title: In silico design of high-affinity ligands for the immobilization of inulinase.
abstract: 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.
authors.affiliation: Voronezh State University, Universitetskaya Pl.1, Voronezh 394006, Russia. Electronic address: marinaholyavka@yahoo.com.
authors.forename: M G
authors.initials: MG
authors.lastname: Holyavka
authors.affiliation: Institute of Cell Biophysics of the Russian Academy of Sciences, Institutskaya St. 3, Pushchino 142290, Moscow region, Russia. Electronic address: ma-ko@bk.ru.
authors.forename: M S
authors.initials: MS
authors.lastname: Kondratyev
authors.affiliation: Institute of Cell Biophysics of the Russian Academy of Sciences, Institutskaya St. 3, Pushchino 142290, Moscow region, Russia. Electronic address: sam4enkoaa@mail.ru.
authors.forename: A A
authors.initials: AA
authors.lastname: Samchenko
authors.affiliation: Institute of Cell Biophysics of the Russian Academy of Sciences, Institutskaya St. 3, Pushchino 142290, Moscow region, Russia. Electronic address: kabanov@mail.ru.
authors.forename: A V
authors.initials: AV
authors.lastname: Kabanov
authors.affiliation: Institute of Cell Biophysics of the Russian Academy of Sciences, Institutskaya St. 3, Pushchino 142290, Moscow region, Russia. Electronic address: komarov@icb.psn.ru.
authors.forename: V M
authors.initials: VM
authors.lastname: Komarov
authors.affiliation: Voronezh State University, Universitetskaya Pl.1, Voronezh 394006, Russia. Electronic address: artyukhov@bio.vsu.ru.
authors.forename: V G
authors.initials: VG
authors.lastname: Artyukhov
mesh_terms: D001230:Aspergillus / Q000201:enzymology*; D001665:Binding Sites; D003198:Computer Simulation; D005656:Fungal Proteins / Q000737:chemistry*; D006026:Glycoside Hydrolases / Q000737:chemistry*; D062105:Molecular Docking Simulation
chemical_list: D005656:Fungal Proteins; D006026:Glycoside Hydrolases; C023086:inulinase
keywords: Computer modeling; Docking; Immobilization; Inulinase; Ligand