Temperature Dependence of the Amide I Frequency as a Probe of Solvent Accessibility of the Protein Backbone

Abstract

Infrared (IR) spectroscopy of proteins often focuses on the relationship between the amide I band and polypeptide secondary structure; IR spectra has been used to probe backbone conformation on a wide range of samples (solution, films, gels, and solids), at a broad range of time scales (from ns to days), and as a function of a variety of perturbations (solvent, ionic strength, presence of lipid membrane). Often ignored is the solvent dependence of the amide I mode. Solvent-backbone hydrogen bonding can have a large effect on the observed amide I frequency (1). In this work, we demonstrate that the temperature dependence of amide I bands can be used to determine the solvent exposure of the peptide backbone. We have compared the IR spectra as a function of temperature in a number of different protein systems, including small, alanine-based peptides that form alpha-helices in solution; short peptides that aggregate to form fibrous, beta-sheet rich fibrous structures; short, dynamic peptides lacking regular secondary structure; membrane-embedded peptides; and globular proteins. When backbone groups are buried from solvent, the amide I band frequencies are independent of temperature (in the range of 5°C to 75°C). By contrast, backbone groups exposed to (and hydrogen-bonded with) solvent water show a temperature dependence similar to that observed in solvated model compounds (2). When this approach is combined with specific isotope-labeling (3), site-specific information about solvent accessibility can be obtained from the variable-temperature IR spectra. (1) A. Starzyk, W. Barber-Armstrong, M. Sridharan and S. M. Decatur, Biochemistry, 2005, 44, 369. (2) K. E. Amunson and J. Kubelka J. Phys. Chem. B, 2007, 111, 9993. (3) S. M. Decatur, Acc. Chem. Res., 2006, 39, 169.