Steered Molecular Dynamics Simulation of Light-harvesting Antenna Protein Complex II
Based on molecular dynamics, the information regarding the ellipsoidal structure of light-harvesting antenna complex II(LHACII) using existing experiments was obtained. The elliptic aberration process of LHACII was investigated. Through using Steered molecular dynamics simulation (SMDS) technique, LHACII was effectively intervened from outside. In the experiment, the whole elliptic aberration process which involves from circular to elliptic shape was simulated to further acquire reasonable elliptic imaging with eccentricity of 0.45~0.68. Additionally, the variation of the spatial arrangement ways of B850 pigment when the elliptic aberration occurred to LHACII was demonstrated. The distance between chlorophyll molecules in the pair with short distance is significantly reduced compared to that of before aberration, moreover, 18 B850 chlorophyll molecules were generally distributed the both sides of the major axis of an ellipse spheroid. In contrast, the distance between chlorophyll molecules in the pair with long distance is farther. These results may fill the gap of the experimental research on the spatial arrangement of pigments and imaging in the aberration of LHACII, providing a structural foundation for energy transfer studies.