Experimental and theoretical study of structural proteomics by mass spectrometry coupled to cross-linking

Author(s)

Alana dos Reis Figueiredo

• Document type: Master's Dissertation
• Press: Campinas, SP.
• Institution: Universidade Estadual de Campinas (UNICAMP). Instituto de Química
• Defense date: 2010-02-25

Examining board members

Fábio Cesar Gozzo; Marcia Regina Soares da Silva; Marcos Nogueira Eberlin

• Advisor: Fábio Cesar Gozzo

Abstract

Mass spectrometry (MS) plays a key role in proteomics because it allows the identification of proteins, peptide sequencing, determination of post-translational modifications and quantitative expression analysis. There is a great interest in using MS to perform analysis beyond the primary structure, i. e. tertiary and quaternary structures, and one of the most promising approaches in this filed is MS coupled to cross-linking technique. In this approach, a bifunctional reagent covalently binds amino acid residues that are close in space and the maximum distance between these residues is given by the arm length of the cross-linking agent. In this study we evaluated the extent and accuracy of the inter-residues distances by both molecular dynamics simulations and MS experiments. Simulated distance ranges showed that there is a minimum distance between residues to which the reagent can bind and a maximum value for each of the studied reagents (DSG, DSS and DSSeb). The experimental data from model proteins (Ubiquitin, Cytochrome C and Myoglobin) also showed that all the detected modified peptides were within the ranges determined by the molecular dynamics simulations, confirming the accuracy of the method. The new space arm length values of the reagent molecules can now be used for the determination of proteins higher structures by the MS coupled to cross-linking technique (AU)

• FAPESP's process: 08/02049-9 - Evaluation of the cross-linking methodology combined to mass spectrometry in obtaining of data of structural proteins.
• Grantee: Alana dos Reis Figueiredo
• Support Opportunities: Scholarships in Brazil - Master