Nature of allosteric inhibition in glutamate racemase: Discovery and characterization of a cryptic inhibitory pocket using atomistic MD simulations and p Ka calculations

Katie L. Whalen, Kenneth B. Tussey, Steven R. Blanke, M. Ashley Spies

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
Pages (from-to)3416-3424
Number of pages9
JournalJournal of Physical Chemistry B
Volume115
Issue number13
DOIs
StatePublished - Apr 7 2011

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry

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