Biology toolbox: Enzyme-substrate interactions and inhibition

How do enzymes and substrates interact?

There are two models for enzyme-substrate interactions:

Model 1: Lock and Key In this model, the shape of the active site and substrate complement in such a way that the substrate fits into the binding site perfectly. There’s some truth in the lock and key model in that enzymes do have active sites, which need to be filled with a substrate and interact with substrate through non-covalent interactions. The problem with this model is that if the substrate fitted the enzyme perfectly, catalysis would be hampered. This is because the enzyme needs to bring about a change to the substrate and not just bind it. The Lock and Key model explains that the enzyme needs to bind substrate, but once the reaction progresses to transition state and product formation, the active site would not be able to accommodate this change. This is the paradox of how enzymes work, they need to be able to bind specifically to substrate, but they also need to be able to turn the substrate into something else (product), which means those two things are at odds with each other. So the enzyme needs to bind the substrate slightly imperfectly in order to be able to turn it over, that is, convert it to product.

Figure 1: A diagram showing the Lock and Key model of enzyme-substrate interaction.

Model 2: Induced Fit In the Induced Fit model, the enzyme active site forms in response to substrate binding. In the diagram, sites a, b and c move in response to binding substrate. So initially the active site is not perfect, but upon binding, it is able to move, which puts the active site under strain. This strain is then able to elicit the energy that’s required for the reaction to occur by stabilizing the transition state and not just binding of the substrate. The enzyme carries out its work by inducing the substrate to take up a transition state on the path to the required product. Figure 2: A diagram showing the Induced Fit model of enzyme substrate interaction

Enzyme Inhibition

One of the best things about enzymes is that they can be regulated. Regulation is important as this is how a cell controls when a reaction takes place and when it does not. Enzymes are regulated by effector molecules which are most commonly inhibitors. One way of regulating enzymes is by inhibiting them. For example, the breakdown of glucose to pyruvate, glycolysis, is a multi-step process that involves 10 enzymes. The first enzyme in this pathway, hexokinase, which phosphorylates glucose to glucose 6-phosphate (G6P), is inhibited by its own product glucose 6-phosphate (G6P). This way the activity of hexokinase is dampened down to control glycolysis.

Figure 3: Hexokinase converts glucose to glucose 6-phosphate during glycolysis Note: G6P is very structurally similar to glucose (G6P= glucose with an added phosphate group).

There are two types of enzyme inhibition mechanism:

• Competitive inhibition
• Non-competitive inhibition

Competitive inhibition

Inhibition by this mechanism involves molecules that are similar to the substrate (substrate analogues) binding to the active site, inhibiting the reaction. They compete with the substrate for binding the enzyme active site. Reaction products that have similar structures to substrates can be used in a feedback loop to inhibit enzyme activity by competing with the substrate for the active binding site. For example G6P (example above) inhibits hexokinase by competing with glucose.

Figure 4: Animation of Competitive Inhibition

Noncompetitive inhibition:

Noncompetitive inhibitors don’t compete with substrate for the active site. Instead they bind to a site distant from the active site. This binding effects a conformational change to the structure of the enzyme that changes the shape of the active site in such a way that the active site can no longer accommodate substrate binding. This process of binding at one site to bring about an effect at a distance is called allostery. Noncompetitive inhibition is also known as allosteric inhibition.

Figure 5: Animation of Non-Competitive Inhibition

An example of allosteric inhibition is the inhibition of the phosphofructokinase (PFK) enzyme (also known as the pacemaker for its important role in regulating the rate of glycolysis, thus “setting the pace”), which catalyzes the ATP-dependent phosphorylation of fructose-6-phosphate to synthesise fructose 1,6-bisphosphate and ADP during glycolysis. When the ratio of ATP to ADP is high, ATP binds to the ATP binding site of this enzyme (which is distant to the active site) and inhibits the enzyme. This means that the cell senses that there is too much ATP around so it stops or slows down glycolysis by inhibiting PFK to stop it from making more ATP. This process is reversible. So when the ratio of ATP:AMP is lowered, the enzyme is activated to make more ATP.