Solvent Networks Tune Thermodynamics of Oligosaccharide Complex Formation in an Extended Protein Binding Site.
Solvent Networks Tune Thermodynamics of Oligosaccharide Complex Formation in an Extended Protein Binding Site.
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DOI：
10.1021/jacs.8b03719
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发表时间：
2018-07
影响因子：
15
通讯作者：
Sonja Kunstmann;U. Gohlke;N. Broeker;Y. Roske;U. Heinemann;M. Santer;S. Barbirz
中科院分区：
文献类型：
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作者：
Sonja Kunstmann;U. Gohlke;N. Broeker;Y. Roske;U. Heinemann;M. Santer;S. Barbirz
在分子水平上，蛋白质 - 聚糖结合的原理仍未被充分理解。将聚糖识别的亲和力和特异性与结构相关联的尝试，受到实验研究普遍缺乏模型系统以及难以描述溶剂影响的阻碍。我们通过实验和计算研究了大肠杆菌噬菌体HK620的尾刺蛋白（TSP）中溶剂在蛋白质 - 聚糖复合物形成过程中的能量贡献。HK620TSP是一个230 kDa的天然右手平行β - 螺旋三聚体，它为细菌细胞表面的O - 抗原多糖提供了延伸的、刚性的结合位点。一组高亲和力突变体对六糖或五糖O - 抗原片段具有非常相似的亲和力，尽管六糖在一个封闭的蛋白质表面腔中引入了一个额外的葡萄糖分支。不同的突变体具有显著不同的热力学结合特征；然而，晶体结构分析表明，在复合物形成时，寡糖或蛋白质的拓扑结构没有发生重大变化。这指向一种溶剂效应。使用基于迁移率的方法进行的分子动力学模拟揭示了一个分布在整个寡糖结合位点的扩展的溶剂位置网络。然而，自由能计算表明，葡萄糖结合腔内的一个小的水网络对热力学特征具有最显著的影响。从葡萄糖结合口袋中置换水所需的能量取决于入口处的氨基酸，这与在不同突变体中将葡萄糖引入口袋时发现的不同量的焓 - 熵补偿是一致的。以前对小分子药物的研究已经表明，少数几个活性水分子可以控制蛋白质复合物的形成。HK620TSP寡糖结合表明，类似的基本原理也适用于聚糖，即少数水分子可以在一个扩展的结合位点中主导热力学特征。
The principles of protein-glycan binding are still not well understood on a molecular level. Attempts to link affinity and specificity of glycan recognition to structure suffer from the general lack of model systems for experimental studies and the difficulty to describe the influence of solvent. We have experimentally and computationally addressed energetic contributions of solvent in protein-glycan complex formation in the tailspike protein (TSP) of E. coli bacteriophage HK620. HK620TSP is a 230 kDa native trimer of right-handed, parallel beta-helices that provide extended, rigid binding sites for bacterial cell surface O-antigen polysaccharides. A set of high-affinity mutants bound hexa- or pentasaccharide O-antigen fragments with very similar affinities even though hexasaccharides introduce an additional glucose branch into an occluded protein surface cavity. Remarkably different thermodynamic binding signatures were found for different mutants; however, crystal structure analyses indicated that no major oligosaccharide or protein topology changes had occurred upon complex formation. This pointed to a solvent effect. Molecular dynamics simulations using a mobility-based approach revealed an extended network of solvent positions distributed over the entire oligosaccharide binding site. However, free energy calculations showed that a small water network inside the glucose-binding cavity had the most notable influence on the thermodynamic signature. The energy needed to displace water from the glucose binding pocket depended on the amino acid at the entrance, in agreement with the different amounts of enthalpy-entropy compensation found for introducing glucose into the pocket in the different mutants. Studies with small molecule drugs have shown before that a few active water molecules can control protein complex formation. HK620TSP oligosaccharide binding shows that similar fundamental principles also apply for glycans, where a small number of water molecules can dominate the thermodynamic signature in an extended binding site.