Jan 252012
 

Imagine that you could get an injection of a protein that would chop up arterial plaques. Imagine that you could drop a plastic bottle into a pool of bacteria that would transform it back into high-grade oil. Imagine that you could take any organic material at all and, with a minimum of planning, transform it into any kind of desired organic chemical with a bare minimum of energy input and no need to purify intermediates. This is the vision behind the applied structural biology of protein design, the holy grail of which is to come up with a way to make enzymes that will perform novel chemistry. A study recently published online in Nature Biotechnology by David Baker’s group (1) suggests that the design process could be improved by crowdsourcing certain parts of the problem to gamers (the paper is paywalled at Nature but freely available via the Foldit site).

To do this, the Baker group used their program Foldit, which they have used previously for predicting three-dimensional protein structures from their amino acid sequences. Rather than predicting a structure from a known sequence, however, the Baker group asked the Foldit players to figure out an amino acid sequence that would generate a desired structure. The goal was to enhance an enzyme that would perform the chemically useful Diels-Alder reaction.

An enzyme is a protein that increases the rate of (catalyzes) a chemical reaction, often by incredible amounts. The best enzymes can increase reaction rates by factors of up to 1017 relative to the same reaction occurring in pure water. Protein design aims to produce artificial enzymes with rate enhancements comparable to their natural counterparts. To do this, biochemists try to design an active site that stabilizes the transition state of a chemical reaction. The transition state is the point of a reaction where the molecules are in their least stable state, and equally likely to revert to substrates or continue on and become products.

Unfortunately, it’s not just as simple as stabilizing a transition state. Enzymes have to bind and release their substrates and products, producing energy landscapes that are at least as complex as the one I have drawn below. Using a protein design protocol they had described in previous publications, Baker’s group managed to produce a weak enzyme. They then asked the Foldit players to help out, by posing some specific challenges to try and stabilize the bound substrates. The Foldit players eventually produced an 18-fold improvement in the enzyme’s kcat/KM value. To understand what that means and what the players accomplished, let’s examine this reaction coordinate:

That’s a busy little figure, but it’s not as bad as it looks. The position up or down in the figure indicates how much energy a state has. The more energy, the less likely the system is to occupy that state. Left to right positions show us how close we are to the desired state of the system, which is to have the product (P) we want separate from the enzyme (E) that catalyzed its production from substrate (S). To move from one stable state to another stable state, you have to push the system over hills (energy barriers) in the landscape, just like pushing a car up a hill. The higher the barrier, the slower that step becomes. For simplicity, this diagram shows only one substrate, but the artificial enzyme had two. We can pretend that the Foldit effort started with an enzyme that resembled the blue curve.

We start with E and S separate from each other in solution (E+S). E and S bind to each other to form ES, releasing binding energy. Here I’ve shown a small barrier between E+S and ES, but in many cases there is no barrier here, or it is negligible. Next S is converted to P, and as you can see there is usually a large energy barrier, at the top of which is the transition state (TS). The height of the barrier is determined by the activation energy, which is affected by the structure of the enzyme-substrate complex. Once P has been formed, the complex dissociates so we have free enzyme and product (E+P). Here I have shown E+P to be a lower-energy state than EP, but this won’t necessarily be true.

In the language of Michaelis-Menten kinetics, this landscape is described by two main parameters. KM, also called the Michaelis constant, describes the balance between E+S and ES, and therefore primarily reflects the binding energy. The larger the binding energy, the more ES will be favored, and the lower KM will be. The turnover number, or kcat (maybe we should call this the Menten constant?) describes the creation of product over time, and in this diagram it depends on the activation energy. Again, the larger the activation energy, the lower kcat will be. However, kcat really just depends on the slowest step of the catalytic cycle. If the largest energy barrier was between EP and E+P, kcat would depend on that barrier. Because kcat/KM is something like a normal rate constant, and combines the values in an easy-to-understand way (a higher kcat/KM means a better enzyme), it’s often used to describe an enzyme’s activity.

So how did the Foldit players improve the activity by a factor of 18? The original enzyme design left part of the active site open to water. Through a series of iterations, the Foldit players filled in this void with a self-stabilizing helix-loop-helix motif (Figure 1b). The upshot of this was that the affinity of the enzyme for both substrates increased. Thus, KM decreased, as shown in Table 1, for both substrates. At the end of the process, the diene bound six times as tightly and the affinity for the dienophile improved by about a factor of three. This accounts for all the observed change in kcat/KM, because kcat was not improved.

Although it may not seem like it, we can also learn a great deal from the fact that kcat did not change. This observation shows that the changes made by the Foldit players did stabilize the TS. Otherwise, the energy barrier would have increased when they stabilized the ES complex. However, the best-case scenario would have been for them to uniquely stabilize TS without improving the energy of ES, because this would effectively lower the energy barrier and increase the reaction rate. Because this didn’t happen, the situation follows the orange curve in the figure above: the ES and TS states have shifted down in energy by the same amount, with no change to the activation energy.

The lack of change in kcat also indicates that the Diels-Alder reaction itself, rather than product dissociation, is rate-limiting for the enzyme. My reasoning here is that the increase in affinity is general. We know that both the ES and TS complexes were stabilized by the changes, so EP probably was too, as shown in the orange curve. If the EP → E+P transition were rate-limiting, these stabilizing mutations would have made the enzyme slower.

The Foldit players made this a better enzyme, but that doesn’t exactly mean that it’s an impressive one. The observed kcat is significantly slower than almost any natural enzyme, and the overall rate enhancement is on the order of 103-104, which is not much better than catalytic antibodies. The success of the Foldit players at improving the affinity of the enzyme for all the bound states suggests that it might be possible to use crowdsourced systems like Foldit to accomplish the more difficult feat of stabilizing a TS, or at least to generate folds that support a pre-defined TS. The ultimate goal is to produce something like the green curve, where substrate binding is stronger and activation energy is lower. I hope that such efforts will be taking place among the Foldit players soon, if they haven’t started already.

Disclaimer: I am part of an ongoing collaboration with David Baker’s group unrelated to the Foldit program.

1) Eiben, C., Siegel, J., Bale, J., Cooper, S., Khatib, F., Shen, B., Players, F., Stoddard, B., Popovic, Z., & Baker, D. (2012). Increased Diels-Alderase activity through backbone remodeling guided by Foldit players Nature Biotechnology DOI: 10.1038/nbt.2109 Also available for free from the Foldit site.

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