The invariant system of coordinates of antibody molecules: Prediction of the ''standard'' C-alpha framework of V-L and V-H domains
The invariant system of coordinates of antibody molecules: Prediction of the ''standard'' C-alpha framework of V-L and V-H domains
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DOI：
10.1073/pnas.93.8.3675
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发表时间：
1996-04-16
影响因子：
11.1
通讯作者：
Leshchiner, D
中科院分区：
文献类型：
--
作者：
Gelfand, IM;Kister, AE;Leshchiner, D
提出了一种不涉及叠加过程的蛋白质结构比较新方法。描述了免疫球蛋白分子的不变坐标系，其基于可变结构域轻链（V-L）-重链（V-H）复合物固有的几何对称性。在不变坐标系中计算了22种免疫球蛋白结构中C-α原子的坐标。我们发现，在这个C-α框架中的76个相同的位置是关于双重轴对称的。通过比较这些分子中的相同位置，我们可以选择轻链中的96个位置和重链中的87个位置，其C-α原子坐标大致相同。为了检查这些位置中C-alpha原子的平均坐标是否符合立体化学要求，我们计算了C-alpha-C-alpha距离。轻链的73个位置和重链的72个位置满足C-alpha-C-alpha距离标准。这些位置上的C-α原子用于构建V-L和V-H复合物的“标准”C-α框架。给出了C-α原子的平均坐标。
A new approach of comparing protein structures that does not involve the procedure of superposition is suggested. An invariant system of coordinates for immunoglobulin molecules that is based on the geometrical symmetry inherent to the variable domain light-chain (V-L)-heavy-chain (V-H) complex is described. The coordinates of the C-alpha atoms in 22 immunoglobulin structures are calculated in the invariant system of coordinates. We found that 76 identical positions in this C-alpha framework are symmetrical about the twofold axis. Comparison of the identical positions in these molecules allows us to select 96 positions in the light chains and 87 positions in the heavy chains whose C-alpha atom coordinates are approximately the same. To check whether the average coordinates of C-alpha atoms in these positions complies with the stereochemical requirements, we calculated C-alpha-C-alpha distances. Seventy-three positions of the light chains and 72 positions of the heavy chains satisfy the C-alpha-C-alpha distance criterion. The C-alpha atoms in these positions are used for constructing the ''standard'' C-alpha framework of V-L and V-H complexes. The average coordinates of C-alpha atoms are presented.