Suppr超能文献

α2→8连接的二唾液酸苷的分子动力学模拟:构象分析及其与蛋白质结合的意义

Molecular dynamics simulations of alpha2 --> 8-linked disialoside: conformational analysis and implications for binding to proteins.

作者信息

Vasudevan Sheeja V, Balaji Petety V

机构信息

Biotechnology Center, Indian Institute of Technology, Bombay, Powai, Mumbai 400 076, India.

出版信息

Biopolymers. 2002 Mar;63(3):168-80. doi: 10.1002/bip.10019.

Abstract

Computational methods have played a key role in elucidating the various three-dimensional structures of oligosaccharides. Such structural information, together with other experimental data, leads to a better understanding of the role of oligosaccharide in various biological processes. The disialoside Neu5Ac-alpha2-->8-Neu5Ac appears as the terminal glycan in glycoproteins and glycolipids, and is known to play an important role in various events of cellular communication. Neurotoxins such as botulinum and tetanus require Neu5Ac-alpha2 --> 8-Neu5Ac for infecting the host. Glycoconjugates containing this disialoside and the enzymes catalyzing their biosynthesis are also regulated during cell growth, development, and differentiation. Unlike other biologically relevant disaccharides that have only two linkage bonds, the alpha2-->8-linked disialoside has four: C2-O, O-C8', C8'-C7', and C7'-C6'. The present report describes the results from nine 1 ns MD simulations of alpha2-->8-linked disialoside (Neu5Ac-alpha2-->8-Neu5Ac); simulations were run using GROMOS96 by explicitly considering the solvent molecules. Conformations around the O-C8' bond are restricted to the +sc/+ap regions due to stereochemical reasons. In contrast, conformations around the C2-O and C8'-C7' bonds were found to be largely unrestricted and all the three staggered regions are accessible. The conformations around the C7'-C6' bond were found to be in either the -sc or the anti region. These results are in excellent agreement with the available NMR and potential energy calculation studies. Overall, the disaccharide is flexible and adopts mainly two ensembles of conformations differing in the conformation around the C7'-C6' bond. The flexibility associated with this disaccharide allows for better optimization of intermolecular contacts while binding to proteins and this may partially compensate for the loss of conformational entropy that may be incurred due to disaccharide's flexibility.

摘要

计算方法在阐明寡糖的各种三维结构方面发挥了关键作用。此类结构信息与其他实验数据一起,有助于更好地理解寡糖在各种生物过程中的作用。二唾液酸Neu5Ac-α2→8-Neu5Ac作为糖蛋白和糖脂中的末端聚糖出现,并且已知在细胞通讯的各种事件中起重要作用。肉毒杆菌和破伤风等神经毒素感染宿主需要Neu5Ac-α2→8-Neu5Ac。含有这种二唾液酸的糖缀合物及其催化生物合成的酶在细胞生长、发育和分化过程中也受到调控。与其他仅具有两个连接键的生物学相关二糖不同,α2→8连接的二唾液酸有四个键:C2-O、O-C8'、C8'-C7'和C7'-C6'。本报告描述了对α2→8连接的二唾液酸(Neu5Ac-α2→8-Neu5Ac)进行的九次1纳秒分子动力学模拟的结果;模拟使用GROMOS96通过明确考虑溶剂分子来运行。由于立体化学原因,O-C8'键周围的构象限于+sc/+ap区域。相比之下,发现C2-O和C8'-C7'键周围的构象在很大程度上不受限制,并且所有三个交错区域都是可及的。发现C7'-C6'键周围的构象处于-sc或反式区域。这些结果与现有的核磁共振和势能计算研究非常吻合。总体而言,二糖是灵活的,主要采用两种构象集合,它们在C7'-C6'键周围的构象不同。与这种二糖相关的灵活性允许在与蛋白质结合时更好地优化分子间接触,这可能部分补偿由于二糖的灵活性可能导致的构象熵损失。

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验