Browsing by Author "Sarabi, Daniel"

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    Structural Dynamics of Rhodopsins using Time-Resolved X-ray Solution Scattering
    (2022-05-11) Sarabi, Daniel
    Light is one of the most important sources of energy and environmental signals, and many organisms adapt in response to the presence of light. This is made possible through specialised proteins called photoreceptors. Rhodopsins are made light-sensitive via the addition of a retinal chromophore, and activated by specific wavelengths of light, which propagates a cascade of structural changes, allowing the protein to carry out it’s function. Microbial rhodopsins have been found to act as light-driven proton pumps, light-gated ion channels or receptors for phototaxis, whereas rhodopsin in higher eukaryotes such as the human eye, is responsible for low-light vision. Time-resolved X-ray solution scattering (TR-XSS) is a sub-field of structural biology which can detect secondary structural changes in proteins as they evolve along their functional pathways in real time. The method addresses many of the limitations of serial crystallography, however, structural modelling is more challenging due to the measured information being one-dimensional. Further challenges arise in structural interpretation of TR-XSS data recorded from integral membrane proteins, due to the presence of a detergent micelle surrounding the protein. In our previous modelling, the interference between the protein and micelle was not addressed, and in this thesis we utilize molecular dynamics simulations to explicitly incorporate the X-ray scattering cross-term between an integral membrane protein and it’s surrounding micelle when modelling against TR-XSS data from photo-activated rhodopsins within a detergent micelle. The influence of the detergent micelle and micelle size on difference X-ray scattering was determined, correction for the solvent excluded volume was made and candidate motions were identified using these protocols for modelling against TR-XSS data of bacteriorhodopsin, SRII in isolation and in complex with it’s transducer protein HrII, and Channelrhodopsin 2. The analysis tools and protocols developed in this thesis should provide a framework for the analysis and structural modelling of light-activated integral membrane proteins as a powerful complement to other biophysical methods.