Molecular Dynamics Simulations of Human Prion Protein under the Different Temperatures

• Main Authors: I-Yen Huang, 黃一晏
• Other Authors: Kuei-Jen Lee
• Format: Others
• Language: zh-TW
• Published: 2009
• Online Access: http://ndltd.ncl.edu.tw/handle/21151142787415080759

碩士 === 亞洲大學 === 生物資訊學系碩士班 === 98 === The symptoms of transmissible spongiform encephalopathies(TSEs) are caused by the progressive death of the brain's nerve cells. When brain tissue collected from a TSEs patient is examined, the spongy appearance of the brain tissue can be found. The prion that is believed to cause TSEs exhibits at least two conformations, the native state and the other conformational state. The TSEs prion promotes refolding of native proteins into the diseased state. Mass of misfolded proteins disrupts cell function and causes cell death. In this study, we performed molecular dynamics simulations by using CHARMM. Calculation of human prion protein in different temperatures associated with the molecular vibration. We obtained human prion protein PDB ID=1i4m structural information from the RCSB protein data bank (PDB). Simulation of water environment use GB imaginary potential. Simulations of human prion protein dynamic behavior were carried out at room temperature (300K) and human body temperature (310K) etc. Each simulation time step was set to 2*10^(−15) seconds. Total steps set to 1.5*10^6 steps. The total simulation time is 3*10^(−9) seconds (3ns). We calculated Root-Mean-Square Deviation (RMSD), Root-Mean-Square Fluctuation (RMSF) and Radius of Gyration (RGYR). It demonstrated that the conformations of human prion protein change under different temperatures.