Definition of the Acceptor Substrate Binding Specificity in Plant Xyloglucan Endotransglycosylases Using Computational Chemistry
Xyloglucan endotransglycosylases (XETs) play key roles in the remodelling and reconstruction of plant cell walls. These enzymes catalyse homo-transglycosylation reactions with xyloglucan-derived donor and acceptor substrates and hetero-transglycosylation reactions with a variety of structurally dive...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-10-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/19/11838 |
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| author | Barbora Stratilová Eva Stratilová Maria Hrmova Stanislav Kozmon |
| author_facet | Barbora Stratilová Eva Stratilová Maria Hrmova Stanislav Kozmon |
| author_sort | Barbora Stratilová |
| collection | DOAJ |
| description | Xyloglucan endotransglycosylases (XETs) play key roles in the remodelling and reconstruction of plant cell walls. These enzymes catalyse homo-transglycosylation reactions with xyloglucan-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 <i>Tropaeolum majus</i> (TmXET6.3) and specific <i>Populus tremula</i> x <i>tremuloides</i> (PttXET16A) XETs, using molecular docking and molecular dynamics (MD) simulations 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 linkages, 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 mannose 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 specific XETs and associate theoretical to experimental data. |
| first_indexed | 2024-03-09T21:37:42Z |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T21:37:42Z |
| publishDate | 2022-10-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-d3c491f8b14c49539a59953b6e6bacf22023-11-23T20:40:09ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-10-0123191183810.3390/ijms231911838Definition of the Acceptor Substrate Binding Specificity in Plant Xyloglucan Endotransglycosylases Using Computational ChemistryBarbora Stratilová0Eva Stratilová1Maria Hrmova2Stanislav Kozmon3Institute of Chemistry, Slovak Academy of Sciences, SK-84538 Bratislava, SlovakiaInstitute of Chemistry, Slovak Academy of Sciences, SK-84538 Bratislava, SlovakiaJiangsu Collaborative Innovation Centre for Regional Modern Agriculture and Environmental Protection, School of Life Science, Huaiyin Normal University, Huai’an 223300, ChinaInstitute of Chemistry, Slovak Academy of Sciences, SK-84538 Bratislava, SlovakiaXyloglucan endotransglycosylases (XETs) play key roles in the remodelling and reconstruction of plant cell walls. These enzymes catalyse homo-transglycosylation reactions with xyloglucan-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 <i>Tropaeolum majus</i> (TmXET6.3) and specific <i>Populus tremula</i> x <i>tremuloides</i> (PttXET16A) XETs, using molecular docking and molecular dynamics (MD) simulations 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 linkages, 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 mannose 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 specific XETs and associate theoretical to experimental data.https://www.mdpi.com/1422-0067/23/19/11838binding free energy calculationsglycoside hydrolase family 16homo- and hetero-transglycosylation reactionsmolecular dockingmolecular dynamics simulationsTmXET6.3 |
| spellingShingle | Barbora Stratilová Eva Stratilová Maria Hrmova Stanislav Kozmon Definition of the Acceptor Substrate Binding Specificity in Plant Xyloglucan Endotransglycosylases Using Computational Chemistry International Journal of Molecular Sciences binding free energy calculations glycoside hydrolase family 16 homo- and hetero-transglycosylation reactions molecular docking molecular dynamics simulations TmXET6.3 |
| title | Definition of the Acceptor Substrate Binding Specificity in Plant Xyloglucan Endotransglycosylases Using Computational Chemistry |
| title_full | Definition of the Acceptor Substrate Binding Specificity in Plant Xyloglucan Endotransglycosylases Using Computational Chemistry |
| title_fullStr | Definition of the Acceptor Substrate Binding Specificity in Plant Xyloglucan Endotransglycosylases Using Computational Chemistry |
| title_full_unstemmed | Definition of the Acceptor Substrate Binding Specificity in Plant Xyloglucan Endotransglycosylases Using Computational Chemistry |
| title_short | Definition of the Acceptor Substrate Binding Specificity in Plant Xyloglucan Endotransglycosylases Using Computational Chemistry |
| title_sort | definition of the acceptor substrate binding specificity in plant xyloglucan endotransglycosylases using computational chemistry |
| topic | binding free energy calculations glycoside hydrolase family 16 homo- and hetero-transglycosylation reactions molecular docking molecular dynamics simulations TmXET6.3 |
| url | https://www.mdpi.com/1422-0067/23/19/11838 |
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