OLIGOSACCHARIDE CONFORMATIONS AND THEIR INTERACTIONS WITH PROTEINS

对低聚糖构象的认识(S) 当它是自由的或附着在糖蛋白或 糖脂对于理解它们与细胞之间的相互作用 细胞凝集素和受体，以及糖苷酶和 糖基转移酶。在这些物质的生物合成和加工过程中 碳水化合物，低聚糖底物的构象起作用 一个重要的角色。在糖蛋白中， 低聚糖可能进一步依赖于蛋白质序列和 糖基化位点周围的结构。因此，至关重要的是 辨别一种特定寡糖的所有可能构象 可以访问与了解糖相关的信息 诱导蛋白质相互作用和糖蛋白生物合成。我们 用分子动力学模拟研究了构象 N-连接低聚糖的偏好--高甘露糖、复合糖和 兼糖受体的杂交型低聚糖 糖基转移酶底物(1)。以下结论如下 从这些分子动力学模拟得出：(I)分子的首选构象 低聚糖不能从其二糖组分中分离出来。 低聚糖残基的添加/删除可导致 国际货币基金组织构象偏好的显著差异 糖苷扭转角。(Ii)N-连接的末端糖 低聚糖可以与壳二糖核心相互作用，从而影响 它们在酶反应中的可用性。(Iii)α-1，6- 分子链有三种不同的CHI构象(180度、60度、-60度) 这会影响低聚糖的整体形状。(四)变更 低聚糖的整体形状不需要仅仅 通过改变α-1，6-链的chi，也通过改变Phi和 在保持c恒定的情况下，PSI。(V)构象分析 在蛋白质-碳水化合物晶体结构中发现的低聚糖， 表明较少被访问的低聚糖构象 有时，与蛋白质分子的结合可能比高度访问的 通过提供更好的互补表面和形状来构象 额外的氢键与蛋白质结合。所获得的信息 来自MD模拟的数据也被用来解释/合理化一些 生化实验观察。利用现有的 实验和计算数据，一条可能的 天冬氨酸生物合成过程中Man9GlcNAc2到Man5GlcNAc2的加工 连接低聚糖已被提出。由于糖胺聚糖， 碳水化合物是蛋白多糖的一部分，在广泛的 一系列生物功能，了解它们的结构和 构象是最重要的。我们进行了构象分析 这些分子的分析，特别是艾杜糖酸酯的构象分析 环在硫酸皮肤素中，因为，它在文献中的构象是 有争议的。我们的分析表明，在皮肤病中α-L-IDUA单位 硫酸盐溶液主要以“轻微扭曲”的1C4形式存在 构象。这与观察到的x射线纤维重复是一致的。 硫酸皮肤素的值，其中α-L-IDUA的1C4构象 单位已被考虑在内。这些信息至关重要，而且 为我们目前关于结合的建模研究提供了基础 肝素或硫酸肝素蛋白多糖对碱性成纤维细胞生长的影响 因子及其受体。

The knowledge about the conformation(s) that an oligosaccharide can access when it is either free or attached to a glycoprotein or glycolipid is important both in understanding their interactions with cellular lectins and receptors, as well with glycosidases and glycosyltransferases. During the biosynthesis and processing of these carbohydrates, the conformation of the oligosaccharide substrate plays an important role. In glycoprotein the conformation of the oligosaccharide may further depend on the protein sequence and the structure surrounding the glycosylation site. Thus it is essential to discern all the possible conformations that a particular oligosaccharide can access, the information that is relevant for understanding sugar induced protein-protein interactions and glycoprotein biosynthesis. We have investigated by molecular dynamics simulations the conformational preferences of N-linked oligosaccharides - high mannose, complex and hybrid type oligosaccharides which are also the sugar acceptor substrates for glycosyltransferases (1). Following conclusions were drawn from these MD simulations: (i) The preferred conformation of the oligosaccharide can not be derived from its disaccharide constituents. Addition/deletion of residues to the oligosaccharide can bring about significant differences in the conformational preferences of inter glycosidic torsion angles. (ii) The terminal sugars of the N-linked oligosaccharides can interact with the chitobiose core thus influencing their availability for the enzymatic reactions. (iii) The alpha-1,6- linkages access three distinct conformations for chi (180o, 60o, - 60o) which affect the overall shape of the oligosaccharide. (iv) Changes in the overall shape of the oligosaccharide need not be brought about only by changing chi of the alpha-1,6-linkage, but also by changing phi and psi while keeping c constant. (v) The conformational analysis of oligosaccharides, found in the protein-carbohydrate crystal structures, show that the less frequently accessed conformation of oligosaccharide at times may bind better to a protein molecule than the highly accessed conformation by providing better complementary surface and form additional hydrogen bonds with the protein. The information obtained from MD simulation have also been used to explain/rationalize some of the biochemical experimental observations. Utilizing the available experimental and computational data, a pathway for the possible processing of Man9GlcNAc2 to Man5GlcNAc2 during the biosynthesis of Asn- linked oligosaccharides has been proposed. Since glycosaminoglycans, the carbohydrate part of proteoglycans, play an important role in a wide range of biological functions, understanding their structure and conformation is of utmost importance. We carried out the conformational analysis of these molecules, specifically the conformation of iduronate ring in dermatan sulfate, since, its conformation in the literature is controversial. Our analysis showed that alpha-L-IdUA unit in dermatan sulfate solution exists predominantly in a 'slightly distorted' 1C4 conformation. This is consistent with the observed x-ray fiber repeat value for dermatan sulfate where 1C4 conformation for the alpha-L-IdUA unit has been taken into consideration. This information is vital and provides the bases for our current modeling studies on the binding of heparin or heparan sulfate proteoglycans to basic fibroblast growth factor and to its receptor.