Deuterium/hydrogen exchange factors (χ) were measured for the backbone amide sites of the membrane-bound forms of the 50-residue fd coat protein and the 23-residue magainin2 peptide in lipid micelles by solution nuclear magnetic resonance spectroscopy. By combining kinetic and thermodynamic effects, deuterium/hydrogen exchange factors overcome the principal limitations encountered in the measurements of kinetic protection factors and thermodynamic fractionation factors for membrane proteins. The magnitudes of the exchange factors can be correlated with the structure and topology of membrane-associated polypeptides. In fd coat protein, residues in the transmembrane helix have exchange factors that are substantially smaller than those in the amphipathic surface helix or the loop connecting the two helices. For the amphipathic helical peptide, magainin2, the exchange factors of residues exposed to the solvent are appreciably larger than those that face the hydrocarbon portion of membrane bilayers. These examples demonstrate that deuterium/hydrogen exchange factors can be measured by solution NMR spectroscopy and used to identify residues in transmembrane helices as well as to determine the polarity of amphipathic helices in membrane proteins.
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We thank Drs. E. Komives for reading the manuscript and helpful remarks, F. Porcelli for helpful discussions in the course of the experiments, and M. Zasloff for the sample of magainin2 used in these experiments. This research was supported by grants RO1 GM29754 and PO1 GM56538 from the National Institute of General Medical Sciences. G. Veglia was supported by a postdoctoral fellowship from NOOPOLIS, Rome, Italy.