Dynamics of ions in the selectivity filter of the KcsA channel Towards a coupled Brownian particle description
Dynamics of ions in the selectivity filter of the KcsA channel Towards a coupled Brownian particle description
复制标题
KcsA 通道选择性过滤器中离子的动力学 走向耦合布朗粒子描述
DOI：
10.1140/epjst/e2013-02040-9
复制
发表时间：
2013
期刊：
影响因子：
--
通讯作者：
Cosseddu S
中科院分区：
文献类型：
--
作者：
Cosseddu S
在离子溶液包围的脂质膜中嵌入KcsA蛋白的分子动力学（MD）模拟的基础上，考虑了离子在KcsA离子通道选择性过滤器中的统计和动力学性质。在无偏MD模拟的基础上，讨论了一种推导离子通过过滤器的布朗动力学模型的新方法。根据附加的假设，离子动力学可以用带有常阻尼和白噪声的欠阻尼朗之万方程或带有分数记忆核的朗之万方程来描述。由无偏MD模拟得到的平均力势与由伞式抽样方法产生的势的比较表明，这些势有显著差异。这些差异的起源是一个悬而未决的问题，需要进一步澄清。
The statistical and dynamical properties of ions in the selectivity filter of the KcsA ion channel are considered on the basis of molecular dynamics (MD) simulations of the KcsA protein embedded in a lipid membrane surrounded by an ionic solution. A new approach to the derivation of a Brownian dynamics (BD) model of ion permeation through the filter is discussed, based on unbiased MD simulations. It is shown that depending on additional assumptions, ion’s dynamics can be described either by under-damped Langevin equation with constant damping and white noise or by Langevin equation with a fractional memory kernel. A comparison of the potential of the mean force derived from unbiased MD simulations with the potential produced by the umbrella sampling method demonstrates significant differences in these potentials. The origin of these differences is an open question that requires further clarifications.