Istituto Officina dei Materiali/CNR UOS SLACS, c/o Department of Physics, University of Cagliari, SP Monserrato-Sestu Km 0.700, Monserrato I-09042, Italy.
J Phys Condens Matter. 2010 Nov 17;22(45):454125. doi: 10.1088/0953-8984/22/45/454125. Epub 2010 Oct 29.
In this paper we investigate the structural and dynamical properties of the two major porins (OmpF and OmpC) in Escherichia coli, using molecular dynamics (MD) simulations. In particular we characterized the atomic fluctuations, correlated motions, temperature dependence, solvent-accessible cross-sectional area and water dynamics in the key regions of the two channels. Our in-depth analysis allows us to highlight the importance of both the key conserved and substituted residues between OmpF and OmpC. The latter is characterized by a narrower and longer constriction region with respect to OmpF. OmpC also showed a higher stability upon increasing temperature. We then present the results of transport properties by using accelerated MD simulations to probe the diffusion of norfloxacin (a fluoroquinolone antibiotic) through the two porins OmpF/OmpC. Our study constitutes a step forward towards understanding the structure-function relationship of the two porins' channels. This will benefit the research of antibacterials with improved permeation properties and nanopores that aim to use these porins as sensing systems.
本文使用分子动力学（MD）模拟研究了大肠杆菌中两种主要孔蛋白（OmpF 和 OmpC）的结构和动力学特性。特别地，我们描述了两个通道关键区域的原子波动、相关运动、温度依赖性、溶剂可及横截面积和水动力学。我们的深入分析突出了 OmpF 和 OmpC 之间关键保守和取代残基的重要性。OmpC 的收缩区域比 OmpF 更窄更长。OmpC 的温度稳定性也随温度升高而提高。然后，我们通过使用加速 MD 模拟来研究诺氟沙星（一种氟喹诺酮类抗生素）通过 OmpF/OmpC 两种孔蛋白的扩散，呈现了输运性质的结果。我们的研究是朝着理解两种孔蛋白通道的结构-功能关系迈出的一步。这将有助于研究具有改善渗透性质的抗菌剂和旨在将这些孔蛋白用作感测系统的纳米孔。
