Deuterium spin probes of side-chain dynamics in proteins. 2. Spectral density mapping and identification of nanosecond time-scale side-chain motions.
In the previous paper in this issue we have demonstrated that it is possible to measure the five different relaxation rates of a deuteron in (13)CH(2)D methyl groups of (13)C-labeled, fractionally deuterated proteins. The extensive set of data acquired in these experiments provides an opportunity to investigate side-chain dynamics in proteins at a level of detail that heretofore was not possible. The data, acquired on the B1 domain of peptostreptococcal protein L, include 16 (9) relaxation measurements at 4 (2) different magnetic field strengths, 25 degrees C (5 degrees C). These data are shown to be self-consistent and are analyzed using a spectral density mapping procedure which allows extraction of values of the spectral density function at a number of frequencies with no assumptions about the underlying dynamics. Dynamics data from 31 of 35 methyls in the protein for which data could be obtained were well-fitted using the two-parameter Lipari-Szabo model (Lipari, G.; Szabo, A. J. Am. Chem. Soc. 1982, 104, 4546). The data from the remaining 4 methyls can be fitted using a three-parameter version of the Lipari-Szabo model that takes into account, in a simple manner, additional nanosecond time-scale local dynamics. This interpretation is supported by analysis of a molecular dynamics trajectory where spectral density profiles calculated for side-chain methyl sites reflect the influence of slower (nanosecond) time-scale motions involving jumps between rotameric wells. A discussion of the minimum number of relaxation measurements that are necessary to extract the full complement of dynamics information is presented along with an interpretation of the extracted dynamics parameters.
Skrynnikov
Nikolai R
NR
Protein Engineering Network Centers of Excellence and Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario, Canada M5S 1A8.
Millet
Oscar
O
Kay
Lewis E
LE
D001426:Bacterial Proteins / Q000737:chemistry*; D003903:Deuterium; D008956:Models, Chemical; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D017434:Protein Structure, Tertiary; D013816:Thermodynamics
D001426:Bacterial Proteins; C055047:Ig L-binding protein, Peptostreptococcus; D003903:Deuterium