Impact of Collective Motions on Protein Function

Title: Impact of Collective Motions on Protein Function Proteins are molecular machines responsible for nearly all of life's processes. Proteins often must change their shape in order to do their work. How certain proteins can change shape so efficiently, and why others cannot, is not known. A possible answer lies in vibrations of these molecules. This project provides necessary data to improve calculations to predict protein shape changes. The work uses a unique experimental setup to measure protein vibrations, as well as a collaborative approach to improve the predictive power of calculations based on the experimental measurements. The research will train graduate students and undergraduates in interdisciplinary research (optical physics, molecular biology, materials science and computational chemistry). In addition, a large number of undergraduates and high school students will participate in experiential learning, with hands-on measurements and calculations on proteins that respond to light such as light harvesting proteins involved in photosynthesis. To increase international and cultural awareness, students, supported by a collaborator in Mexico, will participate in the research and produce instructional media in Spanish. The researchers will investigate the role of intramolecular motions in protein function by applying a unique tool developed to directly measure protein intramolecular vibrational motions: anisotropy terahertz microscopy (ATM). The work will focus on several bench marking proteins which have been extensively studied by other techniques to characterize structure and dynamics. Combined with molecular modeling, ATM measurements of photoactive yellow protein (PYP), chicken egg white lysozyme (CEWL) and dihydrofolate reductase (DHFR) and their mutants will identify long range structural motions that impact function. The measurements on PYP will examine if vibrations within the protein backbone enhance chromophore isomerization for photoactive proteins, such as light sensing protein in the eye, rhodopsin. The proposed measurements will determine if collective vibrations overlap the oscillations of the PYP chromophore, and if photocycling is impacted by detuning the frequencies. The measurements will also examine if remote mutations of CEWL and DHFR affect catalytic rates by perturbing the intramolecular dynamics. The PI and co-PI will refine approaches for calculating the isotropic and anisotropic terahertz absorbance of protein solutions and crystals, and develop methods for analysis of the motions corresponding to the observed resonances.