Tschampel Sarah M, Woods Robert J
Complex Carbohydrate Research Center, University of Georgia, 220 Riverbend Road, Athens, Georgia 30602.
J Phys Chem A. 2003 Oct 30;107(43):9175-81. doi: 10.1021/jp035027u.
Water-mediated interactions play a key role in carbohydrate-lectin binding, where the interactions involve a conserved water that is separated from the bulk solvent and present a bridge between the side chains of the protein and the carbohydrate ligand. To apply quantum mechanical methods to examine the role of conserved waters, we present an analysis in which the relevant carbohydrate atoms are modeled by methanol, and in which the protein is replaced by a limited number of amino acid side chains. Clusters containing a conserved water and a representative amino acid fragment were also examined to determine the influence of amino acid side chains on interaction energies. To quantify the differential binding energies of methanol versus water, quantum mechanical calculations were performed at the B3LYP/6-311++G(3df,3pd)//B3LYP/6-31+G(d) level in which either a methanol molecule was bound to the conserved water (liganded state) or in which a water molecule replaces the methanol (unliganded state). Not surprisingly, the binding of a water to clusters containing charged amino acid side chains was more favorable by 1.55 to 7.23 kcal/mol than that for the binding of a water to the corresponding pure water clusters. In contrast, the binding energy of water to clusters containing polar-uncharged amino acid side chains ranged from 4.35 kcal/mol less favorable to 4.72 kcal/mol more favorable than for binding to the analogous pure water clusters. The overall trend for the binding of methanol versus water, in any of the clusters, favored methanol by an average value of 1.05 kcal/mol. To extend these studies to a complex between a protein (Concanavalin A) and its carbohydrate ligand, a cluster was examined that contained the side chains of three key amino acids, namely asparagine, aspartate, and arginine, as well as a key water molecule, arranged as in the X-ray diffraction structure of Con A. Again, using methanol as a model for the endogenous carbohydrate ligand, energies of -5.94 kcal/mol and -5.70 kcal/mol were obtained for the binding of methanol and water, respectively, to the Con A-water cluster. The extent to which cooperativity enhanced the binding energies has been quantified in terms of nonadditive three-body contributions. In general, the binding of water or methanol to neutral dimers formed cooperative clusters; in contrast, the cooperativity in charged clusters depended on the overall geometry as well as the charge.
水介导的相互作用在碳水化合物-凝集素结合中起着关键作用，其中相互作用涉及一个与大量溶剂分离的保守水分子，它在蛋白质侧链和碳水化合物配体之间形成桥梁。为了应用量子力学方法来研究保守水分子的作用，我们进行了一项分析，其中相关的碳水化合物原子用甲醇模拟，蛋白质用有限数量的氨基酸侧链代替。还研究了含有保守水分子和代表性氨基酸片段的簇，以确定氨基酸侧链对相互作用能的影响。为了量化甲醇与水的差异结合能，在B3LYP/6-311++G(3df,3pd)//B3LYP/6-31+G(d)水平上进行了量子力学计算，其中甲醇分子与保守水分子结合（配体状态）或水分子取代甲醇（未配体状态）。不出所料，水与含有带电氨基酸侧链的簇的结合比与相应的纯水簇的结合更有利，相差1.55至7.23千卡/摩尔。相比之下，水与含有极性不带电氨基酸侧链的簇的结合能比与类似的纯水簇的结合能相差范围为不利4.35千卡/摩尔至有利4.72千卡/摩尔。在任何簇中，甲醇与水结合的总体趋势是甲醇更有利，平均值为1.05千卡/摩尔。为了将这些研究扩展到蛋白质（伴刀豆球蛋白A）与其碳水化合物配体之间的复合物，研究了一个簇，其中包含三个关键氨基酸（即天冬酰胺、天冬氨酸和精氨酸）的侧链以及一个关键水分子，其排列方式与伴刀豆球蛋白A的X射线衍射结构相同。同样，使用甲醇作为内源性碳水化合物配体的模型，甲醇和水与伴刀豆球蛋白A-水簇的结合能分别为-5.94千卡/摩尔和-5.70千卡/摩尔。协同作用增强结合能的程度已根据非加性三体贡献进行了量化。一般来说，水或甲醇与中性二聚体的结合形成了协同簇；相比之下，带电簇中的协同作用取决于整体几何形状以及电荷。
