Investigating Domain-Swapped Proteins by 19F NMR

Abstract

For most proteins under physiological conditions, the native functional state is a single, stable structure. However, certain circumstances may push protein folding into distinctly different structures. The most common alternative structures comprise different multimeric assemblies of identical polypeptide chains. Among thousands of homo-oligomeric protein structures, there is a small, but growing subset of ‘domain-swapped’ proteins1, in which the exchanged subunit in the oligomer is identical to the one in the corresponding monomer. For domain-swapped structures, the only structural difference between the monomer and the pseudo-monomeric unit in the multimer is the region that links the exchanging domains. Although no unifying molecular mechanism of domain swapping has been elucidated, it appears that domain swapping is closely associated with the unfolding/folding process of proteins. For some proteins, distinct intermediates may exist, while for others, complete un/folding may occur. We are studying the dynamics and conformational behavior of specific domain-swapped systems by 19F-NMR in order to gain a better mechanistic understanding of domain swapping. 1. Bennett MJ, Choe S, Eisenberg D. Refined structure of dimeric diphtheria toxin at 2.0 Å resolution. Protein Sci. (1994) 3: 1444-1463.