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Computational studies in protein folding and enzymes engineering involved in bioethanol production

Abstract

This project aims to continue the research that has been developed at IBILCE in the area of theoretical models in molecular biological physics, with emphasis on computational methods. Problems in the area of molecular biological physics have great complexity, and simplified models play an important role in understanding these systems. Such models have served as fundamental tools, from which more elaborate issues can be developed. In this project, the problems to be addressed through simplified models can be divided into three areas: (1) Protein folding, focusing on fundamental questions in the area. The topics covered are: understanding of the diffusion coefficient in the representation of folding, the effects of frustration, hydrophobicity and topology in the folding process, and visualization of the folding funnel. (2) Study of the enzymes involved in the production of bioethanol, in a theoretical and experimental collaboration. We use coarse-grained models in the study of the mechanisms of thermophilic enzymes 1XXN, 1IGO and 2JEN. We will optimize the thermostability of these enzymes {\sl in silico}, we will suggest site-directed mutations to be tested experimentally. We also use simplified models to investigate enzyme activity variations due to conformational changes in the protein domains. (3) Other topics in biological physics involving external collaborators. These include: statistical mechanics applications in bioinformatics and information processing, and the study of ribosome dynamics. (AU)

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Scientific publications (10)
(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 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, . (16/19766-1, 16/13998-8, 17/09662-7, 14/06862-7, 18/11614-3)
MOURO, PAULO RICARDO; CONTESSOTO, VINICIUS DE GODOI; CHAHINE, JORGE; DE OLIVEIRA, RONALDO JUNIO; PEREIRA LEITE, VITOR BARBANTI. Quantifying Nonnative Interactions in the Protein-Folding Free-Energy Landscape. BIOPHYSICAL JOURNAL, v. 111, n. 2, p. 287-293, . (14/06862-7)
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, . (16/19766-1, 14/06862-7)
CORONADO, MONIKA A.; CARUSO, ICARO P.; DE OLIVEIRA, VINICIUS M.; CONTESSOTO, VINICIUS G.; LEITE, VITOR B. P.; KAWAI, LIEGE A.; ARNI, RAGHUVIR K.; EBERLE, RAPHAEL J.. Cold Shock Protein A from Corynebacterium pseudotuberculosis: Role of Electrostatic Forces in the Stability of the Secondary Structure. PROTEIN AND PEPTIDE LETTERS, v. 24, n. 4, p. 358-367, . (16/08104-8, 14/06862-7)
CONTESSOTO, VINICIUS DE GODOI; RAMOS, FELIPE CARDOSO; DE MELO, RICARDO RODRIGUES; DE OLIVEIRA, VINICIUS MARTINS; SCARPASSA, JOSIANE ANIELE; DE SOUSA, AMANDA SILVA; ZANPHORLIN, LETICIA MARIA; SLADE, GABRIEL GOUVEA; PEREIRA LEITE, VITOR BARBANTI; RULLER, ROBERTO. Electrostatic interaction optimization improves catalytic rates and thermotolerance on xylanases. BIOPHYSICAL JOURNAL, v. 120, n. 11, p. 9-pg., . (16/19766-1, 16/13998-8, 17/14253-9, 18/11614-3, 14/06862-7, 19/22540-3, 17/09662-7)
CONTESSOTO, VINICIUS DE GODOI; RAMOS, FELIPE CARDOSO; DE MELO, RICARDO RODRIGUES; DE OLIVEIRA, VINICIUS MARTINS; SCARPASSA, JOSIANE ANIELE; DE SOUSA, AMANDA SILVA; ZANPHORLIN, LETICIA MARIA; SLADE, GABRIEL GOUVEA; PEREIRA LEITE, VITOR BARBANTI; RULLER, ROBERTO. lectrostatic interaction optimization improves catalytic rates and thermotolerance on xylanase. BIOPHYSICAL JOURNAL, v. 120, n. 11, p. 2172-2180, . (17/09662-7, 17/14253-9, 16/19766-1, 19/22540-3, 18/11614-3, 16/13998-8, 14/06862-7)
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, . (13/13151-7, 16/19766-1, 16/13998-8, 17/09662-7, 14/06862-7)
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, . (17/09662-7, 16/13998-8, 16/19766-1, 14/06862-7)
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, . (16/13998-8, 16/19766-1, 14/06862-7, 17/09662-7)
NGO, KHOA; DA SILVA, FERNANDO BRUNO; LEITE, VITOR B. P.; CONTESSOTO, VINICIUS G.; ONUCHIC, JOSE N.. Improving the Thermostability of Xylanase A from Bacillus subtilis by Combining Bioinformatics and Electrostatic Interactions Optimization. Journal of Physical Chemistry B, v. 125, n. 17, p. 4359-4367, . (16/19766-1, 19/22540-3, 14/06862-7, 16/13998-8, 17/09662-7)

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