The Rop-Dimer: A Folded Protein Living Between Two Alternate Structures

Abstract

A central assumption in protein folding is that a protein's native state is unique and stable. The Rop-dimer (Repressor Of Primer) shows strong changes in its folding kinetics and binding ability to RNA upon mutation of its hydrophobic core. Computer simulations investigated the possibility of two competing conformations to explain these results. Given an equivalent energetic bias, both conformations show different kinetic accessibilities in these simulations. Thus Rop's mutational behavior was explained by a preference of the kinetically less favored Wild-Type conformation for slow (un)folding mutants. Faster (un)folding mutants should prefer the kinetically favored conformation. For specific mutants it was suggested that the protein's native state is constituted by two competing conformations. Inspired by these simulations, single-molecule FRET-measurements verified the suggestion of two competing conformations constituting the native ensemble. Despite the need of a large-scale conformational change to get from the one conformation to the other, it shows that for a specific mutant the same dimer can adopt both conformations over time without disassociation of its monomers or changes in environmental conditions.