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Computer simulation of metalloenzymes and of flexible proteins

Abstract

Computer simulation has increasing presence and importance for research in chemistry, biochemistry and molecular biophysics. A clear recognition of this research area was the Nobel prize in Chemistry awarded in 2013 for the development of hybrid methods in molecular simulation.The research proposal presented here will be conducted in the Computational Biochemistry and Biophysics laboratory installed in the Instituto de Química at the Universidade de São Paulo (IQ-USP) and will be carried out by four graduate students already members of the laboratory, besides the principal investigator and foreign collaborators. On this project, we propose to continue our recent developments and applications of innovative methods in molecular simulation to study proteins involved in bio-energetical processes and in molecular recognition.We will investigate the reaction mechanisms of metalloenzymes containing iron-sulfur clusters found in the mitochondrial electron transfer chain and in bacteria. Redox reactions of their substrates, ubiquinone, and of the iron-sulfur clusters in complexes I, II and III will be simulated with atomistic detail and a description by a hybrid potential of quantum chemistry and molecular mechanics (QC/MM). Approximations proposed and implements by our group to study metalloproteins will be used. We also propose to continue the investigation of the forced unfolding of rubredoxin, a simple iron-sulfur protein, in comparison with atomic force microscopy (AFM) experiments to understand its mechanical properties and stability of Fe-S bonds.We will also continue the characterization of the structural flexibility and the complexation to small molecule ligands of the human phosphatase Cdc25B, that is a possible target for the development of antineoplastic inhibitors. Here we will combine molecular simulation with spectroscopical experiments to identify transient states in the flexible C-terminal region and its role in the complexation to ligands. (AU)

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Scientific publications (7)
(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)
CURTOLO, FELIPE; ARANTES, GUILHERME M. Mechanisms for Flavin-Mediated Oxidation: Hydride or Hydrogen-Atom Transfer?. JOURNAL OF CHEMICAL INFORMATION AND MODELING, v. 60, n. 12, p. 6282-6287, DEC 28 2020. Web of Science Citations: 0.
REIS, ANDRE A. O.; SAYEGH, RAPHAEL S. R.; MARANA, SANDRO R.; ARANTES, GUILHERME M. Combining Free Energy Simulations and NMR Chemical-Shift Perturbation To Identify Transient Cation-pi Contacts in Proteins. JOURNAL OF CHEMICAL INFORMATION AND MODELING, v. 60, n. 2, p. 890-897, FEB 2020. Web of Science Citations: 1.
TEIXEIRA, MURILO H.; CURTOLO, FELIPE; CAMILO, SOFIA R. G.; FIELD, MARTIN J.; ZHENG, PENG; LI, HONGBIN; ARANTES, GUILHERME M. Modeling the Hydrolysis of Iron-Sulfur Clusters. JOURNAL OF CHEMICAL INFORMATION AND MODELING, v. 60, n. 2, p. 653-660, FEB 2020. Web of Science Citations: 1.
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. Web of Science Citations: 0.
TEIXEIRA, MURILO HOIAS; ARANTES, GUILHERME MENEGON. Effects of lipid composition on membrane distribution and permeability of natural quinones. RSC ADVANCES, v. 9, n. 29, p. 16892-16899, MAY 28 2019. Web of Science Citations: 2.
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. Web of Science Citations: 12.
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. Web of Science Citations: 5.

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