Computational studies on protein folding and applications in the study of enzymes involved in bioethanol production

• Grant number: 11/17658-3
• Support Opportunities: Regular Research Grants
• Duration: February 01, 2012 - January 31, 2014
• Field of knowledge: Physical Sciences and Mathematics - Physics
• Principal Investigator: Vitor Barbanti Pereira Leite
• Grantee: Vitor Barbanti Pereira Leite
• Host 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

This project aims to continue the research being developed at IBILCE in the area of theoretical molecular biological physics, with emphasis on computational methods. The problems in the area of molecular biological physics have great complexity. History shows that minimalist models play an important role in understanding these complex systems. Such models have served as fundamental tools, from which more elaborate issues could 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 in one and two dimensions, the effects of frustration, hydrophobicity and topology in folding process, and visualization and quantitative descriptors of the folding funnel. (2) Study of the enzymes involved in the production of bioethanol, in a collaboration between theoretical and experimental groups. More specifically, we study the mechanisms associated with two thermophilic enzymes (xynalase and laminarinase). We also use coarse-grained models in combination with SAXS data to investigate the modulation of enzymatic activity by conformational changes of protein domains. (3) Other topics in biological physics involving external collaborators. These include: electron transfer in proteins, statistical mechanics applications in bioinformatics and chemometrics studies. Computational resources are requested, especially a computer cluster, and means (transportation and per diem) to carry out research with external collaborators of the group. (AU)

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)

DE SOUZA, ANGELICA R.; DE ARAUJO, GABRIELA C.; ZANPHORLIN, LETICIA M.; RULLER, ROBERTO; FRANCO, FERNANDA C.; TORRES, FERNANDO A. G.; MERTENS, JEFFREY A.; BOWMAN, MICHAEL J.; GOMES, ELENI; DA SILVA, ROBERTO. Engineering increased thermostability in the GH-10 endo-1,4-beta-xylanase from Thermoascus aurantiacus CBMAI 756. International Journal of Biological Macromolecules, v. 93, n. A, p. 20-26, DEC 2016. (14/02080-4, 14/04272-8, 10/12624-0, 11/17658-3)

MANDELLI, F.; FRANCO CAIRO, J. P. L.; CITADINI, A. P. S.; BUECHLI, F.; ALVAREZ, T. M.; OLIVEIRA, R. J.; LEITE, V. B. P.; PAES LEME, A. F.; MERCADANTE, A. Z.; SQUINA, F. M.. The characterization of a thermostable and cambialistic superoxide dismutase from Thermus filiformis. Letters in Applied Microbiology, v. 57, n. 1, p. 40-46, JUL 2013. (08/58037-9, 11/17658-3)

POLOTTO, FRANCIELE; DRIGO FILHO, ELSO; CHAHINE, JORGE; DE OLIVEIRA, RONALDO JUNIO. Supersymmetric quantum mechanics method for the Fokker-Planck equation with applications to protein folding dynamics. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, v. 493, p. 286-300, MAR 1 2018. (11/17658-3)

ARAUJO, GABRIELA C.; SILVA, RICARDO H. T.; SCOTT, LUIS P. B.; ARAUJO, ALEXANDRE S.; SOUZA, FATIMA P.; DE OLIVEIRA, RONALDO JUNIO. Structure and functional dynamics characterization of the ion channel of the human respiratory syncytial virus (hRSV) small hydrophobic protein (SH) transmembrane domain by combining molecular dynamics with excited normal modes. Journal of Molecular Modeling, v. 22, n. 12, DEC 2016. (10/18169-3, 11/17658-3)

DE SOUZA, ANGELICA R.; DE ARAUJO, GABRIELA C.; ZANPHORLIN, LETICIA M.; RULLER, ROBERTO; FRANCO, FERNANDA C.; TORRES, FERNANDO A. G.; MERTENS, JEFFREY A.; BOWMAN, MICHAEL J.; GOMES, ELENI; DA SILVA, ROBERTO. Engineering increased thermostability in the GH-10 endo-1,4-beta-xylanase from Thermoascus aurantiacus CBMAI 756. International Journal of Biological Macromolecules, v. 93, p. 7-pg., 2016-12-01. (14/04272-8, 10/12624-0, 11/17658-3, 14/02080-4)

HOFFMAM, ZAIRA B.; OLIVEIRA, LEANDRO C.; COTA, JUNIO; ALVAREZ, THABATA M.; DIOGO, JOS A.; NETO, MARIO DE OLIVEIRA; CITADINI, ANA PAULA S.; LEITE, VITOR B. P.; SQUINA, FABIO M.; MURAKAMI, MARIO T.; et al. Characterization of a Hexameric Exo-Acting GH51 alpha-l-Arabinofuranosidase from the Mesophilic Bacillus subtilis. MOLECULAR BIOTECHNOLOGY, v. 55, n. 3, p. 260-267, NOV 2013. (10/51890-8, 11/14200-6, 11/13242-7, 08/58037-9, 11/17658-3)

LIMA, ANGELICA NAKAGAWA; DE OLIVEIRA, RONALDO JUNIO; KIMUS BRAZ, ANTONIO SERGIO; DE SOUZA COSTA, MAURICIO GARCIA; PERAHIA, DAVID; BARBOUR SCOTT, LUIS PAULO. Effects of pH and aggregation in the human prion conversion into scrapie form: a study using molecular dynamics with excited normal modes. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, v. 47, n. 5, p. 583-590, JUL 2018. (11/17658-3)