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Protein Science (2005), 14:1922-1928. Published by Cold Spring Harbor Laboratory Press. Copyright © 2005 The Protein Society
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FOR THE RECORD

Characterization of peptide folding nuclei by hydrogen/deuterium exchange-mass spectrometry

Xue Li1, Robin J. Hood2, William J. Wedemeyer2,3 and J. Throck Watson1,2

1 Departments of Chemistry, 2 Biochemistry, and 3 Physics, Michigan State University, East Lansing, Michigan 48824, USA

(RECEIVED March 15, 2005; FINAL REVISION April 18, 2005; ACCEPTED April 27, 2005)

Covalently linked pairs of well-chosen peptides can be good model systems for protein folding studies because they can adopt stable secondary, side-chain, and tertiary structure under certain conditions. We demonstrate a method for characterizing the structure in such peptide pairs by hydrogen/deuterium exchange of individual amide groups analyzed by collision-induced dissociation tandem mass spectrometry, in concert with circular dichroism spectroscopy. We apply the method to two peptides (and their three possible pairs) from bovine pancreatic trypsin inhibitor to address specific hypotheses regarding the stabilization of local secondary structure by long-range interactions.

Keywords: secondary structure; hydrogen/deuterium exchange; mass spectrometry; collision-induced dissociation; autonomous folding unit; structured peptides; bovine pancreatic trypsin inhibitor (BPTI)

Abbreviations: H-bond, hydrogen bond • HDX, hydrogen/deuterium exchange • NMR, nuclear magnetic resonance • MS, mass spectrometry • MALDI-TOF, matrix-assisted laser-desorption/ionization time-offlight • CID-MS/MS, collision-induced dissociation tandem mass spectrometry • BPTI, bovine pancreatic trypsin inhibitor • TCEP, tris-(2-carboxyethyl)phosphine hydrochloride • TFA, trifluoroacetic acid • GdnHCl, guanidinium hydrochloride • HPLC, high-performance liquid chromatography • CD, circular dichroism • FA, formic acid

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.051458905.

Reprint requests to: J. Throck Watson, Departments of Chemistry and Biochemistry, Michigan State University, East Lansing, MI 48824, USA; e-mail: watsonj{at}msu.edu; fax: (517) 353-9334.


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