Proton character of the peptide unit in the Ca2+-binding sites of calcium pump

The effect of forming calcium pump structures in biological systems on the proton character of the peptide unit has been studied theoretically using the density-functional theory calculations with a large basis set. One acetic acid, one acetate, and three acetamide molecules as well as the modeling peptide unit (MPU) have been employed to mimic the amino acid residues forming the Ca2+-binding sites. To highlight the limiting case of the Ca2+-binding effect on the proton property and the proton countertransport possibility in the direction opposite to the ion, the MPU bounded by the bare or the hydrated Ca2+ has also been investigated. The natural bond orbital (NBO) analysis indicates that the increase of the p-character of the (N-H) sigma orbital results in weakening of the N-H bond which is lengthened when a Ca2+ ion is introduced to the MPU. Calculated NMR shielding sigma(H1) of the MPU shifts upfield upon the Ca2+ ion combination, which reveals the donating of the electron from the amide H as represented by the increase of the calculated positive natural charge for amide H of the MPU. Moreover, the proton affinities (PA) and gas-phase basicities (GB) for the amide nitrogen active site of the MPU are reduced; that is, the acidity of the amide hydrogen gets stronger because of the influence of the Ca2+ ion. To prove the transport possibility of the N-H proton in the direction opposite to the Ca2+ ion along the N-H...O=C hydrogen bond in the helical peptide linkage, NH3 and H2O are used here to assist the dissociation of the amide H of the MPU, and the calculated results show the notable decrease of the deprotonation energies compared to that of the case without this assistance. Moreover, calculated results also reveal that the variation of the quantities discussed here for amide H of the MPU gets smaller when the acidity of Ca2+ ion decreases. Ionization states of the acidic residues forming the Ca2+-binding sites may influence the activity of the amide H of the MPU and further affect the transport tendency of the peptide unit proton in the direction opposite to Ca2+.