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Computer simulation and spectroscopic analysis of proteins involved in bioenergetics and in molecular recognition

Grant number: 12/02501-4
Support type:Regular Research Grants
Duration: May 01, 2012 - April 30, 2014
Field of knowledge:Biological Sciences - Biochemistry - Chemistry of Macromolecules
Principal researcher:Guilherme Menegon Arantes
Grantee:Guilherme Menegon Arantes
Home Institution: Instituto de Química (IQ). Universidade de São Paulo (USP). São Paulo , SP, Brazil


The importance of computer simulation in biochemistry and molecular biophysics is increasing. This proposal aims to strengthen a laboratory of Computational Biochemistry and Biophysics recently opened in the Chemistry Institute of USP (IQ-USP). It is a natural continuation of the previously conceded Aid to Young Researchers. This project is also divided in two different research lines, including the development and application of innovative methods in molecular simulation.In the first research line we propose to study the metalloproteins Cytochrome bc1, Rubredoxinand MitoNEET involved in bioenergetic processes and the electronic phenomena associated with theirprosthetic groups, polynuclear metallic clusters of iron-sulfur. We will employ molecular simulations with a description of hybrid potential of quantum chemistry and molecular mechanics (QC/MM) as well as previously proposed approximations implemented by us and collaborators for the study of metalloproteins.In the second line, we propose to investigate the role of biomolecular intrinsic flexibility inmolecular recognition, in particular in the complexation of small inhibitory molecules to flexible or partially unfolded proteins. We propose the acquisition of nuclear magnetic resonance spectra to guide computational simulations and the generation of configurational ensembles that are able to quantitatively describe the biomolecular recognition process. The model system will be the Cdc25B phosphatase that possesses a very flexible C-terminal and is a target for the design of anti-neoplastic drugs. This project involves three scholarship students already working in the laboratory, one doctoral, one master and one undergraduate students, as well as collaborators in the IQ-USP and abroad. Hopefully in the near future we will have at least one post-doc involved with the first line of the proposed research. (AU)

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Scientific publications (6)
(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)
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. Web of Science Citations: 14.
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. Web of Science Citations: 2.
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. Web of Science Citations: 15.
BHATTACHARJEE, ANIRBAN; CHAVAROT-KERLIDOU, MURIELLE; DEMPSEY, JILLIAN L.; GRAY, HARRY B.; FUJITA, ETSUKO; MUCKERMAN, JAMES T.; FONTECAVE, MARC; ARTERO, VINCENT; ARANTES, GUILHERME M.; FIELD, MARTIN J. Theoretical Modeling of Low-Energy Electronic Absorption Bands in Reduced Cobaloximes. ChemPhysChem, v. 15, n. 14, p. 2951-2958, OCT 6 2014. Web of Science Citations: 7.
NUNES-ALVES, ARIANE; ARANTES, GUILHERME MENEGON. Ligand-Receptor Affinities Computed by an Adapted Linear Interaction Model for Continuum Electrostatics and by Protein Conformational Averaging. JOURNAL OF CHEMICAL INFORMATION AND MODELING, v. 54, n. 8, p. 2309-2319, AUG 2014. Web of Science Citations: 7.
ARANTES, GUILHERME M.; BHATTACHARJEE, ANIRBAN; FIELD, MARTIN J. Homolytic Cleavage of FeS Bonds in Rubredoxin under Mechanical Stress. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, v. 52, n. 31, p. 8144-8146, JUL 29 2013. Web of Science Citations: 9.

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