[Generalized ordering parameter S2 for N-H peptide bonding as measure of the conformational flexibility of proteins: comparison of algorithms of S2 calculation from molecular dynamics simulation data].
NMR spectroscopy in combination with molecular dynamics (MD) simulation technique is a powerful tool for investigation of biomolecule conformations. In the present study we compare the two algorithms of calculation of the generalized order parameter S2 for the peptide N-H bond from MD simulation data. The program based on this algorithm has been written and the effect of an adjustible parameter on results of calculation was studied. HIV-1 protease MD simulation was performed during 7.36 ns using GROMACS 3.1.4. software package. The calculated order parameter values are in good agreement with those obtained by other authors using NMR.
Koval'skiĭ
D B
DB
Ivanova
O S
OS
Dubina
V N
VN
Kanibolotskiĭ
D S
DS
Korneliuk
A I
AI
D000465:Algorithms; D016333:HIV Protease / Q000737:chemistry*; D015497:HIV-1 / Q000201:enzymology*; D006859:Hydrogen / Q000737:chemistry*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009584:Nitrogen / Q000737:chemistry*; D019906:Nuclear Magnetic Resonance, Biomolecular; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation
D010455:Peptides; D006859:Hydrogen; D016333:HIV Protease; D009584:Nitrogen