[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.
Kanibolotskiĭ
D S
DS
Ivanova
O S
OS
Miroshnichenko
N S
NS
Lesniak
V V
VV
D000465:Algorithms; D016333:HIV Protease / Q000737:chemistry*; D006859:Hydrogen / Q000737:chemistry*; D006860:Hydrogen Bonding; D008956:Models, Chemical; D008958:Models, Molecular; D009584:Nitrogen / Q000737:chemistry*; D019906:Nuclear Magnetic Resonance, Biomolecular; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation
D010446:Peptide Fragments; D006859:Hydrogen; D016333:HIV Protease; C514803:p16 protease, Human immunodeficiency virus 1; D009584:Nitrogen