Probing Side-Chain Dynamics of a Ribosome-Bound Nascent Chain Using Methyl NMR Spectroscopy

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Abstract
We report here the use of methyl NMR spectroscopy with a selective-excitation pulsing scheme to extract structural information about a ribosome-bound nascent chain, a complex with a molecular weight of more than 2 MDa and a sample concentration in the micromolar range. The carbon chemical shifts of methyl groups are particularly sensitive to the development of the tertiary structure of a protein it folds, and crucially for systems that are at the limit of acceptable signal-to-noise-ratios, methyl group spectroscopy has higher sensitivity than does backbone amide group-based NMR spectroscopy. Comparison of the side-chain methyl correlations of the ribosome-bound nascent chain to previously obtained backbone amide correlations reveals dynamical perturbations within the hydrophobic core of the folded domain, which are attributed to motional restriction of the nascent chain as a result of ribosome attachment. Methyl NMR spectroscopy therefore provides improved spectral quality and complementary structural information to that of the amide groups and hence promises to provide a greatly enhanced understanding of the molecular basis of cotranslational folding at atomic resolution.