Validation of the CHARMM27 force field for nucleic acids using 2D nuclear overhauser effect spectroscopy

Abstract

Nuclear magnetic resonance spectroscopy offers a powerful method for validation of molecular dynamics simulations as it provides information on the molecular structure and dynamics in solution. We performed 10 ns MD simulations using the CHARMM27 force field of four palindromic oligonucleotides and compared the results with experimental NOESY data using the full relaxation matrix formalism. The correlation coefficients between theoretical and experimental data for the four molecular species under study ranged from 0.82 to 0.98 confirming the high quality of the selected force field and providing a valid basis for the identification of force field imperfections. Hence, we observed an unsatisfactory treatment of deoxyribose conformational equilibrium, which resulted in the overrepresentation of the energetically favorable C3'-endo conformation in the MD trajectory. Our developed approach for force field validation based on NMR NOESY spectral data is applicable to a wide range of molecular systems and appropriate force fields.