Holland Lou, Pham Phuong Thao, Bagdonas Haroldas, Dialpuri Jordan S, Schofield Lucy C, Agirre Jon
York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK.
Protein Sci. 2025 Feb;34(2):e70025. doi: 10.1002/pro.70025.
Tryptophan mannosylation, the covalent addition of an α-ᴅ-mannose sugar to a tryptophan side chain, is a post-translational modification (PTM) that can affect protein stability, folding, and interactions. Compared to other forms of protein glycosylation, it is relatively uncommon but is affected by conformational anomalies and modeling errors similar to those seen in N- and O-glycans in the Protein Data Bank (PDB). In this work, we report methods for detecting, building, and improving mannose structures linked to tryptophans. These methods have been used to mine X-ray crystallographic and cryo-electron microscopy maps in the PDB looking for unmodeled mannosylation, resulting in a number of cases where the modification can be placed in the map with high confidence. Additionally, we address most conformational issues affecting this modification. Finally, the development of a structural template to recognize thrombospondin repeats (TSR) domains where tryptophan mannosylation occurs will allow for the mannosylation of candidate-predicted models, for example, those predicted with AlphaFold.
色氨酸甘露糖化是指在色氨酸侧链上共价添加一个α-D-甘露糖，它是一种翻译后修饰（PTM），能够影响蛋白质的稳定性、折叠和相互作用。与其他形式的蛋白质糖基化相比，它相对不常见，但会受到构象异常和建模错误的影响，类似于蛋白质数据库（PDB）中N-聚糖和O-聚糖所观察到的情况。在这项工作中，我们报告了检测、构建和改进与色氨酸相连的甘露糖结构的方法。这些方法已被用于挖掘PDB中的X射线晶体学和冷冻电子显微镜图谱，以寻找未建模的甘露糖化，从而在许多情况下能够将这种修饰高置信度地定位到图谱中。此外，我们解决了影响这种修饰的大多数构象问题。最后，开发一种结构模板来识别发生色氨酸甘露糖化的血小板反应蛋白重复序列（TSR）结构域，将能够对候选预测模型（例如用AlphaFold预测的模型）进行甘露糖化。
