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Protein Science (2007), 16:2378-2390. Published by Cold Spring Harbor Laboratory Press. Copyright © 2007 The Protein Society
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Scope and utility of hydrogen exchange as a tool for mapping landscapes

Sheila S. Jaswal1 and Andrew D. Miranker

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA

(RECEIVED May 10, 2007; FINAL REVISION July 25, 2007; ACCEPTED August 1, 2007)

The ability to determine conformational parameters of protein-folding landscapes is critical for understanding the link between conformation, function, and disease. Monitoring hydrogen exchange (HX) of labile protons at equilibrium enables direct extraction of thermodynamic or kinetic landscape parameters in two limiting extremes. Here, we establish a quantitative framework for relating HX behavior to landscape. We use this framework to demonstrate that the range of predicted global HX behavior for the majority of a set of characterized two-state proteins under near-native conditions does not readily span between both extremes. For most, stability may be quantitatively determined under physiological conditions, with semiquantitative boundaries on kinetics additionally determined using modest experimental perturbations to shift HX behavior. The framework and relationships derived in the simple context of two-state global folding highlight the importance of understanding HX across the entire continuum of behavior, in order to apply HX to map landscapes.

Keywords: hydrogen exchange; protein folding; two-state; conformational landscape; mass spectrometry


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