Experiments that optically probe the translational motions and internal conformational transitions of biological macromolecules have the potential to enable mechanistic studies of biochemical processes in living cells. This work presents a novel `phase-selective' approach to fluorescence fluctuation spectroscopy that simultaneously monitors protein conformational transitions and nanometer center-of-mass displacements. Polarization- and intensity-modulated photo-excitation is combined with phase-sensitive signal detection to monitor the collective coordinate fluctuations from a large population of fluorescent molecules (N ~ 106). Test experiments are performed on DsRed, a tetrameric complex of fluorescent protein subunits. Thermally induced conformational transitions of the complex lead to fluctuations in the optical dipolar coupling between adjacent chromophore sites. Polarization-resolved equilibrium fluctuation trajectories provide the raw data necessary to determine time-correlation functions and probability distributions of coordinate displacements, which characterize conformational transitions of the DsRed complex.
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