Oligosaccharide Interactions with Proteins

低聚糖与蛋白质的相互作用

• 批准号: 6559116
• 负责人: Pradman 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/6559116
• 关键词: binding proteins; chemical conjugate; chemical structure function; computer simulation; conformation; enzyme substrate complex; galactosyltransferases; glycoproteins; intermolecular interaction; model design /development; molecular dynamics; molecular site; oligosaccharides; physical model; protein metabolism; structural biology

The oligosaccharide moiety of glycoconjugates play important roles in several biological processes of a cell, including the folding and transport of glycoproteins across cellular compartments. The oligosaccharide moieties bind to cellular proteins with high specificity and modulate the homo- and hetro-dimerization of glycoproteins. Due to the conformational flexibility of oligosaccharides, the torsional angles of a disaccharide unit, especially around the a1-6-linkage, adjust in such a way that the side groups of the oligosaccharides orient themselves in a manner that promotes favorable interactions with the binding residues of the protein. Branched oligosaccharides cross-link proteins and generate infinite networks of protein-carbohydrate complexes, resulting in the modulation of various cell responses. Defective glycan synthesis has been shown to have serious pathological consequences and result in several human diseases. Defining the oligosaccharide binding site of b-1,4-Galactosyltransferase(Gal-T1) by docking of oligosaccharides into the binding site: We have continued to use molecular modeling methods to study the binding of oligosaccharides to proteins, in particular the binding of various oligosaccharide substrates to Gal-T1, the 3D-structure of which has recently been determined in our laboratory, either in complex with UDP-galactose and manganese metal ion, or in complex with a-lactalbumin and N-acetylglucosamine (see Project # Z01 BC 009304-05 LECB ). A limited number of oligosaccharides have been shown to be the preferred substrates for Gal-T1. Among the different GlcNAc containing disaccharides only a b-linked disaccharide such as GlcNAcb1,4-GlcNAc or GlcNAcb1,2-Man are preferred over a-linked disaccharides. In fact a-methyl-GlcNAc is less preferred compared to GlcNAc by itself. Also, oligosaccharides such as N-glycans are more preferred acceptor substrates than a (GlcNAc)4. Examination of the GlcNAc binding site in Gal-T1 from the Gal-T1-LA-GlcNAc crystal structure reveals an "open canal shaped" extended sugar binding site that lies behind the GlcNAc binding site, with an average width and length of 10 A and 16 A, respectively. This site is formed by the residues from three regions; residues 280 to 289, residues 319 to 325 and residues 359 to 368. LA binds to this region in the crystal structure of Gal-T1-LA complex, therefore it is expected to compete with the GlcNAc containing oligosaccharides such as chitobiose. In order to understand the size and nature of the oligosaccharide binding site in Gal-T1 we have carried out a modeling study using various disaccharides and N-glycans to dock into the binding site of Gal-T1 without energy minimization of either of the molecules during docking. These studies indicate that GlcNAc with an a-linked substitution such as a-benzyl-GlcNAc can not binding to Gal-T1 since its binding creates a severe steric contacts with the highly conserved residue Tyr286, while as GlcNAc with a -linked substitution such as b-benzyl-GlcNAc can bind without any steric contacts. Docking of a biantennary N-glycan with GlcNAcs at its reducing ends in the extended sugar binding site reveals that the acceptor binding site in Gal-T1 can accommodate a linear pentasaccharide all the way from the GlcNAc moiety to the aspargine linked GlcNAc. The binding site can also accommodate either the a-1-3 arm (GlcNAcb1-2Mana1-3Man b1-4GlcNAcb1-4GlcNAc-N) or a-1-6 arm (GlcNAcb1-2Mana1-6Manb1-4GlcNAcb 1-4GlcNAc-N) of the N-glycan without any steric hindrance. In humans Gal-T1 family members are responsible for the synthesis of Gal moiety in different oligosaccharides, indicating that these enzymes, although transfer Gal to GlcNAc, recognize the remaining oligosaccharide moieties to which GlcNAc is attached to. Therefore the oligosaccharide binding site defined on bovine Gal-T1 will be important in understanding the structure-function of human Gal-T family members. The sequence comparison of the GlcNAc binding site of the family members reveals a little or no sequence variation, while the extended oligosaccharide binding region shows significant variations, indicating that these enzymes may prefer different GlcNAc containing oligosaccharides as their preferred sugar acceptors. However, the exact nature of their preferences based on the homology modeling and their crystal structure determination is underway. 1) Qasba PK. Carbohydrate Polymers 41, 293-309, 2000. Z01 BC 10041-04

糖缀合物的寡糖部分在细胞的几个生物过程中发挥重要作用，包括糖蛋白的折叠和跨细胞区室的运输。寡糖部分以高特异性结合细胞蛋白，并调节糖蛋白的同源和异二聚化。由于低聚糖的构象灵活性，双糖单元的扭转角度，特别是在a1-6键周围，以这样一种方式调整，即低聚糖的侧基以一种促进与蛋白质结合残基有利相互作用的方式定位自己。支链低聚糖交联蛋白质并产生无限的蛋白质-碳水化合物网络，导致各种细胞反应的调节。聚糖合成缺陷已被证明具有严重的病理后果，并导致几种人类疾病。