An In Silico Methodology That Facilitates Decision Making in the Engineering of Nanoscale Protein Materials

Autores
Parladé, Eloi; Voltà Durán, Eric; Cano Garrido, Olivia; Sanchez, Julieta Maria; Unzueta, Ugutz; López Laguna, Hèctor; Serna, Naroa; Cano, Montserrat; Rodríguez Mariscal, Manuel; Vazquez, Esther; Villaverde, Antonio
Año de publicación
2022
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Under the need for new functional and biocompatible materials for biomedical applications, protein engineering allows the design of assemblable polypeptides, which, as convenient building blocks of supramolecular complexes, can be produced in recombinant cells by simple and scalable methodologies. However, the stability of such materials is often overlooked or disregarded, becoming a potential bottleneck in the development and viability of novel products. In this context, we propose a design strategy based on in silico tools to detect instability areas in protein materials and to facilitate the decision making in the rational mutagenesis aimed to increase their stability and solubility. As a case study, we demonstrate the potential of this methodology to improve the stability of a humanized scaffold protein (a domain of the human nidogen), with the ability to oligomerize into regular nanoparticles usable to deliver payload drugs to tumor cells. Several nidogen mutants suggested by the method showed important and measurable improvements in their structural stability while retaining the functionalities and production yields of the original protein. Then, we propose the procedure developed here as a cost-effective routine tool in the design and optimization of multimeric protein materials prior to any experimental testing.
Fil: Parladé, Eloi. Universitat Autònoma de Barcelona; España. Centro de Investigación Biomédica En Red de Bioingeniería, Biomateriales y Nanomedicina; España
Fil: Voltà Durán, Eric. Universitat Autònoma de Barcelona; España. Centro de Investigación Biomédica En Red de Bioingeniería, Biomateriales y Nanomedicina; España
Fil: Cano Garrido, Olivia. Nanoligent S.L; España
Fil: Sanchez, Julieta Maria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones Biológicas y Tecnológicas. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Instituto de Investigaciones Biológicas y Tecnológicas; Argentina. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Departamento de Química. Cátedra de Química Biológica; Argentina. Centro de Investigación Biomédica En Red de Bioingeniería, Biomateriales y Nanomedicina; España. Universitat Autònoma de Barcelona; España
Fil: Unzueta, Ugutz. Centro de Investigación Biomédica En Red de Bioingeniería, Biomateriales y Nanomedicina; España. Universitat Autònoma de Barcelona; España. Institut Dinvestigació Biomèdica Sant Pau; España
Fil: López Laguna, Hèctor. Universitat Autònoma de Barcelona; España. Centro de Investigación Biomédica En Red de Bioingeniería, Biomateriales y Nanomedicina; España
Fil: Serna, Naroa. Nanoligent S.L.; España
Fil: Cano, Montserrat. Nanoligent S.L.; España
Fil: Rodríguez Mariscal, Manuel. Nanoligent S.L.; España
Fil: Vazquez, Esther. Centro de Investigación Biomédica En Red de Bioingeniería, Biomateriales y Nanomedicina; España. Universitat Autònoma de Barcelona; España
Fil: Villaverde, Antonio. Centro de Investigación Biomédica En Red de Bioingeniería, Biomateriales y Nanomedicina; España. Universitat Autònoma de Barcelona; España
Materia
MUTAGENESIS
NANOMATERIALS
NANOMEDICINE
PROTEIN STABILITY
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/213794
Acceder
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network_name_str CONICET Digital (CONICET)
spelling An In Silico Methodology That Facilitates Decision Making in the Engineering of Nanoscale Protein MaterialsParladé, EloiVoltà Durán, EricCano Garrido, OliviaSanchez, Julieta MariaUnzueta, UgutzLópez Laguna, HèctorSerna, NaroaCano, MontserratRodríguez Mariscal, ManuelVazquez, EstherVillaverde, AntonioMUTAGENESISNANOMATERIALSNANOMEDICINEPROTEIN STABILITYhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Under the need for new functional and biocompatible materials for biomedical applications, protein engineering allows the design of assemblable polypeptides, which, as convenient building blocks of supramolecular complexes, can be produced in recombinant cells by simple and scalable methodologies. However, the stability of such materials is often overlooked or disregarded, becoming a potential bottleneck in the development and viability of novel products. In this context, we propose a design strategy based on in silico tools to detect instability areas in protein materials and to facilitate the decision making in the rational mutagenesis aimed to increase their stability and solubility. As a case study, we demonstrate the potential of this methodology to improve the stability of a humanized scaffold protein (a domain of the human nidogen), with the ability to oligomerize into regular nanoparticles usable to deliver payload drugs to tumor cells. Several nidogen mutants suggested by the method showed important and measurable improvements in their structural stability while retaining the functionalities and production yields of the original protein. Then, we propose the procedure developed here as a cost-effective routine tool in the design and optimization of multimeric protein materials prior to any experimental testing.Fil: Parladé, Eloi. Universitat Autònoma de Barcelona; España. Centro de Investigación Biomédica En Red de Bioingeniería, Biomateriales y Nanomedicina; EspañaFil: Voltà Durán, Eric. Universitat Autònoma de Barcelona; España. Centro de Investigación Biomédica En Red de Bioingeniería, Biomateriales y Nanomedicina; EspañaFil: Cano Garrido, Olivia. Nanoligent S.L; EspañaFil: Sanchez, Julieta Maria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones Biológicas y Tecnológicas. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Instituto de Investigaciones Biológicas y Tecnológicas; Argentina. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Departamento de Química. Cátedra de Química Biológica; Argentina. Centro de Investigación Biomédica En Red de Bioingeniería, Biomateriales y Nanomedicina; España. Universitat Autònoma de Barcelona; EspañaFil: Unzueta, Ugutz. Centro de Investigación Biomédica En Red de Bioingeniería, Biomateriales y Nanomedicina; España. Universitat Autònoma de Barcelona; España. Institut Dinvestigació Biomèdica Sant Pau; EspañaFil: López Laguna, Hèctor. Universitat Autònoma de Barcelona; España. Centro de Investigación Biomédica En Red de Bioingeniería, Biomateriales y Nanomedicina; EspañaFil: Serna, Naroa. Nanoligent S.L.; EspañaFil: Cano, Montserrat. Nanoligent S.L.; EspañaFil: Rodríguez Mariscal, Manuel. Nanoligent S.L.; EspañaFil: Vazquez, Esther. Centro de Investigación Biomédica En Red de Bioingeniería, Biomateriales y Nanomedicina; España. Universitat Autònoma de Barcelona; EspañaFil: Villaverde, Antonio. Centro de Investigación Biomédica En Red de Bioingeniería, Biomateriales y Nanomedicina; España. Universitat Autònoma de Barcelona; EspañaMultidisciplinary Digital Publishing Institute2022-05info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/213794Parladé, Eloi; Voltà Durán, Eric; Cano Garrido, Olivia; Sanchez, Julieta Maria; Unzueta, Ugutz; et al.; An In Silico Methodology That Facilitates Decision Making in the Engineering of Nanoscale Protein Materials; Multidisciplinary Digital Publishing Institute; International Journal of Molecular Sciences; 23; 9; 5-2022; 1-121661-65961422-0067CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.mdpi.com/1422-0067/23/9/4958info:eu-repo/semantics/altIdentifier/doi/10.3390/ijms23094958info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T09:56:35Zoai:ri.conicet.gov.ar:11336/213794instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-03 09:56:36.056CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv An In Silico Methodology That Facilitates Decision Making in the Engineering of Nanoscale Protein Materials
title An In Silico Methodology That Facilitates Decision Making in the Engineering of Nanoscale Protein Materials
spellingShingle An In Silico Methodology That Facilitates Decision Making in the Engineering of Nanoscale Protein Materials
Parladé, Eloi
MUTAGENESIS
NANOMATERIALS
NANOMEDICINE
PROTEIN STABILITY
title_short An In Silico Methodology That Facilitates Decision Making in the Engineering of Nanoscale Protein Materials
title_full An In Silico Methodology That Facilitates Decision Making in the Engineering of Nanoscale Protein Materials
title_fullStr An In Silico Methodology That Facilitates Decision Making in the Engineering of Nanoscale Protein Materials
title_full_unstemmed An In Silico Methodology That Facilitates Decision Making in the Engineering of Nanoscale Protein Materials
title_sort An In Silico Methodology That Facilitates Decision Making in the Engineering of Nanoscale Protein Materials
dc.creator.none.fl_str_mv Parladé, Eloi
Voltà Durán, Eric
Cano Garrido, Olivia
Sanchez, Julieta Maria
Unzueta, Ugutz
López Laguna, Hèctor
Serna, Naroa
Cano, Montserrat
Rodríguez Mariscal, Manuel
Vazquez, Esther
Villaverde, Antonio
author Parladé, Eloi
author_facet Parladé, Eloi
Voltà Durán, Eric
Cano Garrido, Olivia
Sanchez, Julieta Maria
Unzueta, Ugutz
López Laguna, Hèctor
Serna, Naroa
Cano, Montserrat
Rodríguez Mariscal, Manuel
Vazquez, Esther
Villaverde, Antonio
author_role author
author2 Voltà Durán, Eric
Cano Garrido, Olivia
Sanchez, Julieta Maria
Unzueta, Ugutz
López Laguna, Hèctor
Serna, Naroa
Cano, Montserrat
Rodríguez Mariscal, Manuel
Vazquez, Esther
Villaverde, Antonio
author2_role author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv MUTAGENESIS
NANOMATERIALS
NANOMEDICINE
PROTEIN STABILITY
topic MUTAGENESIS
NANOMATERIALS
NANOMEDICINE
PROTEIN STABILITY
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Under the need for new functional and biocompatible materials for biomedical applications, protein engineering allows the design of assemblable polypeptides, which, as convenient building blocks of supramolecular complexes, can be produced in recombinant cells by simple and scalable methodologies. However, the stability of such materials is often overlooked or disregarded, becoming a potential bottleneck in the development and viability of novel products. In this context, we propose a design strategy based on in silico tools to detect instability areas in protein materials and to facilitate the decision making in the rational mutagenesis aimed to increase their stability and solubility. As a case study, we demonstrate the potential of this methodology to improve the stability of a humanized scaffold protein (a domain of the human nidogen), with the ability to oligomerize into regular nanoparticles usable to deliver payload drugs to tumor cells. Several nidogen mutants suggested by the method showed important and measurable improvements in their structural stability while retaining the functionalities and production yields of the original protein. Then, we propose the procedure developed here as a cost-effective routine tool in the design and optimization of multimeric protein materials prior to any experimental testing.
Fil: Parladé, Eloi. Universitat Autònoma de Barcelona; España. Centro de Investigación Biomédica En Red de Bioingeniería, Biomateriales y Nanomedicina; España
Fil: Voltà Durán, Eric. Universitat Autònoma de Barcelona; España. Centro de Investigación Biomédica En Red de Bioingeniería, Biomateriales y Nanomedicina; España
Fil: Cano Garrido, Olivia. Nanoligent S.L; España
Fil: Sanchez, Julieta Maria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones Biológicas y Tecnológicas. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Instituto de Investigaciones Biológicas y Tecnológicas; Argentina. Universidad Nacional de Córdoba. Facultad de Ciencias Exactas, Físicas y Naturales. Departamento de Química. Cátedra de Química Biológica; Argentina. Centro de Investigación Biomédica En Red de Bioingeniería, Biomateriales y Nanomedicina; España. Universitat Autònoma de Barcelona; España
Fil: Unzueta, Ugutz. Centro de Investigación Biomédica En Red de Bioingeniería, Biomateriales y Nanomedicina; España. Universitat Autònoma de Barcelona; España. Institut Dinvestigació Biomèdica Sant Pau; España
Fil: López Laguna, Hèctor. Universitat Autònoma de Barcelona; España. Centro de Investigación Biomédica En Red de Bioingeniería, Biomateriales y Nanomedicina; España
Fil: Serna, Naroa. Nanoligent S.L.; España
Fil: Cano, Montserrat. Nanoligent S.L.; España
Fil: Rodríguez Mariscal, Manuel. Nanoligent S.L.; España
Fil: Vazquez, Esther. Centro de Investigación Biomédica En Red de Bioingeniería, Biomateriales y Nanomedicina; España. Universitat Autònoma de Barcelona; España
Fil: Villaverde, Antonio. Centro de Investigación Biomédica En Red de Bioingeniería, Biomateriales y Nanomedicina; España. Universitat Autònoma de Barcelona; España
description Under the need for new functional and biocompatible materials for biomedical applications, protein engineering allows the design of assemblable polypeptides, which, as convenient building blocks of supramolecular complexes, can be produced in recombinant cells by simple and scalable methodologies. However, the stability of such materials is often overlooked or disregarded, becoming a potential bottleneck in the development and viability of novel products. In this context, we propose a design strategy based on in silico tools to detect instability areas in protein materials and to facilitate the decision making in the rational mutagenesis aimed to increase their stability and solubility. As a case study, we demonstrate the potential of this methodology to improve the stability of a humanized scaffold protein (a domain of the human nidogen), with the ability to oligomerize into regular nanoparticles usable to deliver payload drugs to tumor cells. Several nidogen mutants suggested by the method showed important and measurable improvements in their structural stability while retaining the functionalities and production yields of the original protein. Then, we propose the procedure developed here as a cost-effective routine tool in the design and optimization of multimeric protein materials prior to any experimental testing.
publishDate 2022
dc.date.none.fl_str_mv 2022-05
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/213794
Parladé, Eloi; Voltà Durán, Eric; Cano Garrido, Olivia; Sanchez, Julieta Maria; Unzueta, Ugutz; et al.; An In Silico Methodology That Facilitates Decision Making in the Engineering of Nanoscale Protein Materials; Multidisciplinary Digital Publishing Institute; International Journal of Molecular Sciences; 23; 9; 5-2022; 1-12
1661-6596
1422-0067
CONICET Digital
CONICET
url http://hdl.handle.net/11336/213794
identifier_str_mv Parladé, Eloi; Voltà Durán, Eric; Cano Garrido, Olivia; Sanchez, Julieta Maria; Unzueta, Ugutz; et al.; An In Silico Methodology That Facilitates Decision Making in the Engineering of Nanoscale Protein Materials; Multidisciplinary Digital Publishing Institute; International Journal of Molecular Sciences; 23; 9; 5-2022; 1-12
1661-6596
1422-0067
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://www.mdpi.com/1422-0067/23/9/4958
info:eu-repo/semantics/altIdentifier/doi/10.3390/ijms23094958
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute
publisher.none.fl_str_mv Multidisciplinary Digital Publishing Institute
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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