Ab initio density functional theory calculations and vibrational analysis of zinc-bound 4-methylimidazole as a model of a histidine ligand in metalloenzymes

Histidine is often found as a ligand in metalloenzymes. The imidazole side group has two nitrogen atoms capable of being protonated or of participating in metal binding. Hence, histidine can take on various metalbound and protonated forms in proteins. Because of its variable structural state, histidine often functions as a key amino acid residue in enzymatic reactions, Raman and TR spectroscopies have been used as powerful methods to investigate the structure of histidine in proteins. In an attempt to establish the Raman and IR markers reflecting the coordinated and protonated states of histidine, we have calculated the optimized geometry and vibrational frequencies of various forms of zinc(II) complexes of 4-methylimidazole (4-Melm), as a model of a histidine ligand, using the density functional theory (DFT) method. The effects of metal binding on the frequency and N-deuteration shift of the C4C5 stretching mode around 1600 cm(-1) and of the C5N1 stretch around 1100 cm(-1) were satisfactorily reproduced in calculation and explained by changes in the bond distances and the mixing of vibrations. Additionally, the calculated frequency of the Zn-imidazole stretching mode of neutral 4-Melm at 260-255 cm(-1) exhibited an upshift by similar to25 cm(-1) upon its deprotonation, being consistent with the experimental observation. Furthermore, assignments were done for the several ring vibrations in the 1510-1250 cm(-1) region that have previously been used as Raman markers of the metal-bound forms, The results provided a theoretical basis for use of these markers as a basis for determining the structure of histidine in proteins. Atomic charge calculations by the natural population analysis revealed that deprotonation of the Melm ligand decreased the charge of the Zn2+ ion and decreased the acidity of the water ligands. This suggests a possible role of the histidine ligand in controlling the catalytic reactions of metalloenzymes by changing its protonation state.