NMR characterization of partially folded and unfolded conformational ensembles of proteins

Abstract

Studies of unfolded and partially folded proteins provide important insight into the initiation and process of protein folding. This review focuses on the use of nmr in characterization of ensembles of proteins that model the early stages of folding. Analysis of an ensemble includes description of the number of conformations, their structure, relative populations, interconversion rates, and dynamics of subconformations. A chemically synthesized analogue of bovine pancreatic trypsin inhibitor (BPTI), [14-38](Abu), has provided a rare system for characterization of multiple partially folded conformations in slow exchange at near physiological conditions. Multidimensional nmr techniques coupled with selective labeling were used to probe different segments of the polypeptide chain. At each labeled site, there is evidence of slow interconversion between two families of partially folded conformations that in themselves are ensembles of rapidly interconverting conformers. All these conformers display significantly more order in the core relative to the rest of the molecule. For other variants of BPTI that are unfolded at equilibrium, the most ordered structure is also favored in the hydrophobic core residues of the native protein. This is consistent with the hypothesis that the residues that are the first to fold go on to form the most stable, structure-determining part of the protein.