Using sparse nuclear magnetic resonance data and comparative modelling for the determination of structure and dynamics of proteins with application in rational drug design

• Grant number: 11/11343-0
• Support Opportunities: Research Grants - Young Investigators Grants
• Start date: January 01, 2012
• End date: December 31, 2015
• Field of knowledge: Biological Sciences - Biochemistry - Molecular Biology
• Principal Investigator: Rinaldo Wander Montalvão
• Grantee: Rinaldo Wander Montalvão
• Host Institution: Instituto de Física de São Carlos (IFSC). Universidade de São Paulo (USP). São Carlos , SP, Brazil
• Associated researchers: Hélio Crestana Guardia ; Richard Charles Garratt
• Associated scholarship(s): 13/20929-4 - Determination of protein-protein complexes from sparse experimental data, BP.DR; 12/23001-0 - Study and development of a C++/QT/VTK based GUI for protein modelling programs, BP.IC; 12/00137-3 - Using Sparse Nuclear Magnetic Resonance data and Comparative Modelling for the determination of structure and dynamics of proteins with application in rational drug design, BP.JP

Abstract

The main goal of this project is to develop a bioinformatics hybrid system for the simultaneous determination of the tertiary structure and dynamics of proteins of interest for rational drug design. The intention is to develop new approaches to deal with the problem of solving protein structures where traditional methods, such as X-Ray Crystallography and NMR Spectroscopy, fail to produce reliable models.The idea is to generate an ensemble of protein structures that reproduces the experimental data by mixing of two distinctive procedures:*The Protein Comparative Modelling developed during my PhD research at the Professor Sir Tom Blundell's group - Biochemistry Department - Cambridge University - UK. *NMR Restrained Molecular Dynamics created during my post-doc work at the Professors Michele Vendruscolo and Chris Dobson groups - Chemistry Department - Cambridge University - UKI intend to combine these approaches in a tool to be used by experimental groups and pharmaceutical companies for rational drug design. This tool is the natural evolution of the ORCHESTRAR comparative modelling program that I developed during my PhD at Tom Blundell's group and it is licensed by the CNPq and Cambridge University to the software company Tripos (www.tripos.com) as the Advanced Protein Modelling part of SYBYL. (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)

SARAIVA MACEDO TIMMERS, LUIS FERNANDO; NETO, ANTONIO M. S.; MONTALVAO, RINALDO W.; BASSO, LUIZ A.; SANTOS, DIOGENES S.; DE SOUZA, OSMAR NORBERTO. EPSP synthase flexibility is determinant to its function: computational molecular dynamics and metadynamics studies. Journal of Molecular Modeling, v. 23, n. 7, JUL 2017. (11/11343-0, 13/18398-0)