Comprehensive analysis of the N-glycan biosynthetic pathway using bioinformatics to generate UniCorn: A theoretical N-glycan structure database
Comprehensive analysis of the N-glycan biosynthetic pathway using bioinformatics to generate UniCorn: A theoretical N-glycan structure database
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DOI：
10.1016/j.carres.2016.05.012
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发表时间：
2016-08-05
影响因子：
3.1
通讯作者：
Campbell, Matthew P.
中科院分区：
文献类型：
--
作者：
Akune, Yukie;Lin, Chi-Hung;Campbell, Matthew P.
与蛋白质相连的聚糖结构由不同的单糖序列和连接方式组成，这些单糖序列和连接方式是由一系列糖基转移酶从前体核苷糖产生的。这些结构的数据库是解释分析数据和开发生物信息学工具的重要资源。然而，由于没有模板来预测哪些结构是可能的，人类聚糖结构数据库是不完整的，并且在很大程度上依赖于已发表的、经实验确定的聚糖结构数据的整理。在这项工作中，一个由45种人类糖基转移酶组成的文库被用于生成一个由15个或更少单糖残基组成的N -聚糖结构的理论数据库。酶的特异性来源于主要的在线数据库，包括京都基因与基因组百科全书（KEGG）聚糖数据库、功能糖组学联盟（CFG）、碳水化合物活性酶（CAZy）、糖基因数据库（GGDB）和BRENDA。基于已知的活性，超过110万个理论结构和470万个合成反应被生成并存储在我们名为UniCorn的数据库中。此外，我们分析了UniCorn中预测的聚糖结构与UniCarbKB（www.unicarbkb.org）中所含结构之间的差异，UniCarbKB是一个存储文献中报道的经实验描述的聚糖结构的数据库，并且证明了UniCorn可用于辅助确定不明确的结构，同时也可作为一个发现数据库。（C）2016爱思唯尔有限公司。保留所有权利。
Glycan structures attached to proteins are comprised of diverse monosaccharide sequences and linkages that are produced from precursor nucleotide-sugars by a series of glycosyltransferases. Databases of these structures are an essential resource for the interpretation of analytical data and the development of bioinformatics tools. However, with no template to predict what structures are possible the human glycan structure databases are incomplete and rely heavily on the curation of published, experimentally determined, glycan structure data. In this work, a library of 45 human glycosyltransferases was used to generate a theoretical database of N-glycan structures comprised of 15 or less monosaccharide residues. Enzyme specificities were sourced from major online databases including Kyoto Encyclopedia of Genes and Genomes (KEGG) Glycan, Consortium for Functional Glycomics (CFG), Carbohydrate-Active enZymes (CAZy), GlycoGene DataBase (GGDB) and BRENDA. Based on the known activities, more than 1.1 million theoretical structures and 4.7 million synthetic reactions were generated and stored in our database called UniCorn. Furthermore, we analyzed the differences between the predicted glycan structures in UniCorn and those contained in UniCarbKB (www.unicarbkb.org), a database which stores experimentally described glycan structures reported in the literature, and demonstrate that UniCorn can be used to aid in the assignment of ambiguous structures whilst also serving as a discovery database. (C) 2016 Elsevier Ltd. All rights reserved.