Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear (1)H-(15)N NMR Spectroscopy.
Dynamics of Lysine Side-Chain Amino Groups in a Protein Studied by Heteronuclear (1)H-(15)N NMR Spectroscopy.
J Am Chem Soc. 2010 Dec 27;
Authors: Esadze A, Li DW, Wang T, Bru?schweiler R, Iwahara J
Despite their importance in macromolecular interactions and functions, the dynamics of lysine side-chain amino groups in proteins are not well understood. In this study, we have developed the methodology for the investigations of the dynamics of lysine NH(3)(+) groups by NMR spectroscopy and computation. By using (1)H-(15)N heteronuclear correlation experiments optimized for (15)NH(3)(+) moieties, we have analyzed the dynamic behavior of individual lysine NH(3)(+) groups in human ubiquitin at 2 °C and pH 5. We modified the theoretical framework developed previously for CH(3) groups and used it to analyze (15)N relaxation data for the NH(3)(+) groups. For six lysine NH(3)(+) groups out of seven in ubiquitin, we have determined model-free order parameters, correlation times for bond rotation, and reorientation of the symmetry axis occurring on a pico- to nanosecond time scale. From CPMG relaxation dispersion experiment for lysine NH(3)(+) groups, slower dynamics occurring on a millisecond time scale have also been detected for Lys27. The NH(3)(+) groups of Lys48, which plays a key role as the linkage site in ubiquitination for proteasomal degradation, was found to be highly mobile with the lowest order parameter among the six NH(3)(+) groups analyzed by NMR. We compared the experimental order parameters for the lysine NH(3)(+) groups with those from a 1 ?s molecular dynamics simulation in explicit solvent and found good agreement between the two. Furthermore, both the computer simulation and the experimental correlation times for the bond rotations of NH(3)(+) groups suggest that their hydrogen bonding is highly dynamic with a subnanosecond lifetime. This study demonstrates the utility of combining NMR experiment and simulation for an in-depth characterization of the dynamics of these functionally most important side-chains of ubiquitin.
PMID: 21186799 [PubMed - as supplied by publisher]
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PubMed