Molecular dynamics simulations of a branched tetradecasaccharide substrate in the active site of a xyloglucan endo-transglycosylase
(English)In: Molecular Simulation, ISSN 0892-7022Article in journal (Refereed) In press
Molecular dynamics (MD) simulations of the tetradecasaccharide XXXGXXXG in complex with the hybrid aspen xyloglucan endo-transglycosylase PttXET16-34 have been performed and analyzed with respect to structure, dynamics, flexibility and ligand interactions. Notably, the charge state of the so-called “helper residue” Asp87, which lies between the catalytic nucleophile (Glu85) and general acid/base (Glu89) residues on the same beta strand, had a significant effect on PttXET16-34 active site structure. When Asp87 was deprotonated, electrostatic repulsion forced the nucleophile Glu85 away from C-1 of the sugar ring in subsite -1 and the electrophile Glu89 was also weakened due to the formation of a hydrogen bond to Asp87, whereas the protonation of Asp87 resulted in the formation of a hydrogen bond with the catalytic nucleophile and correct positioning of the catalytic machinery. The results suggest that catalysis in glycoside hydrolase family 16, and by extension clan GH-B enzymes, is optimal when the catalytic nucleophile is deprotonated for nucleophilic attack on the substrate, while the “helper residue” and general acid/base residue are both in their conjugate-acid forms to align the nucleophile and deliver a proton to the departing sugar, respectively.
Place, publisher, year, edition, pages
Taylor and Francis.
Xyloglucan, Xyloglucan binding protein, Complex, Molecular Dynamics simulation, Glycam force field
IdentifiersURN: urn:nbn:se:kth:diva-33574OAI: oai:DiVA.org:kth-33574DiVA: diva2:416143
QS 20112011-05-102011-05-102011-05-13Bibliographically approved