PENTACOORDINATED MOLECULES .28. COMPUTER-SIMULATION OF RIBONUCLEASE ACTION ON URIDYLYL-(3'-5')-ADENOSINE (REPRINTED FROM J AM CHEM SOC, VOL100, PG 7393, 1978)

The first step of the hydrolytic action of ribonuclease on the dinucle otide substrate UpA is investigated via molecular mechanics calculatio ns. UpA coordinates were obtained by conformational minimization of th e UpcA coordinates from the X-ray diffraction study of RNase-S with Up cA. Only the amino acid residues in the immediate vicinity of the acti ve site were included in the calculations: histidine-12, histidine-119 , and lysine-41. It is found that histidine-119 and lysine-41 may be m oved into more favorable positions for contact with the phosphate grou p with little change in energy. The transphosphorylation step is initi ated by decreasing the O-2, to Phosphorus distance while simultaneousl y increasing the O-5, to phosphorus distance, resulting in cleavage of the P-O-5, bond and formation of the 2',3'-cyclic intermediate. The p hosphorus atom moves almost 2 Angstrom in forming this cyclic intermed iate, bringing the phosphate unit within the hydrogen-bonding distance of lysine-41. Distances between the dinucleotide and the amino acid r esidues in both the initial structure and the cyclic intermediate supp ort a proposed reaction mechanism involving hydrogen bonding. The reac tion proceeds by an in-line attack of the O-2, oxygen atom on phosphor us and passes through a transition state which lies along the Berry co ordinate. The transition-state structure is determined to be intermedi ate in geometry between a trigonal bipyramid and a square pyramid. Com patible with the enzyme catalysis, the computed ground state, transiti on state, and cyclic intermediate structures have comparable energies.