Samaei-Daryan Samaneh, Goliaei Bahram, Ebrahim-Habibi Azadeh
Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
J Mol Recognit. 2017 Sep;30(9). doi: 10.1002/jmr.2624. Epub 2017 Mar 15.
Structural properties of carbohydrate surface binding sites (SBSs) were investigated with computational methods. Eighty-five SBSs of 44 enzymes in 119 Protein Data Bank (PDB) files were collected as a dataset. On the basis of SBSs shape, they were divided into 3 categories: flat surfaces, clefts, and cavities (types A, B, and C, respectively). Ligand varieties showed the correlation between shape of SBSs and ligands size. To reduce cut-off differences in each SBSs with different ligand size, molecular docking were performed. Molecular docking results were used to refine SBSs classification and binding sites cut-off. Docking results predicted putative ligands positions and displayed dependence of the ligands binding mode to the structural type of SBSs. Physicochemical properties of SBSs were calculated for all docking results with YASARA Structure. The results showed that all SBSs are hydrophilic, while their charges could vary and depended to ligand size and defined cut-off. Surface binding sites type B had highest average values of solvent accessible surface area. Analysis of interactions showed that hydrophobic interactions occur more than hydrogen bonds, which is related to the presence of aromatic residues and carbohydrates interactions.
利用计算方法研究了碳水化合物表面结合位点（SBSs）的结构特性。从119个蛋白质数据库（PDB）文件中的44种酶的85个SBSs中收集作为数据集。根据SBSs的形状，它们被分为3类：平面、裂隙和空腔（分别为A、B和C型）。配体种类显示了SBSs形状与配体大小之间的相关性。为了减少不同配体大小的每个SBSs中的截止差异，进行了分子对接。分子对接结果用于完善SBSs分类和结合位点截止值。对接结果预测了假定配体的位置，并显示了配体结合模式对SBSs结构类型的依赖性。使用YASARA Structure对所有对接结果计算SBSs的物理化学性质。结果表明，所有SBSs都是亲水的，而它们的电荷可能会有所不同，并取决于配体大小和定义的截止值。B型表面结合位点具有最高的溶剂可及表面积平均值。相互作用分析表明，疏水相互作用比氢键更频繁发生，这与芳香族残基的存在和碳水化合物相互作用有关。
