短杆菌肽通道的价态选择性：分子动力学自由能微扰研究
Valence selectivity of the gramicidin channel: a molecular dynamics free energy perturbation study.
作者信息
Roux B
机构信息
Départements de physique et de chimie, Université de Montréal, Québec, Canada.
出版信息
Biophys J. 1996 Dec;71(6):3177-85. doi: 10.1016/S0006-3495(96)79511-5.
Abstract
The valence selectivity of the gramicidin channel is examined using computer simulations based on atomic models. The channel interior is modeled using a gramicidin-like periodic poly (L,D)-alanine beta-helix. Free energy perturbation calculations are performed to obtain the relative affinity of K+ and Cl- for the channel. It is observed that the interior of the gramicidin channel provides an energetically favorable interaction site for a cation but not for an anion. Relative to solvation in bulk water, the carbonyl CO oxygens can provide a favorable interaction to stabilize K+, whereas the amide NH hydrogens are much less effective in stabilizing Cl-. The results of the calculations demonstrate that, as a consequence of the structural asymmetry of the backbone charge distribution, a K+ cation can partition spontaneously from bulk water to the interior of the gramicidin channel, whereas a Cl- anion cannot.
摘要
利用基于原子模型的计算机模拟研究了短杆菌肽通道的价态选择性。通道内部使用类似短杆菌肽的周期性聚（L，D）-丙氨酸β-螺旋进行建模。进行自由能微扰计算以获得K⁺和Cl⁻对通道的相对亲和力。观察到短杆菌肽通道内部为阳离子提供了能量上有利的相互作用位点，而对阴离子则不然。相对于在大量水中的溶剂化，羰基CO氧可以提供有利的相互作用来稳定K⁺，而酰胺NH氢在稳定Cl⁻方面效果要差得多。计算结果表明，由于主链电荷分布的结构不对称，K⁺阳离子可以自发地从大量水中分配到短杆菌肽通道内部，而Cl⁻阴离子则不能。
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