X6A Publications

--- Year 2007 ---

• Thai V, Renesto P, Fowler A, Brown D, Davis T, Gu W, Pollock DD, Kern D, and Raoult D, Eisenmesser E (2007 August 29) (132)

Structural, biochemical, and in vivo characterization of the first virally encoded cyclophilin from the Mimivirus JMB online press

• S. Wang, J. Engohang-Ndong, and I. Smith. (2007) (94)

Structure of the DNA-binding domain of the response regulator PhoP from Mycobacterium tuberculosis. Biochemistry. In process

• Varbanova M, Yamaguchi S, Yang Y, McKelvey K, Hanada A, Borochov R, Yu F, Jikumaru Y, Ross J, Cortes D, Je Ma C, Noel JP, Mander L, Shula ev V, Kamiya Y, Rodermel S, Weiss D, Pichersky E. (2007) (12a)

Methylation of Gibberellins by Arabidopsis GAMT1 and GAMT2. Plant Cell. 19:32-45

• J. Jakoncic , Y. Jouanneau, C. Meyer and V. Stojanoff. (2007) (50)

The catalytic pocket of the ring-hydroxylating dioxygenase from Spingomonas CHY1. Biochemical and Biophysical Research Communications(2007) 352 : 861-866

• Jean Jakoncic, Yves Jouanneau, Christine Meyer, Vivian Stojanoff (2007) (50)

The crystal structure of the ring-hydroxylating dioxygenase from Spingomonas CHY-1 FEBS Journal (2007) 274: 2470-2481

• Korczynska M, Mukhtar TA, Wright GD, Berghuis AM. (2007) (125)

Structural basis for streptogramin B resistance in Staphylococcus aureus by virginiamycin B lyase. Proc Natl Acad Sci U S A. 104(25) : 10388-93

• Susan Rouda and Emmanuel Skordalakes (2007) (180)

Structure of the RNA-Binding Domain of Telomerase: Implications for RNA Recognition and Binding. Structure. 15: 1403-1412

• Valverde, Roberto, Pozdnyakova, Irina, Kajander, Tommi, Venkatraman, Janani, and Regan, Lynne. (2007)

Fragile X Mental Retardation Syndrome: Structure of the KH1-KH2 Domains of Fragile X Mental Retardation Protein Structure. 15: 1090-1098.

• N. Moiseeva and M. Allaire

Using barium ions for heavy-atom derivatization and phasing of xylanase II from Trichoderma longibrachiatum Acta Cryst. (2007). D63: 1025-1028

• A. Jain and V. Stojanoff, 2007

Are you centered? An automatic crystal-centering method for high-throughput macromolecular crystallography
J. Synchrotron Rad, 14: 355-360 [ Read Article ]

--- Year 2006 ---

• Masuda, K., Richter, M., Song, X., Berezov, A., Masuda, K., Murali, R., Greene, M. I. & Zhang, H. (2006) (117)

AHNP-streptavidin: a tetrameric bacterially produced antibody surrogate fusion protein against p185her2/neu. Oncogene 25: 7740-7746

• Ficko-Blean E & Boraston AB (2006)

The Interaction of a Carbohydrate-binding Module from a Clostridium perfringens N-Acetyl-beta-hexosaminidase with Its Carbohydrate Receptor. J Biol Chem. 281(49):37748-57.

• Florence Pojer, Jean-Luc Ferrer, Stephane B. Richard, Dinesh A. Nagegowda, Mee-Lend Chye, Thomas J. Bach, and Joseph P. Noel (2006)

Structural basis for the design of potent and species-specific inhibitors of 3-hydroxy-3-methylglutaryl CoA synthases P NATL ACAD SCI USA, 103(31):11491-11496

• Bianchet, M.A., Krosky, D.J., Ghung, S., Seiple, L., Amzel, L.M., Stivers,J.T. (2006)

Mimicking damaged DNA with a small molecule inhibitor of human UNG2 Nucleic Acids Res 34: pp.5872-5879

• Park, H.H., Wu, H. (2006)

Crystal Structure of RAIDD Death Domain Implicates Potential Mechanism of PIDDosome Assembly J Mol Biol. 357: pp.358-364

• Jakoncic, J., Di Michiel, M., Zhong, Z., Honkimaki, V., Jouanneau, Y. & Stojanoff, V. (2006)

Anomalous Diffraction at Ultra-High Energy for Protein Crystallography. J. Appl. Cryst. 39: 831-841.

• Holyoak, T., Sullivan, S.M., and Nowak, T. ,2006

Structural insights into the mechanism of PEPCK catalysis. Biochemistry, 45: 8254-8263.

• K Horii, ML Kahn, and AB Herr. 2006

Structural basis for platelet collagen responses by the immune-type receptor glycoprotein VI. Blood 108:936-942.

• Schreiter ER, Wang SC, Zamble DB, Drennan CL, 2006

NikR-operator complex structure and the mechanism of repressor activation by metal ions. PNAS, 103: 13676-81.

• Xu, W., Ahmed, S., Moriyama, H., and Chollet, R. 2006

The Importance of the Strictly Conserved, C-terminal Glycine Residue in Phosphoenolpyruvate Carboxylase for Overall Catalysis: MUTAGENESIS AND TRUNCATION OF GLY-961 IN THE SORGHUM C4 LEAF ISOFORM. J Biol Chem 281: 17238-45.

• Alvarez-Venegas, R., Sadder, M., Hlavacka, A., Baluska, F., Xia, Y., Lu, G., Firsov, A., Sarath, G., Moriyama, H., Dubrovsky, J. G., and Avramova, Z. 2006

The Arabidopsis homolog of trithorax, ATX1, binds phosphatidylinositol 5-phosphate, and the two regulate a common set of target genes. Proc Natl Acad Sci U S A 103: 6049-54.

• Adams MA, Singh VK, Keller BO and Jia Z.,2006

Structural and biochemical characterization of gentisate 1,2-dioxygenase from Escherichia coli O157:H7. Mol. Microbiol. 61(6):1469-84.

• Adams MA and Jia Z., 2006

Modulator of Drug Activity B from Escherichia coli: Crystal structure of a prokaryotic homologue of DT-diaphorase. J. Mol. Biol 359(2): 455-65.

• Maximo Barreras, Mario A. Bianchet and Luis Ielpi., 2006

Crystallization and preliminary crystallographic cgaracterization of GumK, a membrane -associated glucorosyltransferase from Xanthomas Campestrid required for xanthan polysaccharide synthesis. Acta Cryst.F. 62: 880-883

• Olia AS, Al-Bassam J, Winn-Stapley DA, Joss L, Casjens SR, Cingolani G.,2006

Binding-induced stabilization and assembly of the phage P22 tail accessory factor gp4. J Mol Biol., 363(2):558-76.

• Shao, C., Zhang, F., Kemp, M.M., Linhardt, R.J., Waisman, D.M., Head, J.F., Seaton, B.A., 2006

Crystallographic analysis of calcium-dependent heparin binding to annexin A2. J.Biol.Chem. v281: pp.31689-31695, 2006

• Wilson, J.J., Kovall, R.A. ,2006

Crystal structure of the CSL-Notch-Mastermind ternary complex bound to DNA. Cell. v124: pp.985-996 , 2006

• Yang, M., Horii, K., Herr, A.B., Kirley, T.L. ,2006

Calcium-dependent dimerization of human soluble calcium activated nucleotidase: characterization of the dimer interface. J.Biol.Chem., v281: pp.28307-28317, 2006

• Sudhamsu, J., Crane, B.R. ,2006

Structure and Reactivity of a Thermostable Prokaryotic Nitric-oxide Synthase That Forms a Long-lived Oxy-Heme Complex. J.Biol.Chem., v281: pp.9623-9632, 2006

• Wang, Y., Zhang, Y., Ha, Y., 2006 Oct

Crystal Structure of a Rhomboid Family Intramembrane Protease. Nature. 444:179-183

• Laptenko, O., Kim, S.-S., Lee, J., Starodubtseva, M., Cava, F., Berenguer, J., Kong, X.P., Borukhov, S., 2006

pH-dependent conformational switch activates the inhibitor of transcription elongation. Embo. J. 25: 2131-2141

• Adams, J.J., Pal, G., Jia, Z., Smith, S.P., 2006 January

Mechanism of bacterial cell-surface attachment revealed by the structure of cellulosomal type II cohesin-dockerin complex. Proc.Natl.Acad.Sci.Usa 103: 305-310

• Nicholson, M.J., Moradi, B., Seth, N.P., Xing, X., Cuny, G.D., Stein, R.L., Wucherpfennig, K.W. , 2006

Small molecules that enhance the catalytic efficiency of HLA-DM. J.Immunol. 176: 4208-4220

• Xi, J., Liu, R., Rossi, M. J., Yang, J., Loll, P. J., Dailey, W. P., & Eckenhoff, R. G. (2006)

High resolution features from low affinity interactions: Photoactive analogs of the haloether anesthetics. ACS Chem. Biol. 1: 377-384.

• Hwang WC, Lin Y, Santelli E, Sui J, Jaroszewski L, Stec B, Farzan M, Marasco WA, Liddington RC. 2006 Nov 10

Structural Basis of Neutralization by a Human Anti-severe Acute Respiratory Syndrome Spike Protein Antibody,80R. J Biol Chem. 281(45):34610-6.

• Payandeh, J.; Fujihashi, M.; Gillon, W.; Pai, E.F., 2006.

The Crystal Structure of (S)-3-O-geranylgeranylglycerol-phosphate-synthase from Archaeoglobus fulgidus Reveals an Ancient Fold for an Ancient Enzyme. J.Biol.Chem., 281:6070-6078.

• Yang, Yue, Yuan, J.S., Ross, J., Noel, J.P., and Pichersky, E., 2006 Apr 15

An Arabidopsis thaliana methyltransferase capable of methylating farnesoic acid. Arch Biochem Biophys. 448(1-2):123-32.

• Natasha Pashkova, Yui Jin S. Ramaswamy, Lois S. Weisman, 2006 Jan.

Structural Basis for myosin V discrimination between distinct cargoes. EMBO Journal. 25:693-700

• K Pant, B Crane.

Nitrosyl-Heme Structures of Bacillus subtilis Nitric Oxide Synthase Have Implications for Understanding Substrate Oxidation. Biochemistry. 45: 2537-2544 (2006)

• R Williams, T Holyoak, G McDonald, C Gui, A Fenton.

Differentiating a Ligand's Chemical Requirements for Allosteric Interactions from Those for Protein Binding. Phenylalanine Inhibition of Pyruvate Kinase. Biochemistry. 45: 5421-5429 (2006)

• S Gabelli, H Azurmendi, M Bianchet, L Amzel, A Mildva.

X-ray, NMR, and Mutational Studies of the Catalytic Cycle of the GDP-Mannose Mannosyl Hydrolase Reaction. Biochemistry. 45: 11290-11303 (2006)

• G Cingolani, D Andrews, S Casjens.

Crystallogenesis of Bacteriophage P22 Tail Accessory Factor gp26 at Acidic and Neutral pH. Acta Cryst. F. 62: 477-482 (2006)

• H Hong, D Patel, L Tamm, B van den Berg.

The Outer Membrane Protein OmpW Forms an Eight-Stranded beta-Barrel with a Hydrophobic Channel. J. Biol. Chem.. 281: 7568-7577 (2006) [ premiere ]

• A Accardi, S Lobet, C Williams, C Miller, R Dutzler.

Synergism Between Halide Binding and Proton Transport in a CLC-type Exchanger. J. Mol. Biol.. 362: 691-699 (2006)

• F Ferreira, G Mendoza-Hernandez, M Castaneda-Bueno, R Aparicio, H Fischer, M Calcagno, G Oliva.

Structural Analysis of N-acetylglucosamine-6-phosphate Deacetylase Apoenzyme from Escherichia coli. J. Mol. Biol.. 359: 308-321 (2006)

• G Subbarao, B van den Berg.

Crystal Structure of the Monomeric Porin OmpG. J. Mol. Biol.. 360: 750-759 (2006)

• J Prada, R Haire, M Allaire, J Jakoncic, V Stojanoff, J Cannon, G Litman, D Ostrov.

Ancient Evolutionary Origin of Diversified Variable Regions Demonstrated by Crystal Structures of an Immune-Type Receptor in Amphioxus. Nat. Immunol.. 7: 875-882 (2006) [ premiere ]

• Y Tang, M Poustovoitov, K Zhao, M Garfinkel, A Canutescu, R Dunbrack, P Adams, R Marmorstein.

Structure of a Human ASF1a-HIRA Complex and Insights into Specificity of Histone Chaperone Complex Assembly. Nat. Struct. Mol. Biol.. 13: 921 (2006) [ premiere ]

• P Pawelek, N Croteau, C Ng-Thow-Hing, C Khursigara, N Moiseeva, M Allaire, J Coulton.

Structure of TonB in Complex with FhuA, E. Coli Outer Membrane Receptor. Science. 312: 1399-1402 (2006) [ premiere ]

--- Year 2005 ---

• Mirza, I.A., Nazi, I., Korczynska, M., Wright, G.D., Berghuis, A.M.

Crystal Structure of Homoserine Transacetylase from Haemophilus influenzae Reveals a New Family of alpha/beta-Hydrolases. Biochemistry. 44: 15768-15773 (2005)

• K Pant, B Crane .

Structure of a Loose Dimer: an Intermediate in Nitric Oxide Synthase Assembly. J. Mol. Biol.. 352: 932-940 (2005)

• J Helliwell.

Protein Crystal Perfection and its Application. Acta Cryst. D. 61: 793-798 (2005)

• A Vahedi-Faridi, V Stojanoff, J Yeh.

The Effects of Flash-Annealing on Glycerol Kinase Crystals. Acta Cryst. D. 61: 982-989 (2005)

• M. Nadella, M.A. Bianchet, S.B.Gabelli, J. Barrila,and L.M. Amzel, 2005 November.

Structure and activity of the axon guidance protein MICAL. Proc Natl Acad Sci USA, 102(46):16830-16835.

• Kuzuyama, T., Noel, J.P. and Richard, S.B. 2005 Jun.

Structural basis for the promiscuous biosynthetic prenylation of aromatic natural products. Nature. 435(7044):983-7.

• Nair, D. T., Johnson, R. E., Prakash, L., Prakash, S.,and Aggarwal, A. K. 2005.

Rev1 Employs a Novel Mechanism of DNA Synthesis Using a Protein Template. Science. 309:2219 -2222

• De Silva, R. S., Kovacikova, G., Lin, W., Taylor, R. K., Skorupski, K., and Kull, F. J. 2005

Crystal Structure of the Virulence Gene Activator Apha from Vibrio Cholerae Reveals It is a Novel Member of the Winged Helix Transcription Factor Superfamily. J.Biol.Chem. 280:13779-13783

• MA. Adams and Z. Jia, 2005 Mar.

Structural and biochemical evidence for a quinone redox cycle in Escherichia coli: Identification of a novel quinol monooxygenase. J.Biol.Chem. 280(9):8359-63.

• Suits, M.D., Pal, G.P., Nakatsu, A., Matte, A., Cygler, M. Jia, Z. 2005.

Identification of an Escherichia coli O 157:H7 heme oxygenase with tandem functional repeats. PNAS, 102: 16955-16960.

• Bzymek, K.P., Moulin, A., Swierczek, S.I., Ringe, D., Petsko, G.A., Holz, R.C. 2005.

Kinetic, Spectroscopic, and X-ray Crystallographic Characterization of the Functional E151H Aminopeptidase from Aeromonas proteolytica. Biochemistry. V44, pp.12030-12040

• Xia Z, Azurmendi HF, Lairson LL, Withers SG, Gabelli SB, Bianchet MA, Amzel LM, Mildvan AS. 2005.

Mutational, Structural, and Kinetic Evidence for a Dissociative Mechanism in the GDP-mannose Mannosyl Hydrolase Reaction. Biochemistry. 44(25):8989-97

• Y. Zhang, H. Moriyama, K. Homma and J. Van Etten, 2005 Aug.

Chlorella virus encoded deoxyuridine triphosphatases exhibit different temperature optima. J. Viol. 79(15):9945-9953.

• E Pozharski, A Moulin, A Hewagama, A Shanafelt, G Petsko, D Ringe.

Diversity of Hapten Recognition: Structural Study of an Anti-Cocaine Antibody M82G2. J. Mol. Biol.. 349(3): 570-582 (2005)

• M. Hahn, MJ. Nicholson, J. Pyrdol,and KW. Wucherpfennig, 2005 May.

Unconventional topology of self peptide-major histocompatibility complex binding by a human autoimmune T cell receptor. Nat Immunol. 6(5):490-496.

• MJ. Nicholson, M. Hahn,and KW. Wucherpfennig, 2005 Oct.

Unusual features of self-peptide/MHC binding by autoimmune T cell receptors. Immunity. 23(4): 351-360.

• Kajander, T., Cortajarena, A.L., Main, E.W.R., Mochrie, S.G.J. and Regan, L. 2005.

A New Folding Paradigm for Repeat Proteins J. Am. Chem. Soc. 127: 10188-90

• Mildvan AS, Xia Z, Azurmendi HF, Saraswat V, Legler PM, Massiah MA, Gabelli SB, Bianchet MA, Kang LW, Amzel LM. 2005.

Structures and mechanisms of Nudix hydrolases. Arch Biochem Biophys. 433(1):129-43

• Effmert, U., Saschenbrecker, S., Ross, J., Negre, F., Fraser, C.M., Noel, J.P., Dudareva, N., and Piechulla, B. 2005

Floral benzenoid carboxyl methyltransferases: From in vitro to in planta function. Phytochemistry. 66: 1211-1230.

• M. Allaire, A. Berntson, A. Jain, J. Jakoncic, C.C. Kao, D. P. Siddons, I. So, V. Venkatagiriyappa, Z. Yin and V. Stojanoff, 2005.

A Modular approach to the beam line automation: The NIGMS Facility at the NSLS Synchrotron Radiation News 18 (2005) 23-27

--- Year 2004 ---

• Yernool, D., Boudker, O., Jin, Y., Gouaux, E, 2004

Structure of a Glutamate Transporter Homologue from Pyrococcus Horikoshii Nature. 431 : 811-818

• James, J. A., Aggarwal, A. K., Linden, R. M., Escalante, C. R. 2004.

Structure of Adeno-Associated Virus Type 2 Rep40-Adp Complex: Insight Into Nucleotide Recognition and Catalysis by Superfamily 3 Helicases Proc.Nat.Acad.Sci.USA. 101:12455-12460

• Gabelli, S. B., Bianchet, M. A., Azurmendi, H. F., Xia, Z., Sarawat, V., Mildvan, A. S., and Amzel, L. M. 2004.

Structure and Mechanism of Gdp-Mannose Glycosyl Hydrolase, a Nudix Enzyme that Cleaves at Carbon Instead of Phosphorus. Structure 12:927 -935

• Clemente, J. C., Moose, R. E., Hemrajani, R., Whitford, L. R., Govindasamy, L., Reutzel, R., McKenna, R., Agbandje-McKenna, M., Goodenow, M. M., and Dunn, B. M. 2004.

Comparing the Accumulation of Active- and Nonactive-Site Mutations in the HIV-1 Protease. Biochemistry. 38:12141-12151

• Hernandez Prada JA, Haire RN, Cannon JP, Litman GW, Ostrov DA. 2004 Oct.

Crystallization and preliminary X-ray analysis of VCBP3 from Branchiostoma floridae. Acta Crystallogr D Biol Crystallog. 60(11):2022-4.

• Pott, M., Hippauf, F., Saschenbrecker, S., Chen, F., Ross, J., Kiefer, I., Slusarenko, A., Noel, J.P., Pichersky, E., Effmert, U., Piechulla, B. 2004

Biochemical and structural characterization of benzenoid carboxyl methyltransferases involved in floral scent production in Stephanotis floribunda and Nicotiana suaveolens. Plant Physiology. 135:1946-1955.

--- Year 2003 ---

• James, J. A., Escalante, C. R., Yoon-Robarts, M., Edwards, T. A., Linden, R. M., and Aggarwal, A. K. 2003.

Crystal Structure of the Sf3 Helicase from Adeno-Associated Virus Type 2 Structure. 11F:1025-1035

• Chen, F, D`Auria, J.C., Tholl, D., Ross, J.R., Gershenzon, J., Noel, J.P., and Pichersky, E. 2003

An Arabidopsis thaliana gene for methylsalicylate biosynthesis, identified by a biochemical genomics approach, has a role in defense. The Plant J. 36:577-588.

• Zubieta, C., Ross, J.R., Koscheski, P., Yang, Y., Pichersky, E., and Noel, J.P. 2003

Structural basis for substrate recognition in the salicylic acid carboxyl methyltransferase family. Plant Cell, 15: 1704-1716.

--- PHD Thesis ---

• Sebastien Boutet, 2005.

Coherent X-Ray Diffractive Imaging and Nucleation of Protein Crystals. PhD thesis (2005)

• Asa Holmner, 2005.

Molecular recognition of carbohydrates - Structural and functional characterisation of bacterial toxins and fungal lectins PhD thesis (2005)