Functional analysis of toxins by clustering of their electrostatic potentials

This is the first time, to our knowledge, that a structural description of the function of protein toxins has been addressed from a new perspective living behind the traditional approach of using common characteristic like α-helixes, β-sheets, and others, and instead using the electrostatic surface...

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Autores:
Martínez-Villate, Germán Camilo
Estévez-Bretón, Carlos Manuel
Tipo de recurso:
Fecha de publicación:
2018
Institución:
Universidad Simón Bolívar
Repositorio:
Repositorio Digital USB
Idioma:
eng
OAI Identifier:
oai:bonga.unisimon.edu.co:20.500.12442/2552
Acceso en línea:
http://hdl.handle.net/20.500.12442/2552
Palabra clave:
Clustering
Toxins
Electrostatic Potential
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License
Licencia de Creative Commons Reconocimiento-NoComercial-CompartirIgual 4.0 Internacional
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dc.title.eng.fl_str_mv Functional analysis of toxins by clustering of their electrostatic potentials
title Functional analysis of toxins by clustering of their electrostatic potentials
spellingShingle Functional analysis of toxins by clustering of their electrostatic potentials
Clustering
Toxins
Electrostatic Potential
title_short Functional analysis of toxins by clustering of their electrostatic potentials
title_full Functional analysis of toxins by clustering of their electrostatic potentials
title_fullStr Functional analysis of toxins by clustering of their electrostatic potentials
title_full_unstemmed Functional analysis of toxins by clustering of their electrostatic potentials
title_sort Functional analysis of toxins by clustering of their electrostatic potentials
dc.creator.fl_str_mv Martínez-Villate, Germán Camilo
Estévez-Bretón, Carlos Manuel
dc.contributor.advisor.none.fl_str_mv Estévez-Bretón, Carlos Manuel
dc.contributor.author.none.fl_str_mv Martínez-Villate, Germán Camilo
Estévez-Bretón, Carlos Manuel
dc.subject.eng.fl_str_mv Clustering
Toxins
Electrostatic Potential
topic Clustering
Toxins
Electrostatic Potential
description This is the first time, to our knowledge, that a structural description of the function of protein toxins has been addressed from a new perspective living behind the traditional approach of using common characteristic like α-helixes, β-sheets, and others, and instead using the electrostatic surface potential (ESP). These potentials have been normally used for 3D visual representation of charge distribution, qualitative interpretations of electrophilic and nucleophilic reactions, and for molecular interactions because of the considerable computational time and effort it takes to calculate them. We calculate the ESP for 16 proteins toxins and compared the 3D shapes of their potentials using the Hausdorff-Gromov distance; then we ran k-means cluster analysis to determine the relation among the shapes of the ESPs. Our results show that the analysis was able to cluster toxins depending on the shape of their ESP and that this clustering is related to the toxins function. There were only 4 toxins that clustered in a different group according to their function, and one that did not cluster with any other group. There was no evidence that taxonomy has a relation with the clusters found.
publishDate 2018
dc.date.issued.none.fl_str_mv 2018-12
dc.date.accessioned.none.fl_str_mv 2019-02-04T14:42:11Z
dc.date.available.none.fl_str_mv 2019-02-04T14:42:11Z
dc.type.eng.fl_str_mv article
dc.type.coar.fl_str_mv http://purl.org/coar/resource_type/c_6501
dc.identifier.uri.none.fl_str_mv http://hdl.handle.net/20.500.12442/2552
url http://hdl.handle.net/20.500.12442/2552
dc.language.iso.eng.fl_str_mv eng
language eng
dc.rights.coar.fl_str_mv http://purl.org/coar/access_right/c_16ec
dc.rights.license.spa.fl_str_mv Licencia de Creative Commons Reconocimiento-NoComercial-CompartirIgual 4.0 Internacional
rights_invalid_str_mv Licencia de Creative Commons Reconocimiento-NoComercial-CompartirIgual 4.0 Internacional
http://purl.org/coar/access_right/c_16ec
dc.publisher.spa.fl_str_mv Ediciones Universidad Simón Bolívar
Facultad Ciencias Básicas y Biomédicas
Programa de Maestría en genética
institution Universidad Simón Bolívar
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spelling Licencia de Creative Commons Reconocimiento-NoComercial-CompartirIgual 4.0 Internacionalhttp://purl.org/coar/access_right/c_16ecEstévez-Bretón, Carlos ManuelMartínez-Villate, Germán Camilo0047a4c5-6864-4dc0-ba06-ccbdf5af3ac7-1Estévez-Bretón, Carlos Manuel5392581e-1412-437e-b346-1398b0e25618-12019-02-04T14:42:11Z2019-02-04T14:42:11Z2018-12http://hdl.handle.net/20.500.12442/2552This is the first time, to our knowledge, that a structural description of the function of protein toxins has been addressed from a new perspective living behind the traditional approach of using common characteristic like α-helixes, β-sheets, and others, and instead using the electrostatic surface potential (ESP). These potentials have been normally used for 3D visual representation of charge distribution, qualitative interpretations of electrophilic and nucleophilic reactions, and for molecular interactions because of the considerable computational time and effort it takes to calculate them. We calculate the ESP for 16 proteins toxins and compared the 3D shapes of their potentials using the Hausdorff-Gromov distance; then we ran k-means cluster analysis to determine the relation among the shapes of the ESPs. Our results show that the analysis was able to cluster toxins depending on the shape of their ESP and that this clustering is related to the toxins function. There were only 4 toxins that clustered in a different group according to their function, and one that did not cluster with any other group. There was no evidence that taxonomy has a relation with the clusters found.engEdiciones Universidad Simón BolívarFacultad Ciencias Básicas y BiomédicasPrograma de Maestría en genéticaClusteringToxinsElectrostatic PotentialFunctional analysis of toxins by clustering of their electrostatic potentialsarticlehttp://purl.org/coar/resource_type/c_6501Abdullah, Z., Hamdan, A.R., 2015. 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Pontificia Universidad Javeriana.ORIGINALPDF.pdfPDF.pdfPDFapplication/pdf5023387https://bonga.unisimon.edu.co/bitstreams/49c6ad7b-1dc3-4020-b84f-0c33aef243f6/downloadd6046544090c1ddf92f1bdf8141b3622MD51LICENSElicense.txtlicense.txttext/plain; charset=utf-81748https://bonga.unisimon.edu.co/bitstreams/d2b9c6ea-1922-4897-b27f-8498664b58bb/download8a4605be74aa9ea9d79846c1fba20a33MD52TEXTFunctional analysis of toxins by clustering of their electrostatic potentials.pdf.txtFunctional analysis of toxins by clustering of their electrostatic potentials.pdf.txtExtracted texttext/plain34139https://bonga.unisimon.edu.co/bitstreams/34f4030d-7557-4b13-b275-3d54a3e3fa99/download5e360e00745a614a1999764c1c7f180bMD53PDF.pdf.txtPDF.pdf.txtExtracted texttext/plain35313https://bonga.unisimon.edu.co/bitstreams/70f8f143-6571-4916-aa6c-17fdf74a4edb/downloadf5c4ba9c4efe1664889964a1c9d5e658MD55THUMBNAILFunctional analysis of toxins by clustering of their electrostatic potentials.pdf.jpgFunctional analysis of toxins by clustering of their electrostatic potentials.pdf.jpgGenerated Thumbnailimage/jpeg1902https://bonga.unisimon.edu.co/bitstreams/03546daa-8479-4c6c-9e57-7718b5251439/downloadc3743cccc1193d7cc6d07f37de5decfaMD54PDF.pdf.jpgPDF.pdf.jpgGenerated Thumbnailimage/jpeg6251https://bonga.unisimon.edu.co/bitstreams/84e6a00e-ede7-47d5-a07b-cdcb137692f3/downloada38f61871b2d0e3922d52d33df407583MD5620.500.12442/2552oai:bonga.unisimon.edu.co:20.500.12442/25522024-07-25 03:45:03.067restrictedhttps://bonga.unisimon.edu.coRepositorio Digital Universidad Simón Bolívarrepositorio.digital@unisimon.edu.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