Generalized crick equations for modeling noncanonical coiled coils
Generalized crick equations for modeling noncanonical coiled coils
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DOI：
10.1006/jsbi.2002.4448
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发表时间：
2002-01-01
影响因子：
3
通讯作者：
Woolfson, DN
中科院分区：
文献类型：
--
作者：
Offer, G;Hicks, MR;Woolfson, DN
克里克设想，α螺旋卷曲螺旋是由α螺旋系统性弯曲产生的，这样每第七个残基在结构上都是等价的，他推导出了骨架原子坐标的方程。克里克的预测被证实实验和卷曲螺旋序列显示有疏水残基交替间隔3和4个残基。尽管如此，在一些卷曲螺旋中，这样的规范七肽重复序列被3或4个残基的插入物中断，产生十和十一个基序。卷曲螺旋的超螺旋随序列模式而变化，在纯粹的基于七或基于十一的基序中分别是左手或右手的。为了对具有混合图案的盘绕线圈进行建模，我们描述了如何针对节距不恒定的情况修改克里克方程。使用梁的弯曲的类比，我们采用倾斜角随着沿着主螺旋的距离沿着线性变化，并且基序的节距取决于α-螺旋链的刚性而受到相邻基序的影响。我们通过拟合GrpE、血凝素和tetrabrachion的双链、三链和四链非典型卷曲螺旋来测试我们的方法。模型的骨架原子和晶体结构的均方根偏差为
Crick envisaged the alpha-helical coiled coil to result from systematic bending of an alpha-helix such that every seventh residue was structurally equivalent, and he derived equations for the coordinates of the backbone atoms. Crick's predictions were vindicated experimentally and coiled-coil sequences were shown to have hydrophobic residues alternately spaced 3 and 4 residues apart. Nonetheless, in some coiled coils such canonical heptad repeats are interrupted by inserts of 3 or 4 residues generating decad and hendecad motifs. The supercoiling of the coiled coils varies with the sequence pattern, being left- or right-handed in purely heptad-based or hendecad-based motifs, respectively. To model coiled coils with a mixture of motifs, we describe how Crick's equations can be modified for cases where the pitch is not constant. Using the analogy of the bending of a beam, we took the tilt angle to change linearly with distance along the major helix and the pitch of a motif to be affected by neighboring motifs depending on the rigidity of the alpha-helical strands. We tested our approach by fitting the two-, three-, and four-stranded noncanonical coiled coils of GrpE, hemagglutinin, and tetrabrachion. The backbone atoms of the model and crystal structures agreed with root mean square deviations of