Liu Sui
July 8th2012
Larsen Lab
Dept. of Chemistry, UC Davis
One Shield Ave.
Davis, CA 95616
The Photoactive Yellow Protein (PYP) and cyanobacteriochromes (CBCR) are biological photosensing proteins that respond to the surrounding light environment around the organism for its growth and survival. Upon light absorption, PYP and CBCR go through large scale conformational changes, which happen via several intermediates over multiple timescales (from picosecond to milliseconds). The goal of this project is to resolve the conformational changes of the PYP and CBCR from initiation to formation of the signaling state (>ms to seconds) with early timescale (picoseconds) transient Förster Resonance Energy Transfer (FRET) technique. We will use a fluorescent probe to measure the protein dynamics and analyze it based on transient FRET dynamics from endogenous tryptophan residues. Fluorescent dyes are commonly used in medical imaging, analytical chemistry and biology, and in our research to dye chromophores and determine distances between them based on the measurement of FRET efficiency. Computational programs such as Visual Molecular Dynamics and MATLAB will be used as output visualization and analyzing tools to determine the protein structural changes. The primary impact of this research is to characterize the transient structural deformation of a protein environment that propagates and initiates the signal transduction pathways.