OLIGOSACCHARIDE CONFORMATIONS AND THEIR INTERACTIONS WITH PROTEINS

低聚糖构象及其与蛋白质的相互作用

• 批准号: 6101031
• 负责人: P K QASBA
• 金额: --
• 依托单位: DIVISION OF BASIC SCIENCES - NCI
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/6101031
• 关键词: aminosugar; binding proteins; computer simulation; conformation; enzyme substrate; glycolipids; glycoprotein structure; intermolecular interaction; lactalbumin; lectin; lysozyme; molecular dynamics; monosaccharides; oligosaccharides; protein structure function

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.

关于寡糖可以构象的知识 当免费或附着在糖蛋白或附上时访问 糖脂对于理解他们与他们的互动很重要 细胞凝集素和受体，以及糖苷酶和受体 糖基转移酶。在这些生物合成和处理过程中 碳水化合物，寡糖底物的构象 一个重要的角色。在糖蛋白中 寡糖可能进一步取决于蛋白质序列和 围绕糖基化位点的结构。因此，必须 辨别特定寡糖的所有可能构象 可以访问与了解糖有关的信息 诱导的蛋白质 - 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构象 N连接寡糖的偏好 - 高甘露糖，复杂和 杂化型寡糖也是糖受体 糖基转移酶的底物（1）。以下结论是 从这些MD模拟中得出：（i） 寡糖不能源自其二糖成分。 寡糖的添加/删除残留物可以带来 间间构象偏好的显着差异 糖苷扭转角。 （ii）N-连接的末端糖 寡糖可以与壳聚糖芯相互作用，从而影响 它们可用于酶促反应。 （iii）alpha-1,6-- 链接访问CHI的三种不同构象（180o，60o，-60o） 影响寡糖的整体形状。 （iv）变化 寡糖的整体形状不必仅带来 通过更改alpha-1,6-链接的CHI，还可以通过更改PHI和 psi同时保持C恒定。 （v）的构象分析 在蛋白质 - 碳水化合物晶体结构中发现的寡糖， 表明寡糖频率较低的构象 有时可能比高度访问的蛋白质分子更好地结合 通过提供更好的互补表面和形式来构象 与蛋白质的额外氢键。获得的信息 MD模拟也已被用来解释/合理化一些 生化实验观测。利用可用的 实验和计算数据，可能 MAN9GLCNAC2在ASN-生物合成期间将MAN9GLCNAC2处理到MAN5GLCNAC2 已经提出了连接的寡糖。自糖胺聚糖以来 蛋白聚糖的一部分碳水化合物，在宽阔的 生物功能的范围，了解其结构和 构象至关重要。我们执行了构象 这些分子的分析，特别是iduronate的构象 在硫酸真皮中环中的环，因为它的文献中的构象为 有争议的。我们的分析表明，α-l-idua单元 硫酸盐溶液主要存在于“略微扭曲” 1C4中 构象。这与观察到的X射线纤维重复一致 硫酸真皮的值，其中1C4构象的alpha-l-idua构象 已经考虑了单位。此信息至关重要，并且 为我们目前关于结合的建模研究提供了基础 肝素或硫酸乙酰肝素蛋白聚糖至碱性成纤维细胞生长 因子及其受体。