Holyavka M G, Kondratyev M S, Samchenko A A, Kabanov A V, Komarov V M, Artyukhov V G
Voronezh State University, Universitetskaya Pl.1, Voronezh 394006, Russia.
Institute of Cell Biophysics of the Russian Academy of Sciences, Institutskaya St. 3, Pushchino 142290, Moscow region, Russia.
Comput Biol Med. 2016 Apr 1;71:198-204. doi: 10.1016/j.compbiomed.2016.02.015. Epub 2016 Feb 27.
Using computer modeling, virtual screening of high-affinity ligands for immobilization of inulinase - an enzyme that cleaves inulin and fructose-containing polymers to fructose - has been performed. The inulinase molecule from Aspergillus ficuum (pdb: 3SC7) taken from the database of protein structures was used as a protein model and the target for flexible docking. The set of ligands studied included simple sugars (activators, inhibitors, products of enzymatic catalysis), as well as high-molecular weight compounds (polycation and polyanion exchange resins, glycoproteins, phenylalanine-proline peptide, polylactate, and caffeine). Based on the comparative analysis of the values of the total energy and the localization of ligand binding sites, we made several assumptions concerning the mechanisms of interaction of the suggested matrices for the immobilization of enzyme molecules and the structural features of such complexes. It was also assumed that the candidates for immobilization agents meeting the industrial requirements may be glycoproteins, for which we propose an additional incorporation of cysteine residues into their structure, aimed to create disulfide «anchors» to the surface.
利用计算机建模，对用于固定菊粉酶（一种将菊粉和含果糖聚合物裂解为果糖的酶）的高亲和力配体进行了虚拟筛选。从蛋白质结构数据库中获取的来自泡盛曲霉的菊粉酶分子（蛋白质数据银行编号：3SC7）被用作蛋白质模型和柔性对接的目标。所研究的配体组包括单糖（激活剂、抑制剂、酶催化产物）以及高分子量化合物（聚阳离子和聚阴离子交换树脂、糖蛋白、苯丙氨酸 - 脯氨酸肽、聚乳酸和咖啡因）。基于对总能量值和配体结合位点定位的比较分析，我们对用于固定酶分子的建议基质的相互作用机制以及此类复合物的结构特征做出了若干假设。还假设符合工业要求的固定化剂候选物可能是糖蛋白，为此我们建议在其结构中额外引入半胱氨酸残基，旨在在表面形成二硫键“锚定”。
