The enzyme catalase is among the most effective enzyme known, with rates approaching 200,000 catalytic events/second/subunit (near the diffusion-controlled limit). . The enzyme catalase is believed to have catalysed a reaction almost every time it encounters a substrate molecule.
The fact that the efficiency of a catalase at perfection limit seems to suggest that the enzyme has found a way to overcome the calculated diffusion limit to achieve more collisions and subsequently reactions Some ways that an enzyme could overcome the diffusion limit are as follows:
1. Enzyme complexes: The E.Coli dihydrolipoyl dehydrogenase enzyme complex is an enzyme complex providing "efficient feed through" of substrates between enzymes. Enzyme complexes are a common cellular mechanism for beating the diffusion limit.
2. Cellular Structure: The fact that catalases are bound by peroxisomes means that they will encounter substrate molecules that will bind to a catalase at a higher rate than they will in free solution. This is because the membrane, with its larger surface area, will attract substrate molecules to the catalase as its greater surface area will increase the likelihood that the diffusing substrate molecules will strike and bind onto it. The membrane also acts as a substrate magnet because it is hydrophilic, meaning that it attracts water. When it does this, it also brings the substrate molecules in the water closer for the catalases.
3. The effectiveness of the local concentration of a substrate is increased by binding sites of relatively low affinity. As a result, they help transfer the substrate to the active site and act like a buffer. Since most enzymes are larger than their substrates, only around 10 amino acids come in contact with the substrates. This very small portion of the enzyme is known as the active site of the enzyme. Some enzymes contain binding sites, which are cofactors needed for catalysis. Some small molecules of substrate even have their own binding sites in certain enzymes and this binding can provide feedback regulation by either increasing or decreasing the enzyme’s activity. The substrate’s relative speed and orientation can also be affected by binding.
4. Increased Effective Size: Sometimes, the N or C terminal ends of the chain may be partially unwound. With a weak substrate binding site near an N or C terminal, a protein in a more extended conformation could have a much larger effective surface area, and therefore a greater rate of encountering a substrate. An examination of the known structure for catalases should show whether the C or N terminal ends could be free in this way, and so increase the sphere of influence.
5. Bubble 'catalysis': When a dilute solution of hydrogen peroxide is shaken, additional energy is added to the system which increases the rate at which the catalase breaks down hydrogen peroxide to release water and oxygen. Also, the shaking of hydrogen peroxide produces oxygen bubbles, which could be a factor amplifying the rate of hydrogen peroxide decomposition, making the catalases appear closer to the diffusion limit than it really is.