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

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• 作者：Hwangseo Park ; Junghun Suh ; and Sangyoub Lee
• 刊名：Journal of the American Chemical Society
• 出版年：2000
• 出版时间：April 26, 2000
• 年：2000
• 卷：122
• 期：16
• 页码：3901 - 3908
• 全文大小：115K
• 年卷期：v.122,no.16(April 26, 2000)
• ISSN：1520-5126

文摘

*On the basis of ab initio calculations at the MP2/6-31G**//RHF/6-31G** level, we study the modelreactions for the catalytic action of aspartatic proteinases. We elucidate the mechanistic features of two competingcatalytic mechanisms by determining the reaction paths. In contrast to the previous theoretical studies whichneglected the electron correlation, the concerted and the stepwise pathways are predicted to be almost equallyfavored in the general acid/general base mechanism. On the other hand, we find that a concerted reactionpathway is preferred to the stepwise one in the nucleophilic mechanism. We also find that both nucleophilicand 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 thepotential 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 energiesis included, the latter is predicted to be the preferred one by 1.9 kcal/mol. The covalent intermediate, whichis the end-point minimum energy complex on the concerted nucleophilic pathway, is found to be a unstableone that is 18.1 kcal/mol higher in free energy than the incipient model enzyme-substrate complex. This factis in accordance with the previous experimental implications that decomposition of the covalent intermediateis much faster than its formation. The present work provides a theoretical support for the persistent argumentthat the possibility of the nucleophilic mechanism cannot be excluded in the catalytic action of asparticproteinases although the required experimental detection of the covalent intermediate has been unsuccessfulso far. It is demonstrated that for all reaction pathways under consideration, the protonation of the nitrogenatom belonging to the peptidic bond is an essential step in crossing the activation barrier for the rupture of apeptide substrate. The relevance of the mechanistic features observed for the model reactions to an enzymaticreaction is discussed.