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.

Nathan A. Baker

Song, Y., Guallar, V. and Baker, N.A. Molecular dynamics simulations of salicylate effects on the micro- and mesoscopic properties of a dipalmitoylphosphatidylcholiine bilayer. Biochemistry 44:13425-13438 (2005).
Zhang, D., Suen, J., Zhang, Y., Song, Y., Radic, Z., Taylor, P., Holst, M.J., Bajaj, C., Baker, N.A. and McCammon, J.A. Tetrameric mouse acetylcholinesterase: Continuum diffusion rate calculations by solving the steady-state smoluchowski equation using finite element methods. Biophys J 88:1659-1665 (2005).
Baker, N.A. Improving implicit solvent simulations: A Poisson-centric view. Curr Op Struc Biology 15:137-143 (2005).

Peter M. Burgers

Garg P. and Burgers, P.M. Ubiquitinated proliferating cell nuclear antigen activates translesion DNA polymerases {eta} and REV1. Proc Natl Acad Sci USA 102:18361-18366 (2005).
Majka, J. and Burgers, P.M. Function of Rad17/Mec3/Ddc1 and its partial complexes in the DNA damage checkpoint. DNA Repair 4:1189-1194 (2005).
Bylund, G.O. and Burgers, P.M. Replication protein A-directed unloading of PCNA by the Ctf18 cohesion establishment complex. Mol Cell Biol 25:5445-5455 (2005).
Garg, P., Stith, C.M., Majka, J. and Burgers, P.M. Proliferating cell nuclear antigen promotes translesion synthesis by DNA polymerase {zeta}. J Biol Chem 280:23446-23450 (2005).
Franco, A.A., Lam, W.M., Burgers, P.M. and Kaufman, P.D. Histone deposition protein Asf1 maintains DNA replisome integrity and interacts with replication factor C. Genes & Development 19:1365-1375 (2005).
Garg, P. and Burgers, P.M. DNA polymerases that propagate the eukaryotic DNA replication fork. Crit Rev Biochem & Mol Biol 40:115-128 (2005).
Jin, Y.H., Garg, P., Stith, C.M., Al-Refai, H., Sterling, J.F., Murray, L.J., Kunkel, T.A., Resnick, M.A., Burgers, P.M. and Gordenin, D.A. The multiple biological roles of the 3'-->5' exonuclease of Saccharomyces cerevisiae DNA polymerase delta require switching between the polymerase and exonuclease domains. Mol Cell Biol 25:461-471 (2005).
Garg, P. and Burgers, P.M. How the cell deals with DNA nicks. Cell Cycle 4:221-224 (2005).

Peter T. Chivers

Rowe, J.L., Starnes, G.L. and Chivers, P.T. Complex transcriptional control links NikABCDE-dependent nickel transport with hydrogenase expression in Escheria coli. J Bacteriol 187:6317-6323 (2005).
Chivers, P. T. and Tahirov, T. H. Structure of Pyrococcus horikoshii NikR: nickel sensing and implications for the regulation of DNA recognition. J. Mol. Biol. 348, 597-607 (2005).

Enrico Di Cera

Page, M.J., Macgillvray, R.T. and Di Cera, E. Determinants of specificity in coagulation proteases. J Thromb Haemost 3:2401-2408 (2005).
Papaconstantinou, M.E., Carrell, C.J., Pineda, A.O., Bobofchak, K.M., Mathews, F.S., Flordellis, C.S., Maragoudakis, M.E., Tsopanoglou, N.E. and Di Cera, E. Thrombin functions through its RGD sequence in a non-canonical conformation. J Biol Chem 280:29393-29396 (2005).
Seibenlist, K.R., Mosesson, M.W., Hernandez, I., Bush, L.A., Di Cera, E., Shainoff, J.R., Diorio, J.P. and Stojanovic, L. Studies on the basis for the properties of fibrin produced from fibriongen containing {gamma}' chains. Blood (Epub)doi: 10.1182/blood-01-0240 (2005).
Mengwasser, K.E., Bush, L.A., Shih, P., Cantwell, A.M. and Di Cera, E. Hirudin binding reveals key determinants of thrombin allostery. J Biol Chem 280:26997-27003 (2005).
Bobofchak, K.M., Pineda, A.O., Mathews, F.S. and Di Cera, E. Energetic and structural consequences of perturbing Gly-193 in the oxyanion hole of serine proteases. J Biol Chem 280:25644-25650 (2005).
de Garavilla, L., Greco, M.N., Sukumar, N., Chen, Z.W., Pineda, A.O., Mathews, F.S., Di Cera, E., Giardino, E.C., Wells, G.I., Haertlein, B.J., Kauffman, J.A., Corcoran, T.W., Derian, C.K., Eckardt, A.J. and Damiano, B.P. A novel, potent dual inhibitor of the leukocyte protease catepsin G and chymase: Molecular mechanism and anti-inflammatory activity in vivo. J Biol Chem. 280:18001-18007 (2005).
Xu, H., Bush, L.A., Pineda, A.O., Caccia, S. and Di Cera, E. Thrombomodulin changes the molecular surface of interaction and the rate of complex formation between thrombin and protein C. J Biol Chem 280:7956-7961 (2005).

Tom Ellenberger

Brieba, L.G., Kokoska, R.J., Bebenek, K., Kunkel, T.A. and Ellenberger, T. A lysine residue in the fingers subdomain of t7 DNA polymerase modulates the miscoding potential of 8-oxo-7,8-dihydroguanosine. Structure (Camb) 13:1653-1659 (2005).
Cherepanov, P., Ambrosio, A.L., Rahman, S., Ellenberger, T. and Engelman, A. Structural basis for the recognition between HIV-1 integrase and transcriptional coactivator p75. PNAS 102:17308-17313 (2005).

Elliot L. Elson

Latacha, K.S., Remond, M.C., Ramasubramanian, A., Chen, A.Y., Elson, E.L. and Tabor, L.A. Role of actin polymerization in bending of the early heart tube. Dev Dynamics 233:1272-1286 (2005).
Marquez, J.P., Genin, G.M., Zahalak, G.I. and Elson, E.L. Thin bio-artificial tissues in plane stress: The relationship between cell and tissue strain, and an improved constitutive model. Biophys J 88:765-777 (2005).
Marquez, J.P., Genin, G.M., Zahalak, G.I. and Elson, E.L. The relationship between cell and tissue strain in three-dimensional bio-artificial tissues. Biophys J 88:778-789 (2005).
Chattopadhyay, K., Saffarian, S., Elson, E.L. and Frieden, C. Measuring unfolding of proteins in the presence of denaturant using fluorescence correlation spectroscopy. Biophys J 88:1413-1422 (2005).
Chattopadhyay, K., Elson, E.L. and Frieden, C. The kinetics of conformational fluctuations in an unfolded protein measured by fluorescence methods. PNAS 102:2385-2389 (2005).

William A. Frazier

Manna, P.P., Dimitry, J., Oldenborg, P.A. and Frazier, W.A. CD47 augments Fas/CD95-mediated apoptosis. J Biol Chem 280:29637-29644 (2005).
Isenberg, J.S., Calzada, M.J., Zhou, L., Guo, N., Lawler, J., Wang, X.Q., Frazier, W.A. and Roberts, D.D. Endogenous thrombospondin-1 is not necessary for proliferation but is permissive for vascular smooth muscle cell responses to platelet-derived growth factor. Matrix Biology 24:110-123 (2005).
Olsson, M. Bruhns, P., Frazier, W.A., Ravetch, J.V. and Oldenborg, P.A. Platelet homeostasis is regulated by platelet expression of CD47 under normal conditions and in passive immune thrombocytopenia. Blood 105:3577-3582 (2005).

Carl Frieden

Justice, S. S., Hunstad, D. A., Harper, J. R., Duguay, A. R., Pinkner, J. S., Bann, J., Frieden, C., Silhavy, T. J. and Hultgren, S. J. Periplasmic peptidyl prolyl cis-trans isomerases are not essential for viability, but SurA is required for pilus biogenesis in Escherichia coli. J Bacteriol 187:7680-7686 (2005).
Li, H. and Frieden, C. Phenylalanine side chain behavior of the intestinal fatty acid binding protein: The effect of urea on backbone and side chain stability. J Biol Chem 280, 38556-38561 (2005).
Shu, Q. and Frieden, C. Relation of enzyme activity of local/global stability of murine adenosine deaminase: 19F NMR studies. J Mol Biol 345:599-610 (2005).
Chattopadhyay, K., Elson, E.L., Frieden, C. The kinetics of conformational fluctuations in an unfolded protein measured by fluorescence methods. PNAS 102:2385-2389 (2005).
Chattopadhyay, K., Saffarian, S., Elson, E.L. and Frieden, C. Measuring unfolding of proteins in the presence of denaturant using fluorescence correlation spectroscopy. Biophys J 88:1413-1422 (2005).
Li, H. and Frieden, C. NMR studies of 4-(19)f-phenylalanine-labeled intestinal fatty acid binding protein: Evidence of conformational heterogeneity in the native state. Biochem 44:2369-2377 (2005).

Roberto Galletto

Galletto, R., Jezewska, M.J., Bujalowski, W. Kinetic mechanism of rat polymerase ß - dsDNA interactions. fluorescence stopped-flow analysis of the cooperative ligand binding to a two-site one-dimensional lattice. Biochemistry 44:1251-1267 (2005).
Galletto, R., Jezewska, M.J., Maillard, R., Bujalowski, W. The nucleotide-binding site of the Escherichia coli DnaC protein. Molecular topography of DnaC protein - nucleotide cofactor complexes. Cell Biochemistry and Biophysics 43:331-354 (2005).
Galletto, R., Jezewska, M.J., Bujalowski, W. Kinetics of allosteric conformational transition of a macromolecule prior to ligand binding. Analysis of stopped-flow kinetic experiments. Cell Biochemistry and Biophysics 42:121-144 (2005)

Kathleen B. Hall

Showalter, S.A. and Hall, K.B. Isotropic reorientational eigenmode dynamics complements NMR relaxation measurements for RNA. Methods in Enzymology 394:465-480 (2005).

Linda C. Kurz

Kurz, L.C., Fite, B., Jean, J., Park, J., Erpelding, T. and Callis, P. Photophysics of tryptophan fluorescence: Link with the catalytic strategy of the citrate synthase from Thermoplasma acidophilum. Biochem 44:1394-1413 (2005).

Timothy M. Lohman

Myong, S., Rasnik, I., Joo, C., Lohman, T. M. and Ha, T. Repetitive shuttling of a motor protein on DNA. Nature 437:1321-1325 (2005).
Wong, J. C., Lucius, A. L. and Lohman, T. M. Energetics of DNA End Binding by E.coli RecBC and RecBCD Helicases Indicate Loop Formation in the 3'-Single-stranded DNA Tail. J Mol Biol 352:765-782 (2005).
Brendza, K.M., Cheng, W., Fischer, C.J., Chesnick, M.A., Niedziela-Majka, A. and Lohman, T.M. Autoinhibition of Escherichia coli Rep monomer helicase activity by its 2B subdomain. PNAS 102:102:10076-10081 (2005).

John E. Majors

Morgan, J.C., Majors, J.E. and Galileo, D.S. Distinct and opposite roles for SH2 and SH3 domains of v-src in embryo survival and hemangiosarcoma formation. Clin Exp Metastasis 22:167-175 (2005).

Garland R. Marshall

Marshall, G.R. and Vakser, I.A. Protein-protein docking methods. In Proteomics and Protein-Protein Interactions: Biology, Chemistry, Bioinformatics and Drug Design. G. Waksman, ed. Springer, NY pp. 115-145(2005).
Marshall, G.R. Introduction to Chemoinformatics in Drug Discovery - a Persona View. In Cheminformatics in Drug Discover, Vol 23. T.I. Oprea, ed. Methods and Principles in Medicinal Chemistry. Wiley-VCH Verlag, Weinheim, Germany pp. 1-22 (2005).
Anderson, L.L., Marshall, G.R. and Baranski, T.J. Using expressed protein ligation to study protein interactions: Semi-synthesis of the G-protein alpha subunit. Protein Peptide Lett. 12:783-787(2005).
Anderson, L.L., Marshall, G.R., Crocker, E., Smith, S.O. and Baranski, T.J. Motion of carboxyl terminus of Ga is restricted upon G-protein activation: A solution NMR study using semi-synthetic Ga subunits J Biol Chem 260:31019-31026 (2005).
Kuster, D.J. and Marshall, G.R. Validated ligand mapping of ACE active site. J Comp-Aided Drug Des 19:609-615 (2005).
Nikiforovich, G.V. and Marshall, G.R. Modeling conformational changes of the flexible loops in the dark-adapted and activated states of rhodopsin. A prototypical G-protein-coupled receptor. Biophysics J 89:3780-3789 (2005).
Nikiforovich, G.V. Mihalik, B., Catt, K.J. and Marshall, G.R. Molecular mechanisms of constitutive activity: Mutations at position 111 of the angiotensin AT₁ receptor. J Peptide Res 66:236-248 (2005).

F. Scott Mathews

Chen, Z.W., Zhao, G., Martinovic, S., Jorns, M.S. and Mathews, F.S. Structure of the sodium borohydride-reduced N-(cyclopropyl)glycine adduct of the flavoenzyme monomeric sarcosine oxidase. Biochemistry 44:15111-15450 (2005).
Papaconstantinou, M.E., Carrell, C.J., Pineda, A.O., Bobofchak, K.M., Mathews, F.S., Flordellis, C.S., Maragoudakis, M.E., Tsopanoglou, N.E. and Di Cera, E. Thrombin functions through its RGD sequence in a non-canonical conformation. J Biol Chem 280:29393-29396 (2005).
Toyama, H., Chen, Z.W., Fukumoto, M., Adachi, O., Adachi, O., Matsushita, K. and Mathews, F.S. Molecualr cloning and structural analysis of quinohemoprotein alcohol dehydrogenase ADH-IIG from Pseudomonas putida HK5 J Mol Biol 352:91-104 (2005).
Hassan-Abdallah, A., Zhao, G. Eschenbrenner, M., Chen, Z.W., Mathews, F.S. and Jorns, M.S. Cloning, expression and crystallization of heterotetrameric sarcosine oxidase from Pseudomonas maltophilia. Protein Expression and Purification 43:33-43 (2005).
Bobofchak, K.M., Pineda, A.O., Mathews, F.S. and Di Cera, E. Energetic and structural consequences of perturbing Gly-193 in the oxyanion hold of serine proteases. J Biol Chem 280:25644-25650 (2005).
Cunane, L.M., Barton, J.D., Chen, Z.W., Le, K.H., Amar, D., Lederer, F. and Mathews, F.S. Crystal structure analysis of recombinant rat kidney long chain hydroxy acid oxidase. Biochem 44:1521-1531 (2005).
Sun, D., Li, X. Mathews, F.S. and Davidson, V.L. Site-directed mutagenesis of proline 94 to alanine in amicyanin converts a true electrion transfer reaction into one that is kinetically coupled. Biochem. 44:7200-7206 (2005).
de Garavilla, L., Greco, M.N., Sukumar, N., Chen, Z.W., Pineda, A.O., Mathews, F.S., Di Cera, E., Giardino, E.C., Wells, G.I., Haertlein, B.J., Kauffman, J.A., Corcoran, T.W., Derian, C.K., Eckardt, A.J. and Damiano, B.P. A novel, potent dual inhibitor of the leukocyte protease catepsin G and chymase: Molecular mechanism and anti-inflammatory activity in vivo. J Biol Chem. 280:18001-18007 (2005).
Cunane, L.M., Chen, Z.W., McIntire, W.S. and Mathews, F.S. p-Cresol methylhydroxylase: Alteration of the structure of the flavoprotein subunit upon its binding to the cytochrome subunit. Biochem 44:2963-2973 (2005).
Sukumar, N., Langan, P., Mathews, F.S., Jones, L.H., Thiyagarajan, P., Schoenborn, B.P. and Davidson, V.L. A preliminary time-of-flight neutron diffraction study on amicyanin from Paracoccus denitrificans. Acta Crystallographica Sec. D-Biological Crystallography 61:640-642 (2005).

Linda J. Pike

Pike, L.J. Growth factor receptors, lipid rafts and caveolae: An evolving story. Biochim Biophys Acta 1746:260-273 (2005).
Macdonald, J.L. and Pike, L.J. A simplified method for the preparation of detergent-free lipid rafts. J Lipid Research 46:1061-1067 (2005).
Pike, L.J., Han, X. and Gross, R.W. EGFR are localized to lipid rafts that contain a balance of inner and outer leaflet lipids: A shotgun lipidomics study. J Biol Chem 280:26796-26804 (2005).

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.

Song, Y., Guallar, V. and Baker, N.A. Molecular dynamics simulations of salicylate effects on the micro- and mesoscopic properties of a dipalmitoylphosphatidylcholiine bilayer. Biochemistry 44:13425-13438 (2005).

Baker, N.A. Improving implicit solvent simulations: A Poisson-centric view. Curr Op Struc Biology 15:137-143 (2005).

Garg P. and Burgers, P.M. Ubiquitinated proliferating cell nuclear antigen activates translesion DNA polymerases {eta} and REV1. Proc Natl Acad Sci USA 102:18361-18366 (2005).

Bylund, G.O. and Burgers, P.M. Replication protein A-directed unloading of PCNA by the Ctf18 cohesion establishment complex. Mol Cell Biol 25:5445-5455 (2005).

Garg, P., Stith, C.M., Majka, J. and Burgers, P.M. Proliferating cell nuclear antigen promotes translesion synthesis by DNA polymerase {zeta}. J Biol Chem 280:23446-23450 (2005).

Franco, A.A., Lam, W.M., Burgers, P.M. and Kaufman, P.D. Histone deposition protein Asf1 maintains DNA replisome integrity and interacts with replication factor C. Genes & Development 19:1365-1375 (2005).

Garg, P. and Burgers, P.M. DNA polymerases that propagate the eukaryotic DNA replication fork. Crit Rev Biochem & Mol Biol 40:115-128 (2005).

Garg, P. and Burgers, P.M. How the cell deals with DNA nicks. Cell Cycle 4:221-224 (2005).

Rowe, J.L., Starnes, G.L. and Chivers, P.T. Complex transcriptional control links NikABCDE-dependent nickel transport with hydrogenase expression in Escheria coli. J Bacteriol 187:6317-6323 (2005).

Chivers, P. T. and Tahirov, T. H. Structure of Pyrococcus horikoshii NikR: nickel sensing and implications for the regulation of DNA recognition. J. Mol. Biol. 348, 597-607 (2005).

Page, M.J., Macgillvray, R.T. and Di Cera, E. Determinants of specificity in coagulation proteases. J Thromb Haemost 3:2401-2408 (2005).

Papaconstantinou, M.E., Carrell, C.J., Pineda, A.O., Bobofchak, K.M., Mathews, F.S., Flordellis, C.S., Maragoudakis, M.E., Tsopanoglou, N.E. and Di Cera, E. Thrombin functions through its RGD sequence in a non-canonical conformation. J Biol Chem 280:29393-29396 (2005).

Seibenlist, K.R., Mosesson, M.W., Hernandez, I., Bush, L.A., Di Cera, E., Shainoff, J.R., Diorio, J.P. and Stojanovic, L. Studies on the basis for the properties of fibrin produced from fibriongen containing {gamma}' chains. Blood (Epub)doi: 10.1182/blood-01-0240 (2005).

Mengwasser, K.E., Bush, L.A., Shih, P., Cantwell, A.M. and Di Cera, E. Hirudin binding reveals key determinants of thrombin allostery. J Biol Chem 280:26997-27003 (2005).

Bobofchak, K.M., Pineda, A.O., Mathews, F.S. and Di Cera, E. Energetic and structural consequences of perturbing Gly-193 in the oxyanion hole of serine proteases. J Biol Chem 280:25644-25650 (2005).

Xu, H., Bush, L.A., Pineda, A.O., Caccia, S. and Di Cera, E. Thrombomodulin changes the molecular surface of interaction and the rate of complex formation between thrombin and protein C. J Biol Chem 280:7956-7961 (2005).

Brieba, L.G., Kokoska, R.J., Bebenek, K., Kunkel, T.A. and Ellenberger, T. A lysine residue in the fingers subdomain of t7 DNA polymerase modulates the miscoding potential of 8-oxo-7,8-dihydroguanosine. Structure (Camb) 13:1653-1659 (2005).

Cherepanov, P., Ambrosio, A.L., Rahman, S., Ellenberger, T. and Engelman, A. Structural basis for the recognition between HIV-1 integrase and transcriptional coactivator p75. PNAS 102:17308-17313 (2005).

Latacha, K.S., Remond, M.C., Ramasubramanian, A., Chen, A.Y., Elson, E.L. and Tabor, L.A. Role of actin polymerization in bending of the early heart tube. Dev Dynamics 233:1272-1286 (2005).

Marquez, J.P., Genin, G.M., Zahalak, G.I. and Elson, E.L. Thin bio-artificial tissues in plane stress: The relationship between cell and tissue strain, and an improved constitutive model. Biophys J 88:765-777 (2005).

Marquez, J.P., Genin, G.M., Zahalak, G.I. and Elson, E.L. The relationship between cell and tissue strain in three-dimensional bio-artificial tissues. Biophys J 88:778-789 (2005).

Chattopadhyay, K., Saffarian, S., Elson, E.L. and Frieden, C. Measuring unfolding of proteins in the presence of denaturant using fluorescence correlation spectroscopy. Biophys J 88:1413-1422 (2005).

Chattopadhyay, K., Elson, E.L. and Frieden, C. The kinetics of conformational fluctuations in an unfolded protein measured by fluorescence methods. PNAS 102:2385-2389 (2005).

Manna, P.P., Dimitry, J., Oldenborg, P.A. and Frazier, W.A. CD47 augments Fas/CD95-mediated apoptosis. J Biol Chem 280:29637-29644 (2005).

Isenberg, J.S., Calzada, M.J., Zhou, L., Guo, N., Lawler, J., Wang, X.Q., Frazier, W.A. and Roberts, D.D. Endogenous thrombospondin-1 is not necessary for proliferation but is permissive for vascular smooth muscle cell responses to platelet-derived growth factor. Matrix Biology 24:110-123 (2005).

Olsson, M. Bruhns, P., Frazier, W.A., Ravetch, J.V. and Oldenborg, P.A. Platelet homeostasis is regulated by platelet expression of CD47 under normal conditions and in passive immune thrombocytopenia. Blood 105:3577-3582 (2005).

Li, H. and Frieden, C. Phenylalanine side chain behavior of the intestinal fatty acid binding protein: The effect of urea on backbone and side chain stability. J Biol Chem 280, 38556-38561 (2005).

Shu, Q. and Frieden, C. Relation of enzyme activity of local/global stability of murine adenosine deaminase: 19F NMR studies. J Mol Biol 345:599-610 (2005).

Chattopadhyay, K., Elson, E.L., Frieden, C. The kinetics of conformational fluctuations in an unfolded protein measured by fluorescence methods. PNAS 102:2385-2389 (2005).

Chattopadhyay, K., Saffarian, S., Elson, E.L. and Frieden, C. Measuring unfolding of proteins in the presence of denaturant using fluorescence correlation spectroscopy. Biophys J 88:1413-1422 (2005).

Li, H. and Frieden, C. NMR studies of 4-(19)f-phenylalanine-labeled intestinal fatty acid binding protein: Evidence of conformational heterogeneity in the native state. Biochem 44:2369-2377 (2005).

Galletto, R., Jezewska, M.J., Bujalowski, W. Kinetic mechanism of rat polymerase ß - dsDNA interactions. fluorescence stopped-flow analysis of the cooperative ligand binding to a two-site one-dimensional lattice. Biochemistry 44:1251-1267 (2005).

Galletto, R., Jezewska, M.J., Maillard, R., Bujalowski, W. The nucleotide-binding site of the Escherichia coli DnaC protein. Molecular topography of DnaC protein - nucleotide cofactor complexes. Cell Biochemistry and Biophysics 43:331-354 (2005).

Galletto, R., Jezewska, M.J., Bujalowski, W. Kinetics of allosteric conformational transition of a macromolecule prior to ligand binding. Analysis of stopped-flow kinetic experiments. Cell Biochemistry and Biophysics 42:121-144 (2005)

Showalter, S.A. and Hall, K.B. Isotropic reorientational eigenmode dynamics complements NMR relaxation measurements for RNA. Methods in Enzymology 394:465-480 (2005).

Kurz, L.C., Fite, B., Jean, J., Park, J., Erpelding, T. and Callis, P. Photophysics of tryptophan fluorescence: Link with the catalytic strategy of the citrate synthase from Thermoplasma acidophilum. Biochem 44:1394-1413 (2005).

Myong, S., Rasnik, I., Joo, C., Lohman, T. M. and Ha, T. Repetitive shuttling of a motor protein on DNA. Nature 437:1321-1325 (2005).

Wong, J. C., Lucius, A. L. and Lohman, T. M. Energetics of DNA End Binding by E.coli RecBC and RecBCD Helicases Indicate Loop Formation in the 3'-Single-stranded DNA Tail. J Mol Biol 352:765-782 (2005).

Brendza, K.M., Cheng, W., Fischer, C.J., Chesnick, M.A., Niedziela-Majka, A. and Lohman, T.M. Autoinhibition of Escherichia coli Rep monomer helicase activity by its 2B subdomain. PNAS 102:102:10076-10081 (2005).

Morgan, J.C., Majors, J.E. and Galileo, D.S. Distinct and opposite roles for SH2 and SH3 domains of v-src in embryo survival and hemangiosarcoma formation. Clin Exp Metastasis 22:167-175 (2005).

Marshall, G.R. and Vakser, I.A. Protein-protein docking methods. In Proteomics and Protein-Protein Interactions: Biology, Chemistry, Bioinformatics and Drug Design. G. Waksman, ed. Springer, NY pp. 115-145(2005).

Marshall, G.R. Introduction to Chemoinformatics in Drug Discovery - a Persona View. In Cheminformatics in Drug Discover, Vol 23. T.I. Oprea, ed. Methods and Principles in Medicinal Chemistry. Wiley-VCH Verlag, Weinheim, Germany pp. 1-22 (2005).

Anderson, L.L., Marshall, G.R. and Baranski, T.J. Using expressed protein ligation to study protein interactions: Semi-synthesis of the G-protein alpha subunit. Protein Peptide Lett. 12:783-787(2005).

Anderson, L.L., Marshall, G.R., Crocker, E., Smith, S.O. and Baranski, T.J. Motion of carboxyl terminus of Ga is restricted upon G-protein activation: A solution NMR study using semi-synthetic Ga subunits J Biol Chem 260:31019-31026 (2005).

Kuster, D.J. and Marshall, G.R. Validated ligand mapping of ACE active site. J Comp-Aided Drug Des 19:609-615 (2005).

Nikiforovich, G.V. and Marshall, G.R. Modeling conformational changes of the flexible loops in the dark-adapted and activated states of rhodopsin. A prototypical G-protein-coupled receptor. Biophysics J 89:3780-3789 (2005).

Nikiforovich, G.V. Mihalik, B., Catt, K.J. and Marshall, G.R. Molecular mechanisms of constitutive activity: Mutations at position 111 of the angiotensin AT1 receptor. J Peptide Res 66:236-248 (2005).

Chen, Z.W., Zhao, G., Martinovic, S., Jorns, M.S. and Mathews, F.S. Structure of the sodium borohydride-reduced N-(cyclopropyl)glycine adduct of the flavoenzyme monomeric sarcosine oxidase. Biochemistry 44:15111-15450 (2005).

Papaconstantinou, M.E., Carrell, C.J., Pineda, A.O., Bobofchak, K.M., Mathews, F.S., Flordellis, C.S., Maragoudakis, M.E., Tsopanoglou, N.E. and Di Cera, E. Thrombin functions through its RGD sequence in a non-canonical conformation. J Biol Chem 280:29393-29396 (2005).

Toyama, H., Chen, Z.W., Fukumoto, M., Adachi, O., Adachi, O., Matsushita, K. and Mathews, F.S. Molecualr cloning and structural analysis of quinohemoprotein alcohol dehydrogenase ADH-IIG from Pseudomonas putida HK5 J Mol Biol 352:91-104 (2005).

Hassan-Abdallah, A., Zhao, G. Eschenbrenner, M., Chen, Z.W., Mathews, F.S. and Jorns, M.S. Cloning, expression and crystallization of heterotetrameric sarcosine oxidase from Pseudomonas maltophilia. Protein Expression and Purification 43:33-43 (2005).

Bobofchak, K.M., Pineda, A.O., Mathews, F.S. and Di Cera, E. Energetic and structural consequences of perturbing Gly-193 in the oxyanion hold of serine proteases. J Biol Chem 280:25644-25650 (2005).

Cunane, L.M., Barton, J.D., Chen, Z.W., Le, K.H., Amar, D., Lederer, F. and Mathews, F.S. Crystal structure analysis of recombinant rat kidney long chain hydroxy acid oxidase. Biochem 44:1521-1531 (2005).

Sun, D., Li, X. Mathews, F.S. and Davidson, V.L. Site-directed mutagenesis of proline 94 to alanine in amicyanin converts a true electrion transfer reaction into one that is kinetically coupled. Biochem. 44:7200-7206 (2005).

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