ABEEMσπ/MM Model Applied To The Study Of Simulations Of Protein Systems And Macular Docking

The ABEEMσπfluctuating charge force field (ABEEMσπ/ MM) be applied to study the structural and properties of the DER F 2, SARS-COV main protease, Plasminogen, Ascaris Trypsin inhibitor and Methianyl-TRNA synthetase in 298K under vacuum conditions for molecular dynamics simulation. we have obtained that the position of all atoms (including the Cαatoms, backbone atoms (C, Cα, N, O), heavy atoms and side chain atoms), bond length, bond angle, dihedral angle and the radii of gyration value by the method of mechanic dynamics simulation, and through compared the crystal structure with the experimental data and simulation results of AMBER force field. The results show good consistency, and indicate that the results of molecular dynamic simulations by ABEEMσπ/MM are very close to the protein structural of experiment. In adiation, the semi-flexible docking studies have been performed in order to understrand the interaction between the recombinant Kringle 1 domain of human plasminogen and five ligands (ε-Aminocaproic Acid (EACA), Trans-4-(Aminomethyl) cyclohexane-1-carboxylic Acid (AMCHA), L-Lysine (Lys), 7-aminoheptanoic acid (7-AHA) and benzylamine) by means of ABEEMσπ/MM. The results show that, the simulated structure is very close to the crystal structure. The calculated binding energy of five complexes is AMCHA > EACA > 7-AHA > Lys > benzylamine, which is in agreement with the value of the equilibrium association constant (Ka) from experiment.This indicates that ABEEMσπ/MM mode can be applied to the study of the protein structure and property, and further applied to the design of new drug molecule.