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https://hdl.handle.net/2440/136652
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Type: | Journal article |
Title: | Definition of the acceptor substrate binding specificity in plant xyloglucan endotransglycosylases using computational chemistry |
Author: | Stratilová, B. Stratilová, E. Hrmova, M. Kozmon, S. |
Citation: | International Journal of Molecular Sciences, 2022; 23(19):11838-1-11838-26 |
Publisher: | MDPI AG |
Issue Date: | 2022 |
ISSN: | 1422-0067 1422-0067 |
Statement of Responsibility: | Barbora Stratilová, Eva Stratilová, Maria Hrmova and Stanislav Kozmon |
Abstract: | Xyloglucan endotransglycosylases (XETs) play key roles in the remodelling and reconstruction of plant cell walls. These enzymes catalyse homo-transglycosylation reactions with xyloglu-can-derived donor and acceptor substrates and hetero-transglycosylation reactions with a variety of structurally diverse polysaccharides. In this work, we describe the basis of acceptor substrate binding specificity in non-specific Tropaeolum majus (TmXET6.3) and specific Populus tremula x tremuloides (PttXET16A) XETs, using molecular docking and molecular dynamics (MD) simula-tions combined with binding free energy calculations. The data indicate that the enzyme-donor (xyloglucan heptaoligosaccharide or XG-OS7)/acceptor complexes with the linear acceptors, where a backbone consisted of glucose (Glc) moieties linked via (1,4)- or (1,3)-β-glycosidic linkag-es, were bound stably in the active sites of TmXET6.3 and PttXET16A. Conversely, the acceptors with the (1,6)-β-linked Glc moieties were bound stably in TmXET6.3 but not in PttXET16A. When in the (1,4)-β-linked Glc containing acceptors, the saccharide moieties were replaced with man-nose or xylose, they bound stably in TmXET6.3 but lacked stability in PttXET16A. MD simulations of the XET-donor/acceptor complexes with acceptors derived from (1,4;1,3)-β-glucans highlighted the importance of (1,3)-β-glycosidic linkages and side chain positions in the acceptor substrates. Our findings explain the differences in acceptor binding specificity between non-specific and spe-cific XETs and associate theoretical to experimental data. |
Keywords: | binding free energy calculations; glycoside hydrolase family 16; homo- and hetero-transglycosylation reactions; molecular docking; molecular dynamics simulations; TmXET6.3; PttXET16A |
Description: | Published: 5 October 2022 |
Rights: | © 2022 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https:// creativecommons.org/licenses/by/ 4.0/). |
DOI: | 10.3390/ijms231911838 |
Grant ID: | http://purl.org/au-research/grants/arc/DP120100900 |
Published version: | https://www.mdpi.com/1422-0067/23/19/11838 |
Appears in Collections: | Agriculture, Food and Wine publications |
Files in This Item:
File | Description | Size | Format | |
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hdl_136652.pdf | Published version | 9.98 MB | Adobe PDF | View/Open |
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