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Fast Helix Formation in the B Domain of Protein A Revealed by Site-Specific Infrared Probes

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Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
Cite this: Biochemistry 2015, 54, 9, 1758–1766
Publication Date (Web):February 23, 2015
Copyright © 2015 American Chemical Society

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    Comparison of experimental and computational protein folding studies can be difficult because of differences in structural resolution. Isotope-edited infrared spectroscopy offers a direct measure of structural changes involved in protein folding at the single-residue level. Here we demonstrate the increased resolution of site-specific infrared probes to the peptide backbone in the B domain of staphylococcal protein A (BdpA). 13C═18O-labeled methionine was incorporated into each of the helices using recombinant protein expression. Laser-induced temperature jumps coupled with infrared spectroscopy were used to probe changes in the peptide backbone on the submillisecond time scale. The relaxation kinetics of the buried helices, solvated helices, and labeled positions were measured independently by probing the corresponding bands assigned in the amide I region. Using these wavelength-dependent measurements, we observe a fast nanosecond phase and slower microsecond phase at each position. We find at least partial formation of helices 1–3 in the fast intermediate state that precedes the transition state. These measurements provide direct, time-resolved experimental evidence of the early formation of partial helical structure in helices 1 and 3, supporting folding models proposed by computer simulations.

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    A van’t Hoff analysis, temperature-dependent FTIR spectra of I32M and A47M BdpA mutants, the protocol for removing EDTA contamination, and figures of relaxation kinetics of WT, Y15M, and A47M BdpA. This material is available free of charge via the Internet at

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