Harmonicity and Anharmonicity in Protein Dynamics: A Normal Mode Analysis and Principal Component Analysis

摘要: A comparison of a normal mode analysis and principal component 200-ps molecular dynamics trajectory bovine pancreatic trypsin inhibitor in vacuum has been made order to further elucidate the harmonic anharmonic aspects proteins. An anharmonicity factor is defined which measures degree modes, be they modes or it shown that system naturally divides into with peak frequencies below 80 cm-1, above this value. In general larger mean-square fluctuation mode, greater its motion. The represent only 12% total number variables, but account for 98% fluctuation. transitional nature motion demonstrated. results strongly suggest large subspace, free energy surface, as probed by simulation, approximated multi-dimensional parabola just rescaled version corresponding approximation conformational surface at single minimum. After 200 ps, rescaling factor, termed "normal factor," apparently converged value whereby within subspace about twice predicted analysis.