Mesodynamics in the SARS nucleocapsid measured by NMR field cycling

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

Processing and fitting of relaxation data Spectra were processed using NMRPipe (Delaglio et al. 1995) software and analyzed using NMRViewJ (Johnson and Blevins 1994) . For R 1 and R 2 , peak intensities were fit to mono-exponential decay equations using an in-house program. Errors in the measurements were assessed from base-plane noise and duplicated points; because of the interleaved acquisition, both approaches resulted in similar errors. Model-free fits were performed using relxn2.2 (Lee et al. 1999 ) and the graphical front-end rvi (Clarkson et al. 2006) ; only relaxation data from 50.7 MHz and above were used in the final fits. Data were weighted by error for v 2 minimization, which for purposes of fitting was defined as the larger of the fitted error or 5%. Excluding flexible residues (Vuister et al. 1993 ), a s m of 11.9 ns was determined by global minimization and used in all subsequent fits. An estimation of tumbling anisotropy using local fits of s m and the 1SSK structure (Huang et al. 2004 ) with the program qfit (Lee et al. 1999 ) indicated D k /D \ of 0.94, and anisotropy was therefore disregarded in subsequent fitting procedures. Errors in single fits were assessed using a Monte Carlo method in which random values consistent with the measured errors were added to the original data and the fit repeated. The total number of Monte Carlo simulations used was 150 for each residue.