Question

The enzyme succinate dehydrogenase acts on succinate and convert it to fumarate tn the TCA cycle . In the presence of malonate the apparent km reduced but the vmax remains unaltered. What can you conclude about the type of inhibition by malonate and the structure of malonate?

Answer 1

In the reaction of oxidation of succinate to fumarate, two hydrogen atoms are removed from substrate by flavin adenine dinucleotide (FAD), a prosthetic group that is tightly attached to succinate dehydrogenase .Flavin adenine dinucleotide (FAD) is an essential cofactor for SDH enzyme.

FAD attachment is stimulated by, the presence of the iron-sulfur subunit and citric acid cycle intermediates such as succinate, malate, or fumarate . The substrate analog malonate is a competitive inhibitor of the succinate dehydrogenase complex.Malonate is a competitive inhibitor of the enzyme succinate dehydrogenase: malonate binds to the active site of the enzyme without reacting, and so competes with succinate, the usual substrate of the enzyme. Malonate, like succinate, is a dicarboxylate that binds to cationic amino acid residues in the active site of the succinate dehydrogenase complex. However, malonate cannot undergo oxidation because it lacks the -CH2 - CH2- group necessary for dehydration. To study the effects of a competitive inhibitior on the activity of succinate dehydrogenase, malonate will be added to a reaction mixture; malonate is sufficiently different from succinate that it cannot de dehydrogenated, i.e. malonate is not metabolized.Enzyme inhibitors are molecular agents that interfere with catalysis, slowing or halting enzymatic reactions. One common type of reversible inhibition is called as competitive. A competitive inhibitor competes with the substrate for the active site of an enzyme.

Competitive inhibition can be analyzed quantitatively by steady-state kinetics. Because the inhibitor binds reversibly to the enzyme, the competition can be biased to favor the substrate simply by adding more substrate. When substrate far exceeds inhibotor, the probability that an inhibitor molecule will bind to the enzyme is minimized and the reaction exhibits a normal Vmax​. However, the substrate at which reaction rate is half that of Vmax​, the apparent Km​, increases in the presence of inhibitor. One common example of competitive inhibition is inhibition of the enzyme succinate dehydrogenase by malonate.

Malonate ions inhibiting the enzyme succinate dehydrogenase. This enzyme catalyses the conversion of succinate ions to fumarate ions. The modern names are:

• malonate: propanedioate

• succinate: butanedioate

• fumarate: trans-butenedioate

• Malonate ions and succinate ions have very similar shapes.

• The similar shape lets the malonate ions bind to the active site, but the lack of the CH2-CH2 bond in the centre of the ion stops any further reaction taking place.The malonate ions therefore block the active site - but remember that this is reversible. The malonate ions will break away and free up the enzyme again. The malonate ions are in competition for the site - they aren't destroying it.

  If the succinate ions have a greater concentration than the malonate ions, by chance they will get access to the site more often than the malonate ions. That means that you can overcome the effect of a competitive inhibitor by increasing the concentration of the substrate.

Structure of Malonate ;

Malonate(2-) is a dicarboxylic acid dianion obtained by the deprotonation of the carboxy groups of malonic acid. It has a role as a human metabolite and a mitochondrial respiratory-chain inhibitor. It is a conjugate base of a malonate.(1-)

Molecular Formula: C3H3O4(−) or C3H2O4-2