基于耗散校正的靶向分子动力学和Langevin方程模拟预测离子通道电导
Predicting ion channel conductance via dissipation-corrected targeted molecular dynamics and Langevin equation simulations
摘要：
离子通道是重要的生理信息传递和功能调控蛋白。为了预测它们的电压-电导特性的微观起源，我们在这里应用耗散校正的靶向分子动力学结合Langevin方程模拟钾通过短杆菌肽A通道的扩散作为测试系统。执行非平衡主成分分析的骨干二面角，我们发现耦合蛋白质离子动力学发生在离子转移。耗散校正的自由能分布对应以及从其他有偏见的模拟方法的预测。在朗之万模拟中引入外部电场，使得能够以I-V特性的形式预测宏观可观测量。
英文摘要：
Ion channels are important proteins for physiological information transfer and functional control. To predict the microscopic origins of their voltage-conductance characteristics, we here applied dissipation-corrected targeted Molecular Dynamics in combination with Langevin equation simulations to potassium diffusion through the Gramicidin A channel as a test system. Performing a non-equilibrium principal component analysis on backbone dihedral angles, we find coupled protein-ion dynamics to occur during ion transfer. The dissipation-corrected free energy profiles correspond well to predictions from other biased simulation methods. The incorporation of an external electric field in Langevin simulations enables the prediction of macroscopic observables in the form of I-V characteristics.
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