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

蛋白质的功能是通过结构变化或波动来表达的。本论文以细菌视紫红质（bacteriorhodopsin）为膜蛋白的模型体系，从实验和理论上研究了膜蛋白结构变化的机理，测定了细菌视紫红质（bacteriorhodopsin）在温度和光照条件下的变性行为。在室温下，细菌视紫红质的结构从光中间态恢复到基态，而在50 ℃左右从激发态的恢复是不完全的。我们可以得出结论，从广泛的光漂白实验在不同的温度下，细菌视紫红质的结构是部分稳定的极性环段，特别是有助于恢复过程的光循环。细菌视紫红质w突变体和化学修饰体高温光漂白的进一步实验 ...更多信息 在此基础上，提出了一种新的理论结构预测方法。假设七个跨膜螺旋是表面极性分布的连续杆，我们计算了七个跨膜螺旋系统的相互作用能。通过最小化相互作用能可以预测7个螺旋的位置和取向。最优选的螺旋构型与细菌视紫红质的实际结构非常相似。在这种方法的框架下，螺旋区域内氨基酸残基的质子化和去质子化强烈影响螺旋构型。事实上，计算表明，在光循环过程中，螺旋的位置和倾斜度的变化与细菌视紫红质中间态的结构分析一致。要理解其作用机制，必须解决环段对结构变化的贡献问题。少

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