[Structural and Physicochemical Characteristics of Conformationally Stable alpha-Helical Oligopeptides].

Abstract

The analysis of conformationally stable (conformational conservative) tetrapeptides selected from protein structures deposited in PDBSelect data bank has been fulfilled. The subset contained 943 tetrapeptide amino acid sequences and there were merely five 3D protein segment representatives for each sequence. As a result, the conclusion has been drawn on the basis of DSSP annotation analysis that in the majority of cases (900 of 943) alpha-helical conformation is obvious. Different than alpha-helix, in particular, the left-handed polyproline II helical conformation was observed in 43 sequences. The physical and chemical properties of conformationally stable peptides taken from the appropriate sample were estimated by the average hydrophobicity/hydrophilicity of tetrapeptides. The results of calculations show that the "neutrality" towards hydrophobicity/hydrophilicity is representative of conformationally stable oligopeptides. It should be noted, that dispersion of hydrophobicity/hydrophilicity distribution is sufficiently lower than for the test subsets. Thus, the conformationally stable oligopeptides present a distinct group of local protein structures which are very close with respect to conformational and physicochemical properties. In accordance with our developed theory of specific long range interactions these peptides are the objects being quite useful for effective mutual molecular recognition.

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