Codon number shapes peptide redundancy in the universal proteome composition.
Identifieur interne : 000700 ( Ncbi/Merge ); précédent : 000699; suivant : 000701Codon number shapes peptide redundancy in the universal proteome composition.
Auteurs : Anthony Kusalik [Canada] ; Brett Trost ; Mik Bickis ; Candida Fasano ; Giovanni Capone ; Darja KanducSource :
- Peptides [ 1873-5169 ] ; 2009.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , analysis : Proteome.
- chemical , genetics : Peptides, Proteome.
- chemical : Codon.
- Amino Acid Sequence, Computational Biology, Databases, Protein, Humans, Molecular Sequence Data, Sequence Analysis, Protein.
Abstract
The proteomes catalogued in the UniRef100 database were collected into a single proteome set and examined for actual versus theoretical pentapeptide occurrences. We found a highly diversified degree of pentapeptide redundancy. Numerically, 953 pentamers are expressed only once in the protein world, whereas 103 pentamers occur more than 50,000 times. Moreover, it seems that 417 potentially possible pentapeptides are not present in the protein world. On the whole, tracing the redundancy profile of the protein world as a function of pentapeptide occurrences reveals a quasi-Gaussian curve, with tails representing scarcely and repeatedly occurring 5-mers. Analysis of physico-chemical-biological parameters shows that codon number is the main factor influencing and favoring specific pentapeptide frequencies in the universal proteome composition. That is, when compared to the set of never-expressed 5-mers, the pentapeptides frequently represented in the universal proteome are endowed with a higher number of multi-codonic amino acids. In contrast, the bulkiness degree and the hydrophobicity level play a smaller role. Unexpectedly, the heat of formation of pentapeptide appears to have the least influence.
DOI: 10.1016/j.peptides.2009.06.035
PubMed: 19591891
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last="Fasano">Candida Fasano</name></author><author><name sortKey="Capone, Giovanni" sort="Capone, Giovanni" uniqKey="Capone G" first="Giovanni" last="Capone">Giovanni Capone</name></author><author><name sortKey="Kanduc, Darja" sort="Kanduc, Darja" uniqKey="Kanduc D" first="Darja" last="Kanduc">Darja Kanduc</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2009">2009</date><idno type="RBID">pubmed:19591891</idno><idno type="pmid">19591891</idno><idno type="doi">10.1016/j.peptides.2009.06.035</idno><idno type="wicri:Area/PubMed/Corpus">002004</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002004</idno><idno type="wicri:Area/PubMed/Curation">002004</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002004</idno><idno type="wicri:Area/PubMed/Checkpoint">001F28</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001F28</idno><idno 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séquence de protéine</term><term>Bases de données de protéines</term><term>Biologie informatique</term><term>Codon</term><term>Données de séquences moléculaires</term><term>Humains</term><term>Peptides (génétique)</term><term>Protéome (analyse)</term><term>Protéome (génétique)</term><term>Séquence d'acides aminés</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>Proteome</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Peptides</term><term>Proteome</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Codon</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>Protéome</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Peptides</term><term>Protéome</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Computational Biology</term><term>Databases, Protein</term><term>Humans</term><term>Molecular Sequence Data</term><term>Sequence Analysis, Protein</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence de protéine</term><term>Bases de données de protéines</term><term>Biologie informatique</term><term>Codon</term><term>Données de séquences moléculaires</term><term>Humains</term><term>Séquence d'acides aminés</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The proteomes catalogued in the UniRef100 database were collected into a single proteome set and examined for actual versus theoretical pentapeptide occurrences. We found a highly diversified degree of pentapeptide redundancy. Numerically, 953 pentamers are expressed only once in the protein world, whereas 103 pentamers occur more than 50,000 times. Moreover, it seems that 417 potentially possible pentapeptides are not present in the protein world. On the whole, tracing the redundancy profile of the protein world as a function of pentapeptide occurrences reveals a quasi-Gaussian curve, with tails representing scarcely and repeatedly occurring 5-mers. Analysis of physico-chemical-biological parameters shows that codon number is the main factor influencing and favoring specific pentapeptide frequencies in the universal proteome composition. That is, when compared to the set of never-expressed 5-mers, the pentapeptides frequently represented in the universal proteome are endowed with a higher number of multi-codonic amino acids. In contrast, the bulkiness degree and the hydrophobicity level play a smaller role. Unexpectedly, the heat of formation of pentapeptide appears to have the least influence.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">19591891</PMID><DateCompleted><Year>2010</Year><Month>02</Month><Day>01</Day></DateCompleted><DateRevised><Year>2009</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1873-5169</ISSN><JournalIssue CitedMedium="Internet"><Volume>30</Volume><Issue>10</Issue><PubDate><Year>2009</Year><Month>Oct</Month></PubDate></JournalIssue><Title>Peptides</Title><ISOAbbreviation>Peptides</ISOAbbreviation></Journal><ArticleTitle>Codon number shapes peptide redundancy in the universal proteome composition.</ArticleTitle><Pagination><MedlinePgn>1940-4</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.peptides.2009.06.035</ELocationID><Abstract><AbstractText>The proteomes catalogued in the UniRef100 database were collected into a single proteome set and examined for actual versus theoretical pentapeptide occurrences. We found a highly diversified degree of pentapeptide redundancy. Numerically, 953 pentamers are expressed only once in the protein world, whereas 103 pentamers occur more than 50,000 times. Moreover, it seems that 417 potentially possible pentapeptides are not present in the protein world. On the whole, tracing the redundancy profile of the protein world as a function of pentapeptide occurrences reveals a quasi-Gaussian curve, with tails representing scarcely and repeatedly occurring 5-mers. Analysis of physico-chemical-biological parameters shows that codon number is the main factor influencing and favoring specific pentapeptide frequencies in the universal proteome composition. That is, when compared to the set of never-expressed 5-mers, the pentapeptides frequently represented in the universal proteome are endowed with a higher number of multi-codonic amino acids. In contrast, the bulkiness degree and the hydrophobicity level play a smaller role. 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