli RecBCD/RecBC-DNA complexes using non-natural DNA: A model for "chi" recognition complexes. J Mol Biol 362:26-43 (2006).

Wagoner, J.A. and Baker, N.A. Assessing implicit models for nonpolar mean solvation forces: The importance of dispersion and volume terms. PNAS, USA 103:8331-8336 (2006).

Konecny, R., Trylska, J, Tama, F., Zhang, D., Baker, N.A., Brooks, C.L. III and McCammon, J.A. Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids. Biopolymers 82:106-120 (2006).

Majka, J. Niedziela-Majka, A. and Burgers, P.M.J. The checkpoint clamp activated Mec1 kinase during initiation of the DNA damage checkpoint. Mol Cell 24:891-901 (2006).

Northam, M. R., Garg, P., Baitin, D. M., Burgers, P. M. and Shcherbakova, P. V. A novel function of DNA polymerase zeta regulated by PCNA. Embo J 25:4316-4325 (2006).

Zhong, X., Garg, P., Stith, C. M., McElhinny, S. A., Kissling, G. E., Burgers, P. M. and Kunkel, T. A.The fidelity of DNA synthesis by yeast DNA polymerase zeta alone and with accessory proteins. Nucleic Acids Res 34:4736-4742 (2006).

Fortune, J.M., Stith, C.M., Kissling, G.E., Burgers, P.M. and Kunkel, T.A. RPA and PCNA suppress formation of large deletion errors by yeast DNA polymrease (delta). Nucleic Acids Res 34:4335-4341 (2006).

Majka, J., Binz, S.K., Wold, M.S. and Burgers, P.M. RPA directs loading of the DNA damage checkpoint clamp to 5'-DNA junctions. J Biol Chem 281:27855-27861 (2006).

Bylund, G.O. Majka, J. and Burgers, P.M. Overproduction and purification of RFC-related clamp loaders and PCNA-related clamps from Saccharomyces cerevisiae. Methods in Enzymology 409:1-11 (2006).

Zhuang, Z., Yoder, B.L., Burgers, P.M. and Benkovic, S.J. The structure of a ring-opened proliferating cell nuclear antigen-replication factor C complex revealed by fluorescence energy transfer. PNAS, USA 103:2546-2451 (2006).

Iwig, J.S., Rowe, J.L. and Chivers, P.T. Nickel homeostasis in Escherichia coli - the rcnR-rcnA efflux pathway and its linkage to NikR function. Molecular Microbiology 62:252-262 (2006).

Bah, A., Garvey, L.C., Ge, J. and Di Cera, E. Rapid kinetics of Na+ binding to thrombin. J Biol Chem 281:40049-40056 (2006).

Page, M.J. and Di Cera, E. Role of Na+ and K+ in enzyme function. Physiol. Rev. 86: 1049-1092 (2006).

Pineda, A.O., Chen, Z.W., Bah, A., Garvey, L.C., Mathews, F.S. and Di Cera, E. Crystal structure of thrombin in a self-inhibited conformation J Biol Chem 281:32922-32928 (2006).

Page, M.J. and Di Cera, E. Is Na(+) a coagulation factor?.Thromb Haemost 95:920-921 (2006).

Feistritzer, C., Schuepbach, R.A., Mosnier, L.O., Bush, L.A., Di Cera, E., Griffin, J.H. and Riewald, M. Protective signaling by activated protein C is mechanistically linked to protein C activation on endothelial cells. J Biol Chem 281:20077-20084 (2006).

Page, M.J., Bleackley, M.R.,Wong, S., Macgillivray, R.T. and Di Cera, E. Conversion of trypsin into a Na(+)-activated enzyme. Biochemistry 45:2987-2993 (2006).

Carrell, C.J., Bush, L.A., Mathews, F.S. and Di Cera, E. High resolution crystal structures of free thrombin in the presence of K(+) reveal the molecular basis of monovalent cation selectivity and an inactive slow form. Biophys Chem 121:177-184 (2006).

Di Cera, E. A structural perspective on enzymes activated by monovalent cations. J Biol Chem 281:1305-1308 (2006).

Gruber, A., Fernandez, J.A., Bush, L., Marzec, U., Griffin, J.H., Hanson, S.R. and Di Cera, E. Limited generation of activated protein C during infusion of the protein C activator thrombin analog W215A/E217A in primates. J Thromb Haemost 4:392-397 (2006).

Bush, L.A., Nelson, R.W. and Di Cera, E. Murine thrombin lacks Na+ activation but retains high catalytic activity. J Biol Chem 281:7183-7188 (2006).

Pascal, J.M. and Ellenberger, T. RNA ligase does the AMP shuffle. Nat Struct Mol Biol 13:950-951 (2006).

Pascal, J.M., Tsodikov, O.V., Hura, G.L., Song, W., Cotner, E.A., Classen, S., Tomkinson, A.E., Tainer, J.A. and Ellenberger, T. A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA. Mol Cell 24:279-291 (2006).

Chen, X., Pascal, J., Vijayakumar, S., Wilson, G.M., Ellenberger, T. and Tomkinson, A.E. Human DNA ligases I, III, and IV--Purification and new specific assays for these enzymes. Methods in Enzymology 409:39-52 (2006).

King, D.A., Hall, B.E., Iwamoto, M.A., Win, K.Z., Chang, J.F. and Ellenberger, T. Domain structure and protein interactions of the silent information regulator SIR3 revealed by screening a nested deletion library of protein fragments. J Biol Chem 281:20107-20119 (2006).

Radman-Livaja, M., Biswas, T., Ellenberger, T., Landy, A. and Aihara, H. DNA arms do the legwork to ensure the directionality of lambda site-specific recombination. Curr Opin Struct Biol 16:42-50 (2006).

Tomkinson, A.E., Vijayakumar, S., Pascal, J.M. and Ellenberger, T. DNA ligases: Structure, reaction mechanism and function. Chem Rev 106:687-699 (2006).

Kim, T.W., Brieba, L.G., Ellenberger, T. and Kool, E.T. Functional evidence for a small and rigid active site in a high fidelity DNA polymerase: Probing T7 DNA polymerase with variably sized base pairs. J Biol Chem 281:2289-2295 (2006).

Wille, J.J., Elson, E.L. and Okamoto, R.J. Cellular and matrix mechanics of bioartificial tissues during continuous cyclic stretch. Ann Biomed Eng 34:1678-1690 (2006).

Marquez, J.P., Genin, G.M., Pryse, K.M. and Elson, E.L. Cellular and matrix contributions to tissue construct stiffness increase with cellular concentration. Ann Biomed Eng 39:2145-2151 (2006).

Asnes, C.F., Marguez, J.P., Elson, E. and Wakatsuki, T. Reconstitution of Frank-Starling mechanism in engineered heart tissues. Biophys J 91:1811-1810 (2006).

Saffarian, S., Qian, H., Collier, I., Elson, E. and Goldberg, G. Powering a burnt bridges Brownian ratchet: A model for an extracellular motor driven by proteolysis of collagen. Phys Rev E Stat Nonlin Soft Matter Phys.73 (4 Pt 1):041909 (2006).

Remond, M.C., Fee, J.A., Elson, E.L. and Taber, L.A. Myosin-based contraction is not necessary for cardiac c-looping in the chick embryo. Anat Embryol 211:443-454 (2006).

Isenberg, J.S., Ridnour, L.A., Dimitry, J., Frazier, W.A., Wink, D.A. and Roberts, D.D. CD47 is necessary for inhibition of nitric oxide-stimulated vascular cell responses by thrombospondin-1. J Biol Chem 281:26069-26080 (2006)

Hagnerud, S., Manna, P.P., Cella, M., Stenberg, A., Frazier, W.A., Colonna, M. and Oldenborg, P.A. Deficit of CD47 results in a defect of marginal zone dendritic cells, blunted immune response to particulate antigen and impairment of skin dendritic cell migration. J Immunol 176:5772-5778. (2006).

Crick, S.L, Jayaraman, M., Frieden, C., Wetzel, R. and Pappu, R.V. Fluorescence correlation spectroscopy shows that monomeric polyglutamine molecules form collapsed structures in aqueous solutions. Proc Natl Acad Sci USA 103:16764-16769 (2006).

Li, H . and Frieden, C. Fluorine-19 NMR studies on the acid state of the intestinal fatty acid binding protein. Biochemistry 45:6272-6278 (2006).

Chattopadhyay, K. and Frieden, C. Steady-state and time-resolved fluorescence studies of the intestinal fatty acid binding protein. Proteins 63:327-335 (2006).

Galletto, R., Amitani, I., Baskin, R.J., Kowalczykowski, S.C. Direct observation of individual RecA filaments assembling on single DNA molecules. Nature 443:875-878 (2006).

Clerte, C. and Hall, K.B. Characterization of multimeric complexes formed by the human PTB1 protein on RNA. RNA 12:457-475 (2006).

Eggington, J.M., Kozlov, A.G., Cox, M.M. and Lohman, T.M. Polar destabilization of DNA duplexes with single-stranded overhangs by the Deinococcus radiodurans SSB protein. Biochemistry 45:14490-14502 (2006).

Kumaran, S., Kozlov, A. G. and Lohman, T. M. Saccharomyces cerevisiae replication protein A binds to single-stranded DNA in multiple salt-dependent modes. Biochemistry 45:11958-11973 (2006).

Wong, C.J., Rice, R.L., Baker, N.A., Ju, T. and Lohman, T.M. Probing 3'-ssDNA loop formation in E. coli RecBCD/RecBC-DNA complexes using non-natural DNA: A model for "chi" recognition complexes. J Mol Biol 362:26-43 (2006).

Kozlov, A.G. and Lohman, T.M. Effects of monovalent anions on a temperature-dependent heat capacity change for excherichia coli SSB tetramer binding to single-stranded DNA. Biochemistry 45:5190-5205 (2006).

Kuznetsov, S. V., Kozlov, A. G., Lohman, T. M. and Ansari, A. Microsecond dynamics of protein-DNA interactions: Direct observation of the wrapping/unwrapping kinetics of single-stranded DNA around the E.coli SSB tetramer. J Mol Biol 359:55-65 (2006).

Downs, M.A., Arimoto, R., Marshall, G.R. and Kisselev, O.G. G-protein alpha and beta-gamma subunits interact with conformationally distinct signaling states of rhodopsin. Vision Res 446:4442-4448 (2006).

Marshall, G.R. and Riley, D.P. Design of protein and enzyme mimetics. In Handbook of Theoretical and Computational Nanotechnology. M. Rieth and W. Sommers, eds., American Scientific Publishers, Vol. 1, Chapter 137, pp. 1-37 (2006).

Anderson, M.A., Ogbay, B., Kisselev, O.G., Cistola, D.P. and Marshall, G.R. Alternative binding mode of des-carboxylate analogs of Gtalpha(340-350) to photoactivated rhodopsin. Chem Biol Drug Des 68:295-307 (2006).

Hata, M. and Marshall, G.R. Do benzodiazepines really mimic beta-turn structures? J Comp-Aided Mol Des 20:321-331 (2006).

Marshall, G.R. and Taylor, C.M. Introduction to Computer-Assisted Drug Design: CADD - Overview & perspective for the future. In Comprehensive Medicinal Chemistry II, Volume 4. J.B. Taylor and D.J. Triggle, eds. Elsevier, Oxford, England, pp. 13-41 (2006).

Vabenoe, J., Nikiforovich, G.V. and Marshall, G.R. A minimalist 3D pharmacophore model for cyclopentapeptide CXCR4 antagonists. Biopolymers (Peptide Sci) 84:459-471 (2006).

Che, Y. and Marshall, G.R. Impact of proline analogs on amide cis-trans isomerism. Biopolymers 81:392-406 (2006).

Nikiforovich, G.V., Zhang, M., Yang, Q., Jagadeesh, G., Chen, H.C. Hunyady, L., Marshall, G.R. and Catt, K.J. Interactions between conserved residues in transmembrane helices 2 and 7 during angiotensin AT(1) receptor activation. Chem Biol Drug Des 68:239-249 (2006).

Vabenoe, J., Nikiforovich, G.V.. and Marshall, G.R. Insight into the binding mode for cyclopentapeptide antogonists of CXCR4 receptor. Chem Biol Drug Des 67:346-354 (2006).

Nikiforovich, G.V.. and Marshall, G.R. 3D modeling of the activated states of constitutively active mutants of rhodopsin. Biochem Biophys Res Commun 345:430-437 (2006).

Ye, Y., Liu, M., Kao, J.L . and Marshall, G.R. Novel trihydroxamate-containing peptides: Design, synthesis, and metal coordination. Biopolymers 84:472-489 (2006).

Anderson, M.A., Ogbay, B., Arimoto, R., Sha, W., Kisselev, O.G. Cistola, D.P. and Marshall, G.R. Relative strength of cation-pi vs salt bridge interactions: The GTalpha(340-350) peptide/rhodopsin system. JACS 128:7531-7541 (2006).

Che, Y., Brooks, B.R. and Marshall, G.R. Development of small molecules designed to modulate protein-protein interactions. J Comput Aided Mol Des 20:109-130 (2006).

Sukumar, N., Chen, Z.W., Ferrari, D., Merli, A., Rossi, G.L., Bellamy, H.D., Chistoserdov, A., Davidson, V.L. and Mathews, F.S. Crystal structure of an electron transfer complex between aromatic amine dehydrogenase and azurin from Alcaligenes faecalis. Biochemistry 45:13500-13510 (2006).

Pineda, A.O., Chen, Z.W., Bah, A., Garvey, L.C., Mathews, F.S. and Di Cera, E. Crystal structure of thrombin in a self-inhibited conformation J Biol Chem 281:32922-32928 (2006).

Hynson, R.M., Mathews, F.S. and Schuman Jorns, M. Identification of a stable flavin-thiolate adduct in heterotetrameric sarcosine oxidase J Mol Biol 362:656-663 (2006).

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Chen, Z.W., Hassan-Abdulah, A., Zhao, G., Jorns, M.S. and Mathews, F.S. Heterotetrameric sarcosine oxidase: Structure of a diflavin metalloenzyme at 1.85 Anstrom resolution. J Mol Biol 360:1000-1018 (2006).

Carrell, C.J., Bush, L.A., Mathews, F.S. and Di Cera, E. High resolution crystal structures of free thrombin in the presence of K(+) reveal the molecular basis of monovalent cation selectivity and an inactive slow form. Biophys Chem 121:177-184 (2006).

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