Definition of the Acceptor Substrate Binding Specificity in Plant Xyloglucan Endotransglycosylases Using Computational Chemistry

• Published in: International journal of molecular sciences 2022-10, Vol.23 (19), p.11838
• Main Authors: Stratilová, Barbora, Stratilová, Eva, Hrmova, Maria, Kozmon, Stanislav
• Format: Article
• Language: English
• Subjects: Binding; binding free energy calculations; Binding sites; Biocatalysts; Carbohydrates; Cell walls; Cellulose; Computational chemistry; Computer applications; Efficiency; Enzymes; Free energy; Glucans; glycoside hydrolase family 16; homo- and hetero-transglycosylation reactions; Linkages; Mannose; Mass spectrometry; Molecular docking; Molecular dynamics; molecular dynamics simulations; Polysaccharides; Scientific imaging; TmXET6.3; Xyloglucan; β-Glucan
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms231911838

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 Tropaeolum majus (TmXET6.3) and specific Populus tremula x tremuloides (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.