OLIGOSACCHARIDE CONFORMATIONS AND THEIR INTERACTIONS WITH PROTEINS

关于寡糖可以在分子中形成的构象的知识 当它是游离的或连接到糖蛋白时， 糖脂对于理解它们与 细胞凝集素和受体，以及糖苷酶， 糖基转移酶在生物合成和加工这些 碳水化合物，寡糖底物的构象发挥作用， 一个重要的角色在糖蛋白中， 寡糖的组成还可以取决于蛋白质序列，并且寡糖的组成还可以取决于蛋白质序列。 糖基化位点周围的结构。因此，必须 辨别出一种特殊的寡糖 可以访问与了解糖相关的信息 诱导蛋白质-蛋白质相互作用和糖蛋白生物合成。我们 通过分子动力学模拟研究了 N-连接寡糖的偏好-高甘露糖、复合物和 也是糖受体的杂合型寡糖 糖基转移酶的底物（1）。以下结论 从这些MD模拟中得出：（i） 寡糖不能从其二糖组分中衍生。 向寡糖中添加/缺失残基可导致 感兴趣的构象偏好的显著差异 糖苷扭转角(ii)N-连接的末端糖 寡糖可以与壳二糖核心相互作用， 它们对于酶促反应的可用性。(iii)阿尔法1，6- 连接获得三种不同的chi构象（180 o，60 o，-60 o） 其影响寡糖的整体形状。(iv)变化 寡糖的整体形状不需要仅仅 通过改变α-1，6-键的chi，还通过改变phi， psi，同时保持c恒定。(v)的构象分析 低聚糖，在蛋白质-碳水化合物晶体结构中发现， 表明低聚糖的不太常见的构象 有时可能比高度接近的蛋白质分子更好地结合蛋白质分子 通过提供更好的互补表面和形式 与蛋白质形成额外的氢键获得的信息 也被用来解释/合理化一些 生化实验观察。利用现有 实验和计算数据，可能的途径 在Asn的生物合成过程中Man 9 GlcNAc 2向Man 5GlcNAc 2的加工 已经提出了连接的寡糖。由于糖胺聚糖， 蛋白聚糖的碳水化合物部分，在广泛的 一系列的生物功能，了解它们的结构， 一致性是最重要的。我们进行了构象分析 分析这些分子，特别是艾杜糖醛酸的构象 环硫酸皮肤素，因为，它的构象在文献中是 争议我们的分析表明，皮肤病患者的α-L-IdUA单位 硫酸盐溶液主要存在于“轻微畸变”的1C 4中 构象这与观察到的X射线纤维重复一致 硫酸皮肤素的值，其中α-L-IdUA的1C 4构象 单位已考虑。这些信息至关重要， 提供了我们目前的结合模型研究的基础， 肝素或硫酸乙酰肝素蛋白聚糖对碱性成纤维细胞生长的抑制作用 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.