화학공학소재연구정보센터
Journal of the American Chemical Society, Vol.116, No.6, 2591-2599, 1994
Simulation Analysis of the Binding Interactions in the RNase-A 3’-Ump Enzyme-Product Complex as a Function of pH
Stochastic boundary simulations are performed to study the binding of 3’-uridine monophosphate to bovine pancreatic ribonuclease A for three protonation states of the enzyme-product complex. Because charged species are involved, the structure of the enzyme-product complex provides a sensitive test of the method used for treating the long-range electrostatic interactions. To avoid spurious effects resulting from group-switch or atom-switch electrostatic potential truncation schemes, an extended electrostatics algorithm is used. It allows for the inclusion of all electrostatic interactions through a pairwise charge-charge interaction at, short distances and charge-group multipole moment interactions at large separations. Since X-ray data are available only at low pH where the phosphate was assumed to be monoanionic, the present simulations provide predictions concerning the structure and interactions of the enzyme-product complex at other pH values. In particular, the role of specific residues in the binding of the product is examined. Maximal binding is found to occur when a phosphate dianion interacts with positively charged His 12 and 119; a fall in binding is expected at low and neutral pH due mainly to the loss of enzyme interactions with the phosphate and base. All three groups of the product (the base, ribose, and phosphate) are involved in binding to the enzyme; Thr 45, Lys 41, and a positively charged histidine (His 12 or His 119) are the respective recognition residues.