Ab Initio Studies on the Catalytic Mechanism of Aspartic Proteinases:  Nucleophilic versus General Acid/General Base Mechanism

Abstract

On the basis of ab initio calculations at the MP2/6-31G**//RHF/6-31G** level, we study the model reactions for the catalytic action of aspartatic proteinases. We elucidate the mechanistic features of two competing catalytic mechanisms by determining the reaction paths. In contrast to the previous theoretical studies which neglected the electron correlation, the concerted and the stepwise pathways are predicted to be almost equally favored in the general acid/general base mechanism. On the other hand, we find that a concerted reaction pathway is preferred to the stepwise one in the nucleophilic mechanism. We also find that both nucleophilic and general-acid/general-base mechanisms may be operative in a peptide hydrolysis by aspartic proteinases. For the model reaction under consideration, the former is energetically more favored if one considers only the potential energy profile along the intrinsic reaction coordinate, as has been done in previous theoretical studies. However, when the entropic contribution due to nuclear motions as well as the zero-point vibrational energies is included, the latter is predicted to be the preferred one by 1.9 kcal/mol. The covalent intermediate, which is the end-point minimum energy complex on the concerted nucleophilic pathway, is found to be a unstable one that is 18.1 kcal/mol higher in free energy than the incipient model enzyme-substrate complex. This fact is in accordance with the previous experimental implications that decomposition of the covalent intermediate is much faster than its formation. The present work provides a theoretical support for the persistent argument that the possibility of the nucleophilic mechanism cannot be excluded in the catalytic action of aspartic proteinases although the required experimental detection of the covalent intermediate has been unsuccessful so far. It is demonstrated that for all reaction pathways under consideration, the protonation of the nitrogen atom belonging to the peptidic bond is an essential step in crossing the activation barrier for the rupture of a peptide substrate. The relevance of the mechanistic features observed for the model reactions to an enzymatic reaction is discussed.

Computing the Role of Near Attack Conformations in an Enzyme-Catalyzed Nucleophilic Bimolecular Reaction

“…An additional water molecule was inserted between the lytic peptide bond and the catalytic dyad as is expected in the general acid/general base (GA/GB) cleavage mechanism. 54 The standard AMBER force field (ff03) 55 was used to describe all parameters. Each system was solvated using atomistic TIP3P water 56 and then electrically neutralized with an ionic concentration of 0.15 M NaCl, resulting in fully atomistic and explicit solvent systems of approximately 40,000 atoms and 14,000 atoms, respectively.…”

Dynamic and Electrostatic Effects on the Reaction Catalyzed by HIV-1 Protease

“…16 The relatively simple structure of the active site is nevertheless the origin of some problems, which are still the source of many scientific debates. Generally, experimental 17, 18, 19, 20 and theoretical 12, 13, 21, 22, 23, 24 studies have provided evidence that peptide bond breaking is the result of a mechanism where a water molecule is activated by an aspartate residue and it then attacks as a nucleophile on a carbonyl carbon of the substrate peptide chain. Nevertheless, in the past 30 years different mechanisms for the reaction catalyzed by aspartic proteases have been suggested.…”

Transition states of native and drug-resistant HIV-1 protease are the same

“…Theoretical studies of the chemical mechanism of HIV-1 protease have included electronic structure calculations (23)(24)(25)(26), quantum mechanics/molecular mechanics (QM/MM) studies (27)(28)(29), and molecular dynamic simulations (30)(31)(32). Early ab initio calculations by Lee et al proposed that the irreversible step of the protease reaction comes after the formation of 3 (24).…”