PackHelix: a tool for helix-sheet packing during protein structure prediction.
PackHelix: a tool for helix-sheet packing during protein structure prediction.
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DOI：
10.1002/prot.23108
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发表时间：
2011-10
影响因子：
2.9
通讯作者：
Max, Nelson
中科院分区：
文献类型：
--
作者：
Hu, Chengcheng;Koehl, Patrice;Max, Nelson
蛋白质的三维结构是围绕其二级结构元素的堆积而组织的。因此，预测拓扑结构和构建涉及α-螺旋和/或β-链的结构基序的几何结构是准确预测蛋白质结构的关键步骤。虽然许多努力都集中在如何包装螺旋和如何详尽地采样形成蛋白质中β折叠的多条链的拓扑结构和几何形状上，但在产生天然样的螺旋包装在折叠上方面几乎没有进展。我们描述了一种方法，可以产生多个螺旋在一个给定的β折叠的αβα三明治型蛋白质折叠。该方法挖掘蛋白质结构中αβ2基序构象的统计分析结果，为螺旋在片上堆积的几何属性提供输入值。然后，它继续进行几何构建器，该几何构建器通过对这些值进行采样并执行一致性检查来生成感兴趣的片材上的螺旋的多个排列，该一致性检查确保螺旋和链之间的适当环几何形状、螺旋之间的最小数量的碰撞以及疏水核心的适当形成。该方法被实现为ProteinShop的一个模块。我们的研究结果表明，它产生的结构与天然结构的RMSD在4-6个RMSD范围内，而不管需要包装的螺旋数量如何，尽管如果蛋白质在序列中的两条连续链之间有几个螺旋，那么这个数量可能会增加，这些螺旋包装在由这两条链形成的片层上。
The three-dimensional structure of a protein is organized around the packing of its secondary structure elements. Predicting the topology and constructing the geometry of structural motifs involving α-helices and/or β-strands are therefore key steps for accurate prediction of protein structure. While many efforts have focused on how to pack helices and on how to sample exhaustively the topologies and geometries of multiple strands forming a β-sheet in a protein, there has been little progress on generating native-like packing of helices on sheets. We describe a method that can generate the packing of multiple helices on a given β-sheet for αβα sandwich type protein folds. This method mines the results of a statistical analysis of the conformations of αβ2 motifs in protein structures to provide input values for the geometric attributes of the packing of a helix on a sheet. It then proceeds with a geometric builder that generates multiple arrangements of the helices on the sheet of interest by sampling through these values and performing consistency checks that guarantee proper loop geometry between the helices and the strands, minimal number of collisions between the helices, and proper formation of a hydrophobic core. The method is implemented as a module of ProteinShop. Our results show that it produces structures that are within 4–6 Å RMSD of the native one, regardless of the number of helices that need to be packed, though this number may increase if the protein has several helices between two consecutive strands in the sequence that pack on the sheet formed by these two strands.
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影响因子：
2.9
作者：
Krivov, Georgii G.;Shapovalov, Maxim V.;Dunbrack, Roland L., Jr.
通讯作者：
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