Computational and statistical analyses of amino acid usage and physico-chemical properties of the twelve late embryogenesis abundant protein classes

Emmanuel Jaspard (1) , David Macherel (1) , Gilles Hunault (2)

1 IRHS - Institut de Recherche en Horticulture et Semences
2 HIFIH - Hémodynamique, Interaction Fibrose et Invasivité tumorales Hépatiques

Late Embryogenesis Abundant Proteins (LEAPs) are ubiquitous proteins expected to play major roles in desiccation tolerance. Little is known about their structure - function relationships because of the scarcity of 3-D structures for LEAPs. The previous building of LEAPdb, a database dedicated to LEAPs from plants and other organisms, led to the classification of 710 LEAPs into 12 non-overlapping classes with distinct properties. Using this resource, numerous physico-chemical properties of LEAPs and amino acid usage by LEAPs have been computed and statistically analyzed, revealing distinctive features for each class. This unprecedented analysis allowed a rigorous characterization of the 12 LEAP classes, which differed also in multiple structural and physico-chemical features. Although most LEAPs can be predicted as intrinsically disordered proteins, the analysis indicates that LEAP class 7 (PF03168) and probably LEAP class 11 (PF04927) are natively folded proteins. This study thus provides a detailed description of the structural properties of this protein family opening the path toward further LEAP structure - function analysis. Finally, since each LEAP class can be clearly characterized by a unique set of physico-chemical properties, this will allow development of software to predict proteins as LEAPs.

Mots clés: INTRINSICALLY DISORDERED PROTEINS; SALSUGINEA DEHYDRINS TSDHN-1; ARABIDOPSIS-THALIANA; GLOBULAR-PROTEINS; DEVELOPMENTAL BIOCHEMISTRY; COTTONSEED EMBRYOGENESIS; SEQUENCE ALIGNMENTS; SECONDARY STRUCTURE; STRESS-PROTEINS; LEA PROTEINS

Domaines: Sciences du Vivant [q-bio]

Emmanuel Jaspard, David Macherel, Gilles Hunault. Computational and statistical analyses of amino acid usage and physico-chemical properties of the twelve late embryogenesis abundant protein classes. PLoS ONE, 2012, 7 (5), ⟨10.1371/journal.pone.0036968⟩. ⟨hal-01209926⟩