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      Bioinformatic characterizations and prediction of K + and Na + ion channels effector toxins

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          Abstract

          Background

          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 birtoxin-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 + and/or Na + channels scorpion toxins, allowing these birtoxin-like peptides to be active on K + and/or Na + channels.

          Results

          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 birtoxin-like peptides appeared to present a new structural motif distinct from those present in K + and Na + channels Toxins. This result, supported by previous experimental data, suggests that birtoxin-like peptides may exert their activity on different sites than those targeted by classic K + or Na + toxins.

          Searching, the nr 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.

          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.

          Conclusion

          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.

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          Most cited references54

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          Database resources of the National Center for Biotechnology Information

          In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data available through NCBI's web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link, Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace, Assembly, and Short Read Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Entrez Probe, GENSAT, Database of Genotype and Phenotype, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting the web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.
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            The PredictProtein server.

            PredictProtein (http://www.predictprotein.org) is an Internet service for sequence analysis and the prediction of protein structure and function. Users submit protein sequences or alignments; PredictProtein returns multiple sequence alignments, PROSITE sequence motifs, low-complexity regions (SEG), nuclear localization signals, regions lacking regular structure (NORS) and predictions of secondary structure, solvent accessibility, globular regions, transmembrane helices, coiled-coil regions, structural switch regions, disulfide-bonds, sub-cellular localization and functional annotations. Upon request fold recognition by prediction-based threading, CHOP domain assignments, predictions of transmembrane strands and inter-residue contacts are also available. For all services, users can submit their query either by electronic mail or interactively via the World Wide Web.
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              A Simplified Monte Carlo Significance Test Procedure

              Adery Hope (1968)
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                Author and article information

                Journal
                BMC Pharmacol
                BMC Pharmacology
                BioMed Central
                1471-2210
                2009
                10 March 2009
                : 9
                : 4
                Affiliations
                [1 ]Laboratory of Epidemiology and Ecology of Parasites, Institut Pasteur de Tunis, Tunis, Tunisia
                [2 ]Laboratory of Venom and Toxins, Institut Pasteur de Tunis, Tunis, Tunisia
                [3 ]Research and Teaching Building, Institut Pasteur de Tunis, 13 Place Pasteur, BP 74, 1002 Belvedere-Tunis, Tunisia
                Article
                1471-2210-9-4
                10.1186/1471-2210-9-4
                2660317
                19284552
                e3063a1e-5dcf-417b-aa2c-ae46650ab65a
                Copyright © 2009 Soli et al; licensee BioMed Central Ltd.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 31 July 2008
                : 10 March 2009
                Categories
                Research Article

                Pharmacology & Pharmaceutical medicine
                Pharmacology & Pharmaceutical medicine

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