Antigen-antibody interface properties: composition, residue interactions, and features of 53 non-redundant structures.
Antigen-antibody interface properties: composition, residue interactions, and features of 53 non-redundant structures.
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DOI：
10.1016/j.bbapap.2011.12.007
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发表时间：
2012-03
期刊：
影响因子：
--
通讯作者：
Mumey B
中科院分区：
文献类型：
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作者：
Ramaraj T;Angel T;Dratz EA;Jesaitis AJ;Mumey B
蛋白质抗原-抗体 (Ag-Ab) 界面的结构包含有关 Ab 如何识别 Ag 以及 Ag 如何折叠以呈现 Ag 识别表面的信息。因此，Ab 表面包含有关 Ab-Ag 界面残基的 Ag 折叠以及它们如何相互作用的信息。为了深入了解这种相互作用的本质，我们分析了由 53 个非冗余的 Ag-Ab 复合物 3D 结构组成的数据集。我们评估了 Ag-Ab 界面的物理和生化特征以及相应界面表面上的氨基酸残基之间存在有利相互作用的程度。界面的氨基酸组成分析证实了 TYR 在含有 Ab 互补位的表面 (PCS) 中占主导地位，其丰度几乎是任何其他残基的两倍。此外，与整个抗体的表面相比，TYR 在 PCS 中的存在量远高于预期（定义为出现倾向），还有芳香族化合物 PHE、TRP，以及较小程度的 HIS 和 ILE。在含Ag表位的表面（ECS）中，相对于整个Ag表面，TRP和TYR的出现倾向略有增加，这意味着比组成最丰富的LYS>ASN>GLU>ASP>ARG的显着性增加。这项检查涵盖了大量不同的独特 Ag-Ab 晶体结构，有助于解释 Ag-Ab 相互作用的生物学范围和特异性。该分析还可以提供对 Ag 结合的噬菌体展示分析中单个氨基酸残基的重要性的测量。
The structures of protein antigen–antibody (Ag–Ab) interfaces contain information about how Ab recognize Ag as well as how Ag are folded to present surfaces for Ag recognition. As such, the Ab surface holds information about Ag folding that resides with the Ab–Ag interface residues and how they interact. In order to gain insight into the nature of such interactions, a data set comprised of 53 non-redundant 3D structures of Ag–Ab complexes was analyzed. We assessed the physical and biochemical features of the Ag–Ab interfaces and the degree to which favored interactions exist between amino acid residues on the corresponding interface surfaces. Amino acid compositional analysis of the interfaces confirmed the dominance of TYR in the Ab paratope-containing surface (PCS), with almost two fold greater abundance than any other residue. Additionally TYR had a much higher than expected presence in the PCS compared to the surface of the whole antibody (defined as the occurrence propensity), along with aromatics PHE, TRP, and to a lesser degree HIS and ILE. In the Ag epitope-containing surface (ECS), there were slightly increased occurrence propensities of TRP and TYR relative to the whole Ag surface, implying an increased significance over the compositionally most abundant LYS>ASN>GLU>ASP>ARG. This examination encompasses a large, diverse set of unique Ag–Ab crystal structures that help explain the biological range and specificity of Ag–Ab interactions. This analysis may also provide a measure of the significance of individual amino acid residues in phage display analysis of Ag binding.