Exploring one-state downhill protein folding in single molecules

Abstract

A one-state downhill protein folding process is barrierless at all conditions, resulting in gradual melting of native structure that permits resolving folding mechanisms step-by-step at atomic resolution. Experimental studies of one-state downhill folding have typically focused on the thermal denaturation of proteins that fold near the speed limit (ca. 10 6 s −1 ) at their unfolding temperature, thus being several orders of magnitude too fast for current single-molecule methods, such as single-molecule FRET. An important open question is whether one-state downhill folding kinetics can be slowed down to make them accessible to single-molecule approaches without turning the protein into a conventional activated folder. Here we address this question on the small helical protein BBL, a paradigm of one-state downhill thermal (un)folding. We decreased 200-fold the BBL folding-unfolding rate by combining chemical denaturation and low temperature, and carried out freediffusion single-molecule FRET experiments with 50-μs resolution and maximal photoprotection using a recently developed Troloxcysteamine cocktail. These experiments revealed a single conformational ensemble at all denaturing conditions. The chemical unfolding of BBL was then manifested by the gradual change of this unique ensemble, which shifts from high to low FRET efficiency and becomes broader at increasing denaturant. Furthermore, using detailed quantitative analysis, we could rule out the possibility that the BBL single-molecule data are produced by partly overlapping folded and unfolded peaks. Thus, our results demonstrate the onestate downhill folding regime at the single-molecule level and highlight that this folding scenario is not necessarily associated with ultrafast kinetics. P rotein folding is an ideal problem for single-molecule approaches because the simple collective behavior that is frequently observed in bulk experiments could hide an underlying complexity of myriads of microscopic folding pathways (1). Thus protein folding has been a major target for modern single-molecule experiments, including force-microscopy (2) and fluorescence (3). Among these, single-molecule FRET (SM-FRET) has the advantage of recapitulating the conventional bulk chemical unfolding experiments at the single-molecule level. SM-FRET methods have already made important contributions to protein folding, such as demonstrating the conversion between native and unfolded populations of two-state-like folding (4), resolving the chemical-denaturant-induced expansion of the unfolded state (5) and its nanosecond conformational dynamics (6), and setting upper bounds for folding transition-path times (7).Another important application is the characterization of the downhill folding scenario predicted by energy landscape theory (1). Downhill folding proteins have a maximal free-energy barrier (i.e., at the denaturation midpoint) below 3RT. (RT is thermal energy, where R is the gas constant and T is the temperature in Kelvin.) The barrier top is thus significantly populated, and ...

When fast is better: protein folding fundamentals and mechanisms from ultrafast approaches

“…The simulations folded most of these proteins into their native structure multiple times and with rates similar to those determined experimentally [177]. A key result was the confirmation that fast-folding proteins cross very small barriers, and that some of them truly fold in the one-state downhill fashion proposed by Muñoz and co-workers [130,139] (Figure 6). In the simulations, collapse and secondary structure occurred together to form a compact form in which a native-like topology was stabilized by a small subset of key long-range native contacts.…”

Slow Proton Transfer Coupled to Unfolding Explains the Puzzling Results of Single-Molecule Experiments on BBL, a Paradigmatic Downhill Folding Protein

“…For BBL, this problem has been circumvented performing SM-FRET experiments at a temperature low enough to slow down its folding kinetics by nearly 100-fold. When carried out at pH 6, SM-FRET experiments unambiguously demonstrated the one-state scenario for BBL unfolding [32]. However, similarly low temperature SM-FRET experiments performed previously on BBL at higher pH have revealed a denaturant-induced conversion between two species with higher and lower FRET efficiency ( E ) [33].…”

β-Structure within the Denatured State of the Helical Protein Domain BBL

“…During the past decade, a large body of data has been compiled and analysed to answer the question of folding cooperativity of this domain. It is being debated whether BBL folds via a barrier-limited two-state mechanism [7][8][9][10][11] or follows a one-state downhill transition without the presence of a free energy barrier [12][13][14][15]. Comparatively little attention has been paid to the denatured state of this domain.…”