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The mining of toxin-like polypeptides from EST database by single residue distribution analysis.

Kozlov S, Grishin E - BMC Genomics (2011)

Bottom Line: The adequacy of motifs for mining toxin-like sequences was confirmed by their ability to identify 100% toxin-like anemone polypeptides in the reference polypeptide database.Analysis of 39939 ESTs of sea anemone Anemonia viridis resulted in identification of five protein precursors of earlier described toxins, discovery of 43 novel polypeptide toxins, and prediction of 39 putative polypeptide toxin sequences.In addition, two precursors of novel peptides presumably displaying neuronal function were disclosed.

View Article: PubMed Central - HTML - PubMed

Affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russia.

ABSTRACT

Background: Novel high throughput sequencing technologies require permanent development of bioinformatics data processing methods. Among them, rapid and reliable identification of encoded proteins plays a pivotal role. To search for particular protein families, the amino acid sequence motifs suitable for selective screening of nucleotide sequence databases may be used. In this work, we suggest a novel method for simplified representation of protein amino acid sequences named Single Residue Distribution Analysis, which is applicable both for homology search and database screening.

Results: Using the procedure developed, a search for amino acid sequence motifs in sea anemone polypeptides was performed, and 14 different motifs with broad and low specificity were discriminated. The adequacy of motifs for mining toxin-like sequences was confirmed by their ability to identify 100% toxin-like anemone polypeptides in the reference polypeptide database. The employment of novel motifs for the search of polypeptide toxins in Anemonia viridis EST dataset allowed us to identify 89 putative toxin precursors. The translated and modified ESTs were scanned using a special algorithm. In addition to direct comparison with the motifs developed, the putative signal peptides were predicted and homology with known structures was examined.

Conclusions: The suggested method may be used to retrieve structures of interest from the EST databases using simple amino acid sequence motifs as templates. The efficiency of the procedure for directed search of polypeptides is higher than that of most currently used methods. Analysis of 39939 ESTs of sea anemone Anemonia viridis resulted in identification of five protein precursors of earlier described toxins, discovery of 43 novel polypeptide toxins, and prediction of 39 putative polypeptide toxin sequences. In addition, two precursors of novel peptides presumably displaying neuronal function were disclosed.

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Conversion of amino acid sequence into a polypeptide pattern using different key residues. SRDA("C") -conversion by the key Cys residues marked by arrows above the original sequence, the number of amino acids separating the adjacent cysteine residues is also indicated; SRDA("C.") takes into account the location of Cys residues and translational termination symbols denoted by points in the amino acid sequence; ("K.") - conversion by the key Lys residues designated by asterisks and the termination symbols.
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Figure 1: Conversion of amino acid sequence into a polypeptide pattern using different key residues. SRDA("C") -conversion by the key Cys residues marked by arrows above the original sequence, the number of amino acids separating the adjacent cysteine residues is also indicated; SRDA("C.") takes into account the location of Cys residues and translational termination symbols denoted by points in the amino acid sequence; ("K.") - conversion by the key Lys residues designated by asterisks and the termination symbols.

Mentions: In many proteins the position of certain (key) amino acid residues in the polypeptide chain is conserved. The arrangement of these residues may be described by a polypeptide pattern, in which the key residues are separated by numbers corresponding to the number of nonconserved amino acids between the key amino acids (see Figure 1).


The mining of toxin-like polypeptides from EST database by single residue distribution analysis.

Kozlov S, Grishin E - BMC Genomics (2011)

Conversion of amino acid sequence into a polypeptide pattern using different key residues. SRDA("C") -conversion by the key Cys residues marked by arrows above the original sequence, the number of amino acids separating the adjacent cysteine residues is also indicated; SRDA("C.") takes into account the location of Cys residues and translational termination symbols denoted by points in the amino acid sequence; ("K.") - conversion by the key Lys residues designated by asterisks and the termination symbols.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3040730&req=5

Figure 1: Conversion of amino acid sequence into a polypeptide pattern using different key residues. SRDA("C") -conversion by the key Cys residues marked by arrows above the original sequence, the number of amino acids separating the adjacent cysteine residues is also indicated; SRDA("C.") takes into account the location of Cys residues and translational termination symbols denoted by points in the amino acid sequence; ("K.") - conversion by the key Lys residues designated by asterisks and the termination symbols.
Mentions: In many proteins the position of certain (key) amino acid residues in the polypeptide chain is conserved. The arrangement of these residues may be described by a polypeptide pattern, in which the key residues are separated by numbers corresponding to the number of nonconserved amino acids between the key amino acids (see Figure 1).

Bottom Line: The adequacy of motifs for mining toxin-like sequences was confirmed by their ability to identify 100% toxin-like anemone polypeptides in the reference polypeptide database.Analysis of 39939 ESTs of sea anemone Anemonia viridis resulted in identification of five protein precursors of earlier described toxins, discovery of 43 novel polypeptide toxins, and prediction of 39 putative polypeptide toxin sequences.In addition, two precursors of novel peptides presumably displaying neuronal function were disclosed.

View Article: PubMed Central - HTML - PubMed

Affiliation: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russia.

ABSTRACT

Background: Novel high throughput sequencing technologies require permanent development of bioinformatics data processing methods. Among them, rapid and reliable identification of encoded proteins plays a pivotal role. To search for particular protein families, the amino acid sequence motifs suitable for selective screening of nucleotide sequence databases may be used. In this work, we suggest a novel method for simplified representation of protein amino acid sequences named Single Residue Distribution Analysis, which is applicable both for homology search and database screening.

Results: Using the procedure developed, a search for amino acid sequence motifs in sea anemone polypeptides was performed, and 14 different motifs with broad and low specificity were discriminated. The adequacy of motifs for mining toxin-like sequences was confirmed by their ability to identify 100% toxin-like anemone polypeptides in the reference polypeptide database. The employment of novel motifs for the search of polypeptide toxins in Anemonia viridis EST dataset allowed us to identify 89 putative toxin precursors. The translated and modified ESTs were scanned using a special algorithm. In addition to direct comparison with the motifs developed, the putative signal peptides were predicted and homology with known structures was examined.

Conclusions: The suggested method may be used to retrieve structures of interest from the EST databases using simple amino acid sequence motifs as templates. The efficiency of the procedure for directed search of polypeptides is higher than that of most currently used methods. Analysis of 39939 ESTs of sea anemone Anemonia viridis resulted in identification of five protein precursors of earlier described toxins, discovery of 43 novel polypeptide toxins, and prediction of 39 putative polypeptide toxin sequences. In addition, two precursors of novel peptides presumably displaying neuronal function were disclosed.

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