Deuterium Spin Probes of Side-Chain Dynamics in Proteins. 2. Spectral Density Mapping and Identification of Nanosecond Time-Scale Side-Chain Motions
journal contributionposted on 2002-05-11, 00:00 authored by Nikolai R. Skrynnikov, Oscar Millet, Lewis E. Kay
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 13CH2D methyl groups of 13C-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 °C (5 °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.
density profilesrelaxation measurementsdynamics datarotameric wellsDeuterium Spin Probesdynamics trajectorydynamics informationfield strengths35 methylsLiparidensity mapping proceduredensity functionrelaxation ratesdynamics parametersB 1 domain13 CH 2 D methyl groups2. Spectral Density Mappingpeptostreptococcal protein L4 methyls