Molecular dynamics simulations of the intramolecular proton transfer and carbanion stabilization in the pyridoxal 5′-phosphate dependent enzymes l-dopa decarboxylase and alanine racemase

Yen Lin Lin, Jiali Gao, Amir Rubinstein, Dan Thomas Major

Research output: Contribution to journalReview articlepeer-review

21 Scopus citations

Abstract

Molecular dynamics simulations using a combined quantum mechanical and molecular mechanical (QM/MM) potential have been carried out to investigate the internal proton transfer equilibrium of the external aldimine species in l-dopa decarboxylase, and carbanion stabilization by the enzyme cofactor in the active site of alanine racemase. Solvent effects lower the free energy of the O-protonated PLP tautomer both in aqueous solution and in the active site, resulting a free energy difference of about - 1 kcal/mol relative to the N-protonated Schiff base in the enzyme. The external aldimine provides the dominant contribution to lowering the free energy barrier for the spontaneous decarboxylation of l-dopa in water, by a remarkable 16 kcal/mol, while the enzyme l-dopa decarboxylase further lowers the barrier by 8 kcal/mol. Kinetic isotope effects were also determined using a path integral free energy perturbation theory on the primary 13C and the secondary 2H substitutions. In the case of alanine racemase, if the pyridine ring is unprotonated as that in the active site, there is destabilizing contribution to the formation of the α-carbanion in the gas phase, although when the pyridine ring is protonated the contribution is stabilizing. In aqueous solution and in alanine racemase, the α-carbanion is stabilized both when the pyridine ring is protonated and unprotonated. The computational studies illustrated in this article show that combined QM/MM simulations can help provide a deeper understanding of the mechanisms of PLP-dependent enzymes. This article is part of a Special Issue entitled: Pyridoxal Phosphate Enzymology.

Original languageEnglish (US)
Pages (from-to)1438-1446
Number of pages9
JournalBiochimica et Biophysica Acta - Proteins and Proteomics
Volume1814
Issue number11
DOIs
StatePublished - Nov 2011

Bibliographical note

Funding Information:
This work has been supported by the National Institutes of Health (Grant GM46736 ) and the Israel Science Foundation .

Keywords

  • Carbanion stabilization
  • Enzymatic decarboxylation
  • Internal proton transfer of PLP
  • QM/MM simulation
  • Racemization

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