Usually when it comes to enzymes, structure is not enough. We want to know where it binds substrates, how it binds and what is the nature of the bond. However, sometimes the process carried out by enzymes is so fast we can’t observe it. And what then? Then theory can observe it.
We really do want to know exact mechanisms of protein actions. For instance, when the protein is involved in a disease we know where and how to stop its action. Usually the mechanism is obtained by multiple tries – very similar substrates are mixed with enzyme and kinetic data is used to deduce functions of particular atoms or groups. However, there is a class of enzymes that action relies on movement of electrons and it’s quite difficult to measure their kinetics.
Ferrodoxins or cytochrome c are just examples of varied group of iron-sulfur protein. They common feature is cluster like this one (taken from Wiki):
The main role of the complex is to keep electrons or transport them from A to B. Because of a lot of possible metastable forms of the cluster it’s hard to get an idea on what’s exactly happening there. In the past it was just suggested that there is a small number of possible forms and there is only one particular pathway of electrons.
And here comes prof. Garnet Chan from Princeton University. He knew that quantum mechanics equations for cluster are impossible to solve. But he found a way to make them “just” hard to solve rather than impossible. He assumed that electron’s behavior can be affected only by other electrons which are close enough to it. Using his equations he found out that there is a lot of possible structure of a cluster with electrons. And these gives a lot of different pathways for electrons. And it’s possible that some of them may be even combination of different pathways. This raises new questions in cluster physics/chemistry: is it totally random which pathway is chosen? or maybe there are some factors that decide? What are differences between pathways and consequences of taking one over another? This questions will be probably answered, with next QM simulations of course!
Garnet Chan’s website on Princeton Chemistry: link
His paper in Nature: link2