New frontiers in structural proteomics: characterizing protein and protein complex structures by mass spectrometry

• Grant number: 14/17264-3
• Support Opportunities: Research Projects - Thematic Grants
• Start date: December 01, 2016
• End date: November 30, 2020
• Field of knowledge: Biological Sciences - Biochemistry - Chemistry of Macromolecules
• Principal Investigator: Fabio Cesar Gozzo
• Grantee: Fabio Cesar Gozzo
• Host Institution: Instituto de Química (IQ). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
• Pesquisadores principais: Kleber Gomes Franchini
• Associated researchers: Brenno Amaro Dasilveira Neto ; Leandro Martinez ; Munir Salomao Skaf ; Paulo Costa Carvalho
• Associated research grant(s): 17/14476-8 - Multi-user quipament approved in grant 2014/17264-3: 2D nanoUPLC system, AP.EMU
• Associated scholarship(s): 20/00144-6 - Structural proteomics: design, synthesis and application of new generation crosslinking agents, BP.PD; 19/07961-2 - Implementation, evaluation and application of mass spectrometric data in protein structure modeling, BP.MS; 18/10209-8 - Molecular and Structural Bases of 1, 2 and 4 Modules from the Polyketide synthesis Enzyme Complex, DEBS, from Saccharopolyspora erythraea, BP.PD; 16/13195-2 - Modeling of protein structure and protein complexes using mass spectrometry data, BP.DR

Abstract

The study of protein interactions is an important field to understand protein functions. This is, however, one area of great experimental difficulties due to inherent complexity of proteins and peptides. High resolution structural tools (i.e. X-Ray diffraction and Nuclear Magnetic Ressonance are the de facto methods for these studies. However, most proteins and protein complexes are not amenable to have their structures solved by these techniques, requiring the use of other alternative methods to structurally characterize proteins and proteins complexes. Mass Spectrometry (MS) is an attractive technique for characterization of proteins due to its intrinsic characteristics, such as sensitivity, speed and broad applicability. Our group have been working on this field in the last 6 years (MS (da Silva et al, 2013, Fioramonte et al., 2012; Santos et al., 2011a; Santos et al., 2011b; Santos et al., 2010; Iglesias et al., 2010; Iglesias et al., 2009). In this project, we intend to use MS to characterize the structure of proteins and protein complexes. These experiments will be performed to obtain distance constrains from cross-linking experiments along with data from hydrogen/deuterium experiments and ion mobility and all these data will be used in a combined fashion to generate structural models of protein and complexes of biological interest. (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)

ADAO, REGINA; ZANPHORLIN, LETICIA M.; LIMA, TATIANI B.; SRIRANGANADANE, DEV; DAHLSTROM, KATHE M.; PINHEIRO, GLAUCIA M. S.; GOZZO, FABIO C.; BARBOSA, LEANDRO R. S.; RAMOS, CARLOS H. I.. Revealing the interaction mode of the highly flexible Sorghum bicolor Hsp70/Hsp90 organizing protein (Hop): A conserved carboxylate clamp confers high affinity binding to Hsp90. JOURNAL OF PROTEOMICS, v. 191, n. SI, p. 191-201, JAN 16 2019. (14/17264-3, 15/15822-1, 12/50161-8)

RASHEED, NADIA; LIMA, TATIANI B.; MERCALDI, GUSTAVO F.; NASCIMENTO, ANDREY F. Z.; SILVA, ANA L. S.; RIGHETTO, GERMANNA L.; BAR-PELED, LIRON; SHEN, KUANG; SABATINI, DAVID M.; GOZZO, FABIO C.; et al. C7orf59/LAMTOR4 phosphorylation and structural flexibility modulate Ragulator assembly. FEBS OPEN BIO, v. 9, n. 9, JULY 2019. (17/21455-7, 14/17264-3, 14/12445-0)

SANTOS, MARLON D. M.; CAMILLO-ANDRADE, AMANDA CAROLINE; KURT, LOUISE U.; CLASEN, MILAN A.; LYRA, EDUARDO; GOZZO, FABIO C.; BATISTA, MICHEL; VALENTE, RICHARD H.; BRUNORO, GISELLE V. F.; BARBOSA, VALMIR C.; et al. Mixed-Data Acquisition: Next-Generation Quantitative Proteomics Data Acquisition. JOURNAL OF PROTEOMICS, v. 222, JUN 30 2020. (14/17264-3)

CLASEN, MILAN A.; KURT, LOUISE U.; SANTOS, MARLON D. M.; LIMA, DIOGO B.; LIU, FAN; GOZZO, FABIO C.; BARBOSA, VALMIR C.; CARVALHO, PAULO C.. Increasing confidence in proteomic spectral deconvolution through mass defect. Bioinformatics, v. 38, n. 22, p. 2-pg., 2022-09-21. (14/50867-3, 14/17264-3)

LIMA, DIOGO B.; MELCHIOR, JOHN T.; MORRIS, JAMIE; BARBOSA, VALMIR C.; CHAMOT-ROOKE, JULIA; FIORAMONTE, MARIANA; SOUZA, TATIANA A. C. B.; FISCHER, JULIANA S. G.; GOZZO, FABIO C.; CARVALHO, PAULO C.; et al. Characterization of homodimer interfaces with cross-linking mass spectrometry and isotopically labeled proteins. Nature Protocols, v. 13, n. 3, p. 431-458, MAR 2018. (14/17264-3, 12/10862-7)

GEWEHR, MAYARA C. F.; TEIXEIRA, ALEXANDRE A. S.; SANTOS, BRUNA A. C.; BIONDO, LUANA A.; GOZZO, FABIO C.; CORDIBELLO, AMANDA M.; EICHLER, ROSANGELA A. S.; RECKZIEGEL, PATRICIA; DA SILVA, RENEE N. O.; DOS SANTOS, NILTON B.; et al. The Relevance of Thimet Oligopeptidase in the Regulation of Energy Metabolism and Diet-Induced Obesity. BIOMOLECULES, v. 10, n. 2, FEB 2020. (14/17264-3, 16/04000-3, 04/04933-2, 15/20657-0)

DOS SANTOS, RICARDO N.; BOTTINO, GUILHERME F.; GOZZO, FABIO C.; MORCOS, FARUCK; MARTINEZ, LEANDRO. Structural complementarity of distance constraints obtained from chemical cross-linking and amino acid coevolution. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, v. 88, n. 4, NOV 2019. (18/14274-9, 10/16947-9, 15/13667-9, 18/24293-0, 13/08293-7, 14/17264-3)

DOS SANTOS, CAMILA RAMOS; DE GIUSEPPE, PRISCILA OLIVEIRA; MOREIRA DE SOUZA, FLAVIO HENRIQUE; ZANPHORLIN, LETICIA MARIA; DOMINGUES, MARIANE NORONHA; SIQUEIRA PIROLLA, RENAN AUGUSTO; HONORATO, RODRIGO VARGAS; COSTA TONOLI, CELISA CALDANA; BUENO DE MORAIS, MARIANA ABRAHAO; DE MATOS MARTINS, VANESA PEIXOTO; et al. The mechanism by which a distinguishing arabinofuranosidase can cope with internal di-substitutions in arabinoxylans. BIOTECHNOLOGY FOR BIOFUELS, v. 11, AUG 11 2018. (13/13309-0, 14/17264-3, 15/26982-0, 14/07135-1)

DOS SANTOS, RICARDO N.; FERRARI, ALLAN J. R.; DE JESUS, HUGO C. R.; GOZZO, FABIO C.; MORCOS, FARUCK; MARTINEZ, LEANDRO. Enhancing protein fold determination by exploring the complementary information of chemical cross-linking and coevolutionary signals. Bioinformatics, v. 34, n. 13, p. 2201-2208, JUL 1 2018. (13/08293-7, 13/05475-7, 16/13195-2, 14/17264-3, 15/13667-9, 10/16947-9)

FIORAMONTE, MARIANA; RAMOS DE JESUS, HUGO CESAR; RAMOS FERRARI, ALLAN JHONATHAN; LIMA, DIOGO BORGES; DREKENER, ROBERTA LOPES; DUARTE CORREIA, CARLOS ROQUE; OLIVEIRA, LUCIANA GONZAGA; DA COSTA NEVES-FERREIRA, ANA GISELE; CARVALHO, PAULO COSTA; GOZZO, FABIO CESAR. XPlex: An Effective, Multiplex Cross-Linking Chemistry for Acidic Residues. Analytical Chemistry, v. 90, n. 10, p. 6043-6050, MAY 15 2018. (14/50249-8, 16/13195-2, 14/17264-3, 12/10862-7, 14/12727-5)

FERRARI, ALLAN J. R.; GOZZO, FABIO C.; MARTINEZ, LEANDRO. Statistical force-field for structural modeling using chemical cross-linking/mass spectrometry distance constraints. Bioinformatics, v. 35, n. 17, p. 3005-3012, SEP 1 2019. (13/08293-7, 13/05475-7, 18/14274-9, 16/13195-2, 14/17264-3, 13/23814-3, 10/16947-9)

ADAO, REGINA; ZANPHORLIN, LETICIA M.; LIMA, TATIANI B.; SRIRANGANADANE, DEV; DAHLSTROM, KATHE M.; PINHEIRO, GLAUCIA M. S.; GOZZO, FABIO C.; BARBOSA, LEANDRO R. S.; RAMOS, CARLOS H. I.. Revealing the interaction mode of the highly flexible Sorghum bicolor Hsp70/Hsp90 organizing protein (Hop): A conserved carboxylate clamp confers high affinity binding to Hsp90. JOURNAL OF PROTEOMICS, v. 191, p. 11-pg., 2019-01-16. (14/17264-3, 12/50161-8, 15/15822-1)

Filed patent(s) as a result of this research project