Bioinformatic characterizations and prediction of K+ and Na+ ion channels effector toxins
Identifieur interne : 000075 ( Main/Exploration ); précédent : 000074; suivant : 000076Bioinformatic characterizations and prediction of K+ and Na+ ion channels effector toxins
Auteurs : Rima Soli [Tunisie] ; Belhassen Kaabi [Tunisie] ; Mourad Barhoumi [Tunisie] ; Mohamed El-Ayeb [Tunisie] ; Najet Srairi-Abid [Tunisie]Source :
- BMC Pharmacology [ 1471-2210 ] ; 2009.
Descripteurs français
- KwdFr :
- Animaux (MeSH), Biologie informatique (MeSH), Canaux potassiques (effets des médicaments et des substances chimiques), Canaux sodiques (effets des médicaments et des substances chimiques), Données de séquences moléculaires (MeSH), Modèles statistiques (MeSH), Motifs d'acides aminés (MeSH), Phylogenèse (MeSH), Similitude de séquences d'acides aminés (MeSH), Structure tertiaire des protéines (MeSH), Venins de scorpion (classification), Venins de scorpion (composition chimique), Venins de scorpion (pharmacologie).
- MESH :
- classification : Venins de scorpion.
- composition chimique : Venins de scorpion.
- effets des médicaments et des substances chimiques : Canaux potassiques, Canaux sodiques.
- pharmacologie : Venins de scorpion.
- Animaux, Biologie informatique, Données de séquences moléculaires, Modèles statistiques, Motifs d'acides aminés, Phylogenèse, Similitude de séquences d'acides aminés, Structure tertiaire des protéines.
English descriptors
- KwdEn :
- Amino Acid Motifs (MeSH), Animals (MeSH), Computational Biology (MeSH), Models, Statistical (MeSH), Molecular Sequence Data (MeSH), Phylogeny (MeSH), Potassium Channels (drug effects), Protein Structure, Tertiary (MeSH), Scorpion Venoms (chemistry), Scorpion Venoms (classification), Scorpion Venoms (pharmacology), Sequence Homology, Amino Acid (MeSH), Sodium Channels (drug effects).
- MESH :
- chemical , chemistry : Scorpion Venoms.
- chemical , classification : Scorpion Venoms.
- chemical , drug effects : Potassium Channels, Sodium Channels.
- chemical , pharmacology : Scorpion Venoms.
- Amino Acid Motifs, Animals, Computational Biology, Models, Statistical, Molecular Sequence Data, Phylogeny, Protein Structure, Tertiary, Sequence Homology, Amino Acid.
Abstract
K+ and Na+ channel toxins constitute a large set of polypeptides, which interact with their ion channel targets. These polypeptides are classified in two different structural groups. Recently a new structural group called
Four multilevel motifs, overrepresented and specific to each group of K+ and/or Na+ ion channel toxins have been identified, using GIBBS and MEME and based on a training dataset of 79 sequences judged as representative of K+ and Na+ toxins.
Unexpectedly
Searching, the
Phylogenetic analysis was used to classify the newly found sequences. Alternatively, classification tree analysis, using CART algorithm adjusted with the training dataset, using the motifs and their 2D structure as explanatory variables, provided a model for prediction of the activity of the new sequences.
The phylogenetic results were in perfect agreement with those obtained by the CART algorithm.
Our results may be used as criteria for a new classification of scorpion toxins based on functional motifs.
Url:
DOI: 10.1186/1471-2210-9-4
PubMed: 19284552
PubMed Central: 2660317
Affiliations:
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Le document en format XML
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sort="Kaabi, Belhassen" uniqKey="Kaabi B" first="Belhassen" last="Kaabi">Belhassen Kaabi</name><affiliation wicri:level="1"><nlm:aff id="I1">Laboratory of Epidemiology and Ecology of Parasites, Institut Pasteur de Tunis, Tunis, Tunisia</nlm:aff><country xml:lang="fr">Tunisie</country><wicri:regionArea>Laboratory of Epidemiology and Ecology of Parasites, Institut Pasteur de Tunis, Tunis</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="I3">Research and Teaching Building, Institut Pasteur de Tunis, 13 Place Pasteur, BP 74, 1002 Belvedere-Tunis, Tunisia</nlm:aff><country xml:lang="fr">Tunisie</country><wicri:regionArea>Research and Teaching Building, Institut Pasteur de Tunis, 13 Place Pasteur, BP 74, 1002 Belvedere-Tunis</wicri:regionArea></affiliation></author><author><name sortKey="Barhoumi, Mourad" sort="Barhoumi, Mourad" uniqKey="Barhoumi M" first="Mourad" last="Barhoumi">Mourad Barhoumi</name><affiliation wicri:level="1"><nlm:aff id="I1">Laboratory of Epidemiology and Ecology of Parasites, Institut Pasteur de Tunis, Tunis, Tunisia</nlm:aff><country xml:lang="fr">Tunisie</country><wicri:regionArea>Laboratory of Epidemiology and Ecology of Parasites, Institut Pasteur de Tunis, Tunis</wicri:regionArea></affiliation></author><author><name sortKey="El Ayeb, Mohamed" sort="El Ayeb, Mohamed" uniqKey="El Ayeb M" first="Mohamed" last="El-Ayeb">Mohamed El-Ayeb</name><affiliation wicri:level="1"><nlm:aff id="I2">Laboratory of Venom and Toxins, Institut Pasteur de Tunis, Tunis, Tunisia</nlm:aff><country xml:lang="fr">Tunisie</country><wicri:regionArea>Laboratory of Venom and Toxins, Institut Pasteur de Tunis, Tunis</wicri:regionArea></affiliation></author><author><name sortKey="Srairi Abid, Najet" sort="Srairi Abid, Najet" uniqKey="Srairi Abid N" first="Najet" last="Srairi-Abid">Najet Srairi-Abid</name><affiliation wicri:level="1"><nlm:aff id="I2">Laboratory of Venom and Toxins, Institut Pasteur de Tunis, Tunis, Tunisia</nlm:aff><country xml:lang="fr">Tunisie</country><wicri:regionArea>Laboratory of Venom and Toxins, Institut Pasteur de Tunis, Tunis</wicri:regionArea></affiliation></author></analytic><series><title level="j">BMC Pharmacology</title><idno type="eISSN">1471-2210</idno><imprint><date when="2009">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Motifs (MeSH)</term><term>Animals (MeSH)</term><term>Computational Biology (MeSH)</term><term>Models, Statistical (MeSH)</term><term>Molecular Sequence Data (MeSH)</term><term>Phylogeny (MeSH)</term><term>Potassium Channels (drug effects)</term><term>Protein Structure, Tertiary (MeSH)</term><term>Scorpion Venoms (chemistry)</term><term>Scorpion Venoms (classification)</term><term>Scorpion Venoms (pharmacology)</term><term>Sequence Homology, Amino Acid (MeSH)</term><term>Sodium Channels (drug effects)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Animaux (MeSH)</term><term>Biologie informatique (MeSH)</term><term>Canaux potassiques (effets des médicaments et des substances chimiques)</term><term>Canaux sodiques (effets des médicaments et des substances chimiques)</term><term>Données de séquences moléculaires (MeSH)</term><term>Modèles statistiques (MeSH)</term><term>Motifs d'acides aminés (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Similitude de séquences d'acides aminés (MeSH)</term><term>Structure tertiaire des protéines (MeSH)</term><term>Venins de scorpion (classification)</term><term>Venins de scorpion (composition chimique)</term><term>Venins de scorpion (pharmacologie)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Scorpion Venoms</term></keywords><keywords scheme="MESH" type="chemical" qualifier="classification" xml:lang="en"><term>Scorpion Venoms</term></keywords><keywords scheme="MESH" type="chemical" qualifier="drug effects" xml:lang="en"><term>Potassium Channels</term><term>Sodium Channels</term></keywords><keywords scheme="MESH" type="chemical" qualifier="pharmacology" xml:lang="en"><term>Scorpion Venoms</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="fr"><term>Venins de scorpion</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Venins de scorpion</term></keywords><keywords scheme="MESH" qualifier="effets des médicaments et des substances chimiques" xml:lang="fr"><term>Canaux potassiques</term><term>Canaux sodiques</term></keywords><keywords scheme="MESH" qualifier="pharmacologie" xml:lang="fr"><term>Venins de scorpion</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Motifs</term><term>Animals</term><term>Computational Biology</term><term>Models, Statistical</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Protein Structure, Tertiary</term><term>Sequence Homology, Amino Acid</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Biologie informatique</term><term>Données de séquences moléculaires</term><term>Modèles statistiques</term><term>Motifs d'acides aminés</term><term>Phylogenèse</term><term>Similitude de séquences d'acides aminés</term><term>Structure tertiaire des protéines</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>K<sup>+ </sup>and Na<sup>+ </sup>channel toxins constitute a large set of polypeptides, which interact with their ion channel targets. These polypeptides are classified in two different structural groups. Recently a new structural group called <italic>birtoxin</italic>-like appeared to contain both types of toxins has been described. We hypothesized that peptides of this group may contain two conserved structural motifs in K<sup>+ </sup>and/or Na<sup>+ </sup>channels scorpion toxins, allowing these <italic>birtoxin-like </italic>peptides to be active on K<sup>+ </sup>and/or Na<sup>+ </sup>channels.</p></sec><sec><title>Results</title><p>Four multilevel motifs, overrepresented and specific to each group of K<sup>+ </sup>and/or Na<sup>+ </sup>ion channel toxins have been identified, using GIBBS and MEME and based on a training dataset of 79 sequences judged as representative of K<sup>+ </sup>and Na<sup>+ </sup>toxins.</p><p>Unexpectedly <italic>birtoxin</italic>-like peptides appeared to present a new structural motif distinct from those present in K<sup>+ </sup>and Na<sup>+ </sup>channels Toxins. This result, supported by previous experimental data, suggests that <italic>birtoxin</italic>-like peptides may exert their activity on different sites than those targeted by classic K<sup>+ </sup>or Na<sup>+ </sup>toxins.</p><p>Searching, the <italic>nr </italic>database with these newly identified motifs using MAST, retrieved several sequences (116 with e-value < 1) from various scorpion species (test dataset). The filtering process left 30 new and highly likely ion channel effectors.</p><p>Phylogenetic analysis was used to classify the newly found sequences. Alternatively, classification tree analysis, using CART algorithm adjusted with the training dataset, using the motifs and their 2D structure as explanatory variables, provided a model for prediction of the activity of the new sequences.</p></sec><sec><title>Conclusion</title><p>The phylogenetic results were in perfect agreement with those obtained by the CART algorithm.</p><p>Our results may be used as criteria for a new classification of scorpion toxins based on functional motifs.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Tunisie</li></country></list><tree><country name="Tunisie"><noRegion><name sortKey="Soli, Rima" sort="Soli, Rima" uniqKey="Soli R" first="Rima" last="Soli">Rima Soli</name></noRegion><name sortKey="Barhoumi, Mourad" sort="Barhoumi, Mourad" uniqKey="Barhoumi M" first="Mourad" last="Barhoumi">Mourad Barhoumi</name><name sortKey="El Ayeb, Mohamed" sort="El Ayeb, Mohamed" uniqKey="El Ayeb M" first="Mohamed" last="El-Ayeb">Mohamed El-Ayeb</name><name sortKey="Kaabi, Belhassen" sort="Kaabi, Belhassen" uniqKey="Kaabi B" first="Belhassen" last="Kaabi">Belhassen Kaabi</name><name sortKey="Kaabi, Belhassen" sort="Kaabi, Belhassen" uniqKey="Kaabi B" first="Belhassen" last="Kaabi">Belhassen Kaabi</name><name sortKey="Srairi Abid, Najet" sort="Srairi Abid, Najet" uniqKey="Srairi Abid N" first="Najet" last="Srairi-Abid">Najet Srairi-Abid</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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