Differentiation of compact and extended conformations of di-ubiquitin conjugates with lysine-specific isopeptide linkages by ion mobility-mass spectrometry

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Modification of ubiquitin, a key cellular regulatory polypeptide of 76 amino acids, to polyubiquitin conjugates by lysine-specific isopeptide linkage at one of its seven lysine residues has been recognized as a central pathway determining its biochemical properties and cellular functions. Structural details and differences of distinct lysine-isopeptidyl ubiquitin conjugates that reflect their different functions and reactivities, however, are only partially understood. Ion mobility spectrometry (IMS) combined with mass spectrometry (MS) has recently emerged as a powerful tool for probing conformations and topology involved in protein interactions by an electric field-driven separation of polypeptide ions through a drift gas. Here we report the conformational characterization and differentiation of Lys63- and Lys48-linked ubiquitin conjugates by IMS-MS. Lys63- and Lys48-linked di-ubiquitin conjugates were prepared by recombinant bacterial expression and by chemical synthesis using a specific chemical ligation strategy, and characterized by high-resolution Fourier transform ion cyclotron resonance mass spectrometry, circular dichroism spectroscopy, and molecular modeling. IMS-MS was found to be an effective tool for the identification of structural differences of ubiquitin complexes in the gas phase. The comparison of collision cross-sections of Lys63- and Lys48-linked di-ubiquitin conjugates showed a more elongated conformation of Lys63-linked di-ubiquitin. In contrast, the Lys48-linked di-ubiquitin conjugate showed a more compact conformation. The IMS-MS results are consistent with published structural data and a comparative molecular modeling study of the Lys63- and Lys48-linked conjugates. The results presented here suggest IMS techniques can provide information that complements MS measurements in differentiating higher-order polyubiquitins and other isomeric protein linkages.

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ISO 690JUNG, Ji Eun, Nicholas A. PIERSON, Andreas MARQUARDT, Martin SCHEFFNER, Michael PRZYBYLSKI, David E. CLEMMER, 2011. Differentiation of compact and extended conformations of di-ubiquitin conjugates with lysine-specific isopeptide linkages by ion mobility-mass spectrometry. In: Journal of The American Society for Mass Spectrometry. 2011, 22(8), pp. 1463-1471. ISSN 1044-0305. eISSN 1879-1123. Available under: doi: 10.1007/s13361-011-0158-0
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@article{Jung2011-08Diffe-16762,
  year={2011},
  doi={10.1007/s13361-011-0158-0},
  title={Differentiation of compact and extended conformations of di-ubiquitin conjugates with lysine-specific isopeptide linkages by ion mobility-mass spectrometry},
  number={8},
  volume={22},
  issn={1044-0305},
  journal={Journal of The American Society for Mass Spectrometry},
  pages={1463--1471},
  author={Jung, Ji Eun and Pierson, Nicholas A. and Marquardt, Andreas and Scheffner, Martin and Przybylski, Michael and Clemmer, David E.}
}
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