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The fact that profiles of the form of Figure 2a are unlikely to exist in most enzymes does not present any conceptual or fundamental problem. This is exactly the profile expected from a protein with RSD and without sufficient binding by distant residues. Of course, the fact that proteins with positive binding energies are not found in most cases, provides a major support for the argument against the RSD proposals.
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Some readers who would start with ref 43 might be confused by our statement about the description of the NAC effect by Kollman and co-workers. However, one should realize that the analysis of the NAC effect by this group started with the clear analysis of ref 42 where the entropic effect (which they called a cratic effect) was added to the free energy profile of the reaction in water. The same approach was used in all of their explicit calculations and summarized in ref 43. Subsequently, ref 44 used the same diagrams to describe the NAC effect, while still considering the same calculations (see Table 1 of ref 44) that were based on the analysis of entropic effects.
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w ≅ -13.3 kcal/mol). Thus, the calculated product binding energy is only about 12 kcal/mol. While this is still an overestimate, it does not indicate a major problem with product inhibition.
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The work of Jorgensen and co-workers seems to represent a misunderstanding of the NAC proposal. That is, these workers used very different NAC geometries in the protein and in water. These geometries were chosen more or less as the minima of the corresponding PMFs. Actually, the minimum of the protein PMF is the most logical definition of the NAC geometry in the water reaction (see ref 32). Otherwise the NAC proposal has little to do with the effect of the protein.
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