利用分子动力学模拟对寡糖和多糖进行构象分析。

Conformational analysis of oligosaccharides and polysaccharides using molecular dynamics simulations.

作者信息

Frank Martin

机构信息

Biognos AB, Generatorsgatan 1, 41705, Göteborg, Sweden,

出版信息

Methods Mol Biol. 2015;1273:359-77. doi: 10.1007/978-1-4939-2343-4_22.

DOI:10.1007/978-1-4939-2343-4_22

PMID:25753720

Abstract

Complex carbohydrates usually have a large number of rotatable bonds and consequently a large number of theoretically possible conformations can be generated (combinatorial explosion). The application of systematic search methods for conformational analysis of carbohydrates is therefore limited to disaccharides and trisaccharides in a routine analysis. An alternative approach is to use Monte-Carlo methods or (high-temperature) molecular dynamics (MD) simulations to explore the conformational space of complex carbohydrates. This chapter describes how to use MD simulation data to perform a conformational analysis (conformational maps, hydrogen bonds) of oligosaccharides and how to build realistic 3D structures of large polysaccharides using Conformational Analysis Tools (CAT).

摘要

复合碳水化合物通常具有大量可旋转键，因此理论上可以产生大量可能的构象（组合爆炸）。因此，在常规分析中，用于碳水化合物构象分析的系统搜索方法仅限于二糖和三糖。另一种方法是使用蒙特卡罗方法或（高温）分子动力学（MD）模拟来探索复合碳水化合物的构象空间。本章描述了如何使用MD模拟数据对寡糖进行构象分析（构象图、氢键），以及如何使用构象分析工具（CAT）构建大型多糖的逼真三维结构。