Alanine racemase free energy profiles from global analyses of progress curves

M. Ashley Spies, Joshua J. Woodward, Mitchell R. Watnik, Michael D. Toney

Research output: Contribution to journalArticle

52 Citations (Scopus)

Abstract

Free energy profiles for alanine racemase from Bacillus stearothermophilus have been determined at pH 6.9 and 8.9 from global analysis of racemization progress curves. This required a careful statistical design due to the problems in finding the global minimum in mean square for a system with eight adjustable parameters (i.e., the eight rate constants that describe the stepwise chemical mechanism). The free energy profiles obtained through these procedures are supported by independent experimental evidence: (1) steady-state kinetic constants, (2) solvent viscosity dependence, (3) spectral analysis of reaction intermediates, (4) equilibrium overshoots for progress curves measured in D 2O, and (5) the magnitudes of calculated intrinsic kinetic isotope effects. The free energy profiles for the enzyme are compared to those of the uncatalyzed and the PLP catalyzed reactions. At pH 6.9, PLP lowers the free energy of activation for deprotonation by 8.4 kcal/mol, while the inclusion of apoenzyme along with PLP additionally lowers it by 11 kcal/mol.

Original languageEnglish (US)
Pages (from-to)7464-7475
Number of pages12
JournalJournal of the American Chemical Society
Volume126
Issue number24
DOIs
StatePublished - Jun 23 2004

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Alanine Racemase
Free energy
Apoenzymes
Geobacillus stearothermophilus
Viscosity
Isotopes
Reaction intermediates
Deprotonation
Kinetics
Bacilli
Enzymes
Spectrum analysis
Rate constants
Chemical activation

ASJC Scopus subject areas

  • Chemistry(all)

Cite this

Alanine racemase free energy profiles from global analyses of progress curves. / Spies, M. Ashley; Woodward, Joshua J.; Watnik, Mitchell R.; Toney, Michael D.

In: Journal of the American Chemical Society, Vol. 126, No. 24, 23.06.2004, p. 7464-7475.

Research output: Contribution to journalArticle

Spies, M. Ashley ; Woodward, Joshua J. ; Watnik, Mitchell R. ; Toney, Michael D. / Alanine racemase free energy profiles from global analyses of progress curves. In: Journal of the American Chemical Society. 2004 ; Vol. 126, No. 24. pp. 7464-7475.
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