Current Status of Carbohydrates Information in the Protein Data Bank
Current Status of Carbohydrates Information in the Protein Data Bank
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DOI：
10.1021/acs.jcim.9b00874
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发表时间：
2020-02-01
影响因子：
5.6
通讯作者：
Verli, Hugo
中科院分区：
文献类型：
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作者：
de Meirelles, Joao L.;Nepomuceno, Felipe C.;Verli, Hugo
碳水化合物因其物理化学、生物学、功能和治疗特性而众所周知。不幸的是，它们的化学性质对这些现象的结构解析提出了严峻的挑战，不仅削弱了我们对碳水化合物的理解，而且也削弱了基于这些分子的新生物技术和治疗应用的发展。近年来，主要从X射线晶体学获得的结构信息的数量和质量都在逐步增加。在这种情况下，目前的工作提出了一个全球性的分析碳水化合物的信息，在蛋白质数据库（PDB）。从高质量的结构，很明显，大部分的数据是高度集中在几组残基类型，其单糖形式，并通过一个小的多样性的糖苷键连接。这些连接的几何形状可以主要与连接的类型，而不是残基，而起皱失真的水平进行了表征，量化，并位于一个伪旋转平衡景观，不仅本地最小值，而且过渡状态。这些定性和定量分析提供了PDB中碳水化合物结构内容的全局图像，可能支持在原子水平上构建碳水化合物相关生物现象的新模型，包括力场参数的新发展。
Carbohydrates are well known for their physicochemical, biological, functional, and therapeutic characteristics. Unfortunately, their chemical nature imposes severe challenges for the structural elucidation of these phenomena, impairing not only the depth of our understanding of carbohydrates but also the development of new biotechnological and therapeutic applications based on these molecules. In the recent past, the amount of structural information, obtained mainly from X-ray crystallography, has increased progressively, as well as its quality. In this context, the current work presents a global analysis of the carbohydrate information available in the Protein Data Bank (PDB). From high quality structures, it is clear that most of the data are highly concentrated on a few sets of residue types, on their monosaccharidic forms, and connected by a small diversity of glycosidic linkages. The geometries of these linkages can be mostly associated with the types of linkages instead of residues, while the level of puckering distortion was characterized, quantified, and located in a pseudorotational equilibrium landscape, not only to local minima but also to transitional states. These qualitative and quantitative analyses offer a global picture of the carbohydrate structural content in the PDB, potentially supporting the building of new models for carbohydrate-related biological phenomena at the atomistic level, including new developments on force field parameters.