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Photoactive yellow protein (PYP) is a model system for studies on functional protein dynamics and the role of protein flexibility during function. Functional conformational change is initiated by anharmonic collective vibrational modes that absorb in the far infrared (FIR) or terahertz (THz) region. We have used THz time-domain spectroscopy (THz-TDS) to investigate changes in the flexibility of PYP with functional state change (initial pG state to pB photo intermediate) induced by dehydration and photo excitation for both thin films and solutions. We find that the THz absorbance follows the dehydration induced capture of the pB state, indicating that the loss of photo cycling with the pB dehydration transition may be associated with the loss of picosecond flexibility. For hydrated films we find that previous reports of THz sensitivity to the pG to pB transition are likely in error and either arise from system drift or heating effects. We find no change in the dielectric response with photo induced occupation of the pB state. We compare these results with computational results and find that the THz dielectric response is dominated by relaxational motions of the solvent and surface side chains.