Use of classical and quantum molecular dynamics simulations to study new glycoside hydrolases identified through omics studies

• Grant number: 24/15257-1
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• Start date: December 01, 2024
• End date: November 30, 2027
• Field of knowledge: Biological Sciences - Biochemistry - Chemistry of Macromolecules
• Principal Investigator: Mário Tyago Murakami
• Grantee: Gustavo Henrique Martins
• Host Institution: Centro Nacional de Pesquisa em Energia e Materiais (CNPEM). Ministério da Ciência, Tecnologia e Inovação (Brasil). Campinas , SP, Brazil
• Associated research grant: 21/04891-3 - Enzymatic mechanisms from the microbiome of aquatic herbivores for depolymerization and metabolism of complex carbohydrates, AP.TEM

Abstract

Multi-omics studies of environments not yet explored have revealed new strategies for the degradation of lignocellulosic biomass, revealing new enzymes, often from unprecedented families, whose molecular mechanisms remain unknown. In this doctoral project, we intend to understand with a high level of detail and precision the mechanisms of enzymes potentially belonging to new families or subfamilies of glycosidic hydrolases, through advanced computational simulation methods that include classical, quantum and hybrid molecular dynamics (QM/MM) . The structures to be used for the simulations will be determined by X-ray crystallography or cryo-electron microscopy, during the execution of the thematic project to which this scholarship is linked. Furthermore, we will be able to use computational simulations to compare and co-validate preliminary data from serial crystallography.