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Biological macromolecules energy landscapes with applications in biotechnology and in biomedicine

Grant number: 16/19766-1
Support type:Regular Research Grants
Duration: March 01, 2017 - February 28, 2019
Field of knowledge:Physical Sciences and Mathematics - Physics
Principal Investigator:Vitor Barbanti Pereira Leite
Grantee:Vitor Barbanti Pereira Leite
Home Institution: Instituto de Biociências, Letras e Ciências Exatas (IBILCE). Universidade Estadual Paulista (UNESP). Campus de São José do Rio Preto. São José do Rio Preto , SP, Brazil

Abstract

Understanding the relationships between structure, energetics and functional dynamics of proteins is one of the biggest challenges in molecular biophysics. The energy landscape approach has contributed significantly to the understanding of complex molecular systems such as protein folding problem, where minimalist and coarse-grained models have played a key role. Using coarse-grained models and statistical physics approaches, the problems addressed in this project can be divided into three groups:(1) Fundamental issues in the protein folding area. The topics covered are: understanding the diffusion coefficient in the representation of folding, study of the effects of frustration and non-native interactions in the folding process, and the visualization of the folding funnel. These methologies will be applied in the study of conformational transitions associated with protein functions.(2) Statistical approaches in bioinformatics and information processing, which complement the mechanistic computational approaches.(3) The tools developed will be integrated and applied in biotechnology and biomedicine problems. The technological application is on the study of enzymes involved in the generation of bioethanol in a theoretical-experimental collaboration. We use coarse-grained models in the study of the thermal stability of enzymes, focusing on 'in silico' stability optimization of enzymes and proposing site directed mutations to be tested experimentally. An immediate on going application aims at evaluating and optimizing enzyme cocktails used in the second generation bioethanol production. In biomedicine, these techniques have applications in various biological systems. We will investigate questions associated with Zika virus proteins, the estrogen receptor and on prospecting vaccines. (AU)

Scientific publications (11)
(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, FERNANDO B.; DE OLIVEIRA, VINICIUS M.; SANCHES, MURILO N.; CONTESSOTO, VINICIUS G.; LEITE, VITOR B. P. Rational Design of Chymotrypsin Inhibitor 2 by Optimizing Non-Native Interactions. JOURNAL OF CHEMICAL INFORMATION AND MODELING, v. 60, n. 2, p. 982-988, FEB 2020. Web of Science Citations: 1.
MOURO, PAULO R.; POVINELLI, ANA P. R.; LEITE, VITOR B. P.; CHAHINE, JORGE. Exploring Folding Aspects of Monomeric Superoxide Dismutase. Journal of Physical Chemistry B, v. 124, n. 4, p. 650-661, JAN 30 2020. Web of Science Citations: 0.
DE OLIVEIRA, VINICIUS M.; CAETANO, DANIEL L. Z.; DA SILVA, FERNANDO B.; MOURO, PAULO R.; DE OLIVEIRA, JR., ANTONIO B.; DE CARVALHO, SIDNEY J.; LEITE, VITOR B. P. pH and Charged Mutations Modulate Cold Shock Protein Folding and Stability: A Constant pH Monte Carlo Study. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, v. 16, n. 1, p. 765-772, JAN 2020. Web of Science Citations: 0.
OLIVEIRA, JR., ANTONIO B.; YANG, HUAN; WHITFORD, PAUL C.; LEITE, VITOR B. P. Distinguishing Biomolecular Pathways and Metastable States. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, v. 15, n. 11, p. 6482-6490, NOV 2019. Web of Science Citations: 1.
YANG, HUAN; BANDARKAR, PRASAD; HORNE, RANSOM; LEITE, VITOR B. P.; CHAHINE, JORGE; WHITFORD, PAUL C. Diffusion of tRNA inside the ribosome is position-dependent. Journal of Chemical Physics, v. 151, n. 8 AUG 28 2019. Web of Science Citations: 0.
DA SILVA, FERNANDO BRUNO; CONTESSOTO, VINICIUS G.; DE OLIVEIRA, VINICIUS M.; CLARKE, JANE; LEITE, VITOR B. P. Non-Native Cooperative Interactions Modulate Protein Folding Rates. Journal of Physical Chemistry B, v. 122, n. 48, p. 10817-10824, DEC 6 2018. Web of Science Citations: 3.
CONTESSOTO, VINICIUS G.; DE OLIVEIRA, VINICIUS M.; FERNANDES, BRUNO R.; SLADE, GABRIEL G.; LEITE, VITOR B. P. TKSA-MC: A web server for rational mutation through the optimization of protein charge interactions. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, v. 86, n. 11, p. 1184-1188, NOV 2018. Web of Science Citations: 2.
TAMBONIS, TIAGO; BOARETO, MARCELO; LEITE, VITOR B. P. Differential Expression Analysis in RNA-seq Data Using a Geometric Approach. JOURNAL OF COMPUTATIONAL BIOLOGY, v. 25, n. 11, p. 1257-1265, NOV 2018. Web of Science Citations: 0.
BRUNI, ALINE THAIS; MARIZ DE CARVALHO, PEDRO OLIVEIRA; PINKE RODRIGUES, CAIO HENRIQUE; PEREIRA LEITE, VITOR BARBANTI. In silico methods in forensic science: Quantum chemistry and multivariate analysis applied to infrared spectra of new amphetamine- and cathinone-derived psychoactive substances. FORENSIC CHEMISTRY, v. 9, p. 21-34, JUN 2018. Web of Science Citations: 2.
DE OLIVEIRA, VINICIUS MARTINS; CONTESSOTO, VINICIUS DE GODOI; DA SILVA, FERNANDO BRUNO; ZAGO CAETANO, DANIEL LUCAS; DE CARVALHO, SIDNEY JURADO; PEREIRA LEITE, VITOR BARBANTI. Effects of pH and Salt Concentration on Stability of a Protein G Variant Using Coarse-Grained Models. BIOPHYSICAL JOURNAL, v. 114, n. 1, p. 65-75, JAN 9 2018. Web of Science Citations: 8.
VINÍCIUS DE GODOI CONTESSOTO; ANTONIO BENTO DE OLIVEIRA JUNIOR; JORGE CHAHINE; RONALDO JUNIO DE OLIVEIRA; VITOR BARBANTI PEREIRA LEITE. Introdução ao problema de enovelamento de proteínas: uma abordagem utilizando modelos computacionais simplificados. Revista Brasileira de Ensino de Física, v. 40, n. 4, p. -, 2018.

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