Folding and Unfolding of the Short Light-Triggered β-Hairpin Peptide AzoChignolin Occurs within 100 ns

Biomolecular infrared spectroscopy: making time for dynamics

Time resolved infrared spectroscopy of biological molecules has provided a wealth of information relating to structural dynamics, conformational changes, solvation and intermolecular interactions. Challenges still exist however arising from the wide range of timescales over which biological processes occur, stretching from picoseconds to minutes or hours. Experimental methods are often limited by vibrational lifetimes of probe groups, which are typically on the order of picoseconds, while measuring an evolving system continuously over some 18 orders of magnitude in time presents a raft of technological hurdles. In this Perspective, a series of recent advances which allow biological molecules and processes to be studied over an increasing range of timescales, while maintaining ultrafast time resolution, will be reviewed, showing that the potential for real-time observation of biomolecular function draws ever closer, while offering a new set of challenges to be overcome.

Mechanism of β-hairpin formation in AzoChignolin and Chignolin

AzoChignolin is a photoswitchable variant of the mini-protein Chignolin with an azobenzene (AMPP) replacing the central loop. AzoChignolin is unfolded with AMPP in the trans-isomer. Transition to the cis-isomer causes β-hairpin folding similar to Chignolin. The AzoChignolin system is excellently suited for comprehensive analysis of folding nucleation kinetics. Utilizing multiple long-time MD simulations of AzoChignolin and Chignolin in MeOH and water, we estimated Markov models to examine folding kinetics of both peptides. We show that while AzoChignolin mimics Chignolin's structure well, the folding kinetics are quite different. Not only folding times but also intermediate states differ, particularly Chignolin is able to fold in MeOH into an α-helical intermediate which is impossible to form in AzoChignolin. The Markov models demonstrate that AzoChignolin's kinetics are generally faster, specifically when comparing the two main microfolding processes of hydrophobic collapse and turn formation. Photoswitchable loops are used frequently to understand the kinetics of elementary protein folding nucleation. However, our results indicate that intermediates and folding kinetics may differ between natural loops and photoswitchable variants.