The prediction of Solenoid Structures in Proteins by a New Helix Fitting Method

将螺旋与数据相匹配的问题出现在蛋白质结构中。螺旋线由几个参数描述：螺旋轴、半径和螺距。到目前为止，所有提出的方案都预先定义了一个螺旋参数。我们已经开发了HELFIT程序，用于将螺旋拟合到C^α坐标。3&lt；10-螺旋的特征是在残基I的主链羰基氧和残基I+3的主链酰胺氢之间至少有两个连续的氢键。主链二面角有系统的、特定于位置的移动。规则的3&10-螺旋的每转残基和半径随着螺旋长度的增加而减小，而螺旋间距和每残基的上升幅度则随着螺旋长度的增加而增加。规则的3&10-螺旋的比例随着螺旋长度的增加而线性减少。能量最小化；表明规则螺旋随着螺旋长度的增加而变得不稳定。这些发现表明，用平均、均匀的二面角来定义3-螺旋是不合适的，并且多肽形成延伸的、规则的3w-螺旋本身是不稳定的。我们提出，在蛋白质中观察到的3&lt；10&gt；-螺旋更好地被称为副螺旋。

The problem of fitting a helix to data arises in protein structure. A helix is described by several parameters : the helix axis, the radius and the pitch. Till now, all programs proposed have predefined one of the helix parameters. We have developed the HELFIT program for fitting helices to C^α coordinates. The 3_<10>-helix is characterized by having at least two consecutive hydrogen bonds between the main-chain carbonyl oxygen of residue i and the main-chain amide hydrogen of residue i+3. There are systematic, position-specific shifts in the backbone dihedral angles. The residues per turn and radius of regular 3_<10>-helices decrease with increasing length of helix, while the helix pitch and rise per residue increase. The fraction of regular 3_<10>-helices decreases linearly with helix length. Energy minimization; show that regular helices become less stable with increasing helix length. These findings indicate that the definition of 3_<10>-helices in terms of average, uniform dihedral angles is not appropriate and that it is inherently unstable for a polypeptide to form an extended, regular 3w-helix. We proposed that the 3_<10>-helices observed in proteins are better referred to parahelices.