A square pyramidal model for ribonuclease action.

A mechanism incorporating a square pyramidal model (SP) is presented for the action of bovine pancreatic ribonuclease. Its formulation is based on structural principles governing pentacoordinate behavior. The model is compared with a previous trigonal bipyramidal (TP) representation with regard to the geometry of the active site and enzyme constraints. Of two variants of the SP model, an adjacent (cis displacement) and in-line (trans displacement) process, the in-line mechanism, as with the TP model, fits existing model studies. Consideration of the energetics of the SP vs. the TP model leads to an estimated energy difference of about 1-2 kcal/mol. This suggests that the preferred model may be intermediate in geometry between the two idealized representations for the enzymatic hydrolysis. Comparisons are made showing that pseudorotation is an unlikely process in either model.