Effect of Electronic Polarization to Human α-Thrombin
DUAN Li-Li1**, LI Zong-Chao1, HE Xiang2, ZHANG Qing-Gang1
1College of Physics and Electronics, Shandong Normal University, Jinan 250014 2Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008
Abstract：The polarized protein-specific charges (PPC) of human α-thrombin (thrombin) and its inhibitor (L86) are made possible by employing the recently developed molecular fractionation with conjugate caps approach incorporated the Poisson–Boltzmann model. Molecular dynamics (MD) simulations of thrombin have been carried out to investigate the dynamics and stability of the thrombin-inhibitor using PPC and AMBER charges respectively. Detailed analysis and comparison of MD results show that the PPC can correctly describe the polarized state of the thrombin and L86. Especially, the root-mean-square deviation of backbone atoms and the hydrogen bonds using PPC are more stable than the AMBER charge. The present results indicate that protein polarization plays critical roles in maintaining the compact structure of thrombin.
2014, Vol. 31 
