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

在蛋白质结构中出现了将螺旋线与数据拟合的问题。螺旋由几个参数描述：螺旋轴、半径和螺距。到目前为止，所有提出的程序都预先定义了一个螺旋参数。我们已经开发了HELFIT程序，用于将螺旋线拟合到C^α坐标。3_<10>螺旋的特征在于在残基i的主链羰基氧和残基i+3的主链酰胺氢之间具有至少两个连续的氢键。骨架二面角有系统的、位置特异性的变化。随着螺旋长度的增加，规则3_螺旋的每圈残基数和半径<10>减小，而螺旋螺距和每残基升程增加。规则的3_<10>-螺旋的比例随螺旋长度线性减少。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，<10>根据平均、均匀二面角来定义3_螺旋是不合适的，并且多肽形成延伸的、规则的3_螺旋是固有不稳定的。我们认为<10>蛋白质中观察到的3_ -螺旋最好称为副螺旋。

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.