Rational evolution by computational methods applied to predict mutations in enzymes to biofuels production

• Grant number: 16/13998-8
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: January 01, 2017
• End date: June 17, 2021
• Field of knowledge: Biological Sciences - Biophysics - Molecular Biophysics
• Agreement: Coordination of Improvement of Higher Education Personnel (CAPES)
• Principal Investigator: Vitor Barbanti Pereira Leite
• Grantee: Vinícius de Godoi Contessoto
• 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
• Associated scholarship(s): 17/09662-7 - Rational Evolution by Computational Methods Applied in Enzymes Related to Bioethanol Production, BE.EP.PD

Abstract

One of the most difficult challenges in science is to find clean and cheap energy sources. The second generation bioethanol seems to be viable a solution to substitute fossil fuel usage. The bioethanol production makes use of sugarcane biomass residues not used directly in fermentation process. This process involves the degradation of cellulose by specific enzymatic hydrolysis. The technological challenge now is to obtain and optimize the enzymes to perform the hydrolysis process with more efficiency. Recent results from CTBE group on Xylanase A enzyme from Bacillus subtilis have shown a group of mutations that improves the thermostability and the catalytic activity. Understanding the effect of each mutation in protein is an important step to be able to develop efficient methods to design optimized enzymes. The motivation of this project is to work on enzymes thermostability optimization, suggesting mutations to be tested experimentaly. This ongoing project seeks to evaluate and optimize enzyme cocktails for second generation bioethanol production. The focus of the optimization is to increase the catalytic activity, the thermostability and pH control, adapting the enzymes to have the optimum activity at the reactor operation conditions. Theoretical methods based on optimization of charge-charge interaction in enzyme surface and based on consensus and ancestral reconstruction sequence will be used. The suggested mutations will be experimentally validated by the CTBE group. (AU)

Scientific publications

(18)

(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)

CHENG, RYAN R.; CONTESSOTO, VINICIUS G.; AIDEN, EREZ LIEBERMAN; WOLYNES, PETER G.; DI PIERRO, MICHELE; ONUCHIC, JOSE N.. Exploring chromosomal structural heterogeneity across multiple cell lines. eLIFE, v. 9, OCT 13 2020. (17/09662-7, 16/13998-8)

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. (16/19766-1, 16/13998-8, 17/09662-7, 17/25130-5, 18/11614-3, 18/18668-1)

CONTESSOTO, VINICIUS G.; FERREIRA, PAULO H. B.; CHAHINE, JORGE; LEITE, VITOR B. P.; OLIVEIRA, RONALDO J.. Small Neutral Crowding Solute Effects on Protein Folding Thermodynamic Stability and Kinetics. Journal of Physical Chemistry B, v. 125, n. 42, p. 11673-11686, OCT 28 2021. (16/13998-8, 19/22540-3, 16/19766-1)

DA SILVA, FERNANDO BRUNO; DE OLIVEIRA, VINICIUS MARTINS; DE OLIVEIRA JUNIOR, ANTONIO BENTO; CONTESSOTO, VINICIUS DE GODOI; LEITE, VITOR B. P.. Processing of Composite Electrodes of Carbon Nanotube Fabrics and Inorganic Matrices via Rapid Joule Heating. Journal of Physical Chemistry B, v. N/A, p. 10-pg., 2023-02-01. (18/11614-3, 16/13998-8, 17/09662-7, 19/22540-3)

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. (16/19766-1, 16/13998-8, 17/09662-7, 14/06862-7, 18/11614-3)

HOENCAMP, CLAIRE; DUDCHENKO, OLGA; ELBATSH, AHMED M. O.; BRAHMACHARI, SUMITABHA; RAAIJMAKERS, JONNE A.; VAN SCHAIK, TOM; CACCIATORE, ANGELA SEDENO; CONTESSOTO, VINICIUS G.; VAN HEESBEEN, ROY G. H. P.; VAN DEN BROEK, BRAM; et al. 3D genomics across the tree of life reveals condensin II as a determinant of architecture type. Science, v. 372, n. 6545, p. 984+, MAY 28 2021. (16/13998-8, 17/09662-7)

FREITAS, FREDERICO CAMPOS; LIMA, ANGELICA NAKAGAWA; CONTESSOTO, VINICIUS DE GODOI; WHITFORD, PAUL C.; DE OLIVEIRA, RONALDO JUNIO. Drift-diffusion (DrDiff) framework determines kinetics and thermodynamics of two-state folding trajectory and tunes diffusion models. Journal of Chemical Physics, v. 151, n. 11, SEP 21 2019. (17/09662-7, 16/13998-8)

DODERO-ROJAS, ESTEBAN; FERREIRA, LUIZA G.; LEITE, VITOR B. P.; ONUCHIC, JOSE N.; CONTESSOTO, VINICIUS G.. Modeling Chikungunya control strategies and Mayaro potential outbreak in the city of Rio de Janeiro. PLoS One, v. 15, n. 1, JAN 28 2020. (17/09662-7, 18/18668-1, 16/13998-8)

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., 2021-06-01. (16/19766-1, 16/13998-8, 17/14253-9, 18/11614-3, 14/06862-7, 19/22540-3, 17/09662-7)

CONTESSOTO, VINICIUS G.; DUDCHENKO, OLGA; AIDEN, EREZ LIEBERMAN; WOLYNES, PETER G.; ONUCHIC, JOSE N.; DI PIERRO, MICHELE. Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues. NATURE COMMUNICATIONS, v. 14, n. 1, p. 12-pg., 2023-01-19. (16/13998-8, 17/09662-7)

OLIVEIRA JUNIOR, ANTONIO B.; CONTESSOTO, VINICIUS G.; MELLO, MATHEUS F.; ONUCHIC, JOSE N.. A Scalable Computational Approach for Simulating Complexes of Multiple Chromosomes. Journal of Molecular Biology, v. 433, n. 6, SI, MAR 19 2021. (16/13998-8, 16/01343-7, 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, JUN 1 2021. (17/09662-7, 17/14253-9, 16/19766-1, 19/22540-3, 18/11614-3, 16/13998-8, 14/06862-7)

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, MAY 6 2021. (16/19766-1, 19/22540-3, 14/06862-7, 16/13998-8, 17/09662-7)

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, NOV 2018. (16/13998-8, 16/19766-1, 14/06862-7, 17/09662-7)

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, 2018-06-18. (16/13998-8, 17/09662-7, 14/06862-7, 16/19766-1)

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. (13/13151-7, 16/19766-1, 16/13998-8, 17/09662-7, 14/06862-7)

OLIVEIRA, JR., ANTONIO B.; ESTRADA, CYNTHIA PEREZ; AIDEN, EREZ LIEBERMAN; CONTESSOTO, VINICIUS G.; ONUCHIC, JOSE N.. Chromosome Modeling on Downsampled Hi-C Maps Enhances the Compartmentalization Signal. Journal of Physical Chemistry B, v. 125, n. 31, p. 8757-8767, AUG 12 2021. (16/13998-8, 17/09662-7)

OLIVEIRA JUNIOR, ANTONIO B.; CONTESSOTO, VINICIUS G.; MELLO, MATHEUS F.; ONUCHIC, JOSE N.. A Scalable Computational Approach for Simulating Complexes of Multiple Chromosomes. Journal of Molecular Biology, v. 433, n. 6, p. 10-pg., 2021-03-18. (16/13998-8, 17/09662-7, 16/01343-7)