Molecular docking and dynamics of a dextranase derived from Penicillium cyclopium CICC-4022.

Autor: Zhang Y; Guangxi Key Laboratory of Polysaccharide Materials and Modification, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, Guangxi, PR China., Zhang D; Guangxi Key Laboratory of Polysaccharide Materials and Modification, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, Guangxi, PR China., Li M; Guangxi Key Laboratory of Polysaccharide Materials and Modification, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, Guangxi, PR China; Key Laboratory of Chemical and Biological Transforming Process of Guangxi Higher Education Institutes, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, Guangxi, PR China. Electronic address: meili@gxun.edu.cn., Qin Q; Guangxi Key Laboratory of Polysaccharide Materials and Modification, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, Guangxi, PR China; Key Laboratory of Chemical and Biological Transforming Process of Guangxi Higher Education Institutes, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, Guangxi, PR China., Jin Y; Guangxi Key Laboratory of Polysaccharide Materials and Modification, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, Guangxi, PR China., Fang Y; Guangxi Key Laboratory of Polysaccharide Materials and Modification, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, Guangxi, PR China., Sun G; Guangxi Key Laboratory of Polysaccharide Materials and Modification, School of Chemistry and Chemical Engineering, Guangxi Minzu University, Nanning 530006, Guangxi, PR China.
Jazyk: angličtina
Zdroj: International journal of biological macromolecules [Int J Biol Macromol] 2023 Dec 31; Vol. 253 (Pt 2), pp. 126493. Date of Electronic Publication: 2023 Aug 28.
DOI: 10.1016/j.ijbiomac.2023.126493
Abstrakt: This study aimed to investigate the recognition mechanism of dextranase (PC-Edex) produced by Penicillium cyclopium CICC-4022 on dextran. Whole genome information of P. cyclopium CICC-4022 was obtained through genome sequencing technology. The coding information of PC-Edex was determined based on the annotation of the protein-coding genes using protein databases. The three-dimensional structure of PC-Edex was obtained via homology modelling. The active site and binding free energy between PC-Edex and dextran were calculated by molecular docking and molecular dynamics techniques. The results showed that the total sequence length and GC content of P. cyclopium CICC-4022 were 29,710,801 bp and 47.02 %, respectively. The annotation of protein-encoding genes showed that P. cyclopium CICC-4022 is highly active and has many carbohydrate transport and metabolic functions, and most of its proteases are glycolytic anhydrases. Furthermore, the gene encoding PC-Edex was successfully annotated. Molecular dynamics simulations indicated that van der Waals interaction was the main driving force of interaction. Residues Ile114, Asp115, Tyr332, Lys344, and Gln403 significantly promoted the binding between dextran and PC-Edex. In summary, this study explored the active site catalyzed by PC-Edex based on the binding pattern of PC-Edex and dextran. Therefore, this study provides genomic information on dextranase and data supporting the rational modification and enhancement of PC-Edex.
Competing Interests: Declaration of competing interest No
(Copyright © 2023 Elsevier B.V. All rights reserved.)
Databáze: MEDLINE
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