Mapping enzyme-substrate interactions: its potential to study the mechanism of enzymes
With the increase of the need to use more sustainable processes for the industry in our society, the modeling of enzymes has become crucial to fully comprehend their mechanism of action and use this knowledge to enhance and design their properties. A lot of methods to study enzymes computationally e...
| Autores: | , , |
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| Tipo de recurso: | capítulo de libro |
| Fecha de publicación: | 2020 |
| País: | España |
| Institución: | Universitat Politècnica de Catalunya (UPC) |
| Repositorio: | UPCommons. Portal del coneixement obert de la UPC |
| Idioma: | inglés |
| OAI Identifier: | oai:upcommons.upc.edu:2117/367437 |
| Acceso en línea: | https://hdl.handle.net/2117/367437 https://dx.doi.org/10.1016/bs.apcsb.2020.06.001 |
| Access Level: | acceso abierto |
| Palabra clave: | Computational chemistry Artificial intelligence Enzymology Enzyme engineering Protein dynamics PELE Enzyme-substrate Molecular modeling Enzims Simulació per ordinador Àrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::Bioinformàtica Àrees temàtiques de la UPC::Enginyeria química::Química analítica::Anàlisi enzimàtica |
| Sumario: | With the increase of the need to use more sustainable processes for the industry in our society, the modeling of enzymes has become crucial to fully comprehend their mechanism of action and use this knowledge to enhance and design their properties. A lot of methods to study enzymes computationally exist and they have been classified on sequence-based, structure-based, and the more new artificial intelligence-based ones. Albeit the abundance of methods to help predict the function of an enzyme, molecular modeling is crucial when trying to understand the enzyme mechanism, as they aim to correlate atomistic information with experimental data. Among them, methods that simulate the system dynamics at a molecular mechanics level of theory (classical force fields) have shown to offer a comprehensive study. In this book chapter, we will analyze these techniques, emphasizing the importance of precise modeling of enzyme-substrate interactions. In the end, a brief explanation of the transference of the information from research studies to the industry is given accompanied with two examples of family enzymes where their modeling has helped their exploitation. |
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