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

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)

Articles published in Agência FAPESP Newsletter about the research grant:
Pesquisa revela mecanismo molecular que leva à insuficiência cardíaca 
Articles published in other media outlets (17 total):
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UOL: Pesquisa revela mecanismo molecular que leva à insuficiência cardíaca (07/Jun/2020)
SBT Interior: Fapesp: Pesquisa revela o mecanismo molecular que leva à insuficiência cardíaca (02/Jun/2020)
Notícias ao Minuto: Estudo mostra que coronavírus pode infectar células do músculo cardíaco (05/Jun/2020)
MTUOL Notícias: Estudo mostra que coronavírus pode infectar células do músculo cardíaco (05/Jun/2020)
Jornal Expresso: Estudo mostra que coronavírus pode infectar células do músculo cardíaco (05/Jun/2020)
Roberto Crispim: Estudo mostra que coronavírus pode infectar células do músculo cardíaco (05/Jun/2020)
Região Noroeste : Pesquisa revela mecanismo que leva à insuficiência cardíaca (03/Jun/2020)
Ternura FM: Fapesp: Pesquisa revela o mecanismo molecular que leva à insuficiência cardíaca (03/Jun/2020)
LabNetwork: Pesquisa revela mecanismo molecular que leva à insuficiência cardíaca (03/Jun/2020)
Pharma Innovation: Pesquisa revela mecanismo molecular que leva à insuficiência cardíaca (03/Jun/2020)
Portal do Governo do Estado de São Paulo: Fapesp: Pesquisa revela o mecanismo molecular que leva à insuficiência cardíaca (02/Jun/2020)
Esteta : Pesquisa revela mecanismo molecular que leva à insuficiência cardíaca (02/Jun/2020)
Folha Nobre: Fapesp: Pesquisa revela o mecanismo molecular que leva à insuficiência cardíaca (02/Jun/2020)
Notícias de Campinas: Fapesp: Pesquisa revela o mecanismo molecular que leva à insuficiência cardíaca (02/Jun/2020)
Atemporal: Pesquisa revela mecanismo molecular que leva à insuficiência cardíaca (02/Jun/2020)
Mix Vale: Fapesp: Pesquisa revela o mecanismo molecular que leva à insuficiência cardíaca (02/Jun/2020)
Portal da Enfermagem: Pesquisa revela mecanismo molecular que leva à insuficiência cardíaca (02/Jun/2020)

Scientific publications (10)
(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)
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.; FISCHER, JULIANA S. G.; CARVALHO, PAULO C. Mixed-Data Acquisition: Next-Generation Quantitative Proteomics Data Acquisition. JOURNAL OF PROTEOMICS, v. 222, JUN 30 2020. Web of Science Citations: 0.
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.; CAMARA, NIELS O. S.; CASTOLDI, ANGELA; BARRETO-CHAVES, MARIA L. M.; DALE, CAMILA S.; SENGER, NATHALIA; LIMA, JOANNA D. C. C.; SEELAENDER, MARILIA C. L.; INADA, ALINE C.; AKAMINE, ELIANA H.; CASTRO, LEANDRO M.; RODRIGUES, ALICE C.; ROSA NETO, JOSE C.; FERRO, EMER S. The Relevance of Thimet Oligopeptidase in the Regulation of Energy Metabolism and Diet-Induced Obesity. BIOMOLECULES, v. 10, n. 2 FEB 2020. Web of Science Citations: 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. Web of Science Citations: 0.
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. Web of Science Citations: 3.
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.; APARICIO, RICARDO; SMETANA, JULIANA H. C. C7orf59/LAMTOR4 phosphorylation and structural flexibility modulate Ragulator assembly. FEBS OPEN BIO, v. 9, n. 9 JULY 2019. Web of Science Citations: 0.
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. Web of Science Citations: 0.
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; FONSECA, LUCAS MIRANDA; BUCHLI, FERNANDA; LOPES DE OLIVEIRA, PAULO SERGIO; GOZZO, FABIO CESAR; MURAKAMI, MARIO TYAGO. The mechanism by which a distinguishing arabinofuranosidase can cope with internal di-substitutions in arabinoxylans. BIOTECHNOLOGY FOR BIOFUELS, v. 11, AUG 11 2018. Web of Science Citations: 2.
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. Web of Science Citations: 6.
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. Web of Science Citations: 6.
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.; DAVIDSON, W. SEAN. Characterization of homodimer interfaces with cross-linking mass spectrometry and isotopically labeled proteins. Nature Protocols, v. 13, n. 3, p. 431-458, MAR 2018. Web of Science Citations: 11.

Please report errors in scientific publications list by writing to: cdi@fapesp.br.
Filed patent(s) as a result of this research project

Solicitação em análise e dentro do prazo legal de sigilo previsto na legislação BR1020180105230 - Universidade Estadual de Campinas (UNICAMP) . Solicitação em análise e dentro do prazo legal de sigilo previsto na legislação - May 2018, 23