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Utilization of modelling tools and molecular dynamics for QM/MM simulations of new enzymes from family GH173

Grant number: 23/00330-2
Support Opportunities:Scholarships in Brazil - Master
Effective date (Start): September 01, 2023
Effective date (End): February 28, 2025
Field of knowledge:Biological Sciences - Biochemistry - Chemistry of Macromolecules
Principal Investigator:Mário Tyago Murakami
Grantee:Gustavo Henrique Barreto Gimenis
Host Institution: Centro Nacional de Pesquisa em Energia e Materiais (CNPEM). Ministério da Ciência, Tecnologia e Inovação (Brasil). Campinas , SP, Brazil

Abstract

Microorganisms capability to act in complex carbohydrates feedstocks and catalyze theirdepolymerization in diverse conditions is a synergistic feature of their enzymatic apparatus.However, due to these systems diversity and complexity, the elucidation of their molecularmechanisms is limited in comparison with the number of enzyme sequences available. Thisphenomenon is even more pronounced for new families of enzymes with unknown structures.The glycoside hydrolase family 173 (GH173) was recently founded by our research group, bya combination of modern multi-omics and biochemical techniques to uncover the capybaramicrobiome molecular strategies. The GH173 characterized members presented beta-galactosidase activity, which is relevant for biorenewables development, food industry, anddrug design. The GH173 harbors a predicted TIM-barrel scaffold, typical from GH-A clan,however the distinguished activities in comparison with homologues and low sequencesidentities with other members reinforce the GH173 foundation and the necessity of detailedstudies to determine its catalytic itinerary. Molecular dynamics simulations with QuantumMechanics / Molecular Mechanics (QM/MM) approaches will be applied in this project toelucidate the mode of action of at least one representative member of this new family. Thecombination of state-of-the-art computational methods with simultaneous experiments willprovide significant advances for the biocatalysis field and a broader comprehension ofmicrobes molecular strategies through unprecedented enzymes.

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