Sun Shengjie, Karki Chitra, Xie Yixin, Xian Yuejiao, Guo Wenhan, Gao Bruce Z, Li Lin
Computational Science Program, University of Texas at El Paso, 500 W University Ave, TX 79968, USA.
Department of Chemistry, University of Texas at El Paso, 500 W University Ave, TX 79968, USA.
Comput Struct Biotechnol J. 2021 Jan 20;19:801-811. doi: 10.1016/j.csbj.2021.01.020. eCollection 2021.
Fast and accurate calculations of the electrostatic features of highly charged biomolecules such as DNA, RNA, and highly charged proteins are crucial and challenging tasks. Traditional implicit solvent methods calculate the electrostatic features quickly, but these methods are not able to balance the high net biomolecular charges effectively. Explicit solvent methods add unbalanced ions to neutralize the highly charged biomolecules in molecular dynamic simulations, which require more expensive computing resources. Here we report developing a novel method, Hybridizing Ions Treatment (HIT), which hybridizes the implicit solvent method with an explicit method to realistically calculate the electrostatic potential for highly charged biomolecules. HIT utilizes the ionic distribution from an explicit method to predict the bound ions. The bound ions are then added in the implicit solvent method to perform the electrostatic potential calculations. In this study, two training sets were developed to optimize parameters for HIT. The performance on the testing set demonstrates that HIT significantly improves the electrostatic calculations. Results on molecular motors myosin and kinesin reveal some mechanisms and explain some previous experimental findings. HIT can be widely used to study highly charged biomolecules, including DNA, RNA, molecular motors, and other highly charged biomolecules. The HIT package is available at http://compbio.utep.edu/static/downloads/download_hit.zip.
快速且准确地计算诸如DNA、RNA和高电荷蛋白质等高度带电生物分子的静电特征是至关重要且具有挑战性的任务。传统的隐式溶剂方法能够快速计算静电特征，但这些方法无法有效地平衡生物分子的高净电荷。显式溶剂方法在分子动力学模拟中添加不平衡离子以中和高度带电的生物分子，这需要更昂贵的计算资源。在此，我们报告开发了一种新方法——杂交离子处理（HIT），该方法将隐式溶剂方法与显式方法相结合，以实际计算高度带电生物分子的静电势。HIT利用显式方法的离子分布来预测结合离子。然后将结合离子添加到隐式溶剂方法中进行静电势计算。在本研究中，开发了两个训练集来优化HIT的参数。测试集上的性能表明HIT显著改善了静电计算。在分子马达肌球蛋白和驱动蛋白上的结果揭示了一些机制并解释了一些先前的实验发现。HIT可广泛用于研究高度带电的生物分子，包括DNA、RNA、分子马达和其他高度带电的生物分子。HIT软件包可在http://compbio.utep.edu/static/downloads/download_hit.zip获取。
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