通过GlyVicinity对碳水化合物残基附近的氨基酸进行统计分析。

Statistical analysis of amino acids in the vicinity of carbohydrate residues performed by GlyVicinity.

作者信息

Rojas-Macias Miguel A, Lütteke Thomas

机构信息

Institute of Veterinary Physiology and Biochemistry, Justus-Liebig-University Giessen, Frankfurter Str. 100, Giessen, 35392, Germany,

出版信息

Methods Mol Biol. 2015;1273:215-26. doi: 10.1007/978-1-4939-2343-4_16.

DOI:10.1007/978-1-4939-2343-4_16

PMID:25753714

Abstract

Protein-carbohydrate interactions are involved in various essential biological events. 3D structural data from the Protein Data Bank (PDB) can help to understand the molecular basis of the specificity of carbohydrate recognition by proteins. Such interactions can be analyzed statistically using GlyVicinity. This chapter exemplifies the usage of this tool to find information on the frequency of the occurrence of specific amino acids in the vicinity of individual carbohydrate residues and to analyze the type of interacting atoms and their spatial distribution around the glycans.

摘要

蛋白质与碳水化合物的相互作用参与了各种重要的生物学事件。来自蛋白质数据库（PDB）的三维结构数据有助于理解蛋白质识别碳水化合物特异性的分子基础。这种相互作用可以使用GlyVicinity进行统计分析。本章举例说明了该工具的用法，以查找有关单个碳水化合物残基附近特定氨基酸出现频率的信息，并分析相互作用原子的类型及其在聚糖周围的空间分布。