Structural Proteomics by Chemical Cross-linking Coupled to Mass Spectrometry: Development, Fundamental Studies and Applications.

• Grant number: 12/10862-7
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: October 01, 2012
• End date: September 30, 2016
• Field of knowledge: Physical Sciences and Mathematics - Chemistry
• Principal Investigator: Fabio Cesar Gozzo
• Grantee: Mariana Fioramonte
• Host Institution: Instituto de Química (IQ). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
• Associated research grant: 08/57805-2 - Institute of Bioanalytics, AP.TEM
• Associated scholarship(s): 15/01601-3 - New frontiers in structural proteomics: advances in in vivo experiments using the genetically encoded unnatural amino acids, BE.EP.DR

Abstract

The study of structures and conformations of proteins and protein complexes is extremely important in biochemistry, since most biochemical processes are governed by such macromolecules interconneted by extensive networks of interaction. Chemical cross-linking coupled to mass spectrometry (MS) is a technique that allows the characterization of structural proteins and protein complexes, especially where these are not capable of being analyzed by high resolution techniques. The experiment is based on reaction of a protein or protein complex with a bifunctional reagent (cross-linking agent, ALC) followed by MS proteomics shotgun analysis. This brings all the advantages of MS to the technique, such as high sensitivity, speed of analysis and ease of use.Although the methodology of cross-linking with MS analysis proves promising to provide structural information of proteins and protein complexes, there are still several limitations to be overcome for it to become of unrestricted use with respect to system size and the protein categories. Among the challenges still to be overcome are the difficulty of detecting and identifying species modified by the ALC's and current restricted ALC's specificity towards aminoacid side chain. This project specifically aims at developing new ALC to allow easier detection and identification of peptides containing cross-linking modification, beside having different selectivities towards aminoacids. These studies will enable the expansion of the applicability of the technique and increase the amount and quality of structural data arising from these experiments.

Scientific publications

(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)

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)

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)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

FIORAMONTE, Mariana. New approaches for chemical cross-linking in structural proteomics. 0000. Doctoral Thesis - Universidade Estadual de Campinas (UNICAMP). Instituto de Química Campinas, SP.