Development and application of computer simulation and spectroscopical analysis to study metalloenzymes and flexible proteins

• Grant number: 14/21900-2
• Support Opportunities: Regular Research Grants
• Start date: February 01, 2015
• End date: January 31, 2017
• Field of knowledge: Biological Sciences - Biochemistry - Chemistry of Macromolecules
• Principal Investigator: Guilherme Menegon Arantes
• Grantee: Guilherme Menegon Arantes
• Host Institution: Instituto de Química (IQ). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• City of the host institution: São Paulo

Abstract

There is an increasing importance of computer simulation in the areas of chemistry, biochemistry and molecular biophysics. The Nobel Prize in Chemistry awarded in 2013 for the development of hybrid methods of molecular simulation is a clear recognition of this importance.The research proposal presented here will be carried out in the Computational Biochemistry and Biophysics laboratory recently installed in the Instituto de Química da Universidade de São Paulo (IQ-USP) and contains five fellow students that already work in the laboratory (1 post-doc, 3 graduate and 1 undergraduate), besides international collaborators. The project focus on the development and the application of innovative molecular simulation methods.We propose to study important biomolecules involved in energetic and molecular recognition processes. The two main metalloproteins studied are rubredoxin and cytochrome bc1 (or mitochondrial complex III). We will investigate electronic phenomena associated with theirs prosthetic groups, iron-sulfur clusters, by molecular simulation with descriptions of hybrid potential of quantum chemistry and molecular mechanics (QC/MM), as well as by approximations proposed and implemented by us to allow the study of metalloproteins. We will also study the structural flexibility and complexation to small ligands of the human phosphatase Cdc25B that is a possible target for the development of antineoplastic inhibitors.For rubredoxin, we will continue the investigation of its forced unfolding in comparison to atomic force microscopy (AFM) experiments. The anisotropic dependence of unfolding and the action of chemical agents in the stability of Fe-S bonds in rubredoxin will be studied. For cytochrome bc1, we plan to elucidate the molecular mechanism of the Q cycle, and the associated coupled electron and proton transfers involving its ubiquinone substrate. The pathway for diffusion and the stoichiometry of complexation between ubiquinone and its redox centers in cytochrome bc1 will also be investigated. For Cdc25B, we will develop procedures to incorporate experimental data derived from nuclear magnetic resonance (NMR) in computer modelling of its structure and complexation to inhibitors. (AU)

Scientific publications

(9)

(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)

SOUZA, VALQUIRIA P.; IKEGAMI, CECILIA M.; ARANTES, GUILHERME M.; MARANA, SANDRO R.. Protein thermal denaturation is modulated by central residues in the protein structure network. FEBS Journal, v. 283, n. 6, p. 1124-1138, MAR 2016. (14/21900-2, 08/55914-9, 14/19439-5)

TEIXEIRA, MURILO HOIAS; ARANTES, GUILHERME MENEGON. Balanced internal hydration discriminates substrate binding to respiratory complex I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, v. 1860, n. 7, p. 541-548, JUL 1 2019. (14/21900-2, 16/24096-5)

SAYEGH, RAPHAEL S. R.; TAMAKI, FABIO K.; MARANA, SANDRO R.; SALINAS, ROBERTO K.; ARANTES, GUILHERME M.. Conformational flexibility of the complete catalytic domain of Cdc25B phosphatases. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, v. 84, n. 11, p. 1567-1575, NOV 2016. (14/19439-5, 08/55914-9, 13/17883-2, 14/21900-2, 12/00543-1)

GALASSI, VANESA VIVIANA; ARANTES, GUILHERME MENEGON. Partition, orientation and mobility of ubiquinones in a lipid bilayer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, v. 1847, n. 12, p. 1560-1573, DEC 2015. (14/21900-2, 12/17833-2, 12/02501-4)

ARANTES, GUILHERME MENEGON; FIELD, MARTIN J.. Ferric-Thiolate Bond Dissociation Studied with Electronic Structure Calculations. Journal of Physical Chemistry A, v. 119, n. 39, p. 10084-10090, OCT 1 2015. (14/21900-2, 12/02501-4)

SOUZA, VALQUIRIA P.; IKEGAMI, CECILIA M.; ARANTES, GUILHERME M.; MARANA, SANDRO R.. Protein thermal denaturation is modulated by central residues in the protein structure network. FEBS Journal, v. 283, n. 6, p. 15-pg., 2016-03-01. (08/55914-9, 14/21900-2, 14/19439-5)

ZHENG, PENG; ARANTES, GUILHERME M.; FIELD, MARTIN J.; LI, HONGBIN. Force-induced chemical reactions on the metal centre in a single metalloprotein molecule. NATURE COMMUNICATIONS, v. 6, JUN 2015. (14/21900-2, 12/02501-4)

NUNES-ALVES, ARIANE; ARANTES, GUILHERME MENEGON. Mechanical Unfolding of Macromolecules Coupled to Bond Dissociation. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, v. 14, n. 1, p. 282-290, JAN 2018. (14/21900-2, 16/24096-5, 14/17008-7)

NUNES-ALVES, ARIANE; ZUCKERMAN, DANIEL M.; ARANTES, GUILHERME MENEGON. Escape of a Small Molecule from Inside T4 Lysozyme by Multiple Pathways. BIOPHYSICAL JOURNAL, v. 114, n. 5, p. 1058-1066, MAR 13 2018. (14/21900-2, 16/24096-5, 14/17008-7, 15/19912-5)