Журнал компьютерных наук и системной биологии

Quantum-Chemical Study of the Propensity of the Amino Acid Pairs for the Peptide Bond Formation

Abstract

Jumber Kereselidze, George Mikuchadze and Lia Bobokhidze

The Modern method of quantum chemistry - the density functional theory (DFT) was used to quantitative describe the formation of the peptide bond between amino acid pairs. In particular the formula of parameter of propensity (Kp), which is a function of six variables: the length and order of the CO and NH bonds, (RCO, RNH, PCO PNH), the activation energy for the formation of the peptide bond (ΔE#), and difference between charges of the carbon atom of the carbonyl group and the amino nitrogen atom (Δq) was constructed. By means of the proposed formula the Kp parameter for 400 amino acid pairs was calculated. Among them only 26 amino acid pairs are most likely to take part in the synthesis of proteins that have been selected based on the value of the parameter Kp. This approach may have important meaning for quantitative description of the amino acid sequences in proteins.