'Good Things Come in Pairs' : UTM research shows enzymatic partners drive chemical reactions

fluoroacetate dehalogenase
Tuesday, February 21, 2017 - 9:44am
Nicolle Wahl

New research from the University of Toronto Mississauga suggests that good things come in pairs when it comes to chemistry. The findings, led by co-authors Emil Pai (UofT, Biochemistry) and Professor Scott Prosser from the Department of Chemical and Physical Sciences and the former director of the Master of Biotechnology program, highlights how paired or “dimeric” enzymes use their empty “seat” to drive a chemical reaction on their occupied half.

“The research advances fundamental concepts regarding the role of enzyme dynamics in catalysis,” says Prosser. “By understanding how binding events regulate enzyme flexibility, we can better design drugs to affect changes on properties of target molecules in fighting disease.”

The findings appear in a recent issue of the journal Science.

Enzymes, of which the vast majority are proteins, speed up chemical reactions in living organisms, without themselves being altered in the process. It turns out that nature tends to package many enzymes as pairs or dimers, and in many cases, dimeric enzymes exhibit cooperativity – that is, after binding the first substrate in the dimer, binding and turnover of the second substrate becomes even faster.

Prosser and his colleagues at UTM recently uncovered another reason for this pairing, in their study of a bacterial enzyme, fluoroacetate dehalogenase. Namely, the empty seat of the dimer becomes dynamic upon binding to the substrate and helps drive forward the reaction. The role of this paired enzyme is to pry away a fluorine atom from an otherwise potent and lethal pesticide, fluoroacetate. This is no small feat – the carbon-fluorine bond is one of the strongest chemical bonds in nature. As an aside, some plants are able to make this poison to protect themselves from grazing herbivores, who don’t have this enzyme and therefore —like humans — could be killed by this poison.

Using X-ray crystallography and nuclear magnetic resonance, the team captured high-resolution snapshots of the paired enzymes during various stages of catalysis. Remarkably, this pair never binds more than one substrate molecule at the same time (i.e. is not cooperative).

Nevertheless, the empty half of the pair appears to still do a fair share of the work in accomplishing this reaction. As the poison binds to the dimer, the empty half sheds water molecules and become more dynamic at the same time, making the reaction more spontaneous. If the enzyme were to suddenly jiggle and lose water molecules in the bound half of the dimer this might spell disaster for the actual bond breaking chemical step – so the empty half of the dimer does the dirty work. The enzyme also prevents binding of a second molecule while it is focused on catalysis of the first molecule.

The team also found that water molecules aren’t just used by the enzyme as “ballast” to drive the reaction. Very subtle networks of these water molecules, shown as constellations in the attached figure, distinguish the enzyme at each step along the reaction pathway. As crystallographic resolution improves, scientists may find that these bound water networks are more involved in protein function than previously imagined.