How well do time-averaged J-coupling restraints work?
A comparison is made of the consequences of using time-averaged and conventional vicinal (3)J-coupling restraints in molecular dynamics refinement of an adenosine nucleoside model system. The target values for the restraints are derived from a 3-ns unrestrained molecular dynamics simulation. A comparison of the results from the restrained refinements and the unrestrained trajectory reveals that while both restraint types (time-averaged and conventional) are capable of acceptably reproducing the averaged values of the restrained parameters, time-averaged J-coupling restraints allow a more realistic and thorough description of conformational fluctuations. The full description of conformational behavior for the sugar ring using time-averaged J-coupling restraints is in excellent agreement with the unrestrained results. J-coupling restraints can result in a localized 'heating effect' about the underlying torsion. This allows a restrained torsion to sample all low-energy rotomers separated by modest barriers in an appropriately weighted mixture that reproduces the J-restraint target value. This will generally be advantageous for experimentally derived data, though it can be misleading if all these low-energy rotomers did not contribute to the ensemble that yields the measured J-value. An analysis of how the force constant used in the restraint terms affects the refinement indicates that smaller force constants are to be preferred, and that constants in the range of K(j)≥0.4 kcal s(2)/mol are acceptably large to overcome the intrinsic preferences of the force field.
Vertex Pharmaceuticals Incorporated, 40 Allston Street, 02139-4211, Cambridge, MA, U.S.A..
D A
DA
Pearlman