Engel Donald E, DeGrado William F
Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
Proteins. 2005 Nov 1;61(2):325-37. doi: 10.1002/prot.20522.
While the geometry and sequence preferences of turns that link two beta-strands have been exhaustively explored, the corresponding preferences for sequences that link helical structures have been less well studied. Here we examine the interhelical geometry of two connected helices as a function of their link's length. The interhelical geometry of a helical pair appears to be significantly influenced by the number of linking residues. Furthermore, for relatively short link lengths, a very limited number of predominant conformations are observed, which can be categorized by their phi/psi angles. No more than two predominant linking backbone conformations are observed for a given link length, and some linking backbone conformations correlate strongly with distinctive interhelical geometric parameters. In this study, sequence and hydrogen-bonding patterns were defined for predominant interhelical link motifs. These results should assist in both protein structure prediction and de novo protein design.
虽然连接两条β链的转角的几何形状和序列偏好已被详尽研究，但连接螺旋结构的序列的相应偏好却较少被深入研究。在此，我们研究了两个相连螺旋的螺旋间几何形状与其连接长度的函数关系。螺旋对的螺旋间几何形状似乎受到连接残基数量的显著影响。此外，对于相对较短的连接长度，观察到的主要构象数量非常有限，这些构象可根据其φ/ψ角进行分类。对于给定的连接长度，观察到的主要连接主链构象不超过两种，并且一些连接主链构象与独特的螺旋间几何参数密切相关。在本研究中，为主要的螺旋间连接基序定义了序列和氢键模式。这些结果应有助于蛋白质结构预测和从头蛋白质设计。
