Application of circular dichroism-based assays to racemases and epimerases: Recognition and catalysis of reactions of chiral substrates by mandelate racemase.

Abstract

Racemases and epimerases have attracted much interest because of their astonishing ability to catalyze the rapid α-deprotonation of carbon acid substrates with high pKa values (∼13-30) leading to the formation of d-amino acids or various carbohydrate diastereomers that serve important roles in both normal physiology and pathology. Enzymatic assays to measure the initial rates of reactions catalyzed by these enzymes are discussed using mandelate racemase (MR) as an example. For MR, a convenient, rapid, and versatile circular dichroism (CD)-based assay has been used to determine the kinetic parameters accompanying the MR-catalyzed racemization of mandelate and alternative substrates. This direct, continuous assay permits real time monitoring of reaction progress, the rapid determination of initial velocities, and immediate recognition of anomalous behaviors. MR recognizes chiral substrates primarily through interactions of the phenyl ring of (R)- or (S)-mandelate with the hydrophobic R- or S-pocket at the active site, respectively. During catalysis, the carboxylate and α-hydroxyl groups of the substrate remain fixed in place through interactions with the Mg2+ ion and multiple H-bonding interactions, while the phenyl ring moves between the R- and S-pockets. The minimal requirements for the substrate appear to be the presence of a glycolate or glycolamide moiety, and a hydrophobic group of limited size that can stabilize the carbanionic intermediate through resonance or strong inductive effects. Similar CD-based assays may be applied to determine the activity of other racemases or epimerases with proper consideration of the molar ellipticity, wavelength, overall absorbance of the sample, and the light pathlength.