A dynamic structure for the acyl-enzyme species of the antibiotic aztreonam with the Citrobacter freundii β-lactamase revealed by infrared spectroscopy and molecular dynamics simulations

Alan Shaun Wilkinson, Patrick K. Bryant, Samy Meroueh, Malcolm G P Page, Shahriar Mobashery, Christopher W. Wharton

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

Infrared difference spectra show that at least 4 conformations coexist for the ester carbonyl group of the stable acyl - enzyme species formed between the antibiotic aztreonam and the class C β-lactamase from Citrobacter freundii. A novel method for the assignment of the bands that arise from the ester carbonyl group has been employed. This has made use of the finding that the infrared absorption intensity of aliphatic esters is surprisingly constant, so a direct comparison with simple model esters has been possible. This has allowed a clear distinction to be made between ester and amide (protein) absorptions. The polarity of the conformer environment varies from hexane-like to strongly hydrogen-bonded. We assume that the conformer with the lowest frequency (1690 cm-1) and hence the strongest hydrogen-bonding is the singular conformer observed in the X-ray crystallographic structure, since a good interaction via two hydrogen bonds with the oxyanion hole is seen. Molecular dynamics simulation by the method of locally enhanced sampling revealed that the motion of the ester carbonyl of the acyl - enzyme species in and out of the oxyanion hole is facile. The simulation revealed two pathways for this motion that would go through intermediates that first break one or the other of the two hydrogen bonds to the oxyanion hole, prior to departure of the carbonyl moiety out of the active site. It is likely that such motion for the acyl - enzyme species might also occur with more typical β-lactam substrates for β-lactamases, but their detection in the more rapid time scale may prove a challenge.

Original languageEnglish (US)
Pages (from-to)1950-1957
Number of pages8
JournalBiochemistry
Volume42
Issue number7
DOIs
StatePublished - Feb 25 2003
Externally publishedYes

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Citrobacter freundii
Aztreonam
Molecular Dynamics Simulation
Molecular dynamics
Infrared spectroscopy
Spectrum Analysis
Esters
Anti-Bacterial Agents
Computer simulation
Enzymes
Hydrogen
Hydrogen bonds
Lactams
Infrared absorption
Hexanes
Hydrogen Bonding
Amides
Conformations
Catalytic Domain
X-Rays

ASJC Scopus subject areas

  • Biochemistry

Cite this

A dynamic structure for the acyl-enzyme species of the antibiotic aztreonam with the Citrobacter freundii β-lactamase revealed by infrared spectroscopy and molecular dynamics simulations. / Wilkinson, Alan Shaun; Bryant, Patrick K.; Meroueh, Samy; Page, Malcolm G P; Mobashery, Shahriar; Wharton, Christopher W.

In: Biochemistry, Vol. 42, No. 7, 25.02.2003, p. 1950-1957.

Research output: Contribution to journalArticle

Wilkinson, Alan Shaun ; Bryant, Patrick K. ; Meroueh, Samy ; Page, Malcolm G P ; Mobashery, Shahriar ; Wharton, Christopher W. / A dynamic structure for the acyl-enzyme species of the antibiotic aztreonam with the Citrobacter freundii β-lactamase revealed by infrared spectroscopy and molecular dynamics simulations. In: Biochemistry. 2003 ; Vol. 42, No. 7. pp. 1950-1957.
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