@article {11054,
	title = {Molecular dynamics simulations of a branched tetradecasaccharide substrate in the active site of a xyloglucan endo-transglycosylase},
	journal = {Molecular Simulation},
	volume = {37},
	number = {12},
	year = {2011},
	note = {Mark, Pekka Zhang, Qiong Czjzek, Mirjam Brumer, Harry Agren, Hans},
	pages = {1001-1013},
	abstract = {Molecular dynamics simulations of the tetradecasaccharide XXXGXXXG in complex with the hybrid aspen xyloglucan endo-transglycosylase PttXET16-34 have been performed and analysed with respect to structure, dynamics, flexibility and ligand interactions. Notably, the charge state of the so-called {\textquoteright}helper residue{\textquoteright} aspartate 87 (Asp87), which lies between the catalytic nucleophile [glutamate 85 (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 away from C1 of the sugar ring in subsite - 1 and the proton-donating ability of Glu89 was also weakened due to the formation of a hydrogen bond with 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, whereas the {\textquoteright}helper residue{\textquoteright} 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.},
	doi = {10.1080/08927022.2011.566605},
	author = {Mark, P. and Zhang, Q. and Czjzek, M. and Brumer, Harry and Agren, H.}
}
