Selected Core and Collaborative Publications

 

2004

 

Bickford, L.C., Mossessova, E., Goldberg, J.  A Structural View of the COPII Vesicle Coat.  Curr. Opin. Struct. Biol. 14: (2) 147-153, 2004.

 

Blaszczyk, J., Li, Y., Wu, Y., Shi, G., Ji, X., Yan, H.  Essential Roles of a Dynamic Loop in the Catalysis of 6-Hydroxymethyl-7,8-Dihydropterin Pyrophosphokinase.  Biochemistry 43: 1469-1477, 2004.

 

Bobkov, A.A., Muhlrad, A., Shvetsov, A., Benchaar, S., Scoville, D., Almo, S. C., Reisler, E.  Cofilin (ADF) Affects Lateral Contacts in F-Actin.  J. Mol. Biol. 337: 93-104, 2004.

 

Botos, I., Melnikov, E.E., Cherry, S., Tropea, J.E., Khalatova, A.G., Rasulova, F., Dauter, Z., Maurizi, M.R., Rotanova, T.V., Wlodawer, A., Gustchina, A.    The Catalytic Domain of EscherichiA coli Lon Protease has a Unique Fold and a Ser-Lys dyad in the Active Site.  J. Biol. Chem. 279: 8140-8148, 2004.

 

Bryngelson, P.A., Arobo, S.E., Pinkham, J.L., Cabelli, D.E., Maroney, M.J. Expression, Reconstitution and Mutation of Recombinant Streptomyces Coelicolor NiSOD.  J. Am. Chem. Soc. 126: 460–461, 2004.

 

Bukowski, M.R., Zhu, S., Koehntop, K.D., Brennessel, W.W., Que, L.  Characterization of an FeIII-OOH Species and its Decomposition Product in a Bleomycin Model System.  Journal of Biological Inorganic Chemistry 9: (1) 39-48, 2004.

 

Chance, M.R., Fiser, A., Sali, A., Pieper, U., Eashwar, N., Xu, G., Radahakanan, T., Marinkovic, N.  High Throughput Computational and Experimental Techniques in Structural Genomics. Genome Research in press, 2004.

 

Chance, M.R., Zak, O., Aisen, P., Liu, R., Xu, G., Guan, J-Q.  Structure of Transferrin: Receptor Complex as Analyzed by Footprinting and Mass Spectrometry. J. Am. Soc. Mass Spectrometry, Vol. 15, 63S, 2004.

 

Darbha, R., Phogat, S., Labrijn, A.F., Shu, Y., Gu, Y., Andrykovitch, M., Zhang, M.Y., Pantophlet, R., Martin, L., Vita, C., Burton, D.R., Dimitrov, D.S., Ji, X.  Crystal Structure of the Broadly Cross-Reactive HIV-1-Neutralizing Fab X5 and Fine Mapping of its Epitope.  Biochemistry 43: 1410-1417, 2004.

 

Derewenda, U., Mateja, A., Devedjiev, Y., Routzahn, K., Evdokimov, A.G., Derewenda, Z.S., Waugh, D.S.  The Structure of Yersinia Pestis V-Antigen, an Essential Virulence Factor and Mediator of Immunity Against Plague. Structure 12: 301-306, 2004.

 

Dokken, K.M., Davis, L.C., Erickson, L.E., Marinkovic, N.  Synchrotron Fourier Transform Infrared Spectroscopy as a Tool to Monitor the Fate of Organic Contaminants in Plants.  Proceedings of Eastern Analytical Conference, 2004.

 

Gogos, A., Gorman, J., Shapiro, L.  Crystal Structure of YfdW Protein from E. coli.  Acta Cryst. D60: 507-511, 2004.

 

Gonzales, P.E., Solomon, A., Sagi, I., Milla, M.E.  Inhibition of the TNFConverting Enzyme (TACE) by its pro Domain.  Journal of Biological Chemistry   in press, 2004.

 

Guan, J.G., Almo, S.C., Chance, M.R.  Synchrotron Radiolysis and Mass Spectrometry: A New Approach to Research on the Actin Cytoskeleton. Acct. Chem. Res. 37: 221-229, 2004.

 

Guan, J-Q., Almo, S., Chance, M.R.  Radical Approaches to Study Actin Cytoskeleton by Mass Spectrometry.  J. Am. Soc. Mass Spectrometry,  Vol. 15, 92S, 2004.

 

Guan, J-Q., Almo, S.C., Reisler, E., Chance, M.R.  Solution Structures of Isolated G- and F-Actin Revealed by Synchrotron Radiolysis and Mass Spectrometry.  Biophysical J. 86: 72a, 2004.

 

Guan, J-Q., Chance, M.R. Footprinting Methods to Examine the Structure and Dynamics of Proteins. Encyclopedia of Molecular Cell Biology and Molecular Medicine, 2nd Ed., R. Meyers, Editor, Wiley Inc., p. 549-568, 2004.

 

Gupta, S., Mangel, W.F., Baniecki, M.L., McGrath, W.J., Takamoto, K.G., Chance, M.R.  DNA Binding Provides a Molecular Strap Activating the Adenovirus Proteinase. Mol. & Cell Proteomics in press, 2004.

 

Gupta, S., Mangel, W.F., McGrath, W.J., Perek, J.L., Lee, D.W., Chance, M.R.  Structural Studies on the Interaction of the Adenovirus Proteinase (AVP) with its Cofactors Using Synchrotron Protein Footprinting.  Biophysical J. 86: 509a, 2004.

 

Himanen, J.P., Chumley, M., Lackmann, M., Li, C., Barton, W.A., Jeffrey, P.D.,Vearing, C., Geleick, D., Feldheim, D., Boyd, A., Henkemeyer, M., Nikolov, D.B.  Repelling Class Discrimination: EphrinA5 Binds to and Activates EphB2 Receptor Signaling.  Nature Neuroscience 7: (5) 501-509, 2004.

 

Kiselar, J.G., Pollard, T.D., Almo, S.C., Chance, M.R.  Probing Interactions of Proteins and their Macromolecular Assemblies Using Synchrotron Radiolysis.  J. Am. Soc. Mass Spectrometry,  Vol. 15, 36S, 2004.

 

Kleinfeld, O., Rulisek, L., Bogin, O., Frenkel, A., Havlas, Z., Burstein, Y., Sagi, I. Higher Metal-Ligand Coordination in the Catalytic Site of Cobalt-Substituted Thermoanaerobacter Brockii Alcohol Dehydrogenase Lowers the Barrier for Enzyme Catalysis.  Biochemistry in press, 2004.

 

Lappi, S.E., Franzen, S.  Eigenvector Mapping: A Method for Discerning Solvent Effects on Vibrational Spectra.  Spectrochimica Acta Part A, 60: 357-370, 2004.

 

Liu, R., Zak, O., Guan, J-Q., Aisen, P., Chance, M.R. Human Transferrin Binding Sites with Transferrin Receptor Detected by Hydroxyl Radical Footprinting and Mass Spectrometry.  Biophysical J. 86: 96a, 2004.

 

Marinkovic, N.S., Sullivan, M.R., Huang, R., Radhakannan, T., Chance, M.R.  Metallomics – High Throughput Determination of Transition Metal Content in Proteins.  Biophysical J. 86: 305a, 2004.

 

Masip, L., Pan, J., Haldar, S., Penner-Hahn, J.E., DeLisa, M.P.,  Georgiou, G.,  Bardwell, J., Collet, J-F  An Engineered Pathway for the Formation of Protein Disulfide Bonds.  Science  303: 1185-1189, 2004.

 

Nesic, D., Hsu, Y., Stebbins, C.E.  Assembly and Function of a Bacterial Genotoxin.  Nature 429: 429-433, 2004.

 

Penner-Hahn, J.E.  Characterization of ‘Spectroscopically Quiet’ Metals in Biology.  Coord. Chem. Rev., in press, 2004.

 

Radhakannan, T., Rajashankar, K., Fedorov, A.A., Dodatko, T., Chance, M.R., Renzoni, A., Cossart, P., Almo, S.C.  The Crystal Structure of PrfA, the Transcriptional Regulator in Listeria Monocytogenes: The Casual Agent of Listeriosis.  Biophysical J. 86: 78a, 2004.

 

Saxena, A.K., Saul, A., Garboczi, D.N.  Related Articles, Links Crystallization and Preliminary X-ray Analysis of the Plasmodium Vivax Sexual Stage 25 kDa Protein Pvs25, a Transmission-Blocking Vaccine Candidate for Malaria. Acta Crystallogr D Biol Crystallogr. 60: 706-708, 2004.

 

Shi, W., Ting, L.M., Kicska, G.A., Lewandowicz, A., Tyler, P.C., Evans, G.B., Furneaux, R.H., Kim, K., Almo, S.C., Schramm, V.L.  Plasmodium Falciparum Purine Nucleoside Phosphorylase: CRYSTAL STRUCTURES, IMMUCILLIN INHIBITORS, AND DUAL CATALYTIC FUNCTION.  J. Biol. Chem. 279: 18103, 2004.

 

Singh, V., Shi, W., Evans, G.B., Tyler, P.C., Furneaux, R.H., Almo, S.C.,  Schramm, V.L.  Picomolar Transition State Analogue Inhibitors of Human 5'-Methylthioadenosine Phosphorylase and X-ray Structure with MT-Immucillin-A.  Biochemistry 43: 9-18, 2004.

 

Smith, F.M., Vearing, C., Lackmann, M., Treutlein, H., Himanen, J.P., Chen, K., Saul, A., Nikolov, D.B., Boyd, A.W.  Dissecting the EphA3/ephrin-A5 Interactions Using a Novel Functional Mutagenesis Screen.  J. Biol. Chem. 279: (19) 9522-9531, 2004.

 

Solomon, A., Rosenblum, G.,Gonzales, P.E., Leonard, J.D., Mobashery, S.,Milla, M.E., Sagi, I.  Pronounced Diversity in Electronic and Chemical Properties Between the Catalytic Zinc Sites of TACE and MMP’s Despite their High Structural Similarity.  Journal of Biological Chemistry in press, 2004.

 

Sun, M-Z., Burk, R., Takamoto, K., Chance, M.R.  Probing HPV E7 Structure and Interaction with pRB by Using Mass Spectrometry Coupled to Synchrotron X-ray Protein Footprinting.  J. Am. Soc. Mass Spectrometry, Vol. 15, 78S, 2004.

 

Takamoto, K.G., Chance, M.R. Footprinting Methods to Examine the Structure and Dynamics of Nucleic Acids.  Encyclopedia of Molecular Cell Biology and Molecular Medicine, 2nd Ed., R. Meyers, Editor, Wiley Inc., p. 521-548, 2004.

 

Taylor S.C., Ferguson, A.D., Bergeron, J.J.M., Thomas, D.Y.  The ER Protein Folding Sensor UDP-glucose Glycoprotein-Glucosyltransferase Modifies Substrates Distant to Local Changes in Glycoprotein Conformation. Nature Struct. & Molecular Biol. 11: 128-134, 2004.

 

Thorson, J.S., Barton, W.A., Hoffmeister, D., Albermann, C., Nikolov, D.B. Structure-Based Enzyme Engineering and Its Impact on In Vitro         Glycorandomization.  ChemBioChem. 5: 16-25, 2004.

 

Weng, T-C, Ph.D. Theses.  X-ray Absorption Spectroscopy Studies on Redox-Active Manganese. Department of Chemistry, University of Michigan,  February 2004.

 

Wetzel, D.L., Striova, J., Higgins, D.A., Collinson, M.M.  Synchrotron Infrared Microspectroscopy Reveals Localized Heterogeneities in an Organically Modified Silicate Film.  Vibrational Spectroscopy in press, 2004.

 

Wlodawer, A., Li, M., Gustchina, A., Oyama, H., Oda, K., Beyer, B.B., Clemente, J., Dunn, B.M.  Two Inhibitor Molecules Bound in the Active Site of Pseudomonas Sedolisin: A Model for the Bi-Product Complex Following Cleavage of a Peptide Substrate. Biochem. Biophys. Res. Comm. 314: 638-645, 2004.

 

Xu, G., Chance, M.R.  Radiolytic Modification of Amino Acid Side-Chains for Probing Protein-Protein Interactions by Hydroxyl Radicals and Mass Spectrometry. J. Am. Soc. Mass Spectrometry, Vol. 15, 23S, 2004.

 

Xu, G., Chance, M.R. Radiolytic Modification of Acidic Amino Acids: New Probes for Protein Footprinting.  Anal. Chem. 76: 1213-1221, 2004

 

Xu, G., Takamoto, K., Chance, M.R.  Radiolytic Modification of Basic and Acidic Amino Acid Residues in Peptides: New Probes for Protein-Protein Charge Interactions.  Proceedings of Pittsburgh Conference, 2004.

 

Yu, P., McKinnon, J.J., Christensen, C.R., Christensen, D.A.  Using Synchrotron FTIR Microspectroscopy to Reveal Chemical Features of Feather Protein Secondary Structure and Relation to Protein Value, Comparison with Other Feed Protein Sources.  British Journal of Nutrition, in press, 2004.

 

Yu, P., McKinnon, J.J., Christensen, C.R., Christensen, D.A. Imaging Molecular Chemistry of Pioneer Corn. Journal of Agricultural and Food Chemistry, in press, 2004.

 

Yu, P., McKinnon, J.J., Christensen, C.R., Christensen, D.A. Use of Synchrotron-Base FTIR Microspectroscopy to Reveal Chemical Features of Feather Protein Secondary Structure and Its Relation to Protein Value. Proceedings of ADSA-ASAS-PSA 2004 Joint Meeting.

 

Yu, P., McKinnon, J.J., Christensen, D.A.  Application of Synchrotron-Based FTIR Microspectroscopy to Animal Feed and Nutrition Science.  Journal of the Science of Food and Agriculture, in press, 2004.

 

Yu, P., McKinnon, J.J., Newkirk, R.W., Christensen, C.R., Christensen, D.A.  Ultrastructural-Chemical Makeup of Canola Seed Tissues Explored with Synchrotron Reflection FTIR Microspectroscopy: A Preliminary Study. Proceedings of ADSA-ASAS-PSA 2004 Joint Meeting.

 

Zhang, X., Schwartz, J.C., Guo, X., Bhatia, S., Cao, E., Chen, L., Zhang, Z.Y., Edidin, M.A., Nathenson, S.G., Almo, S.C.  Structural and Functional Analysis of the Costimulatory Receptor Programmed Death-1. Immunity 20: 337-347, 2004.