Development of an Effective Polarizable Bond Method for Biomolecular Simulation
2013
Xiao, Xudong | Zhu, Tong | Ji, Chang G. | Zhang, John Z. H.
An effective polarizable bond (EPB) model has been developed for computer simulation of proteins. In this partial polarizable approach, all polar groups of amino acids are treated as polarizable, and the relevant polarizable parameters were determined by fitting to quantum calculated electrostatic properties of these polar groups. Extensive numerical tests on a diverse set of proteins (including 1IEP, 1MWE, 1NLJ, 4COX, 1PGB, 1K4C, 1MHN, 1UBQ, 1IGD) showed that this EPB model is robust in MD simulation and can correctly describe the structure and dynamics of proteins (both soluble and membrane proteins). Comparison of the computed hydrogen bond properties and dynamics of proteins with experimental data and with results obtained from the nonpolarizable force field clearly demonstrated that EPB can produce results in much better agreement with experiment. The averaged deviation of the simulated backbone N–H order parameter of the B3 immunoglobobulin-binding domain of streptococcal protein G from experimental observation is 0.0811 and 0.0332 for Amber99SB and EPB, respectively. This new model inherited the effective character of the classic force field and the fluctuating feature of previous polarizable models. Different from other polarizable models, the polarization cost energy is implicitly included in the present method. As a result, the present method avoids the problem of over polarization and is numerically stable and efficient for dynamics simulation. Finally, compared to the traditional fixed AMBER charge model, the present method only adds about 5% additional computational time and is therefore highly efficient for practical applications.
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