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

利用单晶 X 射线分析获得的数据研究糖和氨基酸之间的分子识别模式

基本信息

批准号：
04453158
负责人：
HIRAYAMA Noriaki
金额：
$ 5.12万
依托单位：
Tokai University
依托单位国家：
日本
项目类别：
Grant-in-Aid for General Scientific Research (B)
财政年份：
1992
资助国家：
日本
起止时间：
1992 至 1994
项目状态：
已结题

项目摘要

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.

寡糖的结构研究以及糖和蛋白质之间的识别模式的研究对于理解糖的生物学功能非常重要。在本研究中，我们对生物学上最重要的寡糖之一唾液酸Le^X进行了构象分析，并通过X射线分析确定了蛋白质结构中糖与氨基酸之间的相互作用模式。1.通过分子力学对唾液酸Le^X进行构象分析由于无法获得适合衍射实验的糖链晶体，因此糖链的构象通过分子力学计算进行了研究。通过糖苷键对接单糖组分的X射线结构构建初始模型，并通过分子力学对其进行优化。应用了两种不同的对接模式。结果表明，对接模式对所得的稳定构象有显着影响。2.蛋白质中糖与氨基酸之间的相互作用模式分析利用X射线数据研究了选定的单糖与蛋白质中氨基酸之间的相互作用模式。所有 X 射线数据均取自布鲁克海文国家实验室（美国）编制的蛋白质数据库。考虑的单糖是N-乙酰基-葡糖胺、阿拉伯糖、岩藻糖、半乳糖、葡萄糖、甘露糖、唾液酸和木糖。考虑了氢键、非键相互作用以及糖和芳环之间的相互作用。分析表明，蛋白质中的糖存在一个特定的共同结合袋。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。外层主要由疏水性氨基酸组成。