Higher Accuracy Achieved in the Simulations of Protein Structure Refinement, Protein Folding, and Intrinsically Disordered Proteins Using Polarizable Force Fields
journal contributionposted on 05.12.2018, 00:00 by Anhui Wang, Zhichao Zhang, Guohui Li
The accuracy of molecular mechanics force fields is of vital importance in biomolecular simulations. However, the admittedly more accurate polarizable force fields were recently reported to be less able to reproduce the experimental properties in comparison to additive force fields in some cases. Here, we perform long-time-scale molecular dynamics simulations to systematically evaluate the effect of explicit electronic polarization in polarizable force fields. The results show that the inclusion of electrostatic polarization effect in polarizable force fields can improve their accuracies in protein structure refinement and generate conformational ensembles more approximate to experiments for intrinsically disordered proteins. In contrast, it is difficult for polarizable force fields to approach the native structure, let alone to predict the native state when it is unknown a priori in the real protein structure predictions. We speculate that these effects might be attributed to the preference of protein–water interactions in polarizable force fields.
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biomolecular simulationsProtein Structure Refinementresults showprotein structure refinementIntrinsically Disordered Proteinspolarization effectprotein structure predictionspolarizable force fieldsAccuracy Achievedmechanics force fieldsPolarizable Force Fieldsdynamics simulationsadditive force fields