TY - JOUR
T1 - Nature of allosteric inhibition in glutamate racemase
T2 - Discovery and characterization of a cryptic inhibitory pocket using atomistic MD simulations and p Ka calculations
AU - Whalen, Katie L.
AU - Tussey, Kenneth B.
AU - Blanke, Steven R.
AU - Spies, M. Ashley
PY - 2011/4/7
Y1 - 2011/4/7
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=79953276827&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=79953276827&partnerID=8YFLogxK
U2 - 10.1021/jp201037t
DO - 10.1021/jp201037t
M3 - Article
C2 - 21395329
AN - SCOPUS:79953276827
SN - 1520-6106
VL - 115
SP - 3416
EP - 3424
JO - Journal of Physical Chemistry B
JF - Journal of Physical Chemistry B
IS - 13
ER -