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Top-down structural analysis of posttranslationally modified proteins by Fourier transform ion cyclotron resonance-MS with hydrogen/deuterium exchange and electron capture dissociation

Authors

  • Jingxi Pan,

    1. UVic-Genome BC Proteomics Centre, Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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  • Christoph H. Borchers

    Corresponding author
    • UVic-Genome BC Proteomics Centre, Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
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    • Additional address: University of Victoria, Department of Biochemistry and Microbiology, Petch Building, Room 207, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada.


Correspondence: Dr. Christoph H. Borchers, University of Victoria, University of Victoria—Genome British Columbia Proteomics Centre, #3101–4464 Markham Street, Vancouver Island Technology Park, Victoria, BC V8Z 7X8, Canada

E-mail: christoph@proteincentre.com

Fax: +250-483-3238

Abstract

High-resolution structural characterization of posttranslationally modified proteins represents a challenge for traditional structural biology methods such as crystallography and NMR. In this study, we have used top-down hydrogen/deuterium exchange MS (HDX-MS) with precursor ion selection and electron capture dissociation to determine the impact of oxidative modification on calmodulin (CaM) at an average resolution of 2.5 residues, with complete sequence coverage. The amide deuteration status of native CaM determined by this method correlates well with previously reported crystallographic and NMR data. In contrast, methionine oxidation caused almost complete deuteration of all residues in the protein in 10 s. The oxidative-modification-induced secondary and tertiary structure loss can be largely recovered upon calcium ligation, which also resulted in a substantial increase of amide protection in three of the four calcium-binding loops in oxidatively modified CaM (CaMox). However, the structure of α-helix VI is not restored by cofactor binding. These results are discussed in terms of different target binding and activation capabilities displayed by CaM and CaMox. The isoform-specific top-down HDX structural analysis strategy demonstrated in this study should be readily applicable to other oxidatively modified proteins and other types of PTMs, and may help decipher the structure and function of specific protein isoforms.

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