Elucidation of the structural determinants for the existence of selectivity in endoglucanases through computational approaches

• Grant number: 25/06407-2
• Support Opportunities: Scholarships in Brazil - Scientific Initiation
• Start date: May 01, 2025
• End date: April 30, 2026
• Field of knowledge: Biological Sciences - Biophysics - Molecular Biophysics
• Principal Investigator: Mariana Abrahão Bueno de Morais
• Grantee: Rafaela Beatriz Silva Luz
• Host Institution: Centro Nacional de Pesquisa em Energia e Materiais (CNPEM). Ministério da Ciência, Tecnologia e Inovação (Brasil). Campinas , SP, Brazil

Abstract

Carbohydrates have a wide chemical and structural variety, and to promote the cleavage of the myriad of chemical bonds present in polysaccharides, the glycoside hydrolases (GHs) are currently grouped within approximately 190 families with different architectures. Considering the intrinsic flexibility of the saccharide and the dynamic process of enzymatic catalysis, the interactions between substrate and key residues of the enzyme are fundamental for the selectivity of the glycoside bond cleavage. In addition to cellulose (composed of glucosyl residues linked through ¿-1,4 bonds), glucans with ¿-1,3 bonds and mixed bonds (¿-1,3, ¿-1,4) are abundant in several biological contexts and have relevant biotechnological applications, and understanding their depolymerization process is essential. This project aims to study, by computational methods, the molecular determinants for the selectivity of glucanases to the different chemical bonds of ¿-glucans. To this end, we selected GHs from different families (including recently founded ones) with previously reported activities from the carbohydrate-active enzyme database. By applying an optimized molecular docking strategy with oligosaccharides, to be developed in this project, and performing molecular dynamics simulations with the selected complexes, we intend to map the relevant interactions for each type of chemical bond present in ¿-glucans and obtain productive enzyme-substrate complexes for catalysis. With this information, we can contribute to the development of engineered enzymes that aim at polyspecificity or that are more selective, aiming at increasing catalytic activity. In addition, the generated complexes may, in the future, serve as a starting point for simulations of the catalysis process, using quantum mechanics and molecular mechanics.