Journal Article

entropic contributions in vitamin B₁₂ enzymes still reflect the electrostatic paradigm

Arieh Warshel, Patrick Schopf, Matthew J. L. Mills

2015

Overview

Significance The origin of the catalytic power of B ₁₂ enzymes has been a major puzzle despite our previous finding that this effect is due to electrostatic stabilization of the leaving group. Recent findings of very large entropic contributions to catalysis were presented as an alternative to the electrostatic idea. Here, we use our ability to evaluate entropic contributions by the restraint release (RR) approach to reexamine the nature of the catalytic effect. The RR approach reproduces the observed entropic contributions to the activation barrier and demonstrates that the entropic effect is due to the previously identified electrostatic factors. Thus, we have further substantiated our paradigm for the origin of the catalytic power of B ₁₂ enzymes. The catalytic power of enzymes containing coenzyme B ₁₂ has been, in some respects, the “last bastion” for the strain hypothesis. Our previous study of this system established by a careful sampling that the major part of the catalytic effect is due to the electrostatic interaction between the ribose of the ado group and the protein and that the strain contribution is very small. This finding has not been sufficiently appreciated due to misunderstandings of the power of the empirical valence bond (EVB) calculations and the need of sufficient sampling. Furthermore, some interesting new experiments point toward entropic effects as the source of the catalytic power, casting doubt on the validity of the electrostatic idea, at least, in the case of B ₁₂ enzymes. Here, we focus on the observation of the entropic effects and on analyzing their origin. We clarify that our EVB approach evaluates free energies rather than enthalpies and demonstrate by using the restraint release (RR) approach that the observed entropic contribution to the activation barrier is of electrostatic origin. Our study illustrates the power of the RR approach by evaluating the entropic contributions to catalysis and provides further support to our paradigm for the origin of the catalytic power of B ₁₂ enzymes. Overall, our study provides major support to our electrostatic preorganization idea and also highlights the basic requirements from ab initio quantum mechanics/molecular mechanics calculations of activation free energies of enzymatic reactions.

• Publisher: National Academy of Sciences,National Acad Sciences
• Subject: Biological Sciences / Catalysis / catalytic activity / Computational Biology - methods / Computer Simulation / Databases, Protein / Entropy / enzymes / Hydrogen - chemistry / Methylmalonyl-CoA Mutase - chemistry / Models, Molecular / Quantum Theory / Static Electricity / Thermodynamics / Vitamin B 12 - chemistry / vitamin B12