Analysis of Sub-tc and Supra-tc Motions in Protein Gb1 Using Molecular Dynamics Simulations

The functions of proteins depend on the dynamical behavior of their native states on a wide range of timescales. To investigate these dynamics in the case of the small protein Gb1, we analyzed molecular dynamics simulations with the model- free approach of nuclear magnetic relaxation. We found amplitudes of fast timescale motions (sub-tc, where tc is the rotational correlation time) consistent with S 2 obtained from spin relaxation measurements as well as amplitudes of slow timescale motions (supra-tc) in quantitative agreement with S 2 order parameters derived from residual dipolar coupling measurements. The slow timescale motions are associated with the large variations of the 3 J couplings that follow transitions between different conforma- tional substates. These results provide further characterization of the large structural fluctuations in the native states of proteins that occur on timescales longer than the rotational correlation time.