Molecular Dynamics Simulation On Elliptical Deformation Of Light-harvesting Complex Ⅱ

Light harvesting complex II (LH2) can collect solar energy with high efficiency and quickly transfers energy to light harvesting complex I (LH1) and to reaction center(RC) providing enough energy for original charge reaction. Previous experiments showed that elliptical distortion of purple bacteria LH2 protein would reduce energy transfer efficiency in the process of photoelectric conversion. Accurate LH2 conformation and the structural changes of internal pigment molecules are reliable basis of studying energy transfer. So far, there is no technological studies for detailed elliptical structure of LH2 and its inner spatial arrangement change of B850 pigment molecules. On the basis of elliptical structure of LH2 by previous experiments, dynamics analysis on LH2’s elliptical distortion and LH2 in membrane DMPC and LDAO is studied with the method molecular dynamics in this paper. The main results are as follows:1.By steered molecular dynamics simulation, LH2 is imposed on effective external force and the whole elliptical distortion process from circle to ellipse is simulated. Eventually a rational elliptical conformation with a centrifugation rate of 0.45 to 0.68 and the whole process of pigment B850’s spatial arrangement mode are obtained. Distance between the close-distance pair chlorophyll molecules is significantly shortened compared to before with values all less than 8.119 A.18 chlorophyll molecules B850 are approximately distributed on the major axis of ellipse. Distance between close-distance pair chlorophyll molecules is more close and distance between far-distance pair chlorophyll molecules is farther. Our research is carried on in the molecular level and the experiment cannot do it.2. With our own program, detergent LDAO membranes with thickness of 9 A and 15 A for LH2 are built. Molecular dynamics simulation on LH2 in the above membranes is carried on and we get the following results. LH2 can reach a steady state in the above two membranes. In 9 A membrane, LH2 has stronger fluctuation compared with original configuration. In the two kinds of different thickness of membranes, elliptical distortion can be observed in LH2. The eccentricity of the two ellipses is 0.486 for 9 A and 0.309 for 15 A. In the process, the major axis of ellipse keeps unchanged and stretches in the same direction. Besides, pigment ring B850 has structural distortion. Distance between the majority of close-distance pair chlorophyll molecules is shorter to some extent compared with the original configuration and the others become longer. They are usually distributed around the minor axis; Trp(44,416,509,602,788,835) and Tyr(322,508) can continuously form hydrogen bonds with B850 chlorophyll molecules.3. With our own program, DMPC membranes with thickness of 9 A and 15 A are built for LH2. Molecular dynamics simulation on LH2 in the above membranes is carried on and we get the following results. LH2 can reach a steady state quickly in both membranes with weak and similar fluctuation. In both membranes, elliptical distortion can be observed in LH2. The centrifugation rate for the two ellipses is about 0.29. In the process, the major axis of ellipse stretches in the same direction. Distance between the majority of close-distance pair chlorophyll molecules is shorter to some extent compared with the original configuration. In the 9 A membrane, distance between close-distance pair chlorophyll molecules 858-859 is enlarged to 13 A. In the 15 A membrane, distance between close-distance pair chlorophyll molecules 849-850 is enlarged to 12.76 A and then shortened to 8.305 A, They are usually distributed around the minor axis, Trp(44,416,509,602,788, 835) can continuously form hydrogen bonds with B850 chlorophyll molecules.4. Compared with the pure water solution environment, DMPC and LDAO membranes for LH2 has certain double lipid stability. Elliptical distortion on LH2 is more obvious in LDAO membrances than in DMPC membrances.That conformation changing rules of LH2 and internal B850 chlorophyll molecules in dynamic environment are simulated from the molecular level for the first time is the innovation point in this paper. Furthermore, we have discussed the influence of LH2’s elliptical distortion on distances between close/far-distance pair chlorophyll molecules. Our research is benefit to providing reliable structure information for the following study on energy and charge transfer in chlorophyll rings and lays the basis for further study on energy and charge transfer in LH2-LH1 and LH2-LH1-RC.