Species specific amino acid sequence–protein local structure relationships: An analysis in the light of a structural alphabet

Abstract

To cite this version: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) AbstractProtein 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.Saccharomyces cerevisiae's AAS-PS relationship is close to the general distribution, while striking differences are observed in the case of Arabidopsis thaliana. Plasmodium 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 dependant. These results can give useful insights for improving prediction methodologies which take the species specific information into account.

Global analysis of VHHs framework regions with a structural alphabet

“…PBs assignment was performed with PBxplore tool developed under the guidance of Pierre Poulain (https://github.com/pierrepo/PBxplore, in preparation). PBs are used to translate the 3D structures under a 1D shape like a sequence of amino acids and are particularly more accurate than the secondary structures [40,[62][63] (see Sup Data 2 to see translation of a 3D VHH into a 1D sequence).…”

From local structure to a global framework: recognition of protein folds

“…This observation is quite interesting and the specificities could be exploited in improving the accuracy of approaches for local structure prediction. A study conducted in this direction showed promising results with Plasmodium falciparum, Arabidopsis thaliana and Saccharomyces cerevisiae [223]. Considering the compositions corresponding to both query and template improves profile comparisons [224].…”

Hemolymph proteins in marine crustaceans

“…Most work has focused on oligosaccharide residues of surface-bound glycoproteins and their use by copepods as sex pheromones. Glycoproteins bound to harpacticoid copepod exoskeleton surfaces, particularly the anntenule, genital pore, and caudal ramus, are involved in the recognition of species, sex and stage of potential mates [45,46] . The functional importance of carbohydrate residues on surface-bound glycoproteins of harpacticoid copepods (Tigriopus japonicus and Coullana spp.…”