Studies on Molecular Recognition Patterns between Sugars and Amino Acids by Use of the Data Obtained from Single Crystal X-Ray Analysis

低聚糖的结构研究和糖与蛋白质之间的识别模式研究对于了解糖的生物功能是非常重要的。在本研究中，我们对最具生物意义的低聚糖之一唾液酸乐^X进行了构象分析，并对X-射线分析确定的蛋白质结构中糖与氨基酸的相互作用模式进行了分析。1.唾液酸乐^X的构象分析：由于没有得到适合于衍射实验的糖链晶体，所以用分子力学方法研究了糖链的构象。初始模型是通过糖苷键对接组成单糖的X射线结构构建的，并通过分子力学对其进行了优化。采用了两种不同的对接方式，结果表明，对接方式对得到的稳定构象有显著影响。2.蛋白质中糖和氨基酸的相互作用模式分析利用X射线数据研究了所选择的单糖与蛋白质中氨基酸的相互作用模式。所有的X射线数据均来自美国布鲁克海文国家实验室编制的蛋白质数据库。考虑的单糖是N-乙酰氨基葡萄糖、阿拉伯糖、岩藻糖、半乳糖、葡萄糖、甘露糖、唾液酸和酵素。考虑了氢键、非键相互作用以及糖与芳环之间的相互作用。分析表明，蛋白质中的糖有一个特定的共同结合口袋。口袋由两层氨基酸组成。氨基酸参与氢键的内层主要由亲水性氨基酸组成。外层主要由疏水氨基酸组成。

Structural investigations of oligosaccharides and studies on recognition patterns between sugars and proteins are very essential to the understanding of biological functions sugars. In the present study we have undertaken the conformational analysis of one of the most biologically important oligosaccharides, sialyl Le^X, and the analysis of the interaction patterns between sugars and amino acids in protein structures which have been determined by X-ray analysis.1.Conformational analysis of sialy Le^X by molecular mechanicsSince suitable crystals of the sugar chain for diffraction experiments could not be obtained, the conformation of the sugar chain was investigated by molecular mechanics calculations. The initial models were constructed by docking X-ray structures of the component monosaccharides through glycosidic bonds and they were optimized by molecular mechanics. Two different docking modes were applied.It was shown that the docking mode influence the resultant stable conformations signficantly.2.Analysis of interaction patterns between sugars and amino acids in proteinsInteraction patterns between selected monosaccharides and amino acids in the proteins have been investigated by use of the X-ray data. All the X-ray data were taken from Protein Databank compiled at Brookhaven National Laboratory (USA). The monosaccharides which were taken into consideration are N-acetyl-glucosamine, arabinose, fucose, galactose, glucose, mannose, sialic acid, and zylose. Hydrogen bonds, non-bonded interactions, and interactions between sugars and aromatic rings were taken into account. The analysis showed that there is a specific common binding pocket for sugars in proteins. The pocket is consist of two layrs of amino acids. The inner layr in which amino acids participate in hydrogen bonds is made of mainly hydrophilic amino acids. The outer layr is chiefly consist of hydrophobic amino acids.