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

Sept, D., Baker, N.A. and McCammon, J.A. The physical basis of microtubule structure and stability. Protein Science 12:2257-2261 (2003).

Tai, K., Bond, S.D., MacMillan, H.R., Baker, N.A., Holst, M.J. and McCammon, J.A. Finite element simulations of acetylcholine diffusion in neuromuscular junctions. Biophys J. 84:2234-2241 (2003).

Baker, N.A. and McCammon, J.A. Electrostatic interactions. Methods of Biochemical Analysis 44:427-440 (2003).

Wayne M. Barnes

Kermekchiew, M.B. Tzekov, A. and Barnes, W.M. Cold-sensitive mutants of Taq DNA polymerase provide a hot start for PCR. Nucleic Acids research 31:6139-6147 (2003).

Stratman, J.L., Barnes, W.M. and Simon, T.C. Universal PCR genotyping assay that achieve single copy sensitivity with any primer pair. Transgenic Research 12:521-522 (2003).

Pergams, O.R., Barnes, W.M. and Nyberg, D. Mammalian microevaluation: Rapid change in mouse mitochondrial DNA. Nature 423:397 (2003).

Peter M. Burgers

Majka, J. and Burgers, P.M. Yeast Rad17/Mec3/Ddc1: A sliding clamp for the DNA damage checkpoint. PNAS 100:2249-2254 (2003).

Ayyagari, R., Gomes, X.V., Gordenin, D.A. and Burgers, P.M. Okazaki fragment maturation in yeast. I. Distribution of functions between FEN1 and DNA2. J. Biol. Chem. 278:1618-1625 (2003).

Jin, Y.H., Ayyagari, R., Resnick, M.A., Gordenin, D.A. and Burgers, P.M. Okazaki fragment maturation of yeast. II. Cooperation between the polymerase and 3'-5'-exonuclease activities of Pol delta in the creation of ligatable nick. J. Biol. Chem. 278:1626-1633 (2003).

Peter T. Chivers

Carrington, P.E., Chivers, P.T., Al-Mjeni, F., Sauer, R.T. and Maroney, M.J. Nickel coordination is regulated by the DNA-bound state of NikR. Nat. Struc. Biol. 10:126-130 (2003).

Schreiter, E. D., Sintchak, M. D., Guo Y., Chivers, P. T., Sauer, R. T., and Drennan C. L. Crystal structure of the nickel-responsive transcription factor NikR Nat. Struct. Biol, 10, 794-799 (2003).

Setterdahl, A. T., Chivers, P. T., Hirasawa, M., Lemaire, S. D., Keryer, E., Miginiac-Maslow, M., Kim, S-K., Mason, J., Jacquot, J-P., Longbine, C. C., de Lamotte-Guery, F., and Knaff, D. B. The effect of pH on the oxidation-reduction properties of thioredoxins. Biochemistry 42, 14877-14884 (2003).

Enrico Di Cera

Di Cera, E. Thrombin interactions. Chest 124:11-17 (2003).

Rose, T., LeMosy, E.K., Cantwell, A.M., Banerjee-Roy, D., Skeath, J.B. and Di Cera, E. Three-dimensional models of proteases involved in patterning of the Drosophila embryo. J Biol Chem 278:11320-11330 (2003).

Krem, M.M. and Di Cera, E. Dissecting substrate recognition by thrombin using the inactive mutant S195A. Biophys. Chem. 100:315-323 (2003).

Di Cera, E. Atherosclerosis: Testing the Water. Arter Thromb Vasc Biol. 23:1713-1714 (2003).

Elliot L. Elson

Wagenseil, J.E., Wakatsuki, T., Okamoto, R.J., Zahalzk, G.I. and Elson, E.L. One-dimensional visoelastic behavior of fibroblast populated collagen matrices. J Biomechanical Engineering 125:719-725 (2003).

Wakatsuki, T., Wysolmerski, R.B. and Elson, E.L. Mechanics of cell spreading: Role of myosin II. J. Cell Sci. 116:1617-1625 (2003).

Saffarian, S. and Elson, E.L. Statistical analysis of fluorescence correlation spectroscopy: The standard deviation and bias. Biophysical Journal 84:2030-2042 (2003).

Wakatsuki, T. and Elson, E.L. Reciprocal interactions between cells and extracellular matrix during remodeling of tissue constructs. Biophys. Chem. 100:593-605 (2003).

William A. Frazier

McDonald, J.F., Dimitry, J.M. and Frazier, W.A. An amyloid-like C-terminal domain of thrombospondin-1 displays CD47 agonist activity requiring both VVM motifs. Biochemistry 42:10001-10011 (2003).

Manna, P.P. and Frazier, W.A. The mechanism of CD47-dependent killing of T cells: Heterotrimeric G(i)-dependent inhibiton of protein kinase A. J. Immunol. 170:3544-3453 (2003).

Carl Frieden

Vorobiev, S., Strokopytov, B., Drubin, D.G., Frieden, C., Ono, S., Condeelis, J., Rubenstein, P.A. and Almo, S.C. The structure of nonvertebrate actin: Implications for the ATP hydrolytic mechanism. Proceedings of the National Academy of Sciences of the United States of America 100:5760-5765 (2003).

Nikiforovich, G.V., Andersen, N.H., Fesinmeyer, R.M. and Frieden, C. Possible locally driven folding pathways of TC5b, a 20-residue protein. Proteins 52:292-302 (2003).

Frieden, C. The kinetics of side chain stabilization during protein folding. Biochemistry 42:12439-12446 (2003).

Rajabzadeh, M. Kao, J. and Frieden, C. Consequences of single-site mutations in the intestinal fatty acid binding protein. Biochemistry 42:12192-12199 (2003).

Roberto Galletto

Jezewska, M.J., Galletto, R., Bujalowski, W. Tertiary conformation of the template-primer and gapped DNA substrates in complexes with rat polymerase beta. Fluorescence energy transfer studies using the multiple donor-acceptor approach. Biochemistry 42:11864-78 (2003).

Galletto, R., Jezewska, M.J., and Bujalowski, W. Interactions of the Escherichia coli DnaB helicase hexamer with the replication factor the DnaC protein. Effect of nucleotide cofactors and the ssDNA on protein-protein interactions and the topology of the complex. Journal of Molecular Biology 329:441-465 (2003).

Jezewska, M.J., Galletto, R., Bujalowski, W. Rat polymerase ß binds double-stranded DNA using exclusively the 8-kDa domain. Stoichiometries, intrinsic affinities, and cooperativities. Biochemistry 42:5955-5970 (2003).

Jezewska, M.J., Galletto, R., and Bujalowski, W. Rat polymerase ß – gapped DNA interactions. Antagonistic effects of the 5’ terminal PO4- group and magnesium on the enzyme binding to the gapped DNA with different ssDNA gaps. Cell Biochemistry and Biophysics 38:125-160 (2003).

Katherine Henzler-Wildman

• Henzler-Wildman, K.A., Lee, D.K.and Ramamoorthy, A. Mechanism of membrane bilayer disruption by the human antimicrobial peptide, LL-37. Nat. Struct. Biochemistry 42:6545-6558 (2003).

Timothy M. Lohman

Lucius, A.L., Maluf, N.K., Fischer, C.J. and Lohman, T.M. General methods for analysis of sequential "n-step" kinetic mechanisms: Application to single turnover kinetics of helicase-catalzed DNA unwinding. Biophys. J. 84:2224-223 (2003).

Maluf, N.K., Ali, J.A. and Lohman, T.M. Kinetic mechanism for formation of the active, dimeric UvrD helicase-DNA complex. J. Biol. Chem. 278:31930-31940 (2003).

Maluf, N.K. and Lohman, T.M. Self association equilbria of E. coli UvrD helicase studied by analytical ultracentrifugation. J. Mol. Biol. 325:889-912 (2003).

Maluf, N.K., Fischer, C.J. and Lohman, T.M. A dimer of E. coli UvrD is the active form of the helicase in vitro. J. Mol. Biol. 325:913-935 (2003).

John E. Majors

Hardy, R.W., Marcotrigiano, J., Blight, K.J., Majors, J.E. and Rice, C.M. Hepatitis C virus RNA synthesis in cell-free system isolated from replicon-containing hepatoma cells. J. Virol. 77:2029-2037 (2003).

Garland R. Marshall

Poreddy, A.R., Schall, O.F., Marshall, G.R., Ratledge, C. and Slomczynska, U. Solid-phase synthesis of carboxymycobactin T and analogs as potential antimycobacterial agents. Bioorg. Med. Chem Lett. 13:2553-2556(2003).

Marshall, G.R. and Beusen, D.D. Molecular modeling in drug design. In: Burger's Medicinal Chemistry and Drug Discovery, 6th edition, D.Abraham, Ed., John Wiley & Sons, Inc. New York, Vol. 1, Chapter 3 (2003).

Ye, Y., Liu, M., Kao, J.L.-F. and Marshall, G.R. Peptide-bond modifications for metal coordination: Peptides containing two hydroxamate groups. Biopolymers (Peptide Sci) 71:489-515 (2003).

Marshall, G.R. Solid-phase synthesis: A paradigm shift. J Peptide Sci 9:534-544 (2003).

Nikiforovich, G.V. and Marshall, G.R. Three-dimensional model for meta-II rhodopsin an activated G-protein-coupled receptor. Biochemistry 42:9110-9120 (2003).

Zhang, W-J., Berglund, A., Kao, J.L.-F., Couty, J.-P., Gershengorn, M.C. and Marshall, G.R. Impact of Azaprolin on a isomerism: Conformational analyses and NMR studies of model peptides including TRH analogues. J. Am. Chem. Soc. 125:1221-1235 (2003).

F. Scott Mathews

Xia, Z.X., Dai, W.W., He, Y.N., White, S.A., Mathews, F.S. and Davidson, V.L. X-ray structure of methanol dehydrogenase from paracoccus denitrifcans and molecular amodeling of its interactions with cytochrome c-551i. J Biol Inorganic Chem 8:843-854 (2003).

Sun, D., Ono, K., Okajima, T., Tanizawa, K., Uchida, M. Yamamoto, Y., Mathews, F.S. and Davidson, V.L. Chemical and kinetic reaction mechanisms of quinohemoprotein amine dehydrogenase from Paracocus denitrificans. Biochemistry 42:10896-10903 (2003).

Datta, S., Ikeda, T., Kano, K. and Mathews, F.S. Structure of the phenylhydrazine adduct of the quinohemoprotein amine dehydrogenase from Paracoccus denitrificans at 1.7 A resolution. Acta Crystallographic Section D-Biological Crystallography 59:1551-1556 (2003).

Linda J. Pike

Westover, E.J., Covey, D.F., Brockman, H.L., Brown, R.E. and Pike, L.J. Cholesterol depletion results in site-specific increases in epidermal growth factor receptor phosphorylation due to membrane level effects. JBC 278: 51125-51133 (2003).

Pike, L.J. "Role of lipid domains in EGF receptor signaling" in Handbook of Cell Signaling, R.A. Bradshaw and E.A. Dennis, editors, Academic Press (2003).

Pike, L.J. Lipid Rafts: Bringing order to chaos. J. Lipid Res. 44:655-667 (2003).

Jay W. Ponder

Ponder, J.W. and Case, D.A. Force fields for protein simulatioin. Adv. Prot. Chem. 66:27-85 (2003).

Ren, P. and Ponder, J.W. A polarizable atomic multipole water model for molecular mechanics simulation. J. Phys. Chem. B 107:5933-5947 (2003).