Feb 052008
Blogging on Peer-Reviewed ResearchBecause even the simplest case of enzymatic catalysis involves multiple steps (i.e. association, chemistry, and dissociation), semantic issues have obscured the question of what role protein structural dynamics play. For instance, the opening of the lids in Adenylate kinase appears to be rate-limiting, but there is as yet no evidence that dynamics play any role in the phosphotranfer. Thus, one can argue that dynamics are critical (because they are rate-limiting) or irrelevant (because they contribute nothing to the chemical step). Some authors, Arieh Warshel for example, have argued that the latter finding is general—that the highly successful transition-state stabilization model leaves no place for dynamics in chemical catalysis. Some researchers, however, believe that dynamics may play a significant role in chemistry when catalysis proceeds by other routes, especially hydrogen tunneling. In this vein, Matthew Meyer, Diana Tomchick, and Judith Klinman presented evidence in last week’s Proceedings of the National Academy of Sciences that protein dynamics play a significant role in the chemical step of catalysis for the protein soybean lipoxygenase (SLO-1).

Hydrogen tunneling refers to the idea that a hydrogen may in some instances “tunnel through” an energy barrier, going directly from substrate to product without wasting any time or kT in actually surmounting that barrier. A reaction that primarily reflects tunneling should have three properties. The reaction rate should vary only weakly with temperature, because tunneling mostly divorces the rate from kT. Using an Arrhenius plot, this translates to a low calculated energy of activation. Replacing the reactive hydrogen with deuterium should enormously inhibit the reaction—a large kinetic isotope effect (KIE)—because the doubling of mass makes tunneling less likely. Nonetheless, the difference in the energies of activation (ΔEa) for hydrogen and deuterium calculated from an Arrhenius plot should also be small, if tunneling is the main mechanism. Conceivably an enzyme could enhance the rate of such a reaction by using dynamics to promote favorable vibrational modes for the tunneling to occur, or to temporarily adopt a disfavored structure that puts reactive groups at a better distance for tunneling.

SLO-1 exhibits all three features, and so Klinman’s group has used it as model system to try and understand whether and how enzymes promote tunneling reactions. In this case they have performed a series of mutations of isoleucine 553. In addition to existing data on WT and I553A, they analyzed the KIEs, crystal structures, and activation energies of I553L, I553V, and I553G mutants. They find that the protein as a whole is not much distorted by any of these mutations, nor do any of them appear to have significant effects on the binding pocket or substrate dissociation constant—the Kd for each mutant is around 3 μM, while WT is around 10 μM. Yet as the bulk of the mutated residue decreases, the ΔEa increases significantly. In addition, the kinetic isotope effects decrease much more sharply with temperature than for WT. Again, the magnitude of this increased temperature dependence appears to vary inversely with the bulk of the side chain at I553. From these features, and a decline in the magnitude of the pre-exponential factor, the authors argue that dynamics play an important role in encouraging the tunneling reaction.

Well, you know how I love long-range dynamic effects in proteins. But I don’t quite buy it here. An argument based on negatives is never very satisfying in any case, and here we have a lot of questions. For one thing, to say that the structure hasn’t changed significantly seems overly simplistic to me. The lowest-energy structure may not have been seriously deformed, but absent crystal packing and with a little extra kT around, the average structure might be different. Additionally, these structures were obtained in the absence of ligand. Even though the energetics of binding do not appear to differ significantly for these mutants, the structure of the enzyme or ligand may have changed in the bound state. Even if I accept that the existing structures argue for a completely identical binding site in the free state, and this could realistically be debated, that’s no guarantee that the same is true of the bound state.

I’m not denying that the evidence is strongly suggestive, and getting direct data may be difficult given the size of the protein. However, almost all of these side chains are methylated. That means that perdeuteration of the protein in concert with specific side-chain labeling could be especially fruitful in directly observing the dynamics of the pocket during catalysis. It should also in principle be possible to label other side chains in the region to determine how mutations affect the whole area. It is likely that the substrate can also be labeled, possibly with a nucleus or tag that is poorly relaxed. T2 is likely to be a major challenge here, but not necessarily an insurmountable one, especially since the enzyme appears to be folded and active up to around 50 °C. The presence of the iron is certainly a complicating factor; however, the dynamics should be the same whether catalysis is occurring or not, so possibly it could be substituted with a non-paramagnetic metal. It wouldn’t be the easiest project in the world, but it should be doable.

I think these results are intriguing, and I’d love to hear Warshel’s take on them. Nonetheless, I feel I have to reserve judgment at least until dynamic changes in the pocket that seem to correlate with the kinetic observations are directly demonstrated by NMR or some other method.

Meyer, M.P., Tomchick, D.R., Klinman, J.P. (2008). Enzyme structure and dynamics affect hydrogen tunneling: The impact of a remote side chain (I553) in soybean lipoxygenase-1. Proceedings of the National Academy of Sciences, 105(4), 1146-1151. DOI: 10.1073/pnas.0710643105OPEN ACCESS ARTICLE

  One Response to “Dynamics and tunneling in soybean lipoxygenase”

  1. You know, I've taken quantum chemistry and all, but: when it comes to enzymes, i regard hydrogen tunneling as another word for "magic!"

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