Zinc's Affect on Proton Transfer between Imidazole and Acetate Predicted by ab Initio Calculations

• Published in: The journal of physical chemistry. B 2000-07, Vol.104 (28), p.6662-6667
• Main Authors: El Yazal, Jamal, Roe, Rachel R, Pang, Yuan-Ping
• Format: Article
• Language: English
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/jp994283x

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.