Carbohydrates are key biological mediators of molecular recognition and signaling processes. In this case study, we explore the ability of absolute binding free energy (ABFE) calculations to predict the affinities of a set of five related carbohydrate ligands for the lectin protein, concanavalin A, ranging from 27-atom monosaccharides to a 120-atom complex-type N-linked glycan core pentasaccharide. ABFE calculations quantitatively rank and estimate the affinity of the ligands in relation to microcalorimetry, with a mean signed error in the binding free energy of −0.63 ± 0.04 kcal/mol. Consequently, the diminished binding efficiencies of the larger carbohydrate ligands are closely reproduced: the ligand efficiency values from isothermal titration calorimetry for the glycan core pentasaccharide and its constituent trisaccharide and monosaccharide compounds are respectively −0.14, −0.22, and −0.41 kcal/mol per heavy atom. ABFE calculations predict these ligand efficiencies to be −0.14 ± 0.02, −0.24 ± 0.03, and −0.46 ± 0.06 kcal/mol per heavy atom, respectively. Consequently, the ABFE method correctly identifies the high affinity of the key anchoring mannose residue and the negligible contribution to binding of both β-GlcNAc arms of the pentasaccharide. While challenges remain in sampling the conformation and interactions of these polar, flexible, and weakly bound ligands, we nevertheless find that the ABFE method performs well for this lectin system. The approach shows promise as a quantitative tool for predicting and deconvoluting carbohydrate–protein interactions, with potential application to design of therapeutics, vaccines, and diagnostics.

中文翻译：

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使用绝对结合自由能计算法分析伴刀豆球蛋白 A 的游离寡糖识别


碳水化合物是分子识别和信号传导过程的关键生物介质。在本案例研究中，我们探讨了绝对结合自由能 （ABFE） 计算的能力，以预测凝集素蛋白伴刀豆球蛋白 A 的一组五个相关碳水化合物配体的亲和力，范围从 27 原子单糖到 120 原子复合物型 N-连接聚糖核心五糖。ABFE 计算定量排序并估计与微量热法相关的配体亲和力，结合自由能的平均符号误差为 -0.63 ± 0.04 kcal/mol。因此，较大碳水化合物配体的结合效率降低是紧密再现的：等温滴定量热法对聚糖核心五糖及其组成三糖和单糖化合物的配体效率值分别为-0.14、-0.22和-0.41 kcal/mol/重原子。ABFE 计算预测这些配体效率分别为 -0.14 ± 0.02、-0.24 ± 0.03 和 -0.46 ± 0.06 kcal/mol。因此，ABFE 方法正确识别了关键锚定甘露糖残基的高亲和力和对五糖两个 β-GlcNAc 臂结合的贡献可以忽略不计。虽然在对这些极性、柔性和弱结合配体的构象和相互作用进行采样方面仍然存在挑战，但我们发现 ABFE 方法对这种凝集素系统表现良好。该方法有望作为预测和解复杂碳水化合物-蛋白质相互作用的定量工具，并可能应用于治疗、疫苗和诊断的设计。