Determination of protein-protein complexes from sparse experimental data

• Grant number: 13/20929-4
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: December 01, 2013
• End date: November 30, 2018
• Field of knowledge: Biological Sciences - Biochemistry - Molecular Biology
• Principal Investigator: Glaucius Oliva
• Grantee: Samuel Reghim Silva
• Host Institution: Instituto de Física de São Carlos (IFSC). Universidade de São Paulo (USP). São Carlos , SP, Brazil
• Associated research grant: 11/11343-0 - Using sparse nuclear magnetic resonance data and comparative modelling for the determination of structure and dynamics of proteins with application in rational drug design, AP.JP
• Associated scholarship(s): 16/20366-8 - Determination of Protein-Protein Complexes from Sparse Experimental Data, BE.EP.DR

Abstract

The objective of this project is to develop new computational approaches for determining the structures of protein-protein complexes using sparse experimental information. For that, the student will develop a new computer program using data derived from EPR Double Electron-Electron Resonance (DEER) and Cryo-Electron Microscopy (Cryo-EM). This system will complement the Chemical Shift based approach used by CamDock. We have identified chemical shifts from NMR spectroscopy, EPR Double Electron-Electron Resonance and Cryo-Electron Microscopy as the most promising types of experimental data for this purpose, since they are readily measurable, at least with respect to other observables, and comparatively rich in structural information. Our intention is to provide a new standard tool to the structural biology community to determine the structures of large complexes, which are the basic functional units in the cell, rather than the structures of individual proteins or small complexes, which currently represent the vast majority of the structures in the Protein Data Bank. (AU)

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)

DA SILVA NETO, ANTONIO MARINHO; SILVA, SAMUEL REGHIM; VENDRUSCOLO, MICHELE; CAMILLONI, CARLO; MONTALVAO, RINALDO WANDER. A superposition free method for protein conformational ensemble analyses and local clustering based on a differential geometry representation of backbone. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, v. 87, n. 4, p. 302-312, APR 2019. (13/20929-4, 13/18398-0)

Academic Publications

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

SILVA, Samuel Reghim. Representations of molecular surfaces in spherical harmonics for simulation of protein-protein complexes formation. 2018. Doctoral Thesis - Universidade de São Paulo (USP). Instituto de Física de São Carlos (IFSC/BT) São Carlos.