Species specific amino acid sequence-protein local structure relationships: An analysis in the light of a structural alphabet.: species‟ sequence - structure relationship

Abstract : Protein structure analysis and prediction methods are based on non-redundant data extracted from the available protein structures, regardless of the species from which the protein originates. Hence, these datasets represent the global knowledge on protein folds, which constitutes a generic distribution of amino acid sequence-protein structure (AAS-PS) relationships. In this study, we try to elucidate whether the AAS-PS relationship could possess specificities depending on the specie. For this purpose, we have chosen three different species: Saccharomyces cerevisiae, Plasmodium falciparum and Arabidopsis thaliana. We analyzed the AAS-PS behaviors of the proteins from these three species and compared it to the "expected" distribution of a classical non-redundant databank. With the classical secondary structure description, only slight differences in amino acid preferences could be observed. With a more precise description of local protein structures (Protein Blocks), significant changes could be highlighted. S. cerevisiae's AAS-PS relationship is close to the general distribution, while striking differences are observed in the case of A. thaliana. P. falciparum is the most distant one. This study presents some interesting view-points on AAS-PS relationship. Certain species exhibit unique preferences for amino acids to be associated with protein local structural elements. Thus, AAS-PS relationships are species dependent. These results can give useful insights for improving prediction methodologies which take the species specific information into account.
Type de document :
Article dans une revue
Journal of Theoretical Biology, Elsevier, 2011, 276 (1), pp.209-17. 〈10.1016/j.jtbi.2011.01.047〉
Liste complète des métadonnées

http://www.hal.inserm.fr/inserm-00646218
Contributeur : Alexandre G. De Brevern <>
Soumis le : mardi 29 novembre 2011 - 14:33:05
Dernière modification le : lundi 23 juillet 2018 - 17:04:01
Document(s) archivé(s) le : lundi 5 décembre 2016 - 07:34:02

Identifiants

Collections

Citation

Alexandre De Brevern, Agnel Praveen Joseph. Species specific amino acid sequence-protein local structure relationships: An analysis in the light of a structural alphabet.: species‟ sequence - structure relationship. Journal of Theoretical Biology, Elsevier, 2011, 276 (1), pp.209-17. 〈10.1016/j.jtbi.2011.01.047〉. 〈inserm-00646218〉

Partager

Métriques

Consultations de la notice

232

Téléchargements de fichiers

199