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Review
. 2010 May 1;78(6):1339-75.
doi: 10.1002/prot.22654.

At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?

Shina C L Kamerlin  1 , Arieh Warshel
Affiliations
Review

At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?

Shina C L Kamerlin et al. Proteins. .

Abstract

Enzymes play a key role in almost all biological processes, accelerating a variety of metabolic reactions as well as controlling energy transduction, the transcription, and translation of genetic information, and signaling. They possess the remarkable capacity to accelerate reactions by many orders of magnitude compared to their uncatalyzed counterparts, making feasible crucial processes that would otherwise not occur on biologically relevant timescales. Thus, there is broad interest in understanding the catalytic power of enzymes on a molecular level. Several proposals have been put forward to try to explain this phenomenon, and one that has rapidly gained momentum in recent years is the idea that enzyme dynamics somehow contributes to catalysis. This review examines the dynamical proposal in a critical way, considering basically all reasonable definitions, including (but not limited to) such proposed effects as "coupling between conformational and chemical motions," "landscape searches" and "entropy funnels." It is shown that none of these proposed effects have been experimentally demonstrated to contribute to catalysis, nor are they supported by consistent theoretical studies. On the other hand, it is clarified that careful simulation studies have excluded most (if not all) dynamical proposals. This review places significant emphasis on clarifying the role of logical definitions of different catalytic proposals, and on the need for a clear formulation in terms of the assumed potential surface and reaction coordinate. Finally, it is pointed out that electrostatic preorganization actually accounts for the observed catalytic effects of enzymes, through the corresponding changes in the activation free energies.

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Figures

Fig. 1
Fig. 1
The energy gap between the diabatic product and reactant states in the reaction catalyzed by haloalkane dehalogenase (DhlA), during MD simulations of the enzyme (red), as well as the same reaction in water (blue). This figure was originally presented in Ref. .
Fig. 2
Fig. 2
Autocorrelation function of the energy gap between the reactant and product states in the region of the TS in haloalkane dehalogenase (red), as well as the reference reaction in water (blue). The plot on the top shows the total energy, whereas that on the bottom shows only the electrostatic contribution to the energy. The autocorrelation functions are normalized to 1 at zero time. This figure was originally presented in Ref. .
Fig. 3
Fig. 3
A schematic depiction of the diffusive (A, B) and the inertial models (C, D). These two limiting models are shown in the case where the conformational barrier is much smaller than the chemical one (i.e. Δg≠ conf ≪ Δg≠chem, parts A and C at the top of the figure), and where the two barriers are similar (i.e. Δg≠conf ≈ Δg≠chem, parts B and D at the bottom of the figure). This figure was originally presented in the supporting information of Ref.
Fig. 4
Fig. 4
The behavior of 200fs downhill trajectories run on the ground-state EVB surface of (b) the DhlA system and (a) the relevant reference reaction in water. This figure shows the trajectories separated into solvent and intramolecular solute components, and the time reversal of these trajectories corresponds to the actual reactive trajectories. This figure was originally presented in Ref. .
Fig. 5
Fig. 5
Showing why the trend in the energy contributions along the reaction coordinate of the reaction of CypA, contradict the proposal of Ref. ,. As seen from the figure, the chemical barrier in the protein (which is around 15 kcal/mol) is smaller than that in vacuum (see Ref. 264. Note also that these free energy values are very qualitative, and only brought in, in order to focus the discussion). This means that the contributions of the protein at the TS of the protein/substrate complex, is negative. Thus, if the barrier due to the protein along the chemical coordinate is around 15 kcal/mol in the apo-enzyme (as is implied by Kern’s work), it cannot be similar to the same contribution at the ES system. This means that the study of the apo-enzyme is either (a) unlikely to tell us about the protein contribution along the chemical coordinate in the apo-enzyme, or (b) that the landscape in the corresponding barrier in the apo-enzyme is not related to the barrier in the presence of the substrate.
Fig. 6
Fig. 6
The relationship between the first passage (fp) time, τfp, over the chemical barrier, and the height of the conformational barrier (for the case where Δgchem≠=5kcal/mol). The calculations represent the average from several runs. The figure considers two correlations: (A) The inverse fp time, (τfp)−1, as a function of the conformational barrier, where it is shown that the crossing time of the chemical barrier is independent of the characteristic time of motion along the conformational coordinate as long as kconf > kchem, and (B) τfp and τ fp ′ (which is the fp time when we start the counting from the moment the trajectory reaches the RS). It can be seen that even when kconf < kchem, the time of crossing the chemical barrier is independent of the conformational landscape. This figure was originally presented in Ref. .
Fig. 7
Fig. 7
Highlighted here is the fact that motions to the ES region do not contribute to catalysis. That is, the figure illustrates that in a properly evolved native enzyme, the motions to and from the partially unfolded or unbound configurations are simply a part of the random excursion of the system around the ES minimum. Therefore, there are no fluctuations that “bring the system to the preorganized ES”, as the system is already at the ES (where the fluctuations follow the Boltzmann probability, and the chance of reaching the TS region is determined solely by the free energy of the TS relative to the ES). The same thing holds for the mutants that were used to support the argument that the motion to the ES is relevant to catalysis. In fact, unless the motion to the ES is uphill (which means that the binding free energy is positive), kcat is determined by the motion from the ES and not the motion to the ES (i.e. the reaction goes (a) → (b) → (c) → (d) and not (b) → (c) → (d)). This figure was originally presented in Ref. .
Fig. 8
Fig. 8
The landscapes for the chemical profiles for the monomeric (A) and dimeric (B) forms of chorismate mutase. Here, the profiles are equally spaced according to the rmsd from the native structure for the three regions (I, II, and III) of the enzyme. The orange dashed line designates the 16 kcal/mol height that corresponds to a reasonably low activation barrier, from which it can be seen that the monomer has several catalytic configurations in the second region, whereas the dimer does not have any. This figure was originally presented in Ref. .
Fig. 9
Fig. 9
A schematic representation of the free energy landscape as a function of the conformational and chemical coordinates in a reacting enzyme. The figure depicts trajectories across the conformational coordinate and a continuation of this trajectory along the chemical reaction coordinate. This figure is adopted in part from Ref. .
Fig. 10
Fig. 10
Examining the relationship between the free energy landscape and entropic effects. This figure serves to illustrate the fact that the recent suggestion of the existence of an “entropy funnel” has no relationship to the actual free energy landscape.
Fig. 11
Fig. 11
An illustration of the preorganization effect when considering (a) the stabilization of an ion in water by polarization effects, and (b) the stabilization of an ion in a protein by the cumulative effects of preorganization and polarization. This figure was originally presented in Ref. .
Fig. 12
Fig. 12
A comparison of the energetics of charging (a) the enolate intermediate in the active site of KSI and in water, and (b) the phenolate ligand in the active site of KSI. The preorganization effect is illustrated in the bottom part of each figure, and it can be seen that this effect is significantly smaller in the case of the phenolates, as once the ligand it converted to its non-polar form, it is no longer held in a fixed orientation. This figure was originally presented in Ref. .
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