Molecular Dynamics Simulations Of G_A88and G_B88by ABEEMσπ And OPLS-AA Force Field4

Protein dynamics is to describe the bridge between proteins static structure and dynamicstructure. The dynamic behavior of protein G_A88(PDB code:2JWS) and G_B88(PDB code:2JWS) have been investigated at295K and in3ns, using molecular dynamics by means ofAtom-Bond Electronegativity Equalization Method Fused into Molecular Mechanics i.e.,ABEEMσπ/MM and the explicit ABEEM-7P water solvent model as well as OPLS-AA forcefield. The dynamics properties of these proteins are analyzed, including the root-mean-squaredeviations of bond length, bond angle and torsional angle, root-mean-square deviationsbetween the structure of several kinds of non-hydrogen atoms[Cαatoms, backbone atoms(C,Cα, N, O) and heavy atoms] and experimental data, radius of gyration in aqueous solution andin vacuum, the distribution of hydrophobic and hydrophilic surface area, as well as hydrogenbonds compared to the experimental structures.In this paper, OPLS-AA fixed charge force field is also used for molecular dynamicssimulations of G_A88and G_B88carried out under the same conditions at the same time, and theresults of root-mean-square deviations of bond length, bond angle and torsional angle androot-mean-square deviations between the structure of several kinds of non-hydrogen atomsand experimental data are compared to those obtained from ABEEMσπ force field. Thoseresults demonstrate that both force fields simulate experimental structures correctly, and thesimulated RMSD are close to each other, but the simulated systems are more stable fromABEEMσπ force field than those from OPLS-AA force field according to the fluctuating;Simulated results of radius of gyration in aqueous solution and in vacuum show the“electrostatic compactness” phenolmenon; Those calculations on hydrophobic andhydrophilic surface area also demonstrate the simulated systems are more stable fromABEEMσπ force field than those from OPLS-AA force field according to the fluctuating;Hydrogen bond length is close to the experimental data. These results demonstrate that thesimulated structures of G_A88and G_B88by ABEEMσπ fluctuating charge force field are ingood agreement with the experimental structures, and then explain the rationality of ourmodel and transferability of the parameters.