title: Species specific amino acid sequence-protein local structure relationships: An analysis in the light of a structural alphabet.
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.
authors.affiliation: Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), INSERM, U665, Paris, 6, rue Alexandre Cabanel, F-75015, France. alexandre.debrevern@univ-paris-diderot.fr
authors.forename: Alexandre G
authors.initials: AG
authors.lastname: de Brevern
authors.forename: Agnel Praveen
authors.initials: AP
authors.lastname: Joseph
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D017360:Arabidopsis / Q000378:metabolism; D016000:Cluster Analysis; D030562:Databases, Protein; D008969:Molecular Sequence Data; D010963:Plasmodium falciparum / Q000378:metabolism; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D020543:Proteome / Q000737:chemistry; D012441:Saccharomyces cerevisiae / Q000378:metabolism; D013045:Species Specificity; D013329:Structure-Activity Relationship
chemical_list: D000596:Amino Acids; D011506:Proteins; D020543:Proteome