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

Aquerra, R.M., Kliger, D.S., Holt, J.M. and Ackers, G.K. The molecular code for hemoglobin allostery revealed by linking the thermodynamics and kinetics of quaternary structural change. 2. Cooperative free energies of (α_FeCOβ_Fe)₂ and (α_Feβ_FeCO)₂ T-state tetramers. Biochemistry 43:12065-12080 (2004).
Goldbeck, R.A., Esquerra, R.M., Holt, J.M., Ackers, G.K. and Kliger, D.S. The molecular code for hemoglobin allostery revealed by linking the thermodynamics and kinetics of quaternary structural change. 1. Microstate linear free energy relations. Biochemistry 43:12048-1204.
Ackers, G. K., Holt, J. M., Burgie, E. S. and Yarian, C. S. Analyzing intermediate state cooperativity in hemoglobin. Methods in Enzymology 379:3-28 (2004).

Nathan A. Baker

Song, Y., Zhang, Y., Bajaj, C.L. and Baker, N.A. Continuum diffusion reaction rate calculations of wild-type and mutant mouse acetylcholinesterase: Adaptive finite element analyis. Biophys J 87:1558-1566 (2004).
Wagoner, J. and Baker, N.A. Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models. J Computational Chem 25:1623-1629 (2004).
Zhang, D., Konecny, R., Baker, N.A. and McCammon, J.A. Electostatic interaction between RNA and protein capsid in cowpea chlorotic mottle virus simulated by a coarse-grain RNA model and a Monte Carlo approach. Biopolymers 75:325-337 (2004).
Dolinsky, T.J., Burgers, P.M., Karplus, K. and Baker, N.A. SPrCY: Comparison of structural predictions in the Saccharomyces cerevisiae genome. Bioinformatics 20:2312-2314 (2004).
Song, Y., Zhang, Y., Shen, T., Bajaj, C. L., McCammon, J. A. and Baker, N. A. Finite element solution of the steady-state smoluchowski equation for rate constant calculations. Biophys J 86:2017-2029 (2004).
Vitalis, A., Baker, N.A. and McCammon, J.A. ISIM: a program for grand canonical Monte Carlo simulations of the ionic environment of biomolecules. Molecular Simulation 30:45-61 (2004).
Baker, N.A. Poisson-Boltzmann methods for biomolecular electrostatics. Methods in Enzymology 383:94-118 (2004).

Wayne M. Barnes

Ren, C.P., Chaudhuri, R.R., Fivian, A., Bailey, C.M., Antonio, M., Barnes, W.M. and Pallen, M.J. The ETT2 gene cluster, encoding a second type III secretion system from Escherichia coli, is present in the majority of strains but has undergone widespread mutational attrition. J Bacteriology 186:3547-3560 (2004).

Peter M. Burgers

Garg, P., Stith, C.M., Sabouri, N., Johansson, E. and Burgers, P.M. Idling by DNA polymerase delta maintains a ligatable nick during lagging-strand DNA replication. Genes & Development 18:2764-2773(2004).
Corrette-Bennett, S.E., Borgeson, C., Sommer, D., Burgers, P.M. and Lahue, R.S. DNA polymerase delta, RFC and PCNA are required for repair synthesis of large looped heteroduplexes in Saccharomyces cerevisiae. Nucleic Acids Research 32:6268-6275 (2004).
McCulloch, S.D., Kokoska, R.J., Chilkova, O., Welch, C.M., Johansson, E., Burgers, P.M. and Kunkel, T.A. Enzymatic switching for efficeint and accurate translesion DNA replication. Nucleic Acids Research 32:4665-4675 (2004).
Dolinsky, T.J., Burgers, P.M., Karplus, K. and Baker, N.A. SPrCY: Comparison of structural predictions in the Saccharomyces cerevisiae genome. Bioinformatics 20:2312-2314 (2004).
Dzantiev, L., Constantin, N. Genschel, J., Iver, R.R., Burgers, P.M. and Modrich, P. A defined human system that supports bidirectional mismatch-provoked excision. Mol. Cell. 15:31-41 (2004).
Majka, J. and Burgers, P.M. The PCNA-RFC families of DNA clamps and clamp loaders. Progress in Nucleic Acid Research and Molecular Biology 78:227-260 (2004).
Majka, J., Chung, B. Y. and Burgers, P. M. Requirement for ATP by the DNA damage checkpoint clamp loader. J Biol Chem 279:20921-20926 (2004).
Johansson, E., Garg, P. and Burgers, P. M. The Pol32 subunit of DNA polymerase delta contains separable domains fo rprocessive replication and proliferating cell nuclear antigen (PCNA) binding. J Biol Chem 279:1907-1915 (2004).

Enrico Di Cera

Pineda, A.O., Zhang, E., Guinto, E.R., Savvides, S.N., Tulinsky, A. and Di Cera, E. Crystal structure of the thrombin mutant D221A/D222K: The Asp222:Arg187 ion-pair stabilizes the fast form. Biophys. Chem. 112:253-256 (2004).
Yang, L., Rasad, S., Di Cera, E., Rezaie, A.R. The confomration of the activation peptide of protein C is influenced by Ca²⁺ and Na⁺ binding. J Biol Chem 279:38519-38524 (2004).
Pineda, A.O., Chen, Z.W., Caccia, S., Cantwell, A.M., Savvides, S.N., Waksman, G., Mathews, F.S., Di Cera, E. The anticoagulant thrombin mutant W215A/E217A has a collapsed primary specificity pocket. J Biol Chem 279:39824-39828 (2004).
Pineda, A.O., Carrell, C.J., Bush, L.A., Prasad, S., Caccia, S., Chen, Z.W., Mathews, F.S. and Di Cera, E. Molecular dissection of na⁺ binding to thrombin. J Biol Chem 279:31842-31853 (2004).
Prasad, S., Cantwell, A.M., Bush, L.A., Shih, P., Xu, H. and Di Cera, E. Residue Asp-189 controls both substrate binding and the monovalent cation specificity of thrombin. J Biol Chem 279:10103-10108 (2004).

Elliot L. Elson

Watatsuki, T., Schlessinger, J. and Elson, E.L. The biochemical response of the heart to hypertension and exercise. Trends in Biochem Sci 29:609-617 (2004).
Elson, E.L. Quick tour of fluorescence correlation spectroscopy from its inception. J Biomed Optics 9:857-864 (2004).
Saffarian, S., Collier, I.E., Marmer, B.L., Elson, E.L. and Goldberg, G. Interstitial collagenase is a Brownian ratchet driven by proteolysis of collagen. Science 306:108-111 (2004).
Wagenseil, J.E, Elson, E.L. and Okamoto, R.J. Cell orientation influences the biaxial mechanical properties of fibroblast populated collagen vessels. Annals of Biomed. Engineering 32:720-731 (2004).
Wakatsuki, T., Fee, J.A. and Elson, E.L. Phenotypic screening for pharmaceuticals using tissue constructs. Current Pharmaceutical Biotechnology 5:181-189 (2004).
Emmert, D.A., Fee, J.A., Goeckeler, Z.M., Grojean, J.M., Wakatsuki T., Elson, E.L., Herring, B.P., Gallagher, P.J. and Wysolmerski, R.B. Rho-kinase-mediated Ca2+-independent contraction in rat embryo fibroblasts. American Journal of Physiology - Cell Physiology 286:C8-21 (2004).
Qian, H. and Elson, E. L. Fluorescence correlation spectroscopy with high-order and dual-color correlation to probe nonequilibrium steady states. PNAS 101:2828-2833 (2004).

William A. Frazier

McDonald, J. F., Zheleznyak, A. and Frazier, W. A. Cholesterol-independent interactions with CD47 enhance alpha_vbeta₃ avidity. J Biol Chem 279:17301-17311 (2004).
Manna, P. P. and Frazier, W. A. CD47 mediates killing of breast tumor cells via Gi-dependent inhibition of protein kinase A. Cancer Research 64:1026-1036 (2004).

Carl Frieden

Bann, J.G., Pinkner, J.S., Frieden, C. and Hultgren, S.J. Catalysis of protein folding by chaperones in pathogenic bacteria. PNAS, USA 1001:17389-17393 (2004).
Bann, J.G. and Frieden, C. Folding and domain-domain interactions of the chaperone PapD measured by (19)F NMR. Biochemistry 43:13775-13786 (2004).
Frieden, C., Hoeltzli, S. D. and Bann, J. G. The preparation of 19F-labeled proteins for NMR studies. Methods in Enzymology 380:400-415 (2004).
Shu, Q. and Frieden, C. Urea-dependent unfolding of murine adenosine deaminase: Sequential destabilization as measured by ¹⁹F NMR. Biochemistry 43:1432-1439 (2004).

Roberto Galletto

Jezewska, M.J., Galletto, R., Bujalowski, W. Interactions of the RepA helicase hexamer of plasmid RSF1010 with the ssDNA. Quantitative analysis of stoichiometries, intrinsic affinities, cooperativities, and heterogeneity of the total ssDNA-binding site. Journal of Molecular Biology 343:115-136 (2004).
Galletto, R., Jezewska, M.J., Bujalowski, W. Unzipping mechanism of the double-stranded DNA unwinding by a hexameric helicase: the effect of the 3' arm and the stability of the dsDNA on the unwinding activity of the Escherichia coli DnaB helicase. Journal of Molecular Biology 343:101-114 (2004).
Galletto, R., Jezewska, M.J., Bujalowski, W. Unzipping mechanism of the double-stranded DNA unwinding by a hexameric helicase: quantitative analysis of the rate of the dsDNA unwinding, processivity and kinetic step-size of the Escherichia coli DnaB helicase using rapid quench-flow method. Journal of Molecular Biology 343:83-99 (2004).
Galletto, R., Jezewska, M.J., Bujalowski, W. Multistep sequential mechanism of Escherichia coli helicase PriA protein-ssDNA interactions. Kinetics and energetics of the active ssDNA-searching site of the enzyme. Biochemistry 43:11002-11016 (2004).
Galletto, R., Maillard, R., Jezewska, M.J., Bujalowski, W. Global conformation of the Escherichia coli replication factor DnaC protein in absence and presence of nucleotide cofactors. Biochemistry 43:10988-1001 (2004).

Kathleen B. Hall

Clerte, C. and Hall, K.B. Global and local dynamics of the U1A polyadenylation inhibition element (PIE) RNA and PIE RNA-U1A complexes. Biochem 43:13404-13415 (2004).
Jean, J.M. and Hall, K.B. Stacking-unstacking dynamics of oligodeoxynucleotides trimers. Biochemistry 43:10277-10284 (2004).
Showalter, S.A. and Hall, K.B. Altering the RNA-binding mode of the U1A RBD1 protein. Journal of Molecular Biology 335:465-80 (2004).
Hall, K.B. and Williams, D.J. Dynamics of the IRE RNA hairpin loop probed by 2-aminopurine fluorescence and stochastic dynamics simulations. RNA 10:34-47 (2004).

Katherine Henzler-Wildman

Wolf-Watz M, Thai V, Henzler-Wildman K, Hadjipavlou G, Eisenmesser EZ, Kern D. Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair. Nat. Struct. Mol. Biol. 11:945-949 (2004).
Henzler-Wildman K.A., Martinez G.V., Brown M.F., Ramamoorthy A. Perturbation of the hydrophobic core of lipid bilayers by the human antimicrobial peptide LL-37. Biochemistry 43:8459-8469 (2004).

Timothy M. Lohman

Fischer, C.J., Maluf, N.K. and Lohman, T.M. Mechanism of ATP-dependent translocation of E. coli UvrD monomers along single-stranded DNA. J Mol Biol 344:1287-1309 (2004).
Fischer, C.J. and Lohman, T.M. Mechanism of ATP-dependent translocation of E. coli UvrD monomers along single-stranded DNA. J Mol Biol 344:1265-1286 (2004).
Savvides, S.N., Raghunathan, S., Futterer, K., Kozlov, A.G., Lohman, T.M. and Waksman, G. The C-terminal domain of full-length E. coli SSB is disordered even when bound to DNA. Protein Science 13:1942-1947 (2004).
Lucius, A.L. and Lohman, T.M. Effects of temperature and ATP on the kinetic mechanism and kinetic step-size for E. coli RecBCD helicase-catalyzed DNA unwinding. J. Mol. Biol. 339:751-771 (2004).
Lucius, A.L., Wong, J.C. and Lohman, T.M. Fluorescence stopped-flow studies of single turnover kinetics of E.coli RecBCD helicase-catalyzed DNA unwinding. Journal Mol. Biol. 339:731-750 (2004).
Rasnik, I., Myong, S., Cheng, W., Lohman, T.M. and Ha, T. DNA-binding orientation and domain conformation of the E. coli rep helicase monomer bound to a partial duplex junction: Single-molecule studies of fluorescently labeled enzymes. J Mol Biol 336:395-408 (2004).
Murphy, M.C., Rasnik, I., Cheng, W., Lohman, T.M. and Ha, T. Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy. Biophys J 86:2530-2537 (2004).

Garland R. Marshall

Che, Y. and Marshall, G.R. Impact of Azaproline on peptide conformation. J. Org. Chem. 69:9030-9042 (2004).
Poreddy, A.R., Schall, O.F., Osiek, T.A., Wheatley, J.R., Beusen, D.D., Marshall, G.R. and Slomczynska, U. Hydroxamate-based iron chelators: Combinatorial syntheses of desferrioxamine B analogs and evaluation of their iron affinities. J. Comb. Chem. 6:239-254 (2004).
Berglund, A., Head, R.D., Welsh, E.A. and Marshall, G.R. ProVal: a protein-scoring function for the selection of native and near-native folds. Proteins 54:289-302 (2004).

F. Scott Mathews

Pineda, A.O., Chen, Z.W., Caccia, S., Cantwell, A.M., Savvides, S.N., Waksman, G., Mathews, F.S., Di Cera, E. The anticoagulant thrombin mutant W215A/E217A has a collapsed primary specificity pocket. J Biol Chem 279:39824-39828 (2004).
Carrell, C.J., Wang, X., Jones, L., Jarrett, W.L., Davidson, V.L. and Mathews, F.S. Crystallographic and NMR investigation of cobalt-substituted amicyanin. Biochemistry 43:9381-9389 (2004).
Carrell, C.J., Sun, D., Jiang, S., Davidson, V.L. and Mathews, F.S. Structural studies of two mutants of amicyanin from Paracoccus denitrificans that stabilize the reduced state of the copper. Biochemistry 43:9372-9380 (2004).
Pineda, A.O., Carrell, C.J., Bush, L.A., Prasad, S., Caccia, S., Chen, Z.W., Mathews, F.S. and Di Cera, E. Molecular dissection of na⁺ binding to thrombin. J Biol Chem 279:31842-31853 (2004).
Toyama, H., Mathews, F.S., Adachi, O. and Matsushita, K. Quinohemoprotein alcohol dehydrogenases: Structure, function, and physiology. Archives of Biochemistry and Biophysics 428:10-21 (2004).
Sukumar, N., Dewanti, A. R., Mitra B. and Mathews, F. S. High resolution structures of an oxidied and reduced flavoprotein. The water switch in a soluble form of (S)-mandelate dehydrogenase. J Biol Chem 279:3749-3757 (2004).
Ferrari, D., Di Valentin, M., Carbonera, D., Merli, A., Chen, Z. W., Mathews, F. S., Davidson, V. L. and Rossi, G. L. Electron transfer in crystals of the binary and ternary complexes of methylamine dehydrogenase with amicyanin and cytochrome c551i as detected by EPR spectroscopy. J Biol Inorganic Chem 9:231-237 (2004).

Linda J. Pike

Pike, L.J. and Sadler, J.E. Proteomics, genomics and the future of medical education. Missouri Medicine 101:496-499 (2004).
Pike, L. J. Lipid rafts: Heterogeneity on the high seas. Biochem J 378:281-292 (2004).

Jay W. Ponder

Ren, P. and Ponder, J.W. Temperature and pressure dependence of the AMOEBA water model. J Phys Chem B 108:15671-15682 (2004).

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.

Goldbeck, R.A., Esquerra, R.M., Holt, J.M., Ackers, G.K. and Kliger, D.S. The molecular code for hemoglobin allostery revealed by linking the thermodynamics and kinetics of quaternary structural change. 1. Microstate linear free energy relations. Biochemistry 43:12048-1204.

Ackers, G. K., Holt, J. M., Burgie, E. S. and Yarian, C. S. Analyzing intermediate state cooperativity in hemoglobin. Methods in Enzymology 379:3-28 (2004).

Song, Y., Zhang, Y., Bajaj, C.L. and Baker, N.A. Continuum diffusion reaction rate calculations of wild-type and mutant mouse acetylcholinesterase: Adaptive finite element analyis. Biophys J 87:1558-1566 (2004).

Wagoner, J. and Baker, N.A. Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models. J Computational Chem 25:1623-1629 (2004).

Zhang, D., Konecny, R., Baker, N.A. and McCammon, J.A. Electostatic interaction between RNA and protein capsid in cowpea chlorotic mottle virus simulated by a coarse-grain RNA model and a Monte Carlo approach. Biopolymers 75:325-337 (2004).

Dolinsky, T.J., Burgers, P.M., Karplus, K. and Baker, N.A. SPrCY: Comparison of structural predictions in the Saccharomyces cerevisiae genome. Bioinformatics 20:2312-2314 (2004).

Song, Y., Zhang, Y., Shen, T., Bajaj, C. L., McCammon, J. A. and Baker, N. A. Finite element solution of the steady-state smoluchowski equation for rate constant calculations. Biophys J 86:2017-2029 (2004).

Vitalis, A., Baker, N.A. and McCammon, J.A. ISIM: a program for grand canonical Monte Carlo simulations of the ionic environment of biomolecules. Molecular Simulation 30:45-61 (2004).

Baker, N.A. Poisson-Boltzmann methods for biomolecular electrostatics. Methods in Enzymology 383:94-118 (2004).

Garg, P., Stith, C.M., Sabouri, N., Johansson, E. and Burgers, P.M. Idling by DNA polymerase delta maintains a ligatable nick during lagging-strand DNA replication. Genes & Development 18:2764-2773(2004).

Corrette-Bennett, S.E., Borgeson, C., Sommer, D., Burgers, P.M. and Lahue, R.S. DNA polymerase delta, RFC and PCNA are required for repair synthesis of large looped heteroduplexes in Saccharomyces cerevisiae. Nucleic Acids Research 32:6268-6275 (2004).

McCulloch, S.D., Kokoska, R.J., Chilkova, O., Welch, C.M., Johansson, E., Burgers, P.M. and Kunkel, T.A. Enzymatic switching for efficeint and accurate translesion DNA replication. Nucleic Acids Research 32:4665-4675 (2004).

Dolinsky, T.J., Burgers, P.M., Karplus, K. and Baker, N.A. SPrCY: Comparison of structural predictions in the Saccharomyces cerevisiae genome. Bioinformatics 20:2312-2314 (2004).

Dzantiev, L., Constantin, N. Genschel, J., Iver, R.R., Burgers, P.M. and Modrich, P. A defined human system that supports bidirectional mismatch-provoked excision. Mol. Cell. 15:31-41 (2004).

Majka, J. and Burgers, P.M. The PCNA-RFC families of DNA clamps and clamp loaders. Progress in Nucleic Acid Research and Molecular Biology 78:227-260 (2004).

Majka, J., Chung, B. Y. and Burgers, P. M. Requirement for ATP by the DNA damage checkpoint clamp loader. J Biol Chem 279:20921-20926 (2004).

Johansson, E., Garg, P. and Burgers, P. M. The Pol32 subunit of DNA polymerase delta contains separable domains fo rprocessive replication and proliferating cell nuclear antigen (PCNA) binding. J Biol Chem 279:1907-1915 (2004).

Pineda, A.O., Zhang, E., Guinto, E.R., Savvides, S.N., Tulinsky, A. and Di Cera, E. Crystal structure of the thrombin mutant D221A/D222K: The Asp222:Arg187 ion-pair stabilizes the fast form. Biophys. Chem. 112:253-256 (2004).

Yang, L., Rasad, S., Di Cera, E., Rezaie, A.R. The confomration of the activation peptide of protein C is influenced by Ca2+ and Na+ binding. J Biol Chem 279:38519-38524 (2004).

Pineda, A.O., Chen, Z.W., Caccia, S., Cantwell, A.M., Savvides, S.N., Waksman, G., Mathews, F.S., Di Cera, E. The anticoagulant thrombin mutant W215A/E217A has a collapsed primary specificity pocket. J Biol Chem 279:39824-39828 (2004).

Pineda, A.O., Carrell, C.J., Bush, L.A., Prasad, S., Caccia, S., Chen, Z.W., Mathews, F.S. and Di Cera, E. Molecular dissection of na+ binding to thrombin. J Biol Chem 279:31842-31853 (2004).

Prasad, S., Cantwell, A.M., Bush, L.A., Shih, P., Xu, H. and Di Cera, E. Residue Asp-189 controls both substrate binding and the monovalent cation specificity of thrombin. J Biol Chem 279:10103-10108 (2004).

Watatsuki, T., Schlessinger, J. and Elson, E.L. The biochemical response of the heart to hypertension and exercise. Trends in Biochem Sci 29:609-617 (2004).

Elson, E.L. Quick tour of fluorescence correlation spectroscopy from its inception. J Biomed Optics 9:857-864 (2004).

Saffarian, S., Collier, I.E., Marmer, B.L., Elson, E.L. and Goldberg, G. Interstitial collagenase is a Brownian ratchet driven by proteolysis of collagen. Science 306:108-111 (2004).

Wagenseil, J.E, Elson, E.L. and Okamoto, R.J. Cell orientation influences the biaxial mechanical properties of fibroblast populated collagen vessels. Annals of Biomed. Engineering 32:720-731 (2004).

Wakatsuki, T., Fee, J.A. and Elson, E.L. Phenotypic screening for pharmaceuticals using tissue constructs. Current Pharmaceutical Biotechnology 5:181-189 (2004).

Emmert, D.A., Fee, J.A., Goeckeler, Z.M., Grojean, J.M., Wakatsuki T., Elson, E.L., Herring, B.P., Gallagher, P.J. and Wysolmerski, R.B. Rho-kinase-mediated Ca2+-independent contraction in rat embryo fibroblasts. American Journal of Physiology - Cell Physiology 286:C8-21 (2004).

Qian, H. and Elson, E. L. Fluorescence correlation spectroscopy with high-order and dual-color correlation to probe nonequilibrium steady states. PNAS 101:2828-2833 (2004).

McDonald, J. F., Zheleznyak, A. and Frazier, W. A. Cholesterol-independent interactions with CD47 enhance alphavbeta3 avidity. J Biol Chem 279:17301-17311 (2004).

Manna, P. P. and Frazier, W. A. CD47 mediates killing of breast tumor cells via Gi-dependent inhibition of protein kinase A. Cancer Research 64:1026-1036 (2004).

Bann, J.G., Pinkner, J.S., Frieden, C. and Hultgren, S.J. Catalysis of protein folding by chaperones in pathogenic bacteria. PNAS, USA 1001:17389-17393 (2004).

Bann, J.G. and Frieden, C. Folding and domain-domain interactions of the chaperone PapD measured by (19)F NMR. Biochemistry 43:13775-13786 (2004).

Frieden, C., Hoeltzli, S. D. and Bann, J. G. The preparation of 19F-labeled proteins for NMR studies. Methods in Enzymology 380:400-415 (2004).

Shu, Q. and Frieden, C. Urea-dependent unfolding of murine adenosine deaminase: Sequential destabilization as measured by 19F NMR. Biochemistry 43:1432-1439 (2004).

Galletto, R., Jezewska, M.J., Bujalowski, W. Unzipping mechanism of the double-stranded DNA unwinding by a hexameric helicase: the effect of the 3' arm and the stability of the dsDNA on the unwinding activity of the Escherichia coli DnaB helicase. Journal of Molecular Biology 343:101-114 (2004).

Galletto, R., Jezewska, M.J., Bujalowski, W. Multistep sequential mechanism of Escherichia coli helicase PriA protein-ssDNA interactions. Kinetics and energetics of the active ssDNA-searching site of the enzyme. Biochemistry 43:11002-11016 (2004).

Galletto, R., Maillard, R., Jezewska, M.J., Bujalowski, W. Global conformation of the Escherichia coli replication factor DnaC protein in absence and presence of nucleotide cofactors. Biochemistry 43:10988-1001 (2004).

Clerte, C. and Hall, K.B. Global and local dynamics of the U1A polyadenylation inhibition element (PIE) RNA and PIE RNA-U1A complexes. Biochem 43:13404-13415 (2004).

Jean, J.M. and Hall, K.B. Stacking-unstacking dynamics of oligodeoxynucleotides trimers. Biochemistry 43:10277-10284 (2004).

Showalter, S.A. and Hall, K.B. Altering the RNA-binding mode of the U1A RBD1 protein. Journal of Molecular Biology 335:465-80 (2004).

Hall, K.B. and Williams, D.J. Dynamics of the IRE RNA hairpin loop probed by 2-aminopurine fluorescence and stochastic dynamics simulations. RNA 10:34-47 (2004).

Wolf-Watz M, Thai V, Henzler-Wildman K, Hadjipavlou G, Eisenmesser EZ, Kern D. Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair. Nat. Struct. Mol. Biol. 11:945-949 (2004).

Henzler-Wildman K.A., Martinez G.V., Brown M.F., Ramamoorthy A. Perturbation of the hydrophobic core of lipid bilayers by the human antimicrobial peptide LL-37. Biochemistry 43:8459-8469 (2004).

Fischer, C.J., Maluf, N.K. and Lohman, T.M. Mechanism of ATP-dependent translocation of E. coli UvrD monomers along single-stranded DNA. J Mol Biol 344:1287-1309 (2004).

Fischer, C.J. and Lohman, T.M. Mechanism of ATP-dependent translocation of E. coli UvrD monomers along single-stranded DNA. J Mol Biol 344:1265-1286 (2004).

Savvides, S.N., Raghunathan, S., Futterer, K., Kozlov, A.G., Lohman, T.M. and Waksman, G. The C-terminal domain of full-length E. coli SSB is disordered even when bound to DNA. Protein Science 13:1942-1947 (2004).

Lucius, A.L. and Lohman, T.M. Effects of temperature and ATP on the kinetic mechanism and kinetic step-size for E. coli RecBCD helicase-catalyzed DNA unwinding. J. Mol. Biol. 339:751-771 (2004).

Lucius, A.L., Wong, J.C. and Lohman, T.M. Fluorescence stopped-flow studies of single turnover kinetics of E.coli RecBCD helicase-catalyzed DNA unwinding. Journal Mol. Biol. 339:731-750 (2004).

Rasnik, I., Myong, S., Cheng, W., Lohman, T.M. and Ha, T. DNA-binding orientation and domain conformation of the E. coli rep helicase monomer bound to a partial duplex junction: Single-molecule studies of fluorescently labeled enzymes. J Mol Biol 336:395-408 (2004).

Murphy, M.C., Rasnik, I., Cheng, W., Lohman, T.M. and Ha, T. Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy. Biophys J 86:2530-2537 (2004).

Che, Y. and Marshall, G.R. Impact of Azaproline on peptide conformation. J. Org. Chem. 69:9030-9042 (2004).

Poreddy, A.R., Schall, O.F., Osiek, T.A., Wheatley, J.R., Beusen, D.D., Marshall, G.R. and Slomczynska, U. Hydroxamate-based iron chelators: Combinatorial syntheses of desferrioxamine B analogs and evaluation of their iron affinities. J. Comb. Chem. 6:239-254 (2004).

Berglund, A., Head, R.D., Welsh, E.A. and Marshall, G.R. ProVal: a protein-scoring function for the selection of native and near-native folds. Proteins 54:289-302 (2004).

Pineda, A.O., Chen, Z.W., Caccia, S., Cantwell, A.M., Savvides, S.N., Waksman, G., Mathews, F.S., Di Cera, E. The anticoagulant thrombin mutant W215A/E217A has a collapsed primary specificity pocket. J Biol Chem 279:39824-39828 (2004).

Carrell, C.J., Wang, X., Jones, L., Jarrett, W.L., Davidson, V.L. and Mathews, F.S. Crystallographic and NMR investigation of cobalt-substituted amicyanin. Biochemistry 43:9381-9389 (2004).

Carrell, C.J., Sun, D., Jiang, S., Davidson, V.L. and Mathews, F.S. Structural studies of two mutants of amicyanin from Paracoccus denitrificans that stabilize the reduced state of the copper. Biochemistry 43:9372-9380 (2004).

Pineda, A.O., Carrell, C.J., Bush, L.A., Prasad, S., Caccia, S., Chen, Z.W., Mathews, F.S. and Di Cera, E. Molecular dissection of na+ binding to thrombin. J Biol Chem 279:31842-31853 (2004).

Toyama, H., Mathews, F.S., Adachi, O. and Matsushita, K. Quinohemoprotein alcohol dehydrogenases: Structure, function, and physiology. Archives of Biochemistry and Biophysics 428:10-21 (2004).

Sukumar, N., Dewanti, A. R., Mitra B. and Mathews, F. S. High resolution structures of an oxidied and reduced flavoprotein. The water switch in a soluble form of (S)-mandelate dehydrogenase. J Biol Chem 279:3749-3757 (2004).

Pike, L.J. and Sadler, J.E. Proteomics, genomics and the future of medical education. Missouri Medicine 101:496-499 (2004).

Pike, L. J. Lipid rafts: Heterogeneity on the high seas. Biochem J 378:281-292 (2004).

Ren, P. and Ponder, J.W. Temperature and pressure dependence of the AMOEBA water model. J Phys Chem B 108:15671-15682 (2004).

Yang, L., Rasad, S., Di Cera, E., Rezaie, A.R. The confomration of the activation peptide of protein C is influenced by Ca²⁺ and Na⁺ binding. J Biol Chem 279:38519-38524 (2004).

Pineda, A.O., Carrell, C.J., Bush, L.A., Prasad, S., Caccia, S., Chen, Z.W., Mathews, F.S. and Di Cera, E. Molecular dissection of na⁺ binding to thrombin. J Biol Chem 279:31842-31853 (2004).

McDonald, J. F., Zheleznyak, A. and Frazier, W. A. Cholesterol-independent interactions with CD47 enhance alpha_vbeta₃ avidity. J Biol Chem 279:17301-17311 (2004).

Shu, Q. and Frieden, C. Urea-dependent unfolding of murine adenosine deaminase: Sequential destabilization as measured by ¹⁹F NMR. Biochemistry 43:1432-1439 (2004).

Pineda, A.O., Carrell, C.J., Bush, L.A., Prasad, S., Caccia, S., Chen, Z.W., Mathews, F.S. and Di Cera, E. Molecular dissection of na⁺ binding to thrombin. J Biol Chem 279:31842-31853 (2004).