Molecular modeling of carbohydrate-modifying enzymes

• Grant number: 19/17350-0
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: September 01, 2019
• End date: November 30, 2023
• Field of knowledge: Physical Sciences and Mathematics - Chemistry - Physical-Chemistry
• Principal Investigator: Munir Salomao Skaf
• Grantee: Artur Hermano Sampaio Dias
• Host Institution: Instituto de Química (IQ). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
• Associated research grant: 13/08293-7 - CCES - Center for Computational Engineering and Sciences, AP.CEPID
• Associated scholarship(s): 21/10472-3 - Molecular modeling of GcoA enzyme activity on lignin, BE.EP.DR

Abstract

Here, we propose to apply modern techniques of Molecular Dynamics (MD) simulations to study enzymes of interest to cellulosic biomass conversion. The primary focus of the proposed research lies on CBHs and EGs and other enzymes from fungi and bacteria. Our interest more specifically here is to explore protein-cellulose substrate binding at the atomistic level and to understand the mechanisms of catalytic hydrolysis of the polysaccharides by the enzymes. For that, we propose applying quantum mechanics/molecular mechanics (QM/MM) methods to polysaccharides docked into the corresponding enzyme active sites. Systems such as an oligosaccharide chain docked along the catalytic active tunnel of CBH I and/or CBH II and on EGs are the primary targets. In a later stage, we will also apply metagenomic and metatranscriptomic approaches to help us to understand the best candidates (cellulases, hemicellulases and auxiliary activities) to compose a cocktail. (AU)

Scientific publications

(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)

ARAUJO, EVANDRO A.; DIAS, ARTUR HERMANO SAMPAIO; KADOWAKI, MARCO A. S.; PIYADOV, VASILY; PELLEGRINI, VANESSA O. A.; URIO, MATEUS B.; RAMOS, LUIZ P.; SKAF, MUNIR S.; POLIKARPOV, IGOR. mpact of cellulose properties on enzymatic degradation by bacterial GH48 enzymes: Structural and mechanistic insights from processive Bacillus licheniformis Cel48B cellulas. Carbohydrate Polymers, v. 264, JUL 15 2021. (13/08293-7, 15/13684-0, 14/00769-5, 19/17350-0)

ARAUJO, EVANDRO A.; DIAS, ARTUR HERMANO SAMPAIO; KADOWAKI, MARCO A. S.; PIYADOV, VASILY; PELLEGRINI, VANESSA O. A.; URIO, MATEUS B.; RAMOS, LUIZ P.; SKAF, MUNIR S.; POLIKARPOV, IGOR. Impact of cellulose properties on enzymatic degradation by bacterial GH48 enzymes: Structural and mechanistic insights from processive Bacillus licheniformis Cel48B cellulase. Carbohydrate Polymers, v. 264, p. 13-pg., 2021-04-12. (14/00769-5, 13/08293-7, 15/13684-0, 19/17350-0)