Probing Side-Chain Dynamics in Proteins by the Measurement of Nine Deuterium Relaxation Rates Per Methyl Group

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• 作者：Xinli Liao ; Dong Long ; Da-Wei Li ; Rafael Br眉schweiler ; Vitali Tugarinov
• 刊名：The Journal of Physical Chemistry B
• 出版年：2012
• 出版时间：January 12, 2012
• 年：2012
• 卷：116
• 期：1
• 页码：606-620
• 全文大小：1371K
• 年卷期：v.116,no.1(January 12, 2012)
• ISSN：1520-5207

文摘

We demonstrate the feasibility of the measurement of up to nine deuterium spin relaxation rates in ¹³CHD₂ and ¹³CH₂D methyl isotopomers of small proteins. In addition to five measurable ²H relaxation rates in a ¹³CH₂D methyl group (trib-group person-group-type="allauthors">Millet, O.; Muhandiram, D. R.; Skrynnikov, N. R.; Kay, L. E.trib-group> te>J. Am. Chem. Soc.te> 2002, 124, 6439鈭?8), the measurement of additional four rates of (nearly) single-exponentially decaying magnetization terms in methyl groups of the ¹³CHD₂ variety is reported. Consistency relationships between ²H 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 ¹³CH₂D and ¹³CHD₂ methyls of ubiquitin at 10, 27, and 40 掳C reveals that transverse ²H relaxation rates in ¹³CHD₂ groups are reliable and accurate reporters of the amplitudes of methyl 3-fold axis motions (S_tack">axis^tack">2) for protein molecules with global molecular tumbling times 蟿_C > 9 ns. For smaller molecules, simple correction of transverse ²H relaxation rates in ¹³CHD₂ groups is sufficient for the derivation of robust measures of order. Residue-specific distributions of S_tack">axis^tack">2 are consistent with atomic-detail molecular dynamics (MD) results. Both ¹³CHD₂- and ¹³CH₂D-derived S_tack">axis^tack">2 values are in good overall agreement with those obtained from 1 渭s MD simulations at all the three temperatures, although some differences in the site-specific temperature dependence between MD- and ²H-relaxation-derived S_tack">axis^tack">2 values are observed.