Efforts toward Developing Direct Probes of Protein Dynamics

A direct probe of specific protein vibrations would be of great value for the study of protein dynamics, but such probes have not been available.1 The use of conventional vibrational spectroscopy has been limited by the congestion of the protein vibrational spectrum. Previous studies have used isotopic labeling and differ-ence Fourier transform infrared (FTIR) spectroscopy to examine amide vibrations.2 Other studies have taken advantage of protein-bound ligands or nitrile-derivatized amino acids, which absorb in a region of the IR spectrum unobscured by other protein vibrations (1900-2300 cm-1).3 However, these studies do not directly probe protein vibrations. We have been developing a technique to directly study specific protein vibrations by synthesizing proteins that are site-specifically labeled with carbon-deuterium (C-D) bonds. Like amide bonds, C-D bonds report directly on protein dynamics, but they absor