Seo J, Cohen C
Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02254-9110.
Proteins. 1993 Mar;15(3):223-34. doi: 10.1002/prot.340150302.
Two complementary methods for measuring local pitch based on heptad position in alpha-helical coiled coils are described and applied to six crystal structures. The results reveal a diversity of pitch values: two-stranded coiled coils appear to have pitch values near 150 A; the values for three- and four-stranded coiled coils range closer to 200 A. The methods also provide a rapid and sensitive gauge of local coiled-coil conformation. Polar or charged residues in the apolar interface between coiled-coil helices markedly affect local pitch values, suggesting a connection between pitch uniformity and coiled-coil stability. Moreover, the identification of a skip residue (heptad frame shift) in the hemagglutinin glycoprotein of influenza virus (HA) allows interpretation of local pitch changes. These results on relatively short coiled-coil structures have relevance for the much longer fibrous proteins (many of which have skip residues) whose detailed structures are not yet established. We also show that local pitch values from molecular dynamics predictions of the GCN4 leucine zipper are in striking agreement with the high-resolution crystal structure--a result not readily discerned by direct comparison of atomic coordinates. Taken together, these methods reveal specific aspects of coiled-coil structure which may escape detection by global analyses of pitch.
描述了两种基于α-螺旋卷曲螺旋中七肽位置测量局部螺距的互补方法，并将其应用于六个晶体结构。结果揭示了螺距值的多样性：两链卷曲螺旋的螺距值似乎接近150埃；三链和四链卷曲螺旋的值更接近200埃。这些方法还提供了一种快速且灵敏的局部卷曲螺旋构象测量方法。卷曲螺旋螺旋之间非极性界面中的极性或带电残基显著影响局部螺距值，这表明螺距均匀性与卷曲螺旋稳定性之间存在联系。此外，在流感病毒血凝素糖蛋白（HA）中鉴定出一个跳跃残基（七肽框架移位），这有助于解释局部螺距变化。这些关于相对较短卷曲螺旋结构的结果与更长的纤维状蛋白质（其中许多具有跳跃残基）相关，而这些蛋白质的详细结构尚未确定。我们还表明，GCN4亮氨酸拉链分子动力学预测的局部螺距值与高分辨率晶体结构惊人地一致——这一结果通过直接比较原子坐标不易看出。综上所述，这些方法揭示了卷曲螺旋结构的特定方面，而这些方面可能通过对螺距的全局分析而无法检测到。
