THE ROLE OF LYSINE-41 IN RNASE-A CATALYSIS - A QUANTUM-CHEMICAL STUDYON THE ACTIVE-SITE LIGAND COMPLEX

Several mechanisms have been proposed to explain the action of enzymes at the atomic level. Among them, the recent proposals involving short hydrogen bonds as a step in catalysis by Gerlt and Gassman [1] and pr oton transfer through low barrier hydrogen bonds (LBHBs) [2, 3] have a ttracted attention. There are several limitations to experimentally te sting such hypotheses, Recent developments in computational methods fa cilitate the study of active site-ligand complexes to high levels of a ccuracy, Our previous studies, which involved the docking of the dinuc leotide substrate UpA to the active site of RNase A [4, 5], enabled us to obtain a realistic model of the ligand-bound active site of RNase A. From these studies, based on empirical potential functions, we were able to obtain the molecular dynamics averaged coordinates of RNase A , bound to the ligand UpA. A quantum mechanical study is required to i nvestigate the catalytic process which involves the cleavage and forma tion of covalent bonds. In the present study, we have investigated the strengths of some of the hydrogen bonds between the active site resid ues of RNase A and UpA at the ab initio quantum chemical level using t he molecular dynamics averaged coordinates as the starting point. The 49 atom system and other model systems were optimized at the 3-21G lev el and the energies of the optimized systems were obtained at the 6-31 G level. The results clearly indicate the strengthening of hydrogen b onds between neutral residues due to the presence of charged species a t appropriate positions. Such a strengthening manifests itself in the form of short hydrogen bonds and a low barrier for proton transfer. In the present study, the proton transfer between the 2'-OH of ribose (f rom the substrate) and the imidazole group from the H12 of RNase A is influenced by K41, which plays a crucial role in strengthening the neu tral hydrogen bond, reducing the barrier for proton transfer. (C) 1998 Elsevier Science B.V. All rights reserved.