Chemometric analysis of Hymenoptera toxins and defensins: A model for predicting the biological activity of novel peptides from venoms and hemolymph

Detalhes bibliográficos
Autor(a) principal: Saidemberg, Daniel M. [UNESP]
Data de Publicação: 2011
Outros Autores: Baptista-Saidemberg, Nicoli B. [UNESP], Palma, Mario Sergio [UNESP]
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UNESP
Texto Completo: http://dx.doi.org/10.1016/j.peptides.2011.08.001
http://hdl.handle.net/11449/72627
Resumo: When searching for prospective novel peptides, it is difficult to determine the biological activity of a peptide based only on its sequence. The trial and error approach is generally laborious, expensive and time consuming due to the large number of different experimental setups required to cover a reasonable number of biological assays. To simulate a virtual model for Hymenoptera insects, 166 peptides were selected from the venoms and hemolymphs of wasps, bees and ants and applied to a mathematical model of multivariate analysis, with nine different chemometric components: GRAVY, aliphaticity index, number of disulfide bonds, total residues, net charge, pI value, Boman index, percentage of alpha helix, and flexibility prediction. Principal component analysis (PCA) with non-linear iterative projections by alternating least-squares (NIPALS) algorithm was performed, without including any information about the biological activity of the peptides. This analysis permitted the grouping of peptides in a way that strongly correlated to the biological function of the peptides. Six different groupings were observed, which seemed to correspond to the following groups: chemotactic peptides, mastoparans, tachykinins, kinins, antibiotic peptides, and a group of long peptides with one or two disulfide bonds and with biological activities that are not yet clearly defined. The partial overlap between the mastoparans group and the chemotactic peptides, tachykinins, kinins and antibiotic peptides in the PCA score plot may be used to explain the frequent reports in the literature about the multifunctionality of some of these peptides. The mathematical model used in the present investigation can be used to predict the biological activities of novel peptides in this system, and it may also be easily applied to other biological systems. © 2011 Elsevier Inc.
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spelling Chemometric analysis of Hymenoptera toxins and defensins: A model for predicting the biological activity of novel peptides from venoms and hemolymphInsect venomsPCAPolycationic peptidesSystem biologyToxinschemotactic peptidedefensinHymenoptera venomkininmastoparanpeptidetachykininvenomalgorithmalpha helixantbeebiological activitychemometric analysisdisulfide bondelectricityhemolymphHymenopteraprincipal component analysispriority journalwaspAlgorithmsAmino Acid SequenceAnimalsAnti-Infective AgentsArthropod VenomsBiological AgentsDefensinsDisulfidesHemolymphHydrophobic and Hydrophilic InteractionsIsoelectric PointModels, TheoreticalPeptidesPrincipal Component AnalysisProtein Structure, SecondaryApoideaFormicidaeHexapodaWhen searching for prospective novel peptides, it is difficult to determine the biological activity of a peptide based only on its sequence. The trial and error approach is generally laborious, expensive and time consuming due to the large number of different experimental setups required to cover a reasonable number of biological assays. To simulate a virtual model for Hymenoptera insects, 166 peptides were selected from the venoms and hemolymphs of wasps, bees and ants and applied to a mathematical model of multivariate analysis, with nine different chemometric components: GRAVY, aliphaticity index, number of disulfide bonds, total residues, net charge, pI value, Boman index, percentage of alpha helix, and flexibility prediction. Principal component analysis (PCA) with non-linear iterative projections by alternating least-squares (NIPALS) algorithm was performed, without including any information about the biological activity of the peptides. This analysis permitted the grouping of peptides in a way that strongly correlated to the biological function of the peptides. Six different groupings were observed, which seemed to correspond to the following groups: chemotactic peptides, mastoparans, tachykinins, kinins, antibiotic peptides, and a group of long peptides with one or two disulfide bonds and with biological activities that are not yet clearly defined. The partial overlap between the mastoparans group and the chemotactic peptides, tachykinins, kinins and antibiotic peptides in the PCA score plot may be used to explain the frequent reports in the literature about the multifunctionality of some of these peptides. The mathematical model used in the present investigation can be used to predict the biological activities of novel peptides in this system, and it may also be easily applied to other biological systems. © 2011 Elsevier Inc.Dept. Biology Institute of Biosciences of Rio Claro São Paulo State University (UNESP), Rio Claro, SP 13506-900Instituto Nacional de Ciência e Tecnologia (INCT) em Imunologia/iii, São Paulo, SPDept. Biology Institute of Biosciences of Rio Claro São Paulo State University (UNESP), Rio Claro, SP 13506-900Universidade Estadual Paulista (Unesp)Instituto Nacional de Ciência e Tecnologia (INCT) em Imunologia/iiiSaidemberg, Daniel M. [UNESP]Baptista-Saidemberg, Nicoli B. [UNESP]Palma, Mario Sergio [UNESP]2014-05-27T11:25:58Z2014-05-27T11:25:58Z2011-09-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article1924-1933application/pdfhttp://dx.doi.org/10.1016/j.peptides.2011.08.001Peptides, v. 32, n. 9, p. 1924-1933, 2011.0196-97811873-5169http://hdl.handle.net/11449/7262710.1016/j.peptides.2011.08.0012-s2.0-800526966862-s2.0-80052696686.pdf2901888624506535Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengPeptides2.8511,001info:eu-repo/semantics/openAccess2023-10-01T06:02:03Zoai:repositorio.unesp.br:11449/72627Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T13:38:35.687391Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false
dc.title.none.fl_str_mv Chemometric analysis of Hymenoptera toxins and defensins: A model for predicting the biological activity of novel peptides from venoms and hemolymph
title Chemometric analysis of Hymenoptera toxins and defensins: A model for predicting the biological activity of novel peptides from venoms and hemolymph
spellingShingle Chemometric analysis of Hymenoptera toxins and defensins: A model for predicting the biological activity of novel peptides from venoms and hemolymph
Saidemberg, Daniel M. [UNESP]
Insect venoms
PCA
Polycationic peptides
System biology
Toxins
chemotactic peptide
defensin
Hymenoptera venom
kinin
mastoparan
peptide
tachykinin
venom
algorithm
alpha helix
ant
bee
biological activity
chemometric analysis
disulfide bond
electricity
hemolymph
Hymenoptera
principal component analysis
priority journal
wasp
Algorithms
Amino Acid Sequence
Animals
Anti-Infective Agents
Arthropod Venoms
Biological Agents
Defensins
Disulfides
Hemolymph
Hydrophobic and Hydrophilic Interactions
Isoelectric Point
Models, Theoretical
Peptides
Principal Component Analysis
Protein Structure, Secondary
Apoidea
Formicidae
Hexapoda
title_short Chemometric analysis of Hymenoptera toxins and defensins: A model for predicting the biological activity of novel peptides from venoms and hemolymph
title_full Chemometric analysis of Hymenoptera toxins and defensins: A model for predicting the biological activity of novel peptides from venoms and hemolymph
title_fullStr Chemometric analysis of Hymenoptera toxins and defensins: A model for predicting the biological activity of novel peptides from venoms and hemolymph
title_full_unstemmed Chemometric analysis of Hymenoptera toxins and defensins: A model for predicting the biological activity of novel peptides from venoms and hemolymph
title_sort Chemometric analysis of Hymenoptera toxins and defensins: A model for predicting the biological activity of novel peptides from venoms and hemolymph
author Saidemberg, Daniel M. [UNESP]
author_facet Saidemberg, Daniel M. [UNESP]
Baptista-Saidemberg, Nicoli B. [UNESP]
Palma, Mario Sergio [UNESP]
author_role author
author2 Baptista-Saidemberg, Nicoli B. [UNESP]
Palma, Mario Sergio [UNESP]
author2_role author
author
dc.contributor.none.fl_str_mv Universidade Estadual Paulista (Unesp)
Instituto Nacional de Ciência e Tecnologia (INCT) em Imunologia/iii
dc.contributor.author.fl_str_mv Saidemberg, Daniel M. [UNESP]
Baptista-Saidemberg, Nicoli B. [UNESP]
Palma, Mario Sergio [UNESP]
dc.subject.por.fl_str_mv Insect venoms
PCA
Polycationic peptides
System biology
Toxins
chemotactic peptide
defensin
Hymenoptera venom
kinin
mastoparan
peptide
tachykinin
venom
algorithm
alpha helix
ant
bee
biological activity
chemometric analysis
disulfide bond
electricity
hemolymph
Hymenoptera
principal component analysis
priority journal
wasp
Algorithms
Amino Acid Sequence
Animals
Anti-Infective Agents
Arthropod Venoms
Biological Agents
Defensins
Disulfides
Hemolymph
Hydrophobic and Hydrophilic Interactions
Isoelectric Point
Models, Theoretical
Peptides
Principal Component Analysis
Protein Structure, Secondary
Apoidea
Formicidae
Hexapoda
topic Insect venoms
PCA
Polycationic peptides
System biology
Toxins
chemotactic peptide
defensin
Hymenoptera venom
kinin
mastoparan
peptide
tachykinin
venom
algorithm
alpha helix
ant
bee
biological activity
chemometric analysis
disulfide bond
electricity
hemolymph
Hymenoptera
principal component analysis
priority journal
wasp
Algorithms
Amino Acid Sequence
Animals
Anti-Infective Agents
Arthropod Venoms
Biological Agents
Defensins
Disulfides
Hemolymph
Hydrophobic and Hydrophilic Interactions
Isoelectric Point
Models, Theoretical
Peptides
Principal Component Analysis
Protein Structure, Secondary
Apoidea
Formicidae
Hexapoda
description When searching for prospective novel peptides, it is difficult to determine the biological activity of a peptide based only on its sequence. The trial and error approach is generally laborious, expensive and time consuming due to the large number of different experimental setups required to cover a reasonable number of biological assays. To simulate a virtual model for Hymenoptera insects, 166 peptides were selected from the venoms and hemolymphs of wasps, bees and ants and applied to a mathematical model of multivariate analysis, with nine different chemometric components: GRAVY, aliphaticity index, number of disulfide bonds, total residues, net charge, pI value, Boman index, percentage of alpha helix, and flexibility prediction. Principal component analysis (PCA) with non-linear iterative projections by alternating least-squares (NIPALS) algorithm was performed, without including any information about the biological activity of the peptides. This analysis permitted the grouping of peptides in a way that strongly correlated to the biological function of the peptides. Six different groupings were observed, which seemed to correspond to the following groups: chemotactic peptides, mastoparans, tachykinins, kinins, antibiotic peptides, and a group of long peptides with one or two disulfide bonds and with biological activities that are not yet clearly defined. The partial overlap between the mastoparans group and the chemotactic peptides, tachykinins, kinins and antibiotic peptides in the PCA score plot may be used to explain the frequent reports in the literature about the multifunctionality of some of these peptides. The mathematical model used in the present investigation can be used to predict the biological activities of novel peptides in this system, and it may also be easily applied to other biological systems. © 2011 Elsevier Inc.
publishDate 2011
dc.date.none.fl_str_mv 2011-09-01
2014-05-27T11:25:58Z
2014-05-27T11:25:58Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://dx.doi.org/10.1016/j.peptides.2011.08.001
Peptides, v. 32, n. 9, p. 1924-1933, 2011.
0196-9781
1873-5169
http://hdl.handle.net/11449/72627
10.1016/j.peptides.2011.08.001
2-s2.0-80052696686
2-s2.0-80052696686.pdf
2901888624506535
url http://dx.doi.org/10.1016/j.peptides.2011.08.001
http://hdl.handle.net/11449/72627
identifier_str_mv Peptides, v. 32, n. 9, p. 1924-1933, 2011.
0196-9781
1873-5169
10.1016/j.peptides.2011.08.001
2-s2.0-80052696686
2-s2.0-80052696686.pdf
2901888624506535
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Peptides
2.851
1,001
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 1924-1933
application/pdf
dc.source.none.fl_str_mv Scopus
reponame:Repositório Institucional da UNESP
instname:Universidade Estadual Paulista (UNESP)
instacron:UNESP
instname_str Universidade Estadual Paulista (UNESP)
instacron_str UNESP
institution UNESP
reponame_str Repositório Institucional da UNESP
collection Repositório Institucional da UNESP
repository.name.fl_str_mv Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)
repository.mail.fl_str_mv
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