[New algorithm for calculation of N-H peptide bond order parameter by the method of molecular dynamic modeling]

A new algorithm was proposed for calculation of N-H bond order parameter from molecular dynamics (MD) trajectories. The MD simulation of the HIV-1 protease (3.4.23.16) with monoprotonated active centre was performed for the algorithm verification. It has been shown that the protease in aqueous solution at pH 3.5-6.5 adopts a set of conformations, which are intermediate between the "open" and "closed" ones. The N-H bond order parameters calculated from the MD trajectory are in agreement with experimental NMR data.