[Unstructured regions in elongation factors EF1A from three overkingdom of the living world].
A new characteristic for classification of the Living World which based on the ability of amino acid sequences to form unstructured regions that appear as loops in their 3D structure is described. Our approach is in principle different from RNA and protein phylogenies that are based on the alignment of amino acid sequences from different organisms. Introduction of new structural-functional characteristic in itself is of undoubted interest because megataxonomy and macrophylogeny lack features that may be resolve evolutionary relation between different groups of organisms though apparent abundance of such characteristics are present. We used the program FoldUnfold to search for unstructured regions in the elongation factors EF1A. The reliability of loop prediction was checked against five factors whose structure is known from X-ray analysis. In addition to two cross-bridges between three structural domains in the elongation factors, the program predicts extra loops. Not counting the effector loop that is inherent to all factors, there are six. Three (A, B and C) of the six different loops are revealed in the first domain, one loop (D) in the second, and two loops (E and F) in the third domain of the factor, all six of which are never found in the same factor. Signatures of elongation factors for each Superkingdom of the Living World have been found for several dozen typical representatives from each Superkingdom. These signatures lead to the variation of the number of loops and their localization within the factor domains. The obtained data leads us to believe that the approach based on the prediction of unstructured protein loops--up to six--must have higher resolution than the method based on the indels (insertion + deletion), the number of which equals one for the same elongation factors. In our analysis, the specificity of sequences it is important, in addition to the existence of loops. Since the total number of loops predicted in the factors increases with the complexity of an organism, we propose the following about the role of the loops in evolution: holding to the principle of "thrifty inventiveness", Nature operates with different universal inserts (loops) adapting their number and location among the factor domains as well as their amino acid composition so that the protein will perform special functions: one in protozoa and several in higher organisms.
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D000595:Amino Acid Sequence; D000818:Animals; D001105:Archaea; D001419:Bacteria; D005075:Biological Evolution; D005658:Fungi; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010445:Peptide Elongation Factors / Q000737:chemistry*; D010802:Phylogeny; D010944:Plants; D017434:Protein Structure, Tertiary; D012984:Software
D010445:Peptide Elongation Factors