Dr. Yunfen He

Former Position: 
Research Project and Activities: 
Biomolecular systems properties investigation using various techniques including fluorescence, ATR/FTIR, THz-TDS, ForteBio Octet, Biacore, ELISA, uv-visible, circular dichroism, DSC, and light scattering.
PhD Conferred: 
PhD Thesis Title: 
The Interplay of Protein and Solvent Picosecond Dynamics: Experimental and Theoretical Studies
Thesis Abstract: 

Terahertz gap is located between microwaves and infrared. THz-TDS is based on the generation of subpicosecond terahertz pulses using ultrashort laser pulses with pulse durations of a few femtoseconds. From the spectroscopic point of view terahertz radiation excites the low frequency vibrations of molecules. Terahertz spectroscopy provides a new way to study protein dynamics in this critical frequency range. The strong temperature dependence of molecular flexibility near 200 K for proteins and polynucleotides hydrated above 30% by weight, dynamical transition, is one of the most significant phenomena of biomolecular dynamics. Measurements of the dynamical transition were performed for native, fully denatured and unstructured polypeptides using THz-TDS. The results reveal that the dynamical transition is independent of either tertiary or secondary structure. The transition are also found for shorter chain alanine peptides down to penta-alanine, which indicates that a quantitative predictive theory for the temperature dependence lies in the understanding of the interaction of the side chains of the poly peptide or poly nucleotide with the biological water. The far infrared vibrational modes can be calculated using harmonic or anharmonic normal mode analysis, and the resulting Density of States (DOS) strongly resembles the measured absorbance. A large contrast in the terahertz dielectric response between oxidized and reduced cytochrome c has already been observed experimentally. This large contrast has been associated with a change in the collective structural motions that related to protein flexibility. Molecular simulation results from quasiharmonic analysis and dipole-dipole correlation analysis are compared with the measurements to determine the relative contribution of correlated motions and diffusive motions to the measured dielectric response. The measured hydration dependence is reproduced by hydration dependence of quasiharmonic normal modes, but these modes calculations do not reproduce the oxidation dependence. Whereas dipole-dipole correlation analysis reproduces the oxidation dependence at the lowest hydration level, but surprisingly do not capture the hydration dependence. These results suggest that the hydration dependence in the THz response does in fact arise from changes in the vibrational modes, and the oxidation dependence arises from relaxational motions.

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Curriculum Vitae: 

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