[Superspiralized alpha-spiral. 2. Conformational analysis of a model fragment of the dual-chain parallel superspiralized alpha-spiral].

To estimate the role of nonbonded interactions in the folding of the hydrophobic core of a two-stranded parallel alpha-helical coiled-coil, a conformational analysis was carried out for the model fragment: [formula: see text] with a 2-fold symmetry axis running between the parallel helices, where X denotes nonpolar residues Ala, Leu, Val, Ile, Met, Phe, Tyr, Trp. For every residue X, the energy of interaction between two helices and the complete conformational energy, were mapped as functions of (R, nu 0) where R is radius of coiled coil and nu 0 is the angle that determines orientation of two helices relatively to each other. It was shown that when Phe, Tyr, Ile and Val were located in the d position of repeating heptapeptide, there appeared certain steric restrictions. The obtained results allow one to explain certain peculiarities in the distribution of nonpolar residues in coiled-coil structure in fibrous proteins, i.e., a high percentage of Leu in the hydrophobic core of these structures; preference of a position for Val and Ile compared to d position, and a rare occurrence of Phe in d position.