New methods to assess protein folding and conformational dynamics

A protein’s folding and conformational energy landscape depends on a large number of molecular degrees of freedom and interactions. As a result, different proteins can follow different sequences of events moving toward the native state along the course of folding. For example, the underlying structural organization and ordering can occur locally first and then globally, or vice versa. In addition, the associated conformational transitions can take place over a wide range of timescales. Because of these complexities, arriving at a detailed assessment and understanding of the folding dynamics and mechanism of any protein via a single type of experiment is challenging, and sometimes impossible. As such, over the past two decades, many different experimental methods have been employed to study how proteins fold among which, the laser-induced temperature-jump (T-jump) technique has emerged as a powerful tool to measure protein folding kinetics occurring on the nanosecond and microsecond timescales. Herein, we further expand the utility of the T-jump technique. First, we introduce a new form of the T-jump technique (referred to as VIPT-jump) that can be used to distinguish between different folding mechanisms. Second, we apply the VIPT-jump concept to better understand the folding dynamics of an alanine-based α-helix, and, in conjunction with theoretical modeling, we are able to determine the long-sought microscopic rate constants of the helical nucleation and propagation processes. Third, we develop a new method to extend the time window of observation in a T-jump experiment to the millisecond timescale. In a parallel effort, we demonstrate that quenching the fluorescence of a dye molecule by a tryptophan residue via photoinduced electron transfer mechanism can be used to interrogate the conformational dynamics of proteins that are crucial for function. Applying this method to the M2 proton channel of the Influenza A virus allow us to determine, for the first time, the gating dynamics of the tryptophan tetrad in this membrane protein