Protein–carbohydrate interactions underlie essential biological processes. Elucidating the mechanism of protein–carbohydrate recognition is a prerequisite for modeling and optimizing protein–carbohydrate interactions, which will help in discovery of carbohydrate-derived therapeutics. In this work, we present a survey of a curated database consisting of 6,402 protein–carbohydrate complexes in the Protein Data Bank (PDB). We performed an all-against-all comparison of a subset of nonredundant binding sites, and the result indicates that the interaction pattern similarity is not completely relevant to the binding site structural similarity. Investigation of both binding site and ligand promiscuities reveals that the geometry of chemical feature points is more important than local backbone structure in determining protein–carbohydrate interactions. A further analysis on the frequency and geometry of atomic interactions shows that carbohydrate functional groups are not equally involved in binding interactions. Finally, we discuss the usefulness of protein–carbohydrate complexes in the PDB with acknowledgement that the carbohydrates in many structures are incomplete.

中文翻译：

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蛋白质数据库中蛋白质-碳水化合物相互作用的系统分析

蛋白质-碳水化合物相互作用是基本生物过程的基础。阐明蛋白质-碳水化合物识别的机制是建模和优化蛋白质-碳水化合物相互作用的先决条件，这将有助于发现碳水化合物衍生的治疗方法。在这项工作中，我们对由蛋白质数据库 (PDB) 中的 6,402 个蛋白质-碳水化合物复合物组成的精选数据库进行了调查。我们对非冗余结合位点子集进行了全面比较，结果表明相互作用模式相似性与结合位点结构相似性并不完全相关。结合位点和配体混杂的研究表明，化学特征点的几何形状在确定蛋白质-碳水化合物相互作用方面比局部骨架结构更重要。对原子相互作用的频率和几何形状的进一步分析表明，碳水化合物官能团并不同样参与结合相互作用。最后，我们讨论了 PDB 中蛋白质-碳水化合物复合物的用途，并承认许多结构中的碳水化合物是不完整的。