Vishnepol'skiĭ B M, Pirtskhalava M K
Mol Biol (Mosk). 1993 May-Jun;27(3):638-46.
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.
为了评估非键相互作用在两链平行α-螺旋卷曲螺旋疏水核心折叠中的作用，对模型片段进行了构象分析：[公式：见文本]，其具有在平行螺旋之间运行的二重对称轴，其中X表示非极性残基丙氨酸（Ala）、亮氨酸（Leu）、缬氨酸（Val）、异亮氨酸（Ile）、甲硫氨酸（Met）、苯丙氨酸（Phe）、酪氨酸（Tyr）、色氨酸（Trp）。对于每个残基X，将两个螺旋之间的相互作用能和完整的构象能绘制为（R，ν0）的函数，其中R是卷曲螺旋的半径，ν0是确定两个螺旋相对彼此取向的角度。结果表明，当苯丙氨酸、酪氨酸、异亮氨酸和缬氨酸位于重复七肽的d位置时，会出现一定的空间限制。所得结果有助于解释纤维状蛋白质卷曲螺旋结构中非极性残基分布的某些特性，即这些结构的疏水核心中亮氨酸的比例较高；与d位置相比，缬氨酸和异亮氨酸更倾向于某个位置，并且苯丙氨酸在d位置很少出现。
