Marracino P, Castellani F, Vernier P T, Liberti M, Apollonio F
Department of Information Engineering, Electronics, and Telecommunications, Sapienza University of Rome, Rome, Italy.
Frank Reidy Research Center for Bioelectrics, Old Dominion University, Norfolk, VA, 23508, USA.
J Membr Biol. 2017 Feb;250(1):11-19. doi: 10.1007/s00232-016-9917-y. Epub 2016 Jul 19.
We present here a new method for calculating the radius of a transmembrane pore in a phospholipid bilayer. To compare size-related properties of pores in bilayers of various compositions, generated and maintained under different physical and chemical conditions, reference metrics are needed. Operational metrics can be associated with some observed behavior. For example, pore size can be defined by the largest object that will pass through the length of the pore. The novelty of the present approach resides in the characterization of electropore geometry via a statistical approach, based on essential dynamics rules. We define the pore size geometrically with an algorithm for determining the pore radius. In particular, we extract the radius from the tri-dimensional surface of a defined pore region. The method is applied to a pore formed in a phospholipid bilayer by application of an external electric field. Although the details described here are specific for lipid pores in molecular dynamics simulations, the method can be generalized for any kind of pores for which appropriate structural information is available.
我们在此介绍一种计算磷脂双分子层中跨膜孔半径的新方法。为了比较在不同物理和化学条件下生成并维持的各种组成的双分子层中孔的与尺寸相关的特性，需要参考指标。操作指标可以与某些观察到的行为相关联。例如，孔径可以由能够穿过孔长度的最大物体来定义。本方法的新颖之处在于基于基本动力学规则，通过统计方法对电穿孔几何形状进行表征。我们用一种确定孔半径的算法从几何角度定义孔径。具体而言，我们从定义的孔区域的三维表面提取半径。该方法应用于通过施加外部电场在磷脂双分子层中形成的孔。尽管这里描述的细节特定于分子动力学模拟中的脂质孔，但该方法可以推广到任何可获得适当结构信息的孔。
