Session: Current Topics in Biological Chemistry:

Fast and accurate calculations of the electrostatic features for highly charged biomolecules such as DNA, RNA, highly charged proteins, are crucial but challenging tasks. Traditional implicit solvent methods calculate the electrostatic features fast. But how to balance the high net charges in the biomolecules effectively remains a difficult problem. Most of the explicit solvent methods add extra counter ions to neutralize the highly charged biomolecules in molecular dynamic simulations, which requires more expensive computing resources. Here we developed a novel Hybridizing Ions Treatment (HIT) method, which hybridizes the implicit solvent method with explicit method to realistically calculate the electrostatic potential for highly charged biomolecules. This HIT method utilizes the ionic distribution from an explicit method to obtain the information of bound ions. Such bound ions are then added in the implicit solvent method to perform the electrostatic potential calculations. The performance on the testing set demonstrates that the HIT method significantly improves the electrostatic calculations. This HIT program can be widely used to study highly charged biomolecules, including DNA, RNA, molecular motors, and other highly charged biomolecules.

Shengjie Sun

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