Journal article
Nature of Allosteric Inhibition in Glutamate Racemase: Discovery and Characterization of a Cryptic Inhibitory Pocket Using Atomistic MD Simulations and pK(a) Calculations
The journal of physical chemistry. B, Vol.115(13), pp.3416-3424
04/07/2011
DOI: 10.1021/jp201037t
PMCID: PMC3072873
PMID: 21395329
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 pK(a) 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 pK(a) values of buried residues and catalysis. The potential for future drug development is discussed.
Details
- Title: Subtitle
- Nature of Allosteric Inhibition in Glutamate Racemase: Discovery and Characterization of a Cryptic Inhibitory Pocket Using Atomistic MD Simulations and pK(a) Calculations
- Creators
- Katie L. Whalen - University of Illinois Urbana-ChampaignKenneth B. Tussey - Center for Biophysics and Computational BiologySteven R. Blanke - University of Illinois SystemM. Ashley Spies - University of Illinois Urbana-Champaign
- Resource Type
- Journal article
- Publication Details
- The journal of physical chemistry. B, Vol.115(13), pp.3416-3424
- DOI
- 10.1021/jp201037t
- PMID
- 21395329
- PMCID
- PMC3072873
- NLM abbreviation
- J Phys Chem B
- ISSN
- 1520-6106
- eISSN
- 1520-5207
- Publisher
- American Chemical Society
- Number of pages
- 9
- Grant note
- U54AI057156 / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of Allergy & Infectious Diseases (NIAID) AI076830; AI057156 / NIH; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA
- Language
- English
- Date published
- 04/07/2011
- Academic Unit
- Pharmaceutical Sciences and Experimental Therapeutics; Biochemistry and Molecular Biology; Medicinal and Natural Products Chemistry
- Record Identifier
- 9984293074702771
Metrics
15 Record Views