Modeling and Characterization of Protein Energy Landscape at Low Temperature using Spectral Hole Burning Spectroscopy

Modeling and Characterization of Protein Energy Landscape at Low Temperature using Spectral Hole Burning Spectroscopy Seyed Mahdi Najafi Shooshtari, PhD. Concordia University, 2013. Proteins play various important roles in living organisms. Understanding the way they can perform different tasks is a demanding goal for scientists. Since their structures are changing to certain extent in the process, and some flexibility is essential for proper functioning, knowledge about their static structures is not enough to understand the way they work. One of the tools for studying proteins is optical spectroscopy. However, proteins are almost incapable of light absorption in the visible range which makes them non reachable for direct measurements; therefore, indirect methods must be applied. Pigment embedded into (amorphous) solid can serve as a local reporter on static and dynamic properties of its environment. Using proteins with pigments embedded into them by Nature offers a good alternative to introducing local reporters by chemical or genetic manipulations. In our study we focus on pigment-protein complexes involved in photosynthesis, Thus, the results of this thesis can be used not only for understanding proteins in general (e.g. folding processes), but also have implications in the renewable energy field, ultimately helping us to produce more efficient solar cells. In the course of this thesis spectral hole burning is applied for studying the properties of protein energy landscapes at cryogenic temperatures. This technique is very useful for (partially) removing the ensemble averaging by exciting specified systems selectively. We demonstrate that tunneling and not barrier hopping is most likely responsible for spectral diffusion-related phenomena (including hole burning) observed at low temperatures, that barrier heights most likely obey Gaussian and not square root of V^-1 distribution proposed for other amorphous solids, and discuss which structural elements might participate in small conformational changes. In addition to our experimental studies, we are developing a model that more adequately reflects the multi-well protein energy landscapes than two-level system-based approaches used so far. The results are in reasonable agreement with experiment. Importantly, we demonstrate that protein systems in typical optical low-temperature experiments (hole burning or single molecule / complex spectroscopy) are far from thermodynamic equilibrium. This has to be kept in mind when interpreting the results of any optical experiments.