Zinc's affect on proton transfer between imidazole and acetate predicted by ab initio calculations

Jamal El Yazal, Rachel R. Roe, Yuan-Ping Pang

Research output: Contribution to journalArticle

35 Citations (Scopus)

Abstract

We have recently reported proton dissociation energies of common zinc coordinates, in the presence and absence of the zinc divalent cation, that were obtained from large basis set density functional theory calculations, which suggest a possibility of imidazolate as a zinc coordinate in proteins. To investigate this possibility in further detail, we have searched for potential proton acceptors for the zinc-coordinated imidazole group, as potential proton donors in proteins, through a survey of zinc protein crystal structures and ab initio calculations. Herein, we report the result of our survey of the Protein Data Bank and the ab initio calculations using the B3LYP/6-311+G(d,p) and MP2/6-311+G(d,p) methods. The results reveal that the imidazole - acetate dyad is energetically less stable than the imidazolate-acetic acid dyad when the imidazole and imidazolate are coordinating to the zinc divalent cation, and vice versa in the absence of zinc. The results suggest that the carboxylate group of Asp(Glu) at the second coordination shell of a zinc complex in proteins is not a hydrogen bond acceptor but rather a proton acceptor for the zinc-coordinated imidazole.

Original languageEnglish (US)
Pages (from-to)6662-6667
Number of pages6
JournalJournal of Physical Chemistry B
Volume104
Issue number28
StatePublished - Jul 20 2000

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Proton transfer
imidazoles
Zinc
acetates
zinc
protons
Protons
proteins
Proteins
Divalent Cations
Positive ions
imidazole
cations
acetic acid
Acetic acid
Acetic Acid
carboxylates
Density functional theory
Hydrogen bonds
Crystal structure

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Engineering(all)

Cite this

Zinc's affect on proton transfer between imidazole and acetate predicted by ab initio calculations. / El Yazal, Jamal; Roe, Rachel R.; Pang, Yuan-Ping.

In: Journal of Physical Chemistry B, Vol. 104, No. 28, 20.07.2000, p. 6662-6667.

Research output: Contribution to journalArticle

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AB - We have recently reported proton dissociation energies of common zinc coordinates, in the presence and absence of the zinc divalent cation, that were obtained from large basis set density functional theory calculations, which suggest a possibility of imidazolate as a zinc coordinate in proteins. To investigate this possibility in further detail, we have searched for potential proton acceptors for the zinc-coordinated imidazole group, as potential proton donors in proteins, through a survey of zinc protein crystal structures and ab initio calculations. Herein, we report the result of our survey of the Protein Data Bank and the ab initio calculations using the B3LYP/6-311+G(d,p) and MP2/6-311+G(d,p) methods. The results reveal that the imidazole - acetate dyad is energetically less stable than the imidazolate-acetic acid dyad when the imidazole and imidazolate are coordinating to the zinc divalent cation, and vice versa in the absence of zinc. The results suggest that the carboxylate group of Asp(Glu) at the second coordination shell of a zinc complex in proteins is not a hydrogen bond acceptor but rather a proton acceptor for the zinc-coordinated imidazole.

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