Protein loop modeling by using fragment assembly and analytical loop closure.
Protein loop modeling by using fragment assembly and analytical loop closure.
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DOI：
10.1002/prot.22849
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发表时间：
2010-12
影响因子：
2.9
通讯作者：
Seok, Chaok
中科院分区：
文献类型：
--
作者：
Lee, Julian;Lee, Dongseon;Park, Hahnbeom;Coutsias, Evangelos A.;Seok, Chaok
关键词：
蛋白质环通常参与重要的生物学功能，如分子识别、信号转导或酶作用。环的三维结构可以为理解蛋白质功能背后的分子机制提供必要的信息。在本文中，我们提出了一种新的蛋白质环建模方法，该方法通过片段组装和分析环闭合来生成环构象。片段拼装法大大减少了构象空间，解析环闭合方法有效地找到了几何一致的环构象。我们还推导了闭环空间中任意二面角解析函数的梯度的解析公式。该梯度可用于优化来自实验或数据库的各种限制条件，例如特定残基之间优先相互作用的限制条件或首选主链角度的限制条件。在两组长度从4到12的环路目标上进行测试时，我们证明了当前的环路建模方法优于以往采用基于残数的扭角映射或不同的环路闭合策略的方法。
Protein loops are often involved in important biological functions such as molecular recognition, signal transduction, or enzymatic action. The three dimensional structures of loops can provide essential information for understanding molecular mechanisms behind protein functions. In this paper, we develop a novel method for protein loop modeling, where the loop conformations are generated by fragment assembly and analytical loop closure. The fragment assembly method reduces the conformational space drastically, and the analytical loop closure method finds the geometrically consistent loop conformations efficiently. We also derive an analytic formula for the gradient of any analytical function of dihedral angles in the space of closed loops. The gradient can be used to optimize various restraints derived from experiments or databases, for example restraints for preferential interactions between specific residues or for preferred backbone angles. We demonstrate that the current loop modeling method outperforms previous methods that employ residue-based torsion angle maps or different loop closure strategies when tested on two sets of loop targets of lengths ranging from 4 to 12.
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