Because malate dehydrogenase is closely tied to the citric acid cycle, studies have proposed and experimentally demonstrated that citrate is an allosteric regulator of malate dehydrogenase depending on the concentrations of L-malate and NAD. This may be due to deviations observed in the kinetic behavior of malate dehydrogenase at high oxaloacetate and L-malate concentrations. Experiments have shown that Citrate can both allosterically activate and inhibit the enzymatic activity of malate dehydrogenase. Citrate has been shown to inhibit the oxidation of L-malate when there are low levels of L-malate and NAD. However, in the presence of high levels of malate and NAD, citrate can stimulate the production of oxaloacetate. Although malate dehydrogenase is typically considered a reversible enzyme, it is believed that there is an allosteric regulatory site on the enzyme where citrate can bind to and drive the reaction equilibrium in either direction.
Glutamate has also been shown to inhibit malate dehydrogenase activity. Furthermore, it has been shown that alpha ketoglutarate dehydrogenase can interact with mitochondrial aspartate aminotransferase to form a complex, which can then bind to malate dehydrogenase, forming a ternary complex that reverses inhibitory action on malate dehydrogenase enzymatic activity by glutamate. Additionally, the formation of this complex enables glutamate to react with aminotransferase without interfering activity of malate dehydrogenase. The formation of this ternary complex also facilitates the release of oxaloacetate from malate dehydrogenase to aminotransferase. Kinetically, the binding of malate dehydrogenase to the binary complex of alpha ketoglutarate dehydrogenase and aminotrannferase has been shown to increase reaction rate of malate dehydrogenase because the Km of malate dehydrogenase is decreased when it is bound as part of this complex.