Selected Core and Collaborative Publications

 

2005

Akabayov, B., Doonan, C.J., Pickering, I.J., George, G.N., Sagi, I. Using softer X-ray absorption spectroscopy to probe biological systems. J Synchrotron Radiat. 12: 392-401, 2005.

 

Kharenko, O.A., Kennedy, D.C., Demeler, B., Maroney, M.J., Ogawa, M.Y. Cu(I) Luminescence from the Tetranuclear Cu4S4 Cofactor of a Synthetic 4-Helix Bundle. J. Am. Chem. Soc. 127: 7678-7679, 2005.

Hakemian, A., Tinberg, C., Kondapali, K., Tesler, J., Hoffman, B., Stemmler, T., Rosenzweig, A. The Copper Chelator Methanobactin from Methylosinus Trichosporium OB3b Binds Copper(I). J. Am. Chem. Soc. 127: 17142-3, 2005.

 

Schubot, F., Cherry, S., Austin, B., Tropea, J., Waugh, D. Crystal Structure of the Protease-Resistant Core Domain of Yersinia Pestis Virulence Factor Yopr. Protein Sci. 14: 1679, 2005.

 

Shi, W., Zhan, C., Ignatov, A., Manjasetty, B., Marinkovic, N., Sullivan, M., Huang, R., Chance, M., Metalloproteomics: High-Throughput Structural and Functional Annotation of Proteins in Structural Genomics. Structure. 13: 1473-1486, 2005.

 

Wen, W., Kumarasamy, B., Mukerjee, S., Auinat, M., Ein-Eli, Y. Origin of 5 V Electrochemical Activity Observed in Non-Redox Reactive Divalent Cation Doped LiM0.5-xMn1.5+xO4 (0J. Electrochem. Soc. 152: A1902, 2005.

 

Lansky, D., Mandimutsira, B., Ramdhanie, B., Clausen, M., Penner-Hahn, J., Zvyagin, S., Telser, J., Krzystek, J., Zhan, R., Ou, Z. Synthesis, Characterization, and Physicochemical Properties of Manganese(III) and Manganese(V)-Oxo Corrolazines. Inorg. Chem. 44: 4485-4498, 2005.

 

Thomas, P., Stone, E., Costello, A., Tierney, D., Fast, W. The Quorum-Quenching Lactonase from Bacillus thuringiensis is a Metalloprotein. Biochemistry 44: 7559-7569, 2005.

 

Li, Y., Blaszczyk, J., Wu, Y., Shi, G., Ji, X., Yan, H.  Is the Critical Role of Loop 3 of Escherichia coli 6-Hydroxymethyl-7,8-dihydropterin Pyrophosphokinase in Catalysis Due to Loop-3 Residues Arginine-84 and Tryptophan-89? Site-Directed Muagenesis, Biochemical, and Crystallographic Studies. Biochemistry. 44: 8590-8599, 2005.

 

Strokopytov, B., Fedorov, A., Mahoney, N., Kessels, M., Drubin, D., Almo, S. Phased Translation Function Revisited: Structure Solution of the Cofilin-Homology Domain from Yeast Actin-Binding Protein 1 Using six-Dimensinal Searches. Acta Cryst. D. 61: 285-293, 2005.

 

Pasternak, O., Biesiadka, J., Dolot, F., Hanschuh, L., Bujacz, G., Sikorski, M., Jaskolski, M. Structure of a Yellow Lupin Pathogensis-Related PR-10 Protein Belonging to a Novel Subclass. Acta Cryst. D. 61: 99-107, 2005.

 

Sekar, K., Rajakannan, V., Gayathri, D., Velmurugan, D., Poi, M., Dauter, M., Dauter, Z., Tsai, M. Atomic Resolution (0.97 Angstrom) Structure of the Triple Mutant (K53,56,121M) of Bovine Pancreatic Phopholipase A2. Acta Cryst. F. 61: 3-7, 2005.

 

Kim, J., Sitaraman, S., Hierro, A., Beach, B., Odorizzi, G., Hurley, J. Structural Basis For Endosomal Targeting by The Bro1 Domain. Developmental Cell. 8: 937~947, 2005.

 

Gunter, K., Aschner, M., Miller, L., Eliseev, R., Salter, J., Anderson, K., Hammond, S., Gunter, T. Determining the Oxidation States of Manganese in PC12 and Nerve Growth Factor-Induced PC12 Cells. Free Radical Biology and Medicine. 39: 164-181, 2005.

 

Gustchina, A., Li, M., Wunschmann, S., Chapman, M., Pomes, A., Wlodawer, A. Crystal Structure of Cockroach Allergen Bla g2, an Unusual Zinc Binding Aspartic Protease with a Novel Mode of Self-Inhibition. J. Mol. Biol. 348: 433-444, 2005.

 

Saikrishnan, K., Manjunath, G., Singh, P., Jeyakanthan, J., Dauter, Z., Sekar, K., Muniyappa, K., Vijayan, M. Structure of Mycobacterium smegmatis Single-Stranded DNA-Binding Protein and a Comparative Study Involving Homologus SSBs: Biological Implications of Structural Plasticity and Variability in Quaternary Association. Acta Cryst. D. 61: 1140-1148, 2005.

 

Jensen, M., Costas, M., Ho, R., Kaizer, J., Payeras, A., Umnck, E., Que, Jr., L., Rohde, J., Stubna, A. High-Valent Nonheme Iron. Two Distinct Iron(IV) Species Derived from a Common Iron(II) Precursor. J. Am. Chem. Soc.. 127: 10512-10525, 2005.

 

Fokine, A., Leiman, P., Shneider, M., Ahvazi, B., Boeshans, K., Steven, A., Black, L., Mesyanzhinov, V., Rossman, M. Structural and Functional Similarities Between the Capsid Proteins of Bacteriophages T4 and HK97 Point to a Common Ancestry. Proc Natl Acad Sci USA. 102: 7163-7168, 2005.

 

Longo, A., Leonard, C., Bassi, G., Berndt, D., Krahn, J., Tanaka Hall, T., Weeks, K. Evolution from DNA to RNA Recognition by the bI3 LAGLIDADG Maturase. Nat. Struct. Mol. Biol.. 12: 779, 2005.

 

Guarne, A., Brendler, T., Zhao, Q., Ghirlando, R., Austin, S., Yang, W. Crystal Structure of a SeqA-N Filament: Implications for DNA Replication and Chromosome Organization. EMBO J.. 24: 1502-1511, 2005.

 

Zhan, C., Fedorov, E.V., Shi, W., Ramagopal, U.A., Thirumuruhan, R., Manjasetty, B.A., Almo, S.C., Fiser, A., Chance, M.R., Fedorov, A.A.  The ybeY protein from Escherichia coli is a metalloprotein. Acta Crystallograph Sect F Struct Biol Cryst Commun. 61: 959-63, 2005.

Bonanno, J.B., Almo, S.C., Bresnick, A., Chance, M.R., Fiser, A., Swaminathan, S., Jiang, J., Studier, F.W., Shapiro, L., Lima, C.D., Gaasterland, T.M., Sali, A., Bain, K., Feil, I., Gao, X., Lorimer, D., Ramos, A., Sauder, J.M., Wasserman, S.R., Emtage, S., D'Amico, K.L., Burley, S.K.  New York-Structural GenomiX Research Consortium (NYSGXRC): a large scale center for the protein structure initiative. J Struct Funct Genomics. 6: 225-32, 2005. 

 

Deng, L., Velikovsky, C., Swaminathan, C., Cho, S., Mariuzza, R. Structural Basis for Recognition of the T Cell Adaptor Protein SLP-76 by the SH3 Domain of Phospholipase CGAMMA1. J. Mol. Biol. 352: 2005.

 

Wang, J., Stieglitz, K., Cardia, J., Kantrowitz, E. Structural Basis for Ordered Substrate Binding and Cooperativity in Aspartate Transcarbamoylase. Proc Natl Acad Sci USA. 102: 8881-8886, 2005.

 

Im, Y., Raychaudhuri, S., Prinz, W., Hurley, J. Structural Mechanism for Sterol Sensing and Transport by OSBP-Related Proteins. Nature. 437: 154-158, 2005.

 

Long, S., Campbell, E., MacKinnon, R. Voltage Sensor of Kv1.2: Structural Basis of Electromechanical Coupling. Science. 309: 903, 2005.

 

Long, S., Campbell, E., MacKinnon, R. Crystal Structure of a Mammalian Voltage-Dependent Shaker Family K+ Channel. Science. 309: 897, 2005.

 

Agarwal, R., Binz, T., Swaminathan, S. Structural Analysis of Botulinum Neurotoxin Serotype F Light Chain: Implications on Substrate Binding and Inhibitor Design. Biochemistry. 44: 11758-11765, 2005.

 

Wang, H., Liu, Y., Chen, Y., Robinson, H., Ke, H. Multiple Elements Jointly Determine Inhibitor Selectivity of Cyclic Nucleotide Phosphodiesterases 4 and 7. J. Biol. Chem. 280: 30949, 2005.

 

Brown, J., Zhou, Z., Reshetnikova, L., Robinson, H., Yammani, R., Tobacman, L., Cohen, C. Structure of tropomyosin’s mid-region: bending and binding sites for actin. Proc Natl Acad Sci USA. 102: 18878-18883, 2005.

 

Forster, A., Masters, E., Whitby, F., Robinson, H., Hill, C. The 1.9 Angstrom Structure of a Proteasome-11S Activator Complex and Implications for the Proteasome-Pan/PA700 Interactions. Mol. Cell. Bio. 18: 589, 2005.

 

DiMattia, M., Govindasamy, L., Levy, H., Whitaker-Gurda, B., Kohlbrenner, E., Chiorini, J., McKenna, R., Muzyczka, N., Zolotukhin, S., Agbandje-McKenna, M. Production, Purification, Crystallization and Preliminary X-ray Structural Studies of Adeno-Associated Virus Serotype 5. Acta Cryst. F. F61: 917-921, 2005.

 

Dong, G., Hutagalung, A., Fu, C., Novick, P., Reinisch, K. The Structures of Exocyst Subunit Exo70p and the Exo84p C-terminal Domains Reveal a Common Motif. Nat. Struct. Mol. Biol. 12: 1094, 2005.

 

Gorman, J., Shapiro, L. Crystal Structures of the Tryptophan Repressor binding Protein WrbA and complexes with Flavin Mononucleotide. Protein Sci. 14: 3004-3012, 2005.

 

Nicholson, M., Hahn, M., Wucherpfennig, K. Unusual features of Self-Peptide/MHC Binding by Autoimmune T Cell Receptors. Immunity. 23: 351-360, 2005.

 

Bitto, E., Bingman, C., Robinson, H., Allard, S., Wesenberg, G., Phillips, Jr., G. The Crystal Structure at 2.5 Angstrom Resolution of Human Basophilic Leukemia-Expressed Protein BLES03. Acta Cryst. F. 61: 812, 2005.

 

Mirza, I., Nazi, I., Korczynska, M., Wright, G., Berghuis, A. Crystal Structure of Homoserine Transacetylase from Haemophilus Influenzae Reveals a New Family of alpha/beta-Hydrolases. Biochemistry. 44: 15768-15773, 2005.

 

Robinson, Shi, Sullivan, Nolan, Schneider, Berman, Lynch, Rock, Rosenbaum, Johnson, Chance, and Sweet. An Undulator Beamline for Protein Crystallography at the NSLS: Commissioning and Operation of X29. Synchotron Radiation News, 27-30, 2005.

 

Guan, J.Q., Chance, M.R.  Structural proteomics of macromolecular assemblies using oxidative footprinting and mass spectrometry. Trends Biochem Sci 30: 583-92, 2005.

 

Shcherbakova, I., Brenowitz, M. Perturbation of the hierarchical folding of a large RNA by the destabilization of its Scaffold's tertiary structure. J Mol Biol. 354: 483-96, 2005.

 

Adilakshmi, T., Ramaswamy, P., Woodson, S. A. Protein-independent folding pathway of the 16 S rRNA 5¹ domain.  J. Mol. Biol. 351: 508-519, 2005.

 

Xu, G., Chance, M.R. Radiolytic Modification and Reactivity of Amino Acid Residues Serving as Structural Probes for Protein Footprinting. Anal. Chem. 77: 4549-55, 2005.

 

Xu G, Liu R, Zak O, Aisen P, Chance MR. Structural allostery and binding of the transferring receptor complex. Mol Cell Proteomics. 4: 1959-67, 2005.

 

Marinkovic, N., Gupta, S., Zhan, C., Chance, M. Synchrotron Radiation in Biosciences. Nucl. Instrum. Meth. B. 241: 242-246, 2005.

Marinkovic, N., Chance, M.R. “Synchotron Infared Microscopy”, Encyclopedia of Molecular Cell Biology and Molecular Medicine, 2nd Ed., Vol. 13, R. Meyers, Editor, Wiley Inc., p. 671-708, 2005.

Yu, P. Applications of Cluster Analysis (CLA) and Principal Component Analysis (PCA) in Feed Structure and Feed Molecular Chemistry Research, Using Synchrotron-Based FTIR Microspectroscopy. J. Agr. Food Chem. 53: 7115-7127, 2005.

 

Yu, P. Molecular Chemistry Imaging to Reveal Structural Features of Various Plant Feed Tissues. J. Struct. Biol. 150: 81-89, 2005.

 

Pietrzak, L., Miller, S. Microchemical Structure of Soybean Seeds Revealed in Situ by Ultraspatially Resolved Synchrotron Fourier Transformed Infrared Microspectroscopy. J. Agr. Food Chem. 53: 9304-9311, 2005.

 

Yu, P., Christensen, C., McKinnon, J., Christensen, D.  Ultrastructural-Chemical Makeup of Yellow- (Brassica Rapa) and Brown-Seeded (Brassica Napus) Canola within Cellular Dimensions, Explored with Synchrotron Reflection FTIR Microspectroscopy. Can. J. Plant. Sci. 85: 85: 533-541, 2005.

 

Yu, P. Application of Cluster Analysis (CLA) in Feed Chemical Imaging to Accurately Reveal Structural-Chemical Features of Feeds within Cellular Dimension. J. Agr. Food Chem. 53: 2872-2880, 2005.

 

Dokken, K., Davis, L., Marinkovic, N. Use of Fourier Transform Infrared Microspectroscopy in Plant Growth and Development. Appl. Spectrosc. Rev. 40: 1-26, 2005.

 

Wetzel, D., Post, G., Lodder, R. Synchrotron Infrared Microspectroscopic Analysis of Collagens I, III, and Elastin on the Shoulders of Human Thin-Cap Fibroatheromas. Vib. Spectrosc., 38: 53-59, 2005.

 

Clayton, C.R., Halada, G.P., Gouma, P. Microscopy and Microspectroscopy of  Aluminum and Ferrous Alloys and Their Surface Treatments, in Analytical and Mechanical Characterization of Aluminum and its Alloys, George E. Totten and D. Scott MacKenzie, editors, Marcel Dekker, Inc., New York, 2005.

 

Francis, A.J., Dodge, C.J., McDonald, J.A., Halada, G.P. Decontamination of Uranium-Contaminated Surfaces by Hydroxycarboxylic Acid with Uranium Recovery. Env. Sci. Technol. 39: 5015-5021, 2005.

 

Jones, K.W., Feng, H., Stern, E. A., Neuhäusler, U., Osán, J., Marinkovic, N., Song, Z.  Properties of New York/New Jersey Harbor Sediments.  Acta Physica Polonica A 109: 279-286, 2006.

 

Dokken, K.M., Davis, L.C., Marinkovic, N.S. Synchrotron radiation, infrared microspectroscopy (SR-IMS) as a tool to study the fate and transport of organic contaminants in plants. Spectroscopy 20: 14-20, 2005.

 

Dokken, K.M., Davis, L.C., Erickson, L.E., Castro-Diaz, S., Marinkovic, N.S. Synchrotron Fourier transforms infrared microspectroscopy: A new tool to monitor the fate of organic contaminants in plants. Microchemical Journal 81: 86-91, 2005.

 

Jian, D., Kim, Y., Maxwell, K., Beasley, S., Zhang, R., Gussin, G., Edwards, A., Darst, S.  Crystal Structure of Bacteriophage lamda cII and its DNA Complex. Mol. Cell. 19: 259-269, 2005.

 

Nikolov, D., Li, C., Barton, W., Himanen, J. Crystal Structure of the Ephrin-B1 Ectodomain: Implications for Receptor Recognitin and Signaling. Biochemistry. 44: 10947-10953, 2005.

 

Barton, W., Tzvekova, D., Nikolov, D. Structure of the Angiopoietin-2 Receptor Binding Domain and Identification of Surfaces Involved in Tie2 Recognition. Structure. 13: 825-832, 2005.

 

Hegde, S., Vetting, M., Roderick, S., Mitchenall, L., Maxell, A., Takiff, H., Blanchard, J.  A Fluoroquinolone Resistance Protein from Mycobacterium tuberculosis That Mimics DNA. Science. 308: 1480, 2005.

 

Ramagopal, U., Dauter, Z., Thirumuruhan, R., Fedorov, E., Almo, S. Radiation-Induced Site-Specific Damage of Mercury Derivatives: Phasing and Implications. Acta Cryst. D. 61: 1289-1298, 2005.

 

Sickmier, E., Brekasis, D., Paranawithana, S., Bonanno, J., Paget, M., Burley, S., Kielkopf, C. X-ray Structure of a Rex-Family Repressor/NADH Complex Insights into the Mechanism of Redox Sensing. Structure. 13: 43-54, 2005.

 

Li, S., Schmitz, K., Jeffrey, P., Wiltzius, J., Kussie, P., Ferguson, K. Structural Basis for Inhibition of the Epidermal Growth Factor Receptor by Cetuximab. Cancer Cell. 7: 301-311, 2005.

 

Chlenov, M., Masuda, Y., Murakami, K., Nikiforov, V., Darst, S., Mustaev, A. Structure and Function of Lineage-Specific Sequence Insertions in the Bacterial RNA Polymerase beta' Subunit. J. Mol. Biol.. 353: 138-154, 2005.

 

Sun, J., Wang, W., Yang, H., Liu, S., Liang, F., Fedorov, A., Almo, S., Zhang, Z. Structure and Biochemical Properties of PRL-1, a Phosphatase Implicated in Cell Growth, Differentiation, and Tumor Invasion. Biochemistry. 44: 12009-12021, 2005.

 

Hao, B., Zheng, N., Schulman, B., Wu, G., Miller, J., Pagano, M., Pavletich, N. Structural Basis of the Cks1-Dependent Recognition of P27Kip1 by the SCF skp2 Ubiquitin Ligase. Mol. Cell. 20: 9-19, 2005.

 

Manjasetty, B., Niesen, F., Scheich, C., Roske, Y., Goetz, F., Behlke, J., Sievert, V., Heinemann, U., Buessow, K. X-ray Structure of Engineered Human Aortic Preferentially Expressed Protein-1 (APEG-1). BMC Struct. Bio. 5: 21, 2005.

 

Janjusevic, R., Abramovitch, R., Martin, G., Stebbins, C. A bacterial inhibitor of host programmed cell death defenses is an E3 ubiquitin ligase. Science. 311: 222-226, 2005.

 

Marinkovic, N., Chance M.R., “Synchrotron Infrared Microscopy”, Encyclopedia of Molecular Cell Biology and Molecular Medicine, 2nd Ed., Vol. 13, R. Meyers, Editor, Wiley Inc., p. 671-708, (2005)

Xu, G., Kiselar, J.G., He, Q., and Chance, M.R. Secondary reactions and strategies to improve quantitative protein footprinting. Anal. Chem., 77: 3029-3037, 2005.

Cotter, R.J., Ilchenko, S., Wang, D., Gundry, R.  Tandem Time-of-Flight (TOF/TOF) Mass Spectrometry and Proteomics, Journal of Mass Spectrometry Society of Japan, 53(1): 7-17, 2005.

Cotter, R.J., Ilchenko, S., Wang, D.  The Curved-Field Reflectron: PSD and CID without Scanning, Stepping or Lifting, Int. J. Mass Spectrom. 240: 169-182, 2005.

Xu, G., Chance, M.R., “Radiolytic Modification of Sulfur Containing Acidic Amino Residues in Model peptides:  Fundamental Studies for Protein Footprinting, Anal. Chem., 77: 2437-2449, 2005.