Highly fluctuating protein structures revealed by variable-pressure nuclear magnetic resonance.

Abstract

Although our knowledge of basic folded structures of proteins has dramatically improved, the extent of our corresponding knowledge of higher-energy conformers remains extremely slim. The latter information is crucial for advancing our understanding of mechanisms of protein function, folding, and conformational diseases. Direct spectroscopic detection and analysis of structures of higher-energy conformers are limited, particularly under physiological conditions, either because their equilibrium populations are small or because they exist only transiently in the folding process. A new experimental strategy using pressure perturbation in conjunction with multidimensional NMR spectroscopy is being used to overcome this difficulty. A number of rare conformers are detected under pressure for a variety of proteins such as the Ras-binding domain of RalGDS, beta-lactoglobulin, dihydrofolate reductase, ubiquitin, apomyoglobin, p13(MTCP1), and prion, which disclose a rich world of protein structure between basically folded and globally unfolded states. Specific structures suggest that these conformers are designed for function and are closely identical to kinetic intermediates. Detailed structural determination of higher-energy conformers with variable-pressure NMR will extend our knowledge of protein structure and conformational fluctuation over most of the biologically relevant conformational space.