Mechanistic insights into substrate-assisted catalysis in glycosidases by means of QM/MM molecular dynamics
Carbohydrates are essential molecules in biotechnology and for the proper functioning of living organisms. They are involved in energy storage, being structural components or participating in crucial biological processes such as cellular signaling or the development of diseases. For this reason, car...
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| Tipo de recurso: | tesis doctoral |
| Estado: | Versión publicada |
| Fecha de publicación: | 2021 |
| País: | España |
| Institución: | CBUC, CESCA |
| Repositorio: | TDR. Tesis Doctorales en Red |
| OAI Identifier: | oai:www.tdx.cat:10803/670537 |
| Acceso en línea: | http://hdl.handle.net/10803/670537 |
| Access Level: | acceso abierto |
| Palabra clave: | Enzims Enzimas Enzymes Biologia computacional Biología computacional Computational biology Glúcids Glúcidos Glucydes Glucòsids Glucósidos Glucosydes Dinàmica molecular Dinámica molecular Molecular dynamics Bioquímica Biochemistry Ciències Experimentals i Matemàtiques 547 |
| Sumario: | Carbohydrates are essential molecules in biotechnology and for the proper functioning of living organisms. They are involved in energy storage, being structural components or participating in crucial biological processes such as cellular signaling or the development of diseases. For this reason, carbohydrates have gained great attention among the scientific community. “Carbohydrate-active enzymes” are the catalytic machinery that degrade, synthesize, and modify carbohydrates, even that saccharides show a vast variety of configurations, conformations and stereochemical properties. This thesis is focused on the study of glycosidases, enzymes in charge of hydrolyzing glycosidic bonds. In particular, glycosidases that use the substrate-assisted mechanism, in which the N-acetyl group of the substrate actively participate in catalysis. This reaction mechanism still hinders several mysteries such as the nature of the reaction intermediate, the role of the catalytic residues or the conformational itinerary. The latter corresponds to the conformations that a carbohydrate ring adopts during the enzymatic reaction. Deciphering glycosidase catalytic itineraries and their reaction mechanism boosts the design of specific inhibitors and provides further knowledge of these enzymes. To study glycosidase reaction mechanisms, we used computational techniques based on molecular dynamics, describing the systems with molecular mechanics, quantum mechanics or hybrid methods that combine the benefits from both. We investigated chitinase B from family GH18 that degrades chitin and β-N-acetylglucosaminidases from families GH84 and GH85, which cleave O- and N-glycans, respectively. Furthermore, we elucidated the conformational intrinsic properties of carbohydrates and carbohydrate-based inhibitors related to the substrate-assisted mechanism. In summary, we provide an overview of this reaction mechanism. |
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