Ab initio detection of fuzzy amino acid tandem repeats in protein sequences
Identifieur interne : 000603 ( Main/Curation ); précédent : 000602; suivant : 000604Ab initio detection of fuzzy amino acid tandem repeats in protein sequences
Auteurs : Marco Pellegrini [Italie] ; Maria Elena Renda [Italie] ; Alessio Vecchio [Italie]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2012.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Membrane Proteins, Proteins.
- chemical , genetics : Membrane Proteins, Proteins.
- Algorithms, Amino Acid Sequence, Databases, Protein, Humans, Protein Structure, Secondary.
Abstract
Tandem repetitions within protein amino acid sequences often correspond to regular secondary structures and form multi-repeat 3D assemblies of varied size and function. Developing internal repetitions is one of the evolutionary mechanisms that proteins employ to adapt their structure and function under evolutionary pressure. While there is keen interest in understanding such phenomena, detection of repeating structures based only on sequence analysis is considered an arduous task, since structure and function is often preserved even under considerable sequence divergence (
In this paper we present
Url:
DOI: 10.1186/1471-2105-13-S3-S8
PubMed: 22536906
PubMed Central: 3402919
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PMC:3402919Le document en format XML
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<author><name sortKey="Renda, Maria Elena" sort="Renda, Maria Elena" uniqKey="Renda M" first="Maria Elena" last="Renda">Maria Elena Renda</name>
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<series><title level="j">BMC Bioinformatics</title>
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<term>Amino Acid Sequence</term>
<term>Databases, Protein</term>
<term>Humans</term>
<term>Membrane Proteins (chemistry)</term>
<term>Membrane Proteins (genetics)</term>
<term>Protein Structure, Secondary</term>
<term>Proteins (chemistry)</term>
<term>Proteins (genetics)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term>
<term>Bases de données de protéines</term>
<term>Humains</term>
<term>Protéines ()</term>
<term>Protéines (génétique)</term>
<term>Protéines membranaires ()</term>
<term>Protéines membranaires (génétique)</term>
<term>Structure secondaire des protéines</term>
<term>Séquence d'acides aminés</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Membrane Proteins</term>
<term>Proteins</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Membrane Proteins</term>
<term>Proteins</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Protéines</term>
<term>Protéines membranaires</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Algorithms</term>
<term>Amino Acid Sequence</term>
<term>Databases, Protein</term>
<term>Humans</term>
<term>Protein Structure, Secondary</term>
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<term>Bases de données de protéines</term>
<term>Humains</term>
<term>Protéines</term>
<term>Protéines membranaires</term>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>Tandem repetitions within protein amino acid sequences often correspond to regular secondary structures and form multi-repeat 3D assemblies of varied size and function. Developing internal repetitions is one of the evolutionary mechanisms that proteins employ to adapt their structure and function under evolutionary pressure. While there is keen interest in understanding such phenomena, detection of repeating structures based only on sequence analysis is considered an arduous task, since structure and function is often preserved even under considerable sequence divergence (<italic>fuzzy tandem repeats</italic>
).</p>
</sec>
<sec><title>Results</title>
<p>In this paper we present <italic>PTRStalker</italic>
, a new algorithm for <italic>ab-initio </italic>
detection of <italic>fuzzy tandem repeats </italic>
in protein amino acid sequences. In the reported results we show that by feeding <italic>PTRStalker </italic>
with amino acid sequences from the UniProtKB/Swiss-Prot database we detect novel tandemly repeated structures not captured by other state-of-the-art tools. Experiments with membrane proteins indicate that <italic>PTRStalker </italic>
can detect global symmetries in the primary structure which are then reflected in the tertiary structure.</p>
</sec>
<sec><title>Conclusions</title>
<p><italic>PTRStalker </italic>
is able to detect fuzzy tandem repeating structures in protein sequences, with performance beyond the current state-of-the art. Such a tool may be a valuable support to investigating protein structural properties when tertiary X-ray data is not available.</p>
</sec>
</div>
</front>
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