Determination of Protein-Protein and Protein-Ligand Complexes from Sparse Experimental Data

• Grant number: 13/18398-0
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: November 01, 2013
• End date: August 31, 2017
• Field of knowledge: Biological Sciences - Biophysics - Molecular Biophysics
• Principal Investigator: Glaucius Oliva
• Grantee: Antonio Marinho da Silva Neto
• Host Institution: Instituto de Física de São Carlos (IFSC). Universidade de São Paulo (USP). São Carlos , SP, Brazil

Abstract

The main goal of this project is to analyse the impact of surfaces and docking sites plasticity on protein-protein and protein-ligand interactions. Our intention is to combine data originated from X-Ray Crystallography and NMR Spectroscopy in order to model flexible interactions between a protein and its partner. For that, we will employ a method for NMR Restrained Molecular Dynamics develop in our group with collaboration with Professor Michele Vendruscolo (Chemistry Department - Cambridge University - UK)

Scientific publications

(4)

(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)

DA SILVA NETO, ANTONIO MARINHO; MONTALVAO, RINALDO WANDER; GONDIM MARTINS, DANYELLY BRUNESKA; DE LIMA FILHO, JOSE LUIZ; MADEIROS CASTELLETTI, CARLOS HENRIQUE. A model of key residues interactions for HPVs E1 DNA binding domain-DNA interface based on HPVs residues conservation profiles and molecular dynamics simulations. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, v. 38, n. 12, p. 10-pg., 2019-09-07. (13/18398-0)

DA SILVA NETO, ANTONIO MARINHO; MONTALVAO, RINALDO WANDER; GONDIM MARTINS, DANYELLY BRUNESKA; DE LIMA FILHO, JOSE LUIZ; MADEIROS CASTELLETTI, CARLOS HENRIQUE. A model of key residues interactions for HPVs E1 DNA binding domain-DNA interface based on HPVs residues conservation profiles and molecular dynamics simulations. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, SEP 2019. (13/18398-0)

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)

Academic Publications

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

SILVA NETO, Antonio Marinho da. Differential geometry and information theory application to protein conformational analyses. 2017. Doctoral Thesis - Universidade de São Paulo (USP). Instituto de Física de São Carlos (IFSC/BT) São Carlos.