A general acid-base mechanism for the stabilization of a tetrahedral adduct in a serine-carboxyl peptidase: a computational study.
The QM/MM MD and free energy simulations show that serine-carboxyl peptidases (sedolisins) may stabilize the tetrahedral intermediates and tetrahedral adducts primarily through a general acid-base mechanism involving Asp (Asp164 for kumamolisin-As) rather than the oxyanion-hole interactions as in the cases of serine proteases.
Guo
Haobo
H
Department of Biochemistry and Cellular and Molecular Biology and Center of Excellence for Structural Biology, University of Tennessee, Knoxville, Tennessee 37996, USA.
Wlodawer
Alexander
A
Guo
Hong
H
D000143:Acids / Q000737:chemistry; D000468:Alkalies / Q000737:chemistry; D001665:Binding Sites; D002268:Carboxypeptidases / Q000737:chemistry* / Q000235:genetics; D019295:Computational Biology; D004795:Enzyme Stability; D008956:Models, Chemical; D015394:Molecular Structure; D009154:Mutation; D012694:Serine / Q000737:chemistry; D013816:Thermodynamics
D000143:Acids; D000468:Alkalies; D012694:Serine; D002268:Carboxypeptidases