Mesodynamics in the SARS nucleocapsid measured by NMR field cycling

Clarkson, Michael W.; Lei, Ming; Eisenmesser, Elan Z.; Labeikovsky, Wladimir; Redfield, Alfred; Kern, Dorothee

In addition to extensive mesodynamics in the b-hairpin, the NMR relaxation data revealed motions with similar correlation times for loops encompassing residues 60-64 and 127-130. The MD simulations now provide a rationale for this observation: during the simulations, direct and water-mediated hydrogen bonds form between several residues in the hairpin and these flexible loops. For example, the side-chain of R90 hydrogen-bonds temporarily to residues in both loops (Fig. 7c) . These interactions seem to be responsible for coordinating motions of the Fig. 6 Illustration of crossover behavior of R 1 rates and { 1 H}-15 N NOE field-dependence due to the timescale of internal motions. Relaxation rates (Abragam 1961) are predicted from spectral densities calculated from model-free parameters for a protein with a global correlation time of 11.9 ns, the value for our system. a R 1 values predicted from model 2 for S 2 = 0.85, s e = 13 ps (black line), and model 5 for S 2 f = 0.89, S 2 s = 0.71, and s s = 10 ps (orange line), s s = 100 ps (red line), s s = 500 ps (purple line), s s = 780 ps (green line), and s s = 1.0 ns (cyan line). The black and green lines correspond to actual fitted parameters for residues 142 (in the stable globular part of SARSN) and 94 (in the b-hairpin with complex motions), respectively. Note the crossover point for internal correlation times in the 0.5-1 ns range. b Predicted steady-state { 1 H}-15 N NOE values (same scheme). Note the strong increase in the NOE value with increasing field for internal correlation times in the 0.5-1 ns range. Arrows indicate fields used in this study hairpin and those loops, explaining the similarity of relaxation dispersions at these sites. Strikingly, the MD simulations elucidate the collective nature of the mesodynamics of the entire b-hairpin and the correlation of motions between the hairpin and the 60-64 loop. These correlations can be computed from the time traces of atomic fluctuations within one molecule through a covariance matrix (Fig. 7d) , emphasizing the value of MD simulations to complement the NMR experiments.