Action-Self Quenching: Dimer-Induced Fluorescence Quenching of Chromophores as a Probe for Biomolecular Structure

To obtain a more detailed understanding of how structure influences the function and interaction of biomolecules, it is important to develop structure sensitive techniques to probe these relationships. Alongside <i>in vivo</i> and <i>in vitro</i> techniques, it is instructive to consider <i>in vacuo</i> methodologies: for example native mass spectrometry, ion mobility mass spectrometry, and FRET. Here, we propose a novel technique for probing biomolecular structure based on the changes in photophysics of a chromophore upon dimer formation. Comparison of solution and gas phase measurements on a doubly tagged tripeptide shows that dimer-induced fluorescence quenching is accompanied by an increase in photofragmentation yield. The 12–28 fragment of amyloid beta was used to show that as the charge state was increasedpreviously shown to cause a conformational change from compact random coil to extended helical structurethe disappearance of a band at 495 nm could be correlated with the level of self-quenching. The presence of features in the action spectrum of the +3 charge state of both quenched and unquenched chromophores allowed inference of multiple conformations. Single wavelength measurements on doubly tagged ubiquitin cations were performed to show that the technique is feasible on a small protein. These results demonstrate that self-quenching is a sensitive and fast gas-phase probe of biomolecular structure that can be directly linked to solution phase measurements. Further, it is capable of probing very small changes in conformation, making it complementary to FRET based techniques, which are insensitive at very short chromophore separations.