We have augmented a previously developed polarizable force field (PFF) and applied it to calculating protein pKa shifts and to simulating protein-ion binding. Our work has confirmed that energy-related features of such systems can be successfully reproduced but an accurate explicit representation of the electrostatic polarization is necessary. The errors in the acidity constants were several times lower than those produced by fixed-charges analogues. Binding energies between Cu(I) ion and the Bacillus subtilis CopZ protein computed with the PFF were in a qualitatively better agreement with experiment than those obtained with the fixed-charges force field, and the geometry of the polarizable system was much less distorted. This same was true for binding of the copper to model systems. We believe that our results open road to further accurate simulations of metal ion binding to proteins and ion transport.

Applications of a polarizable force field to computing protein pKa values and modeling protein-ion binding

244th National Meeting (2012)

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