Reply to Huang et al.: Slow proton exchange can duplicate the number of species observed in single-molecule experiments of protein folding

In contrast to the implications of the letter by Huang et al. (1), our previous work unambiguously showed that the protein BBL under denaturing conditions is a single, partly unfolded state (one-state folding) rather than a mix of folded and unfolded molecules (two-state folding) (2). This conclusion was based on ultrahigh-resolution single-molecule (sm) FRET experiments (>1 photon per microsecond) performed on a long BBL construct at pH 6 and using urea as denaturant. We also demonstrated analytically that the single peak in the FRET histograms of BBL could not be explained as two rapidly interconverting states (2).

Additionally, we reported supplementary bulk and smFRET data on the shorter BBL variant of Huang et al. (QNND-BBL), mentioning discrepancies with their guanidinium chloride (GdmCl) denaturation results (2). For these experiments, we used phosphate buffer instead of Mops. We have confirmed that the …

↵¹To whom correspondence should be addressed. E-mail: vmunoz{at}cib.csic.es.