Journal of Physical Chemistry B, Vol.116, No.1, 606-620, 2012
Probing Side-Chain Dynamics in Proteins by the Measurement of Nine Deuterium Relaxation Rates Per Methyl Group
We demonstrate the feasibility of the measurement of up to nine deuterium spin relaxation rates in (13)CHD(2) and (13)CH(2)D methyl isotopomers of small proteins. In addition to five measurable (2)H relaxation rates. in a (13)CH(2)D methyl group (Millet, O.; Muhandiram, D. R.; Skrynnikov, N. R; Kay, L. E. J. Am. Chem. Soc. 2002, 124, 6439-48), the measurement of additional four rates of (nearly) single-exponentially decaying magnetization terms in methyl groups of the (13)CHD(2) variety is reported. Consistency relationships between (2)H spin relaxation rates measured in the two different types of methyl groups are derived and verified experimentally for a subset of methyl-containing side chains in the protein ubiquitin. A detailed comparison of methyl-bearing side-chain dynamics parameters obtained from relaxation measurements in (13)CH(2)D and (13)CHD(2) methyls of ubiquitin at 10, 27, and 40 degrees C reveals that transverse (2)H relaxation rates in (13)CHD(2) groups are reliable and accurate reporters of the amplitudes of methyl 3-fold axis motions (S(axis)(2)) for protein molecules with global molecular tumbling times tau(C)> similar to 9 ns. For smaller molecules, simple correction of transverse (2)H relaxation rates in (13)CHD(2) groups is sufficient for the derivation of robust measures of order. Residue-specific distributions of S(axis)(2) are consistent with atomic-detail molecular dynamics (MD) results. Both (13)CHD(2)- and (13)CH(2)D-derived S(axis)(2) values are in good overall agreement with those obtained from 1 mu s MD simulations at all the three temperatures, although some differences in the site-specific temperature dependence between MD- and (2)H-relaxation-derived S(axis)(2) values are observed.