Dynamics of lysine side-chain amino groups in a protein studied by heteronuclear 1H-15N NMR spectroscopy

Alexandre Esadze, Da Wei Li, Tianzhi Wang, Rafael Brüschweiler, Junji Iwahara

Research output: Contribution to journalArticle

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Abstract

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 NH3 + groups by NMR spectroscopy and computation. By using 1H-15 N heteronuclear correlation experiments optimized for 15NH3 + moieties, we have analyzed the dynamic behavior of individual lysine NH3 + groups in human ubiquitin at 2 °C and pH 5. We modified the theoretical framework developed previously for CH3 groups and used it to analyze 15N relaxation data for the NH3 + groups. For six lysine NH3 + 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 NH3 + groups, slower dynamics occurring on a millisecond time scale have also been detected for Lys27. The NH3 + 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 NH3 + groups analyzed by NMR. We compared the experimental order parameters for the lysine NH3 + groups with those from a 1 μs 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 NH3 + 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.

Original languageEnglish (US)
Pages (from-to)909-919
Number of pages11
JournalJournal of the American Chemical Society
Volume133
Issue number4
DOIs
StatePublished - Feb 2 2011

Fingerprint

Nuclear magnetic resonance spectroscopy
Lysine
Magnetic Resonance Spectroscopy
Proteins
Ubiquitin
Nuclear magnetic resonance
Ubiquitination
Experiments
Computer simulation
Molecular Dynamics Simulation
Hydrogen Bonding
Computer Simulation
Molecular dynamics
Proton Magnetic Resonance Spectroscopy
Hydrogen bonds
Degradation

ASJC Scopus subject areas

  • Chemistry(all)
  • Catalysis
  • Biochemistry
  • Colloid and Surface Chemistry

Cite this

Dynamics of lysine side-chain amino groups in a protein studied by heteronuclear 1H-15N NMR spectroscopy. / Esadze, Alexandre; Li, Da Wei; Wang, Tianzhi; Brüschweiler, Rafael; Iwahara, Junji.

In: Journal of the American Chemical Society, Vol. 133, No. 4, 02.02.2011, p. 909-919.

Research output: Contribution to journalArticle

Esadze, Alexandre ; Li, Da Wei ; Wang, Tianzhi ; Brüschweiler, Rafael ; Iwahara, Junji. / Dynamics of lysine side-chain amino groups in a protein studied by heteronuclear 1H-15N NMR spectroscopy. In: Journal of the American Chemical Society. 2011 ; Vol. 133, No. 4. pp. 909-919.
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