Studies of enzymatic mechanisms for the improvement of bio-fuel production

• Grant number: 11/13242-7
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: October 01, 2011
• End date: July 31, 2013
• Field of knowledge: Physical Sciences and Mathematics - Physics
• Principal Investigator: Vitor Barbanti Pereira Leite
• Grantee: Leandro Cristante de Oliveira
• Host Institution: Centro Nacional de Pesquisa em Energia e Materiais (CNPEM). Campinas , SP, Brazil

Abstract

Obtaining ethanol and sub-products through sugar-cane fermentation is a known and widely employed technique in this country. The demand for bioethanol is stable and increasing. However, in this process, a considerable amount of biomass with a high energetic potential is wasted due the absence of efficient technology. In this work, we will carry out a theoretical-computational study to be performed in collaboration with CTBE experimental groups. The analysis will focus on the regulation/modulation mechanisms of enzymaticactivity by conformational variation of protein domains (CDs and CBMs). Two topics will be analyzed: (1) Conformational fluctuations of the cellulase Bacillus Subtilus CEL5A due to the interaction with the substrate. This system will be investigated using standard Molecular Dynamics techniques with explicit solvent for the holo and apo cases, which will be complemented by structure based models (SBM) and normal mode analysis (NMA). (2) Structural characterization and evaluation of the flexibility of the xylanase-lichenase domains and laminarase TpLam domains (including its variations), which will be performed using molecular dynamics on structure based models combined with Small Angle X-ray Scattering (SAXS)data. The understanding of these enzyme mechanisms may, in principle, be extended to other similar enzymes, helping directly in the development of enzymes with biotechnological potential.

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)

COTA, JUNIO; OLIVEIRA, LEANDRO C.; DAMASIO, ANDRE R. L.; CITADINI, ANA P.; HOFFMAM, ZAIRA B.; ALVAREZ, THABATA M.; CODIMA, CARLA A.; LEITE, VITOR B. P.; PASTORE, GLAUCIA; DE OLIVEIRA-NETO, MARIO; et al. Assembling a xylanase-lichenase chimera through all-atom molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, v. 1834, n. 8, p. 1492-1500, AUG 2013. (11/13242-7, 11/02169-7, 08/58037-9)

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)

DAMASIO, ANDRE R. L.; RUBIO, MARCELO V.; OLIVEIRA, LEANDRO C.; SEGATO, FERNANDO; DIAS, BRUNO A.; CITADINI, ANA P.; PAIXAO, DOUGLAS A.; SQUINA, FABIO M.. Understanding the Function of Conserved Variations in the Catalytic Loops of Fungal Glycoside Hydrolase Family 12. Biotechnology and Bioengineering, v. 111, n. 8, p. 1494-1505, AUG 2014. (11/13242-7, 08/58037-9, 12/12859-3)

DE OLIVEIRA, LEANDRO C.; DA SILVA, VIVIAM M.; COLUSSI, FRANCIELI; CABRAL, ALINE D.; DE OLIVEIRA NETO, MARIO; SQUINA, FABIO M.; GARCIA, WANIUS. Conformational Changes in a Hyperthermostable Glycoside Hydrolase: Enzymatic Activity Is a Consequence of the Loop Dynamics and Protonation Balance. PLoS One, v. 10, n. 2, FEB 27 2015. (12/21054-9, 08/58037-9, 12/03503-0, 11/13242-7)

FRANCO CAIRO, JOAO PAULO L.; OLIVEIRA, LEANDRO C.; UCHIMA, CRISTIANE A.; ALVAREZ, THABATA M.; CITADINI, ANA PAULA DA S.; COTA, JUNIO; LEONARDO, FLAVIA COSTA; COSTA-LEONARDO, ANA M.; CARAZZOLLE, MARCELO F.; COSTA, FERNANDO F.; et al. Deciphering the synergism of endogenous glycoside hydrolase families 1 and 9 from Coptotermes gestroi. Insect Biochemistry and Molecular Biology, v. 43, n. 10, p. 970-981, OCT 2013. (12/19040-0, 11/08609-9, 11/20977-3, 11/13242-7, 10/11469-1, 08/58037-9)

COTA, JUNIO; CORREA, THAMY L. R.; DAMASIO, ANDRE R. L.; DIOGO, JOSE A.; HOFFMAM, ZAIRA B.; GARCIA, WANIUS; OLIVEIRA, LEANDRO C.; PRADE, ROLF A.; SQUINA, FABIO M.. Comparative analysis of three hyperthermophilic GH1 and GH3 family members with industrial potential. NEW BIOTECHNOLOGY, v. 32, n. 1, p. 13-20, JAN 25 2015. (12/21054-9, 11/13242-7, 08/58037-9, 10/18198-3)

COLUSSI, FRANCIELI; DA SILVA, VIVIAM M.; MILLER, IAN; COTA, JUNIO; DE OLIVEIRA, LEANDRO C.; DE OLIVEIRA NETO, MARIO; SQUINA, FABIO M.; GARCIA, WANIUS. Oligomeric state and structural stability of two hyperthermophilic beta-glucosidases from Thermotoga petrophila. Amino Acids, v. 47, n. 5, p. 937-948, MAY 2015. (12/21054-9, 08/58037-9, 12/03503-0, 11/13242-7)