Shirai H, Nakajima N, Higo J, Kidera A, Nakamura H
Department of Bioinformatics, Biomolecular Engineering Research Institute, 6-2-3 Furuedai, Osaka 565, Suita, Japan.
J Mol Biol. 1998 May 1;278(2):481-96. doi: 10.1006/jmbi.1998.1698.
The diversity in the lengths and the amino acid sequences of the third complementarity determining region of the antibody heavy chain (CDR-H3) has made it difficult to establish a relationship between the sequences and the tertiary structures, in contrast to the other CDRs, which are classified by their canonical structures. Enhanced conformational sampling of two different CDR-H3s was performed by multicanonical molecular dynamics (multicanonical MD) simulation while restricting the base structures, with and without the other surrounding CDR segments. The results showed that the multicanonical MD sampled a much larger conformational space than the conventional MD, independent of the initial conformations of the simulations. When the other CDRs surrounding the CDR-H3 segments were included in the calculations, the predominant conformations at 300 K corresponded to the X-ray crystal structures. When only the single CDR-H3 loops were considered with the restricted base structures, a greater number of different conformations were sampled as putative loops, but only a small number of stable conformations appeared at 300 K. Analyses of the resultant conformations revealed a structural role for the glycine, when it is located at position three residues before the last residue of CDR-H3 (Gly-X-X-last residue), coincident with the statistical tendencies of many antibody crystal structures. This reflects the general consistency between the energetically stable conformations and the empirically observed conformations. The current method is expected to be applicable to the structural modeling and the design of antibodies, especially for the inherently flexible loops.
与其他通过典型结构分类的互补决定区（CDR）不同，抗体重链第三互补决定区（CDR-H3）在长度和氨基酸序列上具有多样性，这使得难以确定其序列与三级结构之间的关系。通过多规范分子动力学（multicanonical MD）模拟对两个不同的CDR-H3进行增强构象采样，同时限制基础结构，分别考虑有无其他周围CDR片段的情况。结果表明，多规范MD采样的构象空间比传统MD大得多，且与模拟的初始构象无关。当计算中包含CDR-H3片段周围的其他CDR时，300K时的主要构象与X射线晶体结构相对应。当仅考虑具有受限基础结构的单个CDR-H3环时，作为假定环采样到了更多不同的构象，但在300K时仅出现少量稳定构象。对所得构象的分析揭示了甘氨酸的结构作用，当它位于CDR-H3最后一个残基之前三个残基的位置（甘氨酸-任意氨基酸-任意氨基酸-最后一个残基）时，这与许多抗体晶体结构的统计趋势一致。这反映了能量稳定构象与经验观察到的构象之间的总体一致性。预计当前方法将适用于抗体的结构建模和设计，特别是对于固有柔性的环。
