Dr. Yanting Deng

Theoretically intramolecular structural vibrations of the protein backbone at terahertz (THz) frequencies provide access to functional conformational change, allosteric control and electrostatic and energy state transformation. However the identification of these thermal motions has remained elusive. While the vibrational density of states and isotropic absorption are broad, featureless, and relatively insensitive to protein functional state and mutation, collective vibrations can be isolated based on their directionality using aligned samples (realized with protein crystals) and anisotropic THz microscopy. In this dissertation, I first present the characterization and identification of the thermal collective motions in the picosecond range, for two proteins in the photoactive protein family: photoactive yellow protein (PYP) and orange carotenoid protein (OCP). Specifically I present the intramolecular vibrations measurements for PYP cycling between the ground and photo-activated states. Supporting molecular dynamics simulation and calculation has also been detailed for THz spectral assignment for the holo-protein and the chromophore respectively. For OCP, the picosecond thermal molecular mobility is identified by the net THz absorption and dynamical transition temperature under both photo and chemical activation. I argue that both the susceptibility of OCP to a large conformational change and its interaction with PB are associated with changes in the long-range picosecond structural flexibility. In the last chapter, I present a newly-developed technique: stationary sample anisotropic THz microscopy (SSATM) for fast determination of THz linear dichroism of microscopic samples. The method avoids sample rotation and shortens the measurement time by a factor of 16. SSATM uses a circular polarized THz probe realized by a high transmission (~50%) and broadband (~10 THz) quarter waveplate. The key innovation is the development of near field EO detector response that is independent of the THz polarization by the synchronization of THz and detected NIR polarizations, and the s-p auto balancing module. To structurally and fully map the vibrations of the protein, I present the measurements of lysozyme with the dependence of crystal lattice symmetry groups, and the OCP in the function of photo-intermediate states, and demonstrate the reproducibility and capability of the SSATM of mapping internal structural dynamics of biomacromolecules.