Summary
We describe a new penalty function for use in restrained molecular dynamics simulations which allows experimental J-coupling information to be enforced as a time-averaged, rather than instantaneous, quantity. The pseudo-energy term has been formulated in terms of a calculated J value (a measured quantity) rather than the relevant dihedral angle (a derived quantity). This accounts for the distinct non-linearity of the coupling constant with respect to either Cartesian coordinates or dihedral angles. Example simulations of the cyclic decapeptide antamanide show the procedure's ability to enforce experimental restraints while exploring a large region of conformational space and producing a relatively small disturbance of the physical force field.
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Abbreviations
- MD:
-
molecular dynamics
- rms:
-
root-mean-square
- NOE:
-
nuclear Overhauser effect
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Torda, A.E., Brunne, R.M., Huber, T. et al. Structure refinement using time-averaged J-coupling constant restraints. J Biomol NMR 3, 55–66 (1993). https://doi.org/10.1007/BF00242475
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DOI: https://doi.org/10.1007/BF00242475