title: The entropic contributions in vitamin B12 enzymes still reflect the electrostatic paradigm.
abstract: The catalytic power of enzymes containing coenzyme B12 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 B12 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 B12 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.
authors: Department of Chemistry, University of Southern California, Los Angeles, CA 90089-1062; warshel@usc.edu schopf.patrick@gmail.com.
authors: Patrick
authors: P
authors: Schopf
authors: Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608; and Biomass Science and Conversion Technology Department, Sandia National Laboratories, Livermore, CA 94550.
authors: Matthew J L
authors: MJ
authors: Mills
authors: Department of Chemistry, University of Southern California, Los Angeles, CA 90089-1062; warshel@usc.edu schopf.patrick@gmail.com.
authors: Arieh
authors: A
authors: Warshel
mesh_terms: D002384:Catalysis; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D030562:Databases, Protein; D019277:Entropy; D006859:Hydrogen / Q000737:chemistry; D008765:Methylmalonyl-CoA Mutase / Q000737:chemistry; D008958:Models, Molecular; D011789:Quantum Theory; D055672:Static Electricity; D013816:Thermodynamics; D014805:Vitamin B 12 / Q000737:chemistry*
chemical_list: D006859:Hydrogen; D008765:Methylmalonyl-CoA Mutase; D014805:Vitamin B 12
keywords: EVB; entropy calculations; free-energy methods; vitamin B12 catalysis