Protein nuclear magnetic resonance spectroscopy in the new millennium

Abstract

Solution–state nuclear magnetic resonance (NMR) spectroscopy is a rich source of information that can be exploited to elicit the three–dimensional structure of proteins, the nature of their interactions with other molecules, as well as biological function and dynamic properties. Even though NMR was established in the field of chemistry by the early 1950s it was not until the early 1980s that the first three–dimensional solution structure of a small protein was determined. From that time on, however, NMR has come to play a major role in the field of structure–function research on proteins and other biological macromolecules. It would indeed be difficult to imagine that some of the latest developments in this field, for instance the rapid establishment of many larger proteins as mosaic multi–domain assemblies of independent folding units or our recent understanding of protein folding pathways, without the insights provided by NMR spectroscopy. Despite the substantial impact already contributed by the application of NMR to solve biological problems, it is perhaps still arguable that only a fraction of the experimental parameters that can be derived from NMR spectroscopic examination of proteins have so far been fully exploited. In the last decade, NMR spectroscopy has been boosted by enormous technical improvements, which strive to bypass the classical bottlenecks of structure–function studies of proteins. As a result of these new developments, a greater number of experimental NMR parameters can now be interpreted in a meaningful way, while others have recently become accessible for the first time. The turn of the century therefore appeared poised to witness a new spurt in both the development of new NMR techniques and the expansion of their routine application in protein research. The problems that have been plaguing protein NMR spectroscopists for many years – the bewildering complexity of overcrowded spectra, which can be impossible to analyse, fast nuclear relaxation in large molecules (molecular weight greater than 20 000) leading to low sensitivity, the relative paucity of experimental constraints in the calculation of three–dimensional molecular structures, for example – appear to have been overcome within a few years by the cooperative effect of technological and methodological innovations. These developments include the extension of isotope labelling from 15 N to 13 C and 2 H, the introduction of highly stable superconducting magnets with ever–increasing homogeneous magnetic–field strengths of 20 T (corresponding to a proton NMR frequency of 800 MHz) and higher, and the exploitation of the experimental consequences of newly rediscovered physical phenomena, such as the partial alignment in solution of proteins in strong magnetic fields or liquid crystals, and the interference effects of different mechanisms contributing to nuclear relaxation. It is therefore anticipated that the current pace in the development of NMR spectroscopy into a yet more powerful tool will speed up in the new millennium rather than slow down. In this paper, we will describe the basic principles behind the most important of the recent developments in protein NMR spectroscopy, which include aspects of spectrometer hardware and software, NMR experiments, isotope labelling and data analysis. These facets will then be discussed in terms of sample applications to illustrate their use as practical tools in addressing biological and biophysical phenomena at the molecular level.