HOW WELL DO TIME-AVERAGED J-COUPLING RESTRAINTS WORK

A comparison is made of the consequences of using time-averaged and co nventional vicinal 3J-coupling restraints in molecular dynamics refine ment of an adenosine nucleoside model system. The target values for th e restraints are derived from a 3-ns unrestrained molecular dynamics s imulation. A comparison of the results from the restrained refinements and the unrestrained trajectory reveals that while both restraint typ es (time-averaged and conventional) are capable of acceptably reproduc ing 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 b ehavior for the sugar ring using time-averaged J-coupling restraints i s in excellent agreement with the unrestrained results. J-coupling res traints can result in a localized 'heating effect' about the underlyin g torsion. This allows a restrained torsion to sample all low-energy r otomers separated by modest barriers in an appropriately weighted mixt ure that reproduces the J-restraint target value. This will generally be advantageous for experimentally derived data, though it can be misl eading if all these low-energy rotomers did not contribute to the ense mble that yields the measured J-value. An analysis of how the force co nstant used in the restraint terms affects the refinement indicates th at smaller force constants are to be preferred, and that constants in the range of K(j) greater-than-or-equal-to 0.4 kcal s2/mol are accepta bly large to overcome the intrinsic preferences of the force field.