Coarse Graining Methods for Studies of Structural Changes in Intermediate States of Membrane Proteins

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The function of a protein is expressed through the structural change or fluctuation. In this work, we studied experimentally and theoretically the mechanism of the structural change of membrane proteins, using bacteriorhodopsin as a model system of the membrane protein.We measured the denaturation behaviors of bacteriorhodopsin, a typical intrinsic membrane protein, changing the temperature and the light illumination conditions. At room temperature, the structure of bacteriorhodopsin recovered from photointermediate states to the ground state, while the recovery from the excited states was incomplete at the temperature around 50 ℃. We could conclude from extensive photobleaching experiments at various temperatures that the structure of bacteriorhodopsin is partly stabilized by polar loop segments which particularly contribute to the recovering process of the photocycle. Further experiments of the photobleaching at high temperature for mutated and chemically modified bacteriorhodopsin w … More ill lead to the physical mechanism of the photocycle.A novel method for theoretical structure prediction was developed on the basis of the preivious results of denaturation experiments. Supposing that seven transmembrane helices are continuum rods with the polarity distribution of their surfaces, we calculated the interaction energy of a seven-helix system. The positioning and orientation of seven helices could be predicted by minimizing the interaction energy. The most preferable configuration of helices was very similar to the actual structure of bacteriorhodopsin. In the framework of this method, the protonation and deprotonation of amino acid residues within the helical regions strongly affect the helix configuration. In fact, the calculation suggested that the positioning and the tilting of helices change during the photocycle in accordance with the structural analyzes of intermediate states of bacteriorhodopsin. The problem of the contribution of loop segments to the structural change should be solved for the understanding of the functioning mechanism. Less