Offer G, Sessions R
Department of Clinical Veterinary Science, University of Bristol, UK.
J Mol Biol. 1995 Jun 23;249(5):967-87. doi: 10.1006/jmbi.1995.0352.
In order to predict the structure of alpha-helical coiled-coil proteins from their sequences, it is necessary to know how the side-chains pack in the interface between the alpha-helical strands. Since in alpha-fibrous proteins leucine is the most common residue at both the a and d positions of the heptad repeat, which form the inner core of the interface, we determined the lowest-energy conformation for a two-stranded coiled-coil with the sequence (LAALAAA)5. Coiled-coils were constructed using the Crick equations with a range of pitches, major helical radii and relative rotations of the two strands, and with different starting side-chain conformations. On energy minimisation, convergence occurred to a small number of structures. The lowest-energy coiled-coil had 2-fold rotational symmetry, an average pitch of 131 A and an average radius of 4.52 A; the leucine side-chain conformations were tt and g+t at the a and d positions. This coiled-coil was used as a former to determine the lowest-energy side-chain conformations for the 63 combinations of a and d residues that occur in the repeating heptad sequence of rat skeletal myosin. The leucine residues at the a and d positions of the central heptad were replaced by the a-d pair of interest and molecular dynamics simulations performed to allow the side-chains of these residues to explore conformational space. The lowest-energy side-chain conformation of a residue at an a or d position depends on the nature of the partnering residue, consistent with the fact that these side-chains pack against one another. In most cases the lowest-energy structure was symmetric but in a few cases the side-chains were asymmetrically disposed in the two strands. The local pitch is very sensitive to the nature of the residues in the inner core and varies over a twofold range. In contrast, the radius and relative rotation of the two strands were relatively insensitive to sequence.
为了从序列预测α-螺旋卷曲螺旋蛋白的结构，有必要了解α-螺旋链之间界面处侧链的堆积方式。由于在α-纤维状蛋白中，亮氨酸是七肽重复序列a和d位置最常见的残基，而这两个位置构成了界面的内核，我们确定了序列为(LAALAAA)5的双链卷曲螺旋的最低能量构象。使用Crick方程构建卷曲螺旋，改变一系列的螺距、主螺旋半径以及两条链的相对旋转角度，并采用不同的起始侧链构象。在能量最小化时，收敛到少数几种结构。能量最低的卷曲螺旋具有2次旋转对称性，平均螺距为131 Å，平均半径为4.52 Å；亮氨酸侧链在a和d位置的构象分别为tt和g+t。这个卷曲螺旋被用作模板，来确定大鼠骨骼肌肌球蛋白重复七肽序列中出现的a和d残基的63种组合的最低能量侧链构象。将中央七肽a和d位置的亮氨酸残基替换为感兴趣的a-d对，并进行分子动力学模拟，以使这些残基的侧链能够探索构象空间。a或d位置残基的最低能量侧链构象取决于配对残基的性质，这与这些侧链相互堆积的事实一致。在大多数情况下，最低能量结构是对称的，但在少数情况下，侧链在两条链中不对称分布。局部螺距对内核中残基的性质非常敏感，变化范围达两倍。相比之下，两条链的半径和相对旋转对序列相对不敏感。
