Are time-averaged restraints necessary for nuclear magnetic resonance refinement? A model study for DNA.

A recently suggested method for refinement of structural data obtained from two-dimensional nuclear magnetic resonance experiments using molecular dynamics (MD) is explored. In this method, the time-averaged values of the appropriate internal co-ordinates of the molecule, calculated from the MD trajectory, are driven by restraints towards the experimental target values. This contrasts with most refinement procedures currently in use, where restraints are applied based on the instantaneous values of the appropriate co-ordinates. Both refinement methods are applied to the EcoRI restriction site DNA hexamer d(GAATTC)2, using target nuclear Overhauser enhancement distances derived from a one nanosecond unrestrained MD simulation of this structure. The resulting refined structures are compared to the results of the unrestrained MD trajectory, which serves as our "experimental" data. We show that although both methods can yield an average structure with the correct gross morphology, the new method allows both a much more realistic picture of inherent flexibility, and reproduces fine conformational detail better, such as sequence dependency. We also analyze the very long MD trajectory generated here (longer than any previously reported for a DNA oligomer), and find that significantly shorter simulations, typical of those frequently performed, may not yield acceptably reliable values for certain structural parameters.