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Computer simulations of cytochrome bc1 and of Cdc25B phosphatase with spectroscopical validation

Grant number: 12/17833-2
Support type:Scholarships in Brazil - Post-Doctorate
Effective date (Start): May 01, 2013
Effective date (End): April 30, 2016
Field of knowledge:Biological Sciences - Biochemistry - Chemistry of Macromolecules
Principal Investigator:Guilherme Menegon Arantes
Grantee:Vanesa Viviana Galassi
Home Institution: Instituto de Química (IQ). Universidade de São Paulo (USP). São Paulo , SP, Brazil

Abstract

The relevance of computer simulations in biochemistry and molecular biophysics is increasing. Accordingly, the proposal herein described is part of a regular research project already supported by FAPESP in order to consolidate a laboratory of Computational Biochemistry and Biophysics recently installed in the Institute of Chemistry in the University of Sao Paulo (IQ-USP). Here we will take advantage of the experience previously acquired by the proponent during her PhD with computer simulations and spectroscopical methods of membrane proteins to develop two lines of research that are part of the project mentioned above. In the first line, we propose to study the metalloprotein cytochrome bc1 , essential to photosynthetic and cellular respiration processes, and the electronic phenomena associated with one of its prosthetic groups, the Rieske-type [2Fe-2S] iron-sulfur cluster. We will first employ molecular mechanical computations to build a realistic model of cytochrome bc1 embeddedin lipid membranes and to probe the diffusion of its natural substrate, ubiquinone. Then, we will simulate the rate-limiting step of the catalysed Q-cycle with a hybrid potential of quantum chemistry and molecular mechanics (QC/MM). These detailed studies will shed bright light in the mechanism catalysed by cytochrome bc1. In the second line, we propose to investigate the role of protein intrinsic flexibility in molecular recognition. In particular, the Cdc25B phosphatase will be studied. This protein possesses a partially unfolded C-terminal. Cdc25B is also a target for the design of anti-neoplastic drugs.A combination of several spectroscopical data, including circular dichroism, infrared, fluorescence and X-ray scattering, will be acquired. These data will be compared in order to validate and guide computer simulations already under development in our laboratory that describe quantitatively the Cdc25B conformational states and recognition process. Although related to different subjects, the two lines of research proposed are linked by our continuous development of novel methodologies of computer simulations and the complementary usage of quantitative experimental measurements for their test and calibration.

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)
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.

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