Electrostatic Basis for Enzyme Catalysis Arieh Warshel,* Pankaz K. Sharma, Mitsunori Kato, Yun Xiang, Hanbin Liu, and Mats H. M. Olsson Department of Chemistry, University of Southern California, SGM Building 418, 3620 McClintock Avenue, Los Angeles, California 90089-1062 Received November 7, 2005 Contents 1. Introduction 3210 2. Formulating the Problem and Illustrating the Nature of Different Reference States 3211 3. Evaluating Activation Free Energies in Enzyme Active Sites by the EVB and MO QM/MM Methods 3216 4. Electrostatic Contributions of Preorganized Active Sites 3218 4.1. General Studies 3218 4.2. Quantifying the Source of Electrostatic Contributions to Catalysis 3220 4.3. The Cost of Electrostatic Preorganization Is Paid by the Folding Energy 3223 4.4. Metal Ion Catalyses 3223 4.5. Some Comments on the Energetics of Zwitterionic Transition States 3224 4.6. Allosteric Control of Catalytic Activity Is Also Associated with Electrostatic Effects 3224 5. What About Other Proposals? 3226 5.1. Ground-State Destabilization by Steric Strain Does Not Provide a Large Catalytic Effect 3226 5.2. Dynamical Effects Do Not Contribute Significantly to Enzyme Catalysis 3226 5.3. Correlated Modes Clearly Exist in Proteins, but They Also Exist in Solution 3228 5.4. Near Attack Conformations (NACs) Correspond to TS Stabilization 3229 5.5. The Entropy Contributions of Bringing the Reactants Together Do Not Lead to a Large Catalytic Effect 3229 5.6. Reactant State Destabilization by Desolvation Effects Does Not Provide a Large Catalytic Effect 3229 5.7. A Consistently Defined Low-Barrier Hydrogen Bond (LBHB) Proposal Leads to Anticatalytic Effects 3231 5.8. A Consistently Defined Covalent Catalysis Does Not Account for Large Catalytic Effects 3231 6. Problems with the Catalytic Antibody Proposals Reflect Difficulties with Creating a Proper Preorganized Environment 3232 7. Conclusions 3232 8. Acknowledgments 3232 9. References 3232 1. Introduction Enzymatic reactions play a fundamentally important role in controlling and performing most life processes. 1-3 Thus, understanding how enzymes work has both fundamental and practical importance. In this respect it is crucial to understand what is the origin of the enormous catalytic power of enzymes, which remains one of the challenges of modern biophysics. Although many elements of this puzzle were elucidated by biochemical and structural studies, the source of the catalytic power of enzymes has not been widely understood and, clearly, has not been agreed upon by the scientific community (e.g., see ref 4). The current consensus is sometimes reduced to statements such as, “the enzyme binds the transition state stronger than the ground state” or “the catalytic groups are perfectly oriented”. However, such statements are not sufficient to explain this catalytic power since the real question is how this differential binding is accomplished and what are the actual catalytic groups. The issue of the origin of enzyme catalysis is, in fact, sometimes confused and trivialized by attributing it to the selection of the reference state (see below) and implying that the enormous acceleration by 10 orders of magnitude is well understood since binding energies of ligands by proteins can reach 15 kcal/mol. 5 As will be discussed in this review, the issue is not the binding energy itself but rather the change in binding energy on moving from the reactant state to the transition state. Unfortunately, most attempts to account for the catalytic power of enzymes cannot rationalize binding energies of more than a few kilocalories per mole. The problem becomes more challenging after realizing that some enzymes catalyze their reactions by more than 20 orders of magnitude and that this catalytic effect is entirely due to the active site environment and has very little to do with covalent arguments of the type promoted in refs 5 and 6. Earlier attempts to quantify the contributions to enzyme catalysis were reviewed in, e.g., refs 1 and 7-11. However, this review will explore the origin of the catalytic power of enzymes in a somewhat more systematic way. It will start by clarifying recent confusions regarding the reference state by introducing a catalytic scale that does not include the well- understood effect of having different mechanisms in the enzyme and in solution as well as the effect of the binding of the reactant state. This will allow us to focus on the effect of the enzyme environment, which must represent the true catalytic effect (see below). We will demonstrate that the effect of the enzyme environment can be much larger than the estimated 15 kcal/mol provided in ref 5. Furthermore, we will point out that a correct rationalization of “even” this 15 kcal/mol effect is an enormous challenge. We will then * To whom correspondence should be addressed. E-mail: warshel@usc.edu. Phone: (213) 740-4114. Fax: (213) 740-2701. 3210 Chem. Rev. 2006, 106, 3210-3235 10.1021/cr0503106 CCC: $59.00 © 2006 American Chemical Society Published on Web 06/15/2006