Selected Case Center for Proteomics and Center for Synchrotron Biosciences Publications

 

2006

Lamour, V., Hogan, B. P., Erie, D. A., Darst, S. A. Crystal structure of Thermus aquaticus Gfh1, a Gre-factor homolog that inhibits rather than stimulates transcript cleavage. J. Molec. Biol. 356: 179-188, 2006.

 

Lilic, M., Vujanac, M., and Stebbins, C. E. A Common Structural Motif in the binding of Virulence Factors to Bacterial Secretion Chaperones.  Mol. Cell. 21: 653-64, 2006.

 

Patel, S., Ciatto, C., Chen, C., Bahna, F., Rajebhosale, M., Arkus, N., Schieren, I., Jessell, T., Honig, B. Type II Cadherin Ectodomain Structures: Implications for Classical Cadherin Specificity. Cell 124: 1255-1268, 2006.
 

Manjasetty, B., Bussow, K., Fieber-ErdMan, M., Roske, Y., Gobam, J., Scheich, C., Gotz, F., Niesen, F., Heinemann, U. Crystal Structure of Homo Sapiens PTD012 Reveals a Zinc-Containing Hydrolase Fold. Protein Sci. 15: 914-920, 2006.
 

Hoelz, A., Janz, J., Lawrie, S., Corwin, B., Lee, A., Sakmar, T. Crystal Structure of the SH3 Domain of beta PIX in Complex with a High Affinity Peptide from PAK2. J. Mol. Biol. 358: 509-522, 2006.
 

Roden, M., Brims, D., Fedorov, A., DiLorenzo, T., Almo, S., Nathenson, S., Anovitz, L., Wesolowski, D. Structural Analysis of H2-Db Class I Molecules Containing Two Different Allelic Forms of the type 1 Diabetes Susceptibility Factor beta-2 Microglobulin: Implications for the Mechanism Underlying Viriations in Antigen Presentation. Mol. Immunol. 43: 1370-1378, 2006.
 

McManus, E., Luisi, B., Perham, R. Structure of a Putative Lipoate Protein Ligase from Thermoplasma acidophilum and the Mechanism of Target Selection for Post-Translational Modification. J. Mol. Biol. 356: 625-637, 2006. 

 

Leduc, Y., Phenix, C., Puttick, J., Nienaber, K., Palmer, D., Delbaere, L. Crystallization, Preliminary X-ray Diffraction and Structure Solution of MosA, a Dihydrodipicolinate Synthase from Sinorhizobium Meliloti L5-30. Acta Cryst. F. F62: 49-51, 2006.

 

Mariana Margarit, S., Davidson, W., Frego, L., Stebbins, C.E. A Steric Antagonism of Actin Polymerization by a Salmonella Virulence Protein. Structure, 14(8):1219-29, 2006.

Manjasetty, B.A., Shi, W. Zhan, C., Fiser, A., Chance, M.R. “A High-Throughput Approach to Protein Structure Analysis”, Genetic Engineering, Vol. 28: 105-128, (2006).

Takamoto, K.G., Chance, M.R. “Radiolytic protein footprinting with mass spectrometry to probe the structure of macromolecular complexes”, Annual Review of Biophysics and Biomolecular Structure, Volume 35, 251-276 (2006).

Zheng, Q.Y., Rozanas, C.R., Thalmann, I., Chance, M.R., and Alagramam, K.N., “Inner ear proteomics of mouse models for deafness, a discovery strategy.” Brain Res. 1091(1):113-21 (2006).

Mukherjee, P.K., Mohamed, S., Chandra, J., Kuhn, D., Liu, S., Antar, O.S., Munyon, R., Mitchell, A.P., Andes, D., Chance, M.R., Rouabhia, M. and Ghannoum, M.A.  “Alcohol dehydrogenase modulates the ability of the pathogen Candida Albicans to form biofilm on catheter surfaces through an ethanol-based mechanism.”  Infection and Immunity. 74(7): 3804-16 (2006).
 

Hajkova, D., K. C. Rao, K. C. S., and Miyagi, M. The pH Dependency of the Carboxyl Oxygen Exchange Reaction Catalyzed by Lysyl Endopeptidase and Trypsin. J. Proteome Res., 5(7): 1667-1673, (2006).

Shi W., et al., Chance M.R. Beamline X29: a novel undulator source for X-ray crystallography. J. Synchrotron Radiation, V13:365-372 (2006).

Gobezie, R., Millett, P. J., Sarracino, D. S., Evans, C., and Thornhill, T. S. Proteomics: applications to the study of rheumatoid arthritis and osteoarthritis The Journal of the American Academy of Orthopaedic Surgeons 14(6): 325-332 (2006).

 

Periyannan, G., Costello, A., Tierney, D., Yang, K., Bennett, B., Crowder, M. Sequential Binding of Cobalt(II) to Metallo-beta-lactamase CcrA. Biochemistry 45: 1313-1320, 2006. 

Shearer, J., Long, L. A Superoxide Dismutase Maquette That Reproduces the Spectroscopic and Functional Properties of the Metalloenzyme. Inorg. Chem. 45: 2358 – 2360, 2006. 

Grembecka, J., Cierpicki, T., Drvedjiev, Y., Derewenda, U., Kang, B., Bushweller, J., Derewenda, Z. The Binding of the PDZ Tandem of Syntenin to Target Proteins. Biochemistry 45: 3674-3683, 2006. 

Stone, E., Costello, A., Tierney, D., Fast, W. Substrate-Assisted Cysteine Deprotonation in the Mechanism of Dimethylargininase (DDAH) from Pseudomonas aeruginosa. Biochemistry. 45: 5618-5630, 2006. 

Liu, Y., Cheney, M., Gaudet, J., Chruszcz, M., Lukasik, S., Suglyama, D., Lary, J., Cole, J., Dauter, Z. The Tetramer Structure of the Nervy Homology Two Domain, NHR2, is Critical for AML1/ETO's Activity. Cancer Cell 9: 249-260, 2006. 

Sekar, K., Yogavel, M., Gayathri, D., Velmurugan, D., Krishna, R., Poi, M., Dauter, Z., Dauter, M., Tsai, M. Atomic Resolution Structure of the Double Mutant (K53,56M) of Bovine Pancreatic Phospholipase A2. Acta Cryst. F. 62: 1-5, 2006. 

Velmurugan, D., Rajakannan, V., Gayathri, D., Banumathi, S., Yamane, T., Dauter, Z., Dauter, M., Sekar, K. Ab Initio Structure Determination of the Triple Mutant (K53,56,121M) of Bovine Pancreatic Phospholipase A(2) at Atomic and High Resolution Using ACORN. Current Science 90: 1091-1099, 2006. 

 

Shen, X., Hanson, J., Suib, S.L. In-situ Synthesis of Mixed-Valent Manganese Oxide Nanocrystals: An in-situ Synchrotron X-ray Diffraction Study. J. Am. Chem. Soc. 128: 4570-4571, 2006.

 

Costello, A.L., Periyannan, G., Yang, K.W., Crowder, M.W., Tierney, D.L. Site Selective Binding of Zn(II) to Metallo-b-Lactamase L1 from Stenotrophomonas maltophilia. J. Biol. Inorg. Chem. 11: 351-358, 2006.

 

Frost, B.J., Bautista, C.M., Huang, R., Shearer, J. Manganese Complexes of 1,3,5-triaza-7-phosphaadamantane (PTA): The First Nitrogen Bound Transition Metal Complex of PTA. Inorganic Chemistry 45: 3481 – 3483, 2006.

Stone, E.M., Costello, A.L., Tierney, D.L., Fast, W. Substrate-Assisted Cysteine Deprotonation in the Mechanism of Dimethylargininase (DDAH) from Pseudomonas aeruginosa. Biochemistry, 45(17): 5618-30, 2006.

Cook, J.D., Bencze, K.Z., Jankovic, A., Crater, A.K., Busch, C., Bradley, P.B., Spaller, M., Stemmler, T.L. Monomeric yeast frataxin is an iron binding protein. Biochemistry, 45(25): 7767-77, 2006.

 

Chai, S.C., Bruyere, J.R., Maroney, M.J. Probes of the catalytic site of cysteine dioxygenase. J. Biol. Chem., 281(23): 15774-9, 2006.

Manjasetty, B.A., Chance, M.R. Crystal Structure of E. coli L-Arabinose Isomerase (ECAI), the putative target of biological tagatose production, J. Mol. Biol. 360(2): 297-309, 2006.

Manjasetty, B.A. Turnbull, A., Bussow, K., Chance, M.R. Recent advances in protein structure analysis in recent research developments in biochemistry. 6: SG Pandalai, Ed., Research Signpost, Kerala, India, 2006.

Zhu, H., Nandakumar, J., Aniukwu, J., Wang, L., Glickman, M., Lima, C., Shuman, S. Atomic Structure and Nonhomologous End-Joining Function of the Polymerase Component of Bacterial DNA Ligase D. Proc Natl Acad Sci USA. 103: 1711-1716, 2006.
 

Hu, G., Lin, G., Wang, M., Dick, L., Xu, R., Nathan, C., Li, H. Structure of the Mycobacterium tuberculosis proteasome and mechanism of inhibition by a peptidyl boronate. Molecular Microbiology. 59: 1417-1428, 2006.
 

Nam, Y., Silz, P., Song, L., Aster, J., Blacklow, S. Structural Basis for Cooperativity in Recruitment of MAML Co-activators to Notch Transcription Complexes. Cell. 124: 973-983, 2006.
 

Sanghani, P., Davis, W., Zhai, L., Robinson, H. Structure-Function Relationships in Human Glutathione-Dependent Formaldehyde Dehydrogenase. Role of Glu-67 and Arg-368 in the Catalytic Mechanism. Biochemistry. 45: 4819-4830, 2006.
 

Kim, J., Malashkevich, V., Roday, S., Lisbin, M., Schramm, V., Almo, S. Structural and Kinetic Characterization of Escherichia coli TadA, the Wobble-Specific tRNA Deaminase. Biochemistry. 45: 6407-6416, 2006.
 

Cordero-Morales, J., Cuello, L., Zhao, Y., Jogini, V., Cortes, D., Roux, B., Perozo, E. Molecular Determinants of Gating at the Potassium-Channel Selectivity Filter. Nat. Struct. Mol. Biol. 13: 311, 2006.
 

Pawelek, P., Croteau, N., Ng-Thow-Hing, C., Khursigara, C., Moiseeva, N., Allaire, M., Coulton, J. Structure of TonB in Complex with FhuA, E. Coli Outer Membrane Receptor. Science. 312: 1399, 2006.
 

Fisher, C., Beglova, N., Blacklow, S. Structure of an LDLR-RAP Complex Reveals a General Mode for Ligand Recognition by Lipoprotein Receptors. Mol. Cell. 22: 277-283, 2006.
 

Safo, M., Ko, T., Musayev, F., Zhao, Q., Wang, A., Archer, G. Structure of the Mecl Repressor from Staphylococcus aureus in Complex with the Cognate DNA Operator of mec. Acta Cryst. F. 62: 320-324, 2006.
 

Gill, H., Boron, W. Preliminary X-ray Diffraction Analysis of the Cytoplasmic N-terminal Domain of the Na/HCO3 Cotransporter NBCe1-A. Acta Cryst. F. 62: 534-537, 2006.
 

Leduc, Y., Phenix, C., Puttick, J., Nienaber, K., Palmer, D., Delbaere, L. Crystallization, Preliminary X-ray Diffraction and Structure Solution of MosA, a Dihydrodipicolinate Synthase from Sinorhizobium Meliloti L5-30. Acta Cryst. F. F62: 49-51, 2006.

Adilakshmi, T., Lease, R. A., Woodson, S. A. Hydroxyl radical footprinting in vivo: mapping macromolecular structures with synchrotron radiation.  Nucl. Acids Res. 34: e64, 2006.

 

Nguyenle, T., Laurberg, M., Brenowitz, M., Noller, H.F. Following the Dynamics of Changes in Solvent Accessibility of 16 S and 23 S rRNA During Ribosomal Subunit Association Using Synchrotron-generated Hydroxyl Radicals. J Mol Biol., 359(5):1235-48, 2006.

 

Shcherbakova, I., Mitra, S., Beer, R.H., Brenowitz, M. Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins. Nucl. Acids Res. 34(6): e48, 2006.

 

Laederach, A., Shcherbakova, I., Liang, M.P., Brenowitz, M., Altman, R.B. Local kinetic measures of macromolecular structure reveal partitioning among multiple parallel pathways from the earliest steps in the folding of a large RNA molecule. J Mol Biol. 358: 1179-90, 2006.

 

Kwok, L.W., Shcherbakova, I., Lamb, J.S., Park, H.Y., Andresen, K., Smith, H., Brenowitz, M., Pollack, L. Concordant exploration of the kinetics of RNA folding from global and local perspectives. J Mol Biol. 355: 282-93, 2006.

 

Yu, P. An Emerging Method for Rapid Characterization of Feed Structures and Feed Component Matrix at a Cellular Level and Relation to Feed Quality and Nutritive Value. Archives of Animal Nutrition. 60: 229-244, 2006.

Seaman, S., Dyar, M., Marinkovic, N., Dunbar, N. An FTIR Study of Hydrogen in Anorthosite and Associated Melt Inclusions. Am. Mineral. 91: 12-20, 2006.