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...

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Detalles Bibliográficos
Autores: Roda, Sergi, Santiago, Gerard, Guallar, Víctor|||0000-0002-4580-1114
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
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spelling Mapping enzyme-substrate interactions: its potential to study the mechanism of enzymesRoda, SergiSantiago, GerardGuallar, Víctor|||0000-0002-4580-1114Computational chemistryArtificial intelligenceEnzymologyComputational chemistryEnzyme engineeringProtein dynamicsPELEEnzyme-substrateMolecular modelingEnzimsSimulació per ordinadorÀrees temàtiques de la UPC::Informàtica::Aplicacions de la informàtica::BioinformàticaÀrees temàtiques de la UPC::Enginyeria química::Química analítica::Anàlisi enzimàticaWith 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.Peer ReviewedObjectius de Desenvolupament Sostenible::9 - Indústria, Innovació i InfraestructuraAcademic Press Inc.20202020-09-0120222022-05-17book parthttp://purl.org/coar/resource_type/c_3248AMhttp://purl.org/coar/version/c_ab4af688f83e57aainfo:eu-repo/semantics/bookPartapplication/pdfhttps://hdl.handle.net/2117/367437https://dx.doi.org/10.1016/bs.apcsb.2020.06.00132951809reponame:UPCommons. Portal del coneixement obert de la UPCinstname:Universitat Politècnica de Catalunya (UPC)Inglésengopen accesshttp://purl.org/coar/access_right/c_abf2Attribution-NonCommercial-NoDerivs 3.0 Spainhttp://creativecommons.org/licenses/by-nc-nd/3.0/es/Attribution-NonCommercial-NoDerivs 3.0 Spainhttps://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccessoai:upcommons.upc.edu:2117/3674372026-05-27T15:37:01Z
dc.title.none.fl_str_mv Mapping enzyme-substrate interactions: its potential to study the mechanism of enzymes
title Mapping enzyme-substrate interactions: its potential to study the mechanism of enzymes
spellingShingle Mapping enzyme-substrate interactions: its potential to study the mechanism of enzymes
Roda, Sergi
Computational chemistry
Artificial intelligence
Enzymology
Computational chemistry
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
title_short Mapping enzyme-substrate interactions: its potential to study the mechanism of enzymes
title_full Mapping enzyme-substrate interactions: its potential to study the mechanism of enzymes
title_fullStr Mapping enzyme-substrate interactions: its potential to study the mechanism of enzymes
title_full_unstemmed Mapping enzyme-substrate interactions: its potential to study the mechanism of enzymes
title_sort Mapping enzyme-substrate interactions: its potential to study the mechanism of enzymes
dc.creator.none.fl_str_mv Roda, Sergi
Santiago, Gerard
Guallar, Víctor|||0000-0002-4580-1114
author Roda, Sergi
author_facet Roda, Sergi
Santiago, Gerard
Guallar, Víctor|||0000-0002-4580-1114
author_role author
author2 Santiago, Gerard
Guallar, Víctor|||0000-0002-4580-1114
author2_role author
author
dc.subject.none.fl_str_mv Computational chemistry
Artificial intelligence
Enzymology
Computational chemistry
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
topic Computational chemistry
Artificial intelligence
Enzymology
Computational chemistry
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
description 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.
publishDate 2020
dc.date.none.fl_str_mv 2020
2020-09-01
2022
2022-05-17
dc.type.none.fl_str_mv book part
http://purl.org/coar/resource_type/c_3248
AM
http://purl.org/coar/version/c_ab4af688f83e57aa
dc.type.openaire.fl_str_mv info:eu-repo/semantics/bookPart
format bookPart
dc.identifier.none.fl_str_mv https://hdl.handle.net/2117/367437
https://dx.doi.org/10.1016/bs.apcsb.2020.06.001
32951809
url https://hdl.handle.net/2117/367437
https://dx.doi.org/10.1016/bs.apcsb.2020.06.001
identifier_str_mv 32951809
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution-NonCommercial-NoDerivs 3.0 Spain
http://creativecommons.org/licenses/by-nc-nd/3.0/es/
Attribution-NonCommercial-NoDerivs 3.0 Spain
https://creativecommons.org/licenses/by-nc-nd/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
Attribution-NonCommercial-NoDerivs 3.0 Spain
http://creativecommons.org/licenses/by-nc-nd/3.0/es/
https://creativecommons.org/licenses/by-nc-nd/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Academic Press Inc.
publisher.none.fl_str_mv Academic Press Inc.
dc.source.none.fl_str_mv reponame:UPCommons. Portal del coneixement obert de la UPC
instname:Universitat Politècnica de Catalunya (UPC)
instname_str Universitat Politècnica de Catalunya (UPC)
reponame_str UPCommons. Portal del coneixement obert de la UPC
collection UPCommons. Portal del coneixement obert de la UPC
repository.name.fl_str_mv
repository.mail.fl_str_mv
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