Katie Whalen - Nature of Allosteric Inhibition in Glutamate Racemase: Discovery and Characterization of a Cryptic Inhibitory Pocket Using Atomist MD Simulations and pKa Calculations

Version 1

      Publication Details (including relevant citation   information):

      J. Phys. Chem. B, 2011, 115 (13), pp 3416–3424

      DOI: 10.1021/jp201037t

      Publication Date (Web): March 11, 2011

      Copyright © 2011 American Chemical Society

      Abstract:

      Enzyme inhibition via allostery, in which the ligand binds   remotely from the active site, is a poorly understood phenomenon   and represents a significant challenge to structure-based drug   design. Dipicolinic acid (DPA), a major component of   Bacillus spores, is shown to inhibit glutamate racemase   from Bacillus anthracis, a monosubstrate/monoproduct   enzyme, in a novel allosteric fashion. Glutamate racemase has   long been considered an important drug target for its integral   role in bacterial cell wall synthesis. The DPA binding mode was   predicted via multiple docking studies and validated via   site-directed mutagenesis at the binding locus, while the   mechanism of inhibition was elucidated with a combination of Blue   Native polyacrylamide gel electrophoresis, molecular dynamics   simulations, and free energy and pKa  calculations. Inhibition by DPA not only reveals a novel cryptic   binding site but also represents a form of allosteric regulation   that exploits the interplay between enzyme conformational   changes, fluctuations in the pKa values of   buried residues and catalysis. The potential for future drug   development is discussed.

      Address (URL): http://dx.doi.org/10.1021/jp201037t