Determination of protein secondary structure by Fourier transform infrared spectroscopy: A critical assessment

Abstract

The ultimate goal of structural studies of proteins is to gain insight into protein three-dimensional structure at highresolution level. This can often be accomplished by the application of techniques such as X-ray crystallography or multidimensional nuclear magnetic resonance (NMR) spectroscopy. However, high-resolution studies of proteins are not always feasible. For example, crystallographic studies require high-quality single crystals which for many proteins (e.g., the vast majority of membrane proteins) are not available. Furthermore, the question arises as to whether the relatively “static” structure in single crystals adequately represents the protein conformation in a complex and dynamic environment of living cells. There is a growing realization [e.g., Martinek et al. (1989)l that in vivo most proteins act in an interfacial environmeht where they form dynamic complexes with biological membranes, nucleic acids, polysaccharides, or other proteins. Aqueous buffers, from which protein crystals are usually grown, do not necessarily mimic well the conditions of protein functioning in vivo. NMR offers a somewhat better flexibility in studying protein structure in “biologically relevant” environments. However, the interpretation of NMR spectra of larger proteins is very complex, and the assignment of interproton distances generated by the NMR experiment is not always feasible; at present the technique is restricted to small proteins of less than approximately 15-20 kDa.