Fluorescence Measurements and Molecular Dynamics Simulations of Protein Conformational Fluctuations

摘要

The amount of useful information derived from tandem mass spectrometry (MS/MS) measurements of biomolecules depends in part on the ion structure and dynamics. We report laser-induced fluorescence measurements of trapped, unsolvated biomolecular ions derivatized with a fluorescent dye. This technique is particularly sensitive to local interactions between the dye and a natural quencher, Trp, and also between the dye and protenated side chains. This has been the basis for our development of methods1,2 to apply these interactions to probe the dynamics of conformational fluctuations of proteins in a solvent-free environment as a function of temperature and charge state. Recently we have added the experimental capability to perform measurements of the excited state decay rates and also the dispersed spectrum of the dye to help isolate the Trp quenching interaction from the dye-charge effects. These experiments are complemented by molecular dynamics (MD) simulations to elucidate the details of the conformational fluctuations which lead to the experimentally observed changes in fluorescence intensity and lifetime.