In silico design of high-affinity ligands for the immobilization of inulinase.

Autor: Holyavka MG; Voronezh State University, Universitetskaya Pl.1, Voronezh 394006, Russia. Electronic address: marinaholyavka@yahoo.com., Kondratyev MS; Institute of Cell Biophysics of the Russian Academy of Sciences, Institutskaya St. 3, Pushchino 142290, Moscow region, Russia. Electronic address: ma-ko@bk.ru., Samchenko AA; Institute of Cell Biophysics of the Russian Academy of Sciences, Institutskaya St. 3, Pushchino 142290, Moscow region, Russia. Electronic address: sam4enkoaa@mail.ru., Kabanov AV; Institute of Cell Biophysics of the Russian Academy of Sciences, Institutskaya St. 3, Pushchino 142290, Moscow region, Russia. Electronic address: kabanov@mail.ru., Komarov VM; Institute of Cell Biophysics of the Russian Academy of Sciences, Institutskaya St. 3, Pushchino 142290, Moscow region, Russia. Electronic address: komarov@icb.psn.ru., Artyukhov VG; Voronezh State University, Universitetskaya Pl.1, Voronezh 394006, Russia. Electronic address: artyukhov@bio.vsu.ru.
Jazyk: angličtina
Zdroj: Computers in biology and medicine [Comput Biol Med] 2016 Apr 01; Vol. 71, pp. 198-204. Date of Electronic Publication: 2016 Feb 27.
DOI: 10.1016/j.compbiomed.2016.02.015
Abstrakt: 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.
(Copyright © 2016 Elsevier Ltd. All rights reserved.)
Databáze: MEDLINE
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