García-Hernández E, Zubillaga R A, Rodríguez-Romero A, Hernández-Arana A
Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, México D.F., México 04510.
Glycobiology. 2000 Oct;10(10):993-1000. doi: 10.1093/glycob/10.10.993.
A global census of stereochemical metrics including interface size, hydropathy, amino acid propensities, packing and hydrogen bonding was carried out on 32 x-ray-elucidated structures of lectin-carbohydrate complexes covering eight different lectin families. It is shown that the interactions at primary binding subsites are more efficient than at other subsites. Another salient behavior found for primary subsites was a marked negative correlation between the interface size and the polar surface content. It is noteworthy that this demographic rule is delineated by lectins with unrelated phylogenetic origin, indicating that independent interface architectures have evolved through common optimization paths. The structural properties of lectin-carbohydrate interfaces were compared with those characterizing a set of 32 protein homodimers. Overall, the analysis shows that the stereochemical bases of lectin-carbohydrate and protein-protein interfaces differ drastically from each other. In comparison with protein-protein complexes, lectin-carbohydrate interfaces have superior packing efficiency, better hydrogen bonding stereochemistry, and higher interaction cooperativity. A similar conclusion holds in the comparison with protein-protein heterocomplexes. We propose that the energetic consequence of this better interaction geometry is a larger decrease in free energy per unit of area buried, feature that enables lectins and carbohydrates to form stable complexes with relatively small interface areas. These observations lend support to the emerging notion that systems differing from each other in their stereochemical metrics may rely on different energetic bases.
对涵盖八个不同凝集素家族的32个通过X射线解析的凝集素-碳水化合物复合物结构进行了包括界面大小、亲水性、氨基酸倾向、堆积和氢键在内的立体化学指标的全球普查。结果表明，主要结合亚位点处的相互作用比其他亚位点处的更有效。在主要亚位点发现的另一个显著行为是界面大小与极性表面含量之间存在明显的负相关。值得注意的是，这一统计规律由具有不相关系统发育起源的凝集素所界定，表明独立的界面结构是通过共同的优化路径进化而来的。将凝集素-碳水化合物界面的结构特性与一组32个蛋白质同二聚体的特性进行了比较。总体而言，分析表明凝集素-碳水化合物界面和蛋白质-蛋白质界面的立体化学基础彼此有很大差异。与蛋白质-蛋白质复合物相比，凝集素-碳水化合物界面具有更高的堆积效率、更好的氢键立体化学和更高的相互作用协同性。与蛋白质-蛋白质异源复合物的比较也得出了类似的结论。我们提出，这种更好的相互作用几何结构的能量后果是每单位埋藏面积的自由能下降幅度更大，这一特征使凝集素和碳水化合物能够以相对较小的界面面积形成稳定的复合物。这些观察结果支持了一种新出现的观点，即立体化学指标不同的系统可能依赖于不同的能量基础。
