310-helices in proteins are parahelices
310-helices in proteins are parahelices
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DOI：
10.1002/prot.21026
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发表时间：
2006-08-15
影响因子：
2.9
通讯作者：
Matsushima, Norio
中科院分区：
文献类型：
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作者：
Enkhbayar, Purevjav;Hikichi, Kunio;Matsushima, Norio
3(10)-螺旋的特征在于残基 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。螺旋参数 - 螺距、每转残基、半径和与最佳拟合螺旋的均方根偏差 (rmsd) - 通过使用 HELFIT 程序确定。所有 3(10)-螺旋根据 rmsd/(N - 1)(1/2) 分为规则或不规则，其中 N 是螺旋长度。对于两者来说，主干二面角都存在系统的、特定于位置的变化。对于5、6和7个残基长的螺旋，平均phi、psi系统地从类似于z-58度、类似于-32度到类似于-90度、类似于-4度。螺旋也有相同的一般模式，N = 8 和 9；然而，在 N = 9 中，残基 6、7 和 8 会重复该趋势，大致重复残基 2、3 和 4 的 phi、psi。规则 3(10)-螺旋的每转残基和半径随着螺旋长度的增加而减小，而每个残基的螺旋螺距和上升增加。也就是说，随着 N 从 5 增加到 8，常规 3(10)-螺旋变得更细更长。常规 31, 螺旋的比例随螺旋长度线性减小。所有较长的螺旋，N >= 9 都是不规则的。能量最小化表明，随着螺旋长度的增加，规则螺旋变得不太稳定。这些发现表明，以平均、均匀的二面角来定义 3(10)-螺旋是不合适的，并且多肽形成延伸的、规则的 3(10)-螺旋本质上是不稳定的。在蛋白质中观察到的 3(10)-螺旋最好称为副螺旋。
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. The helical parameters - pitch, residues per turn, radius, and root mean square deviation (rmsd) from the best-fit helix - were determined by using the HELFIT program. All 3(10)-helices were classified as regular or irregular based on rmsd/(N - 1)(1/2) where N is the helix length. For both there are systematic, position-specific shifts in the backbone dihedral angles. The average phi, psi shift systematically from similar to z-58 degrees, similar to -32 degrees to similar to -90 degrees, similar to -4 degrees for helices 5, 6, and 7 residues long. The same general pattern is seen for helices, N = 8 and 9; however, in N = 9, the trend is repeated with residues 6, 7, and 8 approximately repeating the phi, psi of residues 2, 3, and 4. 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. That is, regular 3(10)-helices become thinner and longer as N increases from 5 to 8. The fraction of regular 31,helices decreases linearly with helix length. All longer helices, N >= 9 are irregular. Energy minimizations 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 3(10)-helix. The 3(10)-helices observed in proteins are better referred to parahelices.