Department of Biochemistry and Molecular Biology

Chair: Barry Rosen, PhD
4374 Scott Hall
(313) 577-1511

Articles Published

Azzone GF and Lee, CP.  Lars Ernster (1920 - 1998).  TIBS  24:166-167, 1999.

Bednar J*, Studitsky VM*, Grigoryev SA, Felsenfeld G, Woodcock CL. Nature of the nucleosomal barrier to transcription: direct observation of paused intermediates by electron cryo-microscopy.  Molecular Cell 4:77-386, 1999. *These authors equally contributed to the paper.

Brown LS, Needleman R and Lanyi JK.  Functional roles of aspartic acid residues at the cytoplasmic surface of bacteriorhodopsin.  Biochemistry 38(21):6855-61.

Brown LS, Needleman R and Lanyi JK.  Origins of deuterium kinetic isotope effects on the proton transfers of the bacteriorhodopsin photocycle.  Biochemistry 39(5):938-45, 2000.

Chang VW-H, Wu R and Ho YS.  Recycling of anion-exchange resins for plasmid DNA purification.  BioTechniques 26:1056, 1999.

Chon YS, Kandori H, Sasaki J, Lanyi JK, Needleman R and Maeda A.  Existence of two L photointermediates of halorhodopsin from halobacterium salinarium, differing in their protein and water FTIR bands.  Biochemistry 38(29):9449-55, 1999.

Dioumaev A, Brown LS, Needleman R and Lanyi JK.  Fourier transform infrared spectra of a late intermediate of the bacteriorhodopsin photocycle suggest transient protonation of Asp-212.  Biochemistry 38(31):10070-8, 1999.

Darville MI, Ho YS and Elzirik D.  NF-B is required for cytokine-induced manganese superoxide dismutase expression in insulin-producing cells.  Endocrinology 141:153-162, 2000.

Davis MD, VanderKuur JA and Brooks SC.  Ligand structure influences autologous down-regulation of estrogen receptor-alpha  messenger RNA.  J Steroid Biochem Mol Biol, 70:27-37, 1999.

Draghici S, Cumberland L and Kovari LC. Correlation of HIV protease structure with Indinavir resistance: a data mining and neural networks approach (Submitted to Proceedings of SPIE 2000).

Draghici S, Cumberland L, and Kovari LC. Data Mining HIV drug resistance with neural networks (Submitted to Proceedings of the IJCNN 2000).

Ghosh M, Shen J and Rosen BP.  Pathways of As(III) detoxification in Saccharomyces cerevisiae.  Proc Natl Acad Sci USA 96:5001-5006, 1999.

Green BN, Bordoli RS, Hanin LG, Lallier FH, Toulmond A and Vinogradov SN.  Electrospray ionization mass spectrometric determination of the molecular mass of the ~200kDa globin dodecamer subassemblies in hexagonal bilayer hemoglobins.  J Biol Chem 274:28206-28212, 1999.

Green BN, Kuchumov AR, Klemm D and Vinogradov SN.  An electrospray ionization mass spectrometric study of the giant, extracellular, hexagonal bilayer hemoglobin of the leech Haemopis grandis provides a complete enumeration of its subunits.  Int J Mass Spectrom Ion Proc 188:105-112, 1999.

Haimeur A, Guimond C, Pilote S, Mukhopadhyay R., Rosen BP, Poulin R and Ouellette, M. Elevated levels of polyamines and trypanothione resulting from overexpression of ornithine decarboxylase in arsenite resistant Leishmania.  Mol Microbiol, 34:726-735, 1999.

Henschen A, Theodor I, and Edwards BFP and Pirkle H.  Crotalase, a fibrinogen-clotting venom enzyme: primary structure and evidence for a fibrinogen recognition exosite different from thrombin, Thrombosis and Haemostasis 81:81-86, 1999.

Jaeschke H, Ho YS, Fisher MA, Lawson JA and Farhood, A.   Glutathione perodidase-deficient mice are more susceptible to neutrophil-mediated hepatic parenchymal cell injury during endotoxemia:  Importance of an intracellular oxidant stress.  Hepatology 29:443-450, 1999.

Johnson RM, Panchoosingh H. Goyette G and Ravindranath Y.  Increased deformability in fetal erythrocytes:  its occurrence in glycolytic enzyme deficiencies and accelerated erythropoiesis.  Ped Res 45:106-113, 1999.

Kandori H, Kinoshita N, Yamazaki Y, Maeda A, Shichida Y, Needleman R, Lanyi JK, Bizounok, M, Herzfeld, J, Raap, J and Lugtenburg J.  Structural change of tereonine 89 upon photoisomerization in bacteriorhodopsin as revealed by polarized FTIR spectroscopy.  Biochemistry, 38(30):9676-83, 1999.

Lehoux IE and Mitra B.  (S)-Mandelate Dehydrogenase from Pseudomonas putida: Mechanistic Studies with Alternate Substrates and pH and Kinetic Isotope Effects, Biochemistry 38, 5836-5848, 1999.

Lehoux IE and Mitra B. (S)-Mandelate Dehydrogenase from Pseudomonas putida: Mutations of the Catalytic Base Histidine274 and Chemical Rescue of Activity, Biochemistry 38:9948-9955, 1999.

Li J and Rosen BP. Steric limitations in the interaction of the ATP binding domains of the ArsA ATPase.  J Biol Chem  273:6796-6800, 1998.

Li J and Rosen BP. The linker peptide of the ArsA ATPase.  Mol Microbiol 35:361-367, 2000.

Liu G, Schwartz JA and Brooks SC.   p53 down regulates  ER responsive genes by interfering with the binding of  ER to ERE.  Biochem Biophys Res Comm 264:359-364, 1999.

MacArthur RD, Crane LR, Kosmyna JM, Kovari LC, Podzorski R.  The avoidance of Zidovudine in Nevirapine-containing antiretroviral regimens may allow for the successful use of Efavirenz in subsequent antiretroviral regimens (Submitted to Lancet).

Mukhopadhyay R and Rosen BP.  The Saccharomyces cerevisiae ACR2 gene encodes an arsenate reductase, FEMS Microbiol Lett  168:127-136, 1998.

Oka T. Kamikubo H, Tokunaga F, Lanyi JK, Needleman R and Kataoka M.  Conformational change of helix G in the bacteriorhodopsin photocycle: investigation with heavy atom labeling and x-ray diffraction.  Biophys J 76(2):1018-23, 1999.

Rensing C, Fan B, Sharma R, Mitra B and Rosen BP.  CopA:  an Escherichia coli Cu(I)-translocating P-type ATPase.  Proc Natl Acad Sci USA 97:652-656, 2000.

Rensing C, Mitra B and Rosen BP.  A Zn(II)-translocating P-type ATPase from Proteus mirabilis.  Biochemistry and Cell Biology, 76:787-790, 1999.

Rensing C, Sun Y, Mitra B and Rosen BP.  Pb(II)-translocating P-type ATPases.  J Biol Chem  273:32614-32617, 1998.

Sharma R, Rensing C, Rosen BP and Mitra B.  The ATP hydrolytic activity of purified ZntA, a Pb(II)/Cd(II)/Zn(II)-translocating ATPase from Escherichia coli, J Biol Chem 275:3873-3878, 2000.

Sharma R, Rensing C, Rosen BP and Mitra B. The ATP hydrolytic activity of purified ZntA, a Pb(II)/Cd(II)/Zn(II)-translocating ATPase from Escherichia coli, J Biol Chem 275:3873-3878, 2000.

Shi J, Vlamis-Gardikas A, Aslund F, Holmgren A and Rosen BP.  Reactivity of glutaredoxins 1, 2 and 3 from Escherichia coli shows that glutaredoxin 2 is the primary hydrogen donor to ArsC-catalyzed arsenate reduction.  J Biol Chem 274:36039-36042, 1999.

Stevens SY, Hu W, Gladysheva T, Rosen BP, Zuiderweg ER and Lee L.  Secondary structure and fold homology of the ArsC protein from the Escherichia coli arsenic resistance plasmid R773.  Biochemistry 38:10178-10186, 1999.

Studitsky VM. Preparation and analysis of positioned nucleosomes. in Chromatin protocols, Humana Press, 17-27, 1999.

Takashima S, Kuchumov AR and Vinogradov SN. The apparently symmetrical hexagonal bilayer hemoglobin from Lumbricus terrestris has a large dipole moment.  Biophys Chem 77:27-35, 1999.

Tanio M, Inoue S, Yokota K, Seki T, Tuzi S, Needleman R, Lanyi JK, Naito A and Saito H.  Long-distance effects of site-directed mutations on backbone conformation in bacteriorhodopsin from solid state NMR of [1-13C] Val-labeled proteins.  Biophys J 77(1):431-42, 1999.

Tanio M, Tuzi S, Yamaguchi S, Kawaminami R, Naito A, Needleman R, Lanyi JK and Saito H.  Conformational changes of bacteriorhodopsin along the proton-conduction chain as studied with (13)C NMR of [3-(13)C] Ala-labeled protein:arg(82) may function as an information mediator.  Biophys J 77(3):1577-84, 1999.

Taveau J-C Kuchumov AR, Lamy JN, Boisset N and Vinogradov SN.  Three-dimensional reconstruction of Lumbricus terrestris hemoglobin at 22( resolutions: intramolecular localization of the globin and linker chains.  J Mol Biol  289:1343-1360, 1999.

Taveau J-C, Kuchumov AR, Lamy JN, Wall JS, Weber RE and. Vinogradov SN.  The role of the linker subunits in the reassembly of the 3.6MDa hexagonal bilayer hemoglobin from Lumbricus terrestris.  J Mol Biol, 289:1361-1374, 1999.

Tuzi S, Yamaguchi S, Tanio M, Konishi H, Inoue D, Naito A, Needleman R, Lanyi JK and Saito H.  Location of a cation-binding site in the loop between helices F and G of bacteriorhodopsin as studied by 13C NMR.  Biophys J 76(3):1523-31, 1999.

Walmsley AR, Zhou TQ, Borges-Walmsley I. and Rosen BP.  The ATPase mechanism of ArsA, the catalytic subunit of the arsenite pump.  J Biol Chem  274:16153-16161, 1999.

Varo, GL, Brown S, Needleman r, and Lanyi JK.  Binding of calcium ions to bacteriorhodopsin,  Biophys J 76(6):3219-26, 1999.

Wang Z-G, Schmid KJ and Ackerman, SH.  The Drosophila gene 2A5 complements the defect in mitochondrial F1-ATPase assembly in yeast lacking the molecular chaperone Atp11p, FEBS Lett, 452:305-308, 1999.

Winters MA, Coolley KL, Girard YA, Hamdan H, Kovari LC and Merigan TC.  Genotypic, phenotypic, and structural analysis of a deletion in the (3-(4 region of the HIVŠ1 reverse transcriptase gene that is associated with resistance to nucleoside reverse transcriptase inhibitors. (Submitted to Journal of Virology).

Xiong Y, Peterson PL and Lee CP.  Effect of N-acetyl L cysteine on mitochondrial function following traumatic brain injury in rats.  J Neurotrauma 16:1067-1082, 1999.

Xu Y and Mitra B.  A Highly Active Soluble Mutant of the Membrane-Associated (S)-Mandelate Dehydrogenase from Pseudomonas putida.  Biochemistry 38:12367-12376, 1999.

Zhang J, Graham GG, Montine TJ and Ho YS.  Enhanced N-methyl-4-phenyl-1,2,3,6-tetrahydropyridine toxicity in mice deficient in copper-zinc superoxide dismutase or glutathione peroxidase.  J  Neuropathol Exp Neurol 59:58-66, 2000.

Zhou TQ and Rosen BP.  Asp45 is a Mg2+ ligand in the ArsA ATPase.  J Biol Chem 274,13854-13858, 1999.

Zhou TQ, Rosen BP and Gatti DL.  Crystallization and preliminary X-ray analysis of the catalytic subunit of the ATP-dependent arsenite pump encoded by the Escherichia coli plasmid R773.  Acta Crystallogr D Biol Crystallogr 55:921-924, 1999.

Articles In Press

Hanin LG and Vinogradov SN.  Combinatorics of giant hexagonal bilayer hemoglobins.  Math Biosci (in press).

Verweij BH, Muizelaar JP, Vinas FC, Peterson PL, Xiong Y and Lee CP. Dose response and time window curves for SNX-111 in the treatment of mitochondrial dysfunction after experimental traumatic brain injury: a new surrogate outcome measure for preclinical trials.  J Neurosurgery (in press).

Verweij BH, Muizelaar JP, Vinas FC, Xiong Y and. Lee CP.  Cerebral mitochondrial dysfunction after traumatic brain injury in humans. J Neurosurgery (in press)

Wang Z-G and Ackerman SH.  The assembly factor Atp11p binds to the {beta} subunit of the mitochondrial F1 ATPase, J Biol Chem (in press)

Weber RE and Vinogradov SN.  Nonvertebrate hemoglobins: functions and molecular adaptations.  Physiol Rev (in press).

Xiong Y, Peterson PL and. Lee CP. Alterations in cerebral energy metabolism induced by traumatic brain injury.  J Neurological Research. (in press).

Yoshida T, Maulik N, Engleman RM, Ho YS and Das DK.  Targeted disruption of the mouse Sod1 gene makes the hearts vulnerable to ischemic reperfusion injury.  Circ Res (in press).

Zal F, Green BN, Martineu P, Lallier FH, Toulmond A, Vinogradov SN and Childress, JJ. Hemoglobin structure diversity among deep-sea hydrothermal vent alvinellid worms.  Eur J Biochemistry (in press).

Abstracts

Chen, Z, Chua, CC, Ho, Y-S, Hamdy, RC and Chua, BHL.  Overexpression of glutathione peroxidase protects against myocardial I/R injury in adult and aged mice.  The FASEB J  13:A753, 1999.

Cheng, P, Doyle, M, Panthangi, V, Rahman, A, MacArthur, RD, Kosmyna, JM, Crane, LR, Podzorski, R, Draghici, S and Kovari, LC.  Mechanisms of HIV-1 protease drug resistance. Infectious Diseases Society of America Annual Meeting, Philadelphia, 1999.

Cumberland, LT, Draghici, S and Kovari, LC.  Using data mining and neural networks techniques to predict resistance and cross-resistance of HIV-1 protease. Data Mining and Knowledge Discovery: Theory, Tools, and Technology II. OR29, Dasarathy, 1999.

Kovari, LC, Draghici, S, Cheng, P, Doyle, M, Panthangi, V, Rahman, A, Lloyd, R, Holler, TP, Pavlovsky, AR, MacArthur, L, Crane and Kosmyna, J.  Structure-function study of HIV protease drug resistance. Data Mining in Crystallography, Erice, Italy, 1999.

Lee, CP, Xiong Y and. Peterson PL.  Oxidative stress and perturbation of cellular calcium homeostasis in mitochondrial dysfunction induced by traumatic brain injury.  J Neurochem 72: S86B, 1999.

Liu, G. Schwartz, JA and Brooks, SC. Physical interaction between hERa and p53 and its functional effect:  Keystone Symposium Endocrine Disruptors Granlibakken Resort, CA, February, 1999.

MacArthur, RD, Kosmyna, JM, Crane, LR and Kovari, LC.  The presence or absence of Zidovudine in a Nevirapine-containing antiretroviral regimen determines which of two Nevirapine-limiting mutations occurs in virologic failure. ICAAC, San Francisco, 1999.

MacArthur, RD, Kosmyna, JM, Crane, LR, Kovari, LC, Podzorski, R. Sequencing of non-nucleoside reverse transcriptase inhibitors based on specific mutational patterns fails to lower plasma HIV-RNA levels in persons extensively pre-treated with antiretrovirals who are failing virologically on nevirapine-containing antiretroviral regimens. European AIDS Conference, Lisbon, 1999.

Sheluho, DS, Wang, Z-G, and Ackerman, SH, Probing the action of Atp11p and Atp12p in mitochondrial F1-ATPase assembly, FASEB J, 13:A1523, Abstract No 1099, 1999.

Winters, MA, Kim, E, Chou, S, Warford, A, Kagan, R, Fenwick, R, Kovari, LC and Merigan, TC.  Insertions between codons 35 and 38 of the protease gene in HIV-1 strains from patients failing antiretroviral therapy. 7th Conference on Retroviruses and Opportunistic Infections, San Francisco, 2000.

Xiong, Y, Peterson, PL, Lin H, Chen, B and Lee CP. Effects of traumatic brain injury [TBI] on apoptosis-regulating proteins in rats.  J Neurotrauma 16:1004, 1999.

Books and Chapters

Bhattacharjee, H., Ghosh, M, Mukhopadhyay, R and Rosen, BP.  Arsenic pumps from E. coli to humans. In Transport of Molecules Across Membranes, JK Broome-Smith, S Baumber, CJ. Stirling and BF. Ward, eds, Society for General Microbiology 58, 58-79 1999.

Jaeschke, H, Ho, Y-S, Fisher, MA, Lawson, JA and Farhood, A.  Reactive oxygen and inflammatory liver injury.  In Cells of the Hepatic Sinusoid.  Vol 7 (E. Weiss, DL Knook and R. Fraser, eds)  Kupffer Cell Foundation, Leiden, The Netherlands, pp 211-215, 1999.

Kuroda, M, Xu, C and Rosen, BP.  Mechanisms of bacterial resistance to heavy metals.  J. Biochem (Tokyo), 123:16-23, 1998.

Lehoux, I and Mitra, B.  Mechanistic Roles of the Conserved Residue Arginine 277 in S-Mandelate Dehydrogenase from Pseudomonas putida, Flavins and Flavoproteins (S. Ghisla, P. Kroneck, P.

Macheroux & H. Sund, ed) Agency for Scientifc Publications, Berlin,  471-474, 2000.

Mukhopadhyay, R, Li, J, Bhattacharjee, H and Rosen, BP. Metalloid Resistance Mechanisms. in Resolving the Antibiotic Paradox, Rosen, BP and Mobashery, S, eds, Plenum Press, pp 159-181, 1998.

Rensing, C and Rosen, BP, Transport of Soft Metals in Prokaryotes.  in Molecular Biology and Toxicology of Metals, RK. Zalpus and DJ Koropatnick, eds.  Taylor and Francis, London. in press, 1999.

Rensing, C, Ghosh, M and Rosen, BP.  Families of soft metal ATPases.  J Bacteriol 181, 5891-5897, 1999.

Rosen, BP, Bhattacharjee, H and Kuroda, M. Arsenic ATPases in Methods in Enzymology, 292:82-97,1998.

Rosen, BP, Bhattacharjee, H., Zhou, TQ and Walmsely, AR.  Mechanism of the ArsA ATPase, Biochem Biophys Acta, 1461:207-215, 1999.

Rosen, BP, Families of arsenic transporters.  Trends in Microbiology, 7:207-212, 1999.

Rosen, BP. The role of efflux in bacterial resistance to soft metals and metalloids. in Essays in Biochemistry, Vol. 34:  Metalloproteins; SJ Higgins and DP Ballou, eds in press, 1999.

Vinogradov. SN.  Self-assembly.  In: The Encyclopedia of Molecular Biology, (T. Creighton ed), J. Wiley & Sons, Inc, New York, pp 2307-2311, 1999.

Xu, C and Rosen, BP. Metalloregulation of Soft Metal Resistance Pumps.  in Proceedings of the Second International Symposium on Metals and Genetics, B Sarkar, ed, Plenum Press, in press, 1999.

Xu, Y and Mitra, B. (S)-Mandelate Dehydrogenase from Pseudomonas putida: The role of the membrane-binding segment and Glycine81 in the reactivity toward oxygen, Flavins and Flavoproteins (S. Ghisla, P. Kroneck, P. Macheroux & H. Sund, ed) Agency for Scientifc Publications, Berlin, 487-490, 2000.

Driessen, AJM, Rosen, BP and Konings, WN.  Diversity of transport mechanisms:  common structural principals.  Trends in Biochem Sci, in press.

Ghosh, M and Rosen, BP. Microbial resistance mechanisms for heavy metals and metalloids.  For Handbook of Heavy Metals in the Environment, Ed., B. Sarkar, in press.

Xiong, Y Peterson, PL and. Lee, CP.  Mitochondrial dysfunction following experimental traumatic brain injury: efficacy of blood brain barrier-penetrating antioxidant.  In Mitochondrial Ubiquinone [Coenzyme Q 10]: Biochemical, Functional, Medical, and Therapeutic Aspects in Human Health and Diseases [eds. M. Ebadi, J. Marwah and RK. Chopra] Peominent Press, AZ, 2000, in press.