Glycoblocks: a schematic three-dimensional representation for glycans and their interactions.
Glycoblocks: a schematic three-dimensional representation for glycans and their interactions.
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DOI：
10.1107/s2059798316013553
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发表时间：
2017-02-01
期刊：
影响因子：
--
通讯作者：
Agirre J
中科院分区：
文献类型：
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作者：
McNicholas S;Agirre J
随着结构糖科学最终获得普及，需要一种清晰的方式来描述聚糖及其在三维空间中的相互作用比以往任何时候都更加迫切。这里介绍了糖块表示法，它结合了简化的键合网络描述和熟悉的二维聚糖符号，将其带入三维空间。由共价连接的聚糖提供的近距离相互作用对于糖蛋白的正确折叠是必不可少的，并且在识别过程中也起着关键作用。因此，能够以清晰的方式可视化蛋白质-聚糖和聚糖-聚糖接触对于理解这些生物过程非常重要。在结构方面，糖基化糖通过氢键将蛋白质粘合在一起，而非共价结合的聚糖经常利用额外的堆积相互作用。找到这些多组分情况的清晰分子视图通常是不容易的;除了需要显示相互作用的蛋白质残基之外，聚糖可能包含许多支链糖，每个支链糖由十个以上的非H原子组成，并提供三个以上的潜在键合伙伴。随着结构糖科学最终获得普及，并稳步提高糖蛋白三维结构的沉积速率，需要一种清晰的方式来描述这些相互作用比以往任何时候都更加迫切。这里介绍了一种名为Glycoblocks的示意图，它将简化的键合网络描述（涵盖氢键和堆叠相互作用）与糖生物学社区使用的熟悉的二维聚糖符号相结合，并由CCP 4分子图形项目（CCP 4 mg）带入三维空间。
With structural glycoscience finally gaining popularity, the need for a clear way of depicting glycans and their interactions in three dimensions is more pressing than ever. Here the Glycoblocks representation is introduced, which combines a simplified bonding-network depiction with the familiar two-dimensional glycan notation brought into three-dimensions. The close-range interactions provided by covalently linked glycans are essential for the correct folding of glycoproteins and also play a pivotal role in recognition processes. Being able to visualise protein–glycan and glycan–glycan contacts in a clear way is thus of great importance for the understanding of these biological processes. In structural terms, glycosylation sugars glue the protein together via hydrogen bonds, whereas non-covalently bound glycans frequently harness additional stacking interactions. Finding an unobscured molecular view of these multipartite scenarios is usually far from trivial; in addition to the need to show the interacting protein residues, glycans may contain many branched sugars, each composed of more than ten non-H atoms and offering more than three potential bonding partners. With structural glycoscience finally gaining popularity and steadily increasing the deposition rate of three-dimensional structures of glycoproteins, the need for a clear way of depicting these interactions is more pressing than ever. Here a schematic representation, named Glycoblocks, is introduced which combines a simplified bonding-network depiction (covering hydrogen bonds and stacking interactions) with the familiar two-dimensional glycan notation used by the glycobiology community, brought into three dimensions by the CCP4 molecular graphics project (CCP4mg).