A structural biology laboratory network for the study of the 3D structures of proteins

• Grant number: 00/10266-8
• Support Opportunities: Genome Research Grants
• Start date: November 01, 2000
• End date: March 31, 2008
• Field of knowledge: Biological Sciences - Biochemistry - Molecular Biology
• Principal Investigator: Nilson Ivo Tonin Zanchin
• Grantee: Nilson Ivo Tonin Zanchin
• Host Institution: Associação Brasileira de Tecnologia de Luz Síncrotron (ABTLuS). Ministério da Ciência, Tecnologia e Inovação (Brasil). Campinas , SP, Brazil
• Associated scholarship(s): 01/13731-6 - Bioinformatics in the structural biology laboratory network for the study of the 3D structures of proteins project, BP.TT

Abstract

We envisage finding the structures of proteins which: I) have potential of playing a functional role in the induction and/or sustenance of malignant phenotypes in humans; II) are functionally important in plants and bacteria. For some of these proteins, attempts will be made to determine structures that may reveal new folds; III) exhibit high potential of having its structure determined by synchrotron radiation protein crystallography or multinuclear multidimensional high-resolution nuclear magnetic resonance spectroscopy (NMR). The choice of these proteins will be mainly based on the results of the F APESP Genomics Programs such as Xylella fastidiosa, Xanthomonas citri, Sugar Cane EST and the FAPESP/LICR Human Cancer. These Programs have produced an enormous amount of information, which need to be exploited from a structural and functional point of view. The knowledge of the structures of these proteins would disclose an attractively practical output, the rational design of inhibitors of the proteins, i.e. potential anti-cancer drugs in the case of the FAPESP/LICR Human Cancer project or herbicides/pesticides in the other cases. In parallel, we are also proposing to organize the Sao Paulo State Laboratory Network for Structural Biology, aimed at increasing the throughput of proteins to be analyzed and to expand the number of groups, in the State of Sao Paulo, involved in the area of Structural Biology. The F APESP genome programs have been important to increase significantly the number of laboratories with expertise in DNA sequencing and annotation. A further development in molecular biology involves increasing capabilities in protein structure determination, which, in turn, requires expertise in protein expression and purification. All these aspects are central to the present project. The creation of a network of laboratories is critical for the accomplishment of these goals. In addition, we hope that the laboratories that will be part of the network will be seeking to develop their interest in the study of the structural aspects of proteins. Thus, it is expected that they may work further down the project pipeline attempting either to crystallize proteins and collect diffraction data and/or to study the proteins in solution by means of NMR spectroscopy; with the final aim of solving their 3D structure(s). (AU)

Scientific publications

(12)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

DE OLIVEIR, JULIANA FERREIRA; CASTILHO, BEATRIZ A.; SFORCA, MAURICIO L.; KRIEGER, MARCO AURELIO; ZERI, ANA CAROLINA; GUIMARAES, BEATRIZ G.; ZANCHIN, NILSON I. T.. Characterization of the Trypanosoma cruzi ortholog of the SBDS protein reveals an intrinsically disordered extended C-terminal region showing RNA-interacting activity. Biochimie, v. 91, n. 4, p. 475-483, APR 2009. (02/12597-7, 00/10266-8, 98/14138-2)

RINALDI, FABIO C.; MEZA, ANDREIA N.; GUIMARAES, BEATRIZ G.. Structural and Biochemical Characterization of Xylella fastidiosa DsbA Family Members: New Insights into the Enzyme-Substrate Interaction. BIOCHEMISTRY, v. 48, n. 15, p. 3508-3518, 2009. (00/10266-8, 98/14138-2)

DE OLIVEIRA, ALINE L.; GALLO, MARIANA; PAZZAGLI, LUIGIA; BENEDETTI, CELSO E.; CAPPUGI, GIANNI; SCALA, ANIELLO; PANTERA, BARBARA; SPISNI, ALBERTO; PERTINHEZ, THELMA A.; CICERO, DANIEL O.. The Structure of the Elicitor Cerato-platanin (CP), the First Member of the CP Fungal Protein Family, Reveals a Double psi beta-Barrel Fold and Carbohydrate Binding. Journal of Biological Chemistry, v. 286, n. 20, p. 17560-17568, MAY 20 2011. (00/10266-8)

GIUSEPPE, PRISCILA O.; VON ATZINGEN, MARINA; NASCIMENTO, ANA LUCIA T. O.; ZANCHIN, NILSON I. T.; GUIMARAES, BEATRIZ G.. The crystal structure of the leptospiral hypothetical protein LIC12922 reveals homology with the periplasmic chaperone SurA. Journal of Structural Biology, v. 173, n. 2, p. 312-322, FEB 2011. (00/10266-8, 98/14138-2)

DOMINGUES, MARIANE NORONHA; DE SOUZA, TIAGO ANTONIO; CERNADAS, RAUL ANDRES; PEIXOTO DE OLIVEIRA, MARIA LUIZA; DOCENA, CASSIA; FARAH, CHUCK SHAKER; BENEDETTI, CELSO EDUARDO. The Xanthomonas citri effector protein PthA interacts with citrus proteins involved in nuclear transport, protein folding and ubiquitination associated with DNA repair. MOLECULAR PLANT PATHOLOGY, v. 11, n. 5, p. 663-675, SEP 2010. (07/06686-0, 00/10266-8, 98/14138-2)

SMETANA‚ J.H.C.; ZANCHIN‚ N.I.T.. Interaction analysis of the heterotrimer formed by the phosphatase 2A catalytic subunit‚ α4 and the mammalian ortholog of yeast Tip41 (TIPRL). FEBS Journal, v. 274, n. 22, p. 5891-5904, 2007. (00/10266-8, 98/14138-2)

SOUZA, C. S.; FERREIRA, L. C. S.; THOMAS, L.; BARBOSA, J. A. R. G.; BALAN, A.. Crystallization, data collection and data processing of maltose-binding protein (MalE) from the phytopathogen Xanthomonas axonopodis pv. citri. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, v. 65, p. 3-pg., 2009-02-01. (01/07540-3, 00/10266-8)

SOUZA, C. S.; FERREIRA, L. C. S.; THOMAS, L.; BARBOSA, J. A. R. G.; BALAN, A.. Crystallization, data collection and data processing of maltose-binding protein (MalE) from the phytopathogen Xanthomonas axonopodis pv. citri. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, v. 65, n. 2, p. 105-107, FEB 2009. (01/07540-3, 00/10266-8)

STEHLING, ELIANA G.; SFORCA, MAURICIO L.; ZANCHIN, NILSON I. T.; OYAMA, JR., SERGIO; PIGNATELLI, ANGELA; BELLUZZI, OTTORINO; POLVERINI, EUGENIA; CORSINI, ROMINA; SPISNI, ALBERTO; PERTINHEZ, THELMA A.. Looking over Toxin-K+ Channel Interactions. Clues from the Structural and Functional Characterization of alpha-KTx Toxin Tc32, a Kv1.3 Channel Blocker. BIOCHEMISTRY, v. 51, n. 9, p. 1885-1894, MAR 6 2012. (00/10266-8)

HESLING, CÉDRIC; OLIVEIRA, CARLA C.; CASTILHO, BEATRIZ A.; ZANCHIN, NILSON I. T.. The Shwachman-Bodian-Diamond syndrome associated protein interacts with HsNip7 and its down-regulation affects gene expression at the transcriptional and translational levels. Experimental Cell Research, v. 313, n. 20, p. 4180-4195, Dec. 2007. (00/10266-8, 98/14138-2)

CERNADAS, RAUL ANDRES; CAMILLO, LUCIANA RODRIGUES; BENEDETTI, CELSO EDUARDO. Transcriptional analysis of the sweet orange interaction with the citrus canker pathogens Xanthomonas axonopodis pv. citri and Xanthomonas axonopodis pv. aurantifolii. MOLECULAR PLANT PATHOLOGY, v. 9, n. 5, p. 609-631, SEP 2008. (00/10266-8, 98/14138-2)

CERNADAS, RAUL ANDRES; BENEDETTI, CELSO EDUARDO. Role of auxin and gibberellin in citrus canker development and in the transcriptional control of cell-wall remodeling genes modulated by Xanthomonas axonopodis pv. citri. Plant Science, v. 177, n. 3, p. 190-195, SEP 2009. (00/10266-8, 98/14138-2)