Strategies for carbohydrate model building, refinement and validation.
Strategies for carbohydrate model building, refinement and validation.
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DOI：
10.1107/s2059798316016910
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发表时间：
2017-02-01
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影响因子：
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通讯作者：
Agirre J
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作者：
Agirre J
本文讨论了结构生物学家在处理碳水化合物时可能面临的许多典型困难，重点是在X射线晶体学和低温电子显微镜预计将在未来十年重叠的分辨率范围内解决问题。糖是生物分子中最复杂的立体化学家族，对任何试图理解其命名，反应或分支结构的人来说都是巨大的挑战。目前的晶体学程序提供了一个抽象层，允许不专业的结构生物学家从头开始或几乎不需要人工干预就可以自动构建完整的蛋白质或核酸模型组件。然而，对于糖来说，这仍然不是普遍正确的。在过去，对碳水化合物特定构建和验证工具的需求已经被强调了很多次，同时引入了新一代的实验方法，这些方法在过去十年中一直在增加蛋白质-糖复合物和糖蛋白的生产。虽然已经取得了一些初步的进展，以满足这些需求，正确建模和精制碳水化合物仍然是一个挑战。本文将解决结构生物学家在处理碳水化合物时可能面临的许多典型困难，重点是在X射线晶体学和低温电子显微镜预计将在未来十年重叠的分辨率范围内解决问题。
This article addresses many of the typical difficulties that a structural biologist may face when dealing with carbohydrates, with an emphasis on problem solving in the resolution range where X-ray crystallography and cryo-electron microscopy are expected to overlap in the next decade. Sugars are the most stereochemically intricate family of biomolecules and present substantial challenges to anyone trying to understand their nomenclature, reactions or branched structures. Current crystallographic programs provide an abstraction layer allowing inexpert structural biologists to build complete protein or nucleic acid model components automatically either from scratch or with little manual intervention. This is, however, still not generally true for sugars. The need for carbohydrate-specific building and validation tools has been highlighted a number of times in the past, concomitantly with the introduction of a new generation of experimental methods that have been ramping up the production of protein–sugar complexes and glycoproteins for the past decade. While some incipient advances have been made to address these demands, correctly modelling and refining carbohydrates remains a challenge. This article will address many of the typical difficulties that a structural biologist may face when dealing with carbohydrates, with an emphasis on problem solving in the resolution range where X-ray crystallography and cryo-electron microscopy are expected to overlap in the next decade.