Sutherland Jeffrey, Arteca Gustavo A
Département de chimie et biochimie, Laurentian University, Sudbury, Ontario, Canada.
J Mol Graph Model. 2002 Oct;21(2):101-10. doi: 10.1016/s1093-3263(02)00126-2.
In an Ohmic model, channel conductivity can be described in terms of the geometry of a conducting cable. The essential features of such devices are the arc length of the curve describing the channel's longitudinal path, and the cross-sectional areas transversal to this curve. In a first approximation, conducting channels can be represented by an average molecular shape with estimated lengths and cross-sectional areas. Whereas the physical shortcomings of this approach are known, its accuracy limitations in practice have not been established. In this work, we discuss an improved model for the channel's shape, one that allows us to gauge how much of the Ohmic conductivity can be assigned purely to geometrical features. In the present algorithm, we investigate all regions inside the pore that are accessible to ions using various choices for the molecular surface of the inner channel. We discuss the agreement with experimental conductances in the case of 12 channels (cholera toxin B-subunit pentamer, Staphylococcus aureus alpha-hemolysin, Streptomyces lividans KcsA channel, seven porins, gramicidin A, and phospholamban). Our results can be regarded as a benchmark for the best performance that can be expected from a geometrical model of conductance. Consequently, significant deviations from experimental trends can safely be assigned to non-geometrical factors, namely the specific composition of the ion channel and the detailed electrostatic interactions between the channel and a particular ion.
在欧姆模型中，通道电导率可以根据导电电缆的几何形状来描述。此类装置的基本特征是描述通道纵向路径的曲线的弧长，以及垂直于该曲线的横截面积。在一阶近似中，导电通道可以用具有估计长度和横截面积的平均分子形状来表示。尽管这种方法的物理缺陷是已知的，但其在实际中的精度限制尚未确定。在这项工作中，我们讨论了一种改进的通道形状模型，该模型使我们能够衡量欧姆电导率中有多少可以纯粹归因于几何特征。在当前算法中，我们使用内通道分子表面的各种选择来研究孔内离子可及的所有区域。我们讨论了在12种通道（霍乱毒素B亚基五聚体、金黄色葡萄球菌α-溶血素、变铅青链霉菌KcsA通道、七种孔蛋白、短杆菌肽A和受磷蛋白）的情况下与实验电导的一致性。我们的结果可被视为电导几何模型所能达到的最佳性能的基准。因此，与实验趋势的显著偏差可以安全地归因于非几何因素，即离子通道的特定组成以及通道与特定离子之间的详细静电相互作用。
