Department of Physics and Earth Sciences, Jacobs University Bremen, 28759 Bremen, Germany.
J Chem Theory Comput. 2020 Apr 14;16(4):2751-2765. doi: 10.1021/acs.jctc.9b00992. Epub 2020 Mar 13.
To reach their site of action, it is essential for antibiotic molecules to cross the bacterial outer membrane. The progress of enhanced sampling techniques in molecular dynamics simulations enables us to understand these translocations at an atomic level. To this end, calculations of free energy surfaces for these permeation processes are of key importance. Herein, we investigate the translocation of a variety of anionic solutes through the outer membrane pore OprO of the Gram-negative bacterium using the metadynamics and umbrella sampling techniques at the all-atom level. Free energy calculations have been performed employing these two distinct methods in order to illustrate the difference in computed free energies, if any. The investigated solutes range from a single atomic chloride ion over a multiatomic monophosphate ion to a more bulky fosmidomycin antibiotic. The role of complexity of the permeating solutes in estimating accurate free energy profiles is demonstrated by performing extensive convergence analysis. For simple monatomic ions, good agreement between the well-tempered metadynamics and the umbrella sampling approaches is achieved, while for the permeation of the monophosphate ion differences start to appear. In the case of larger molecules such as fosmidomycin it is a tough challenge to achieve converged free energy profiles. This issue is mainly due to neglecting orthogonal degrees of freedom during the free energy calculations. Nevertheless, the freely driven metadynamics approach leads to clearly advantageous results. Additionally, atomistic insights of the translocation mechanisms of all three solutes are discussed.
为了到达作用部位，抗生素分子必须穿过细菌的外膜。增强采样技术在分子动力学模拟中的进展使我们能够在原子水平上理解这些转移。为此，计算这些渗透过程的自由能表面对于关键重要的。在本文中，我们使用元动力学和伞状采样技术在全原子水平上研究了各种阴离子溶质通过革兰氏阴性菌 OprO 外膜孔的迁移。为了说明如果存在任何差异，我们使用这两种不同的方法进行了自由能计算。研究的溶质范围从单个原子的氯离子到多原子的单磷酸盐离子，再到更大体积的福米地霉素抗生素。通过进行广泛的收敛性分析，证明了渗透溶质的复杂性在估计准确的自由能曲线中的作用。对于简单的单原子离子，经过良好调整的元动力学和伞状采样方法之间达成了很好的一致性，而对于单磷酸盐离子的渗透，差异开始出现。对于福米地霉素等较大的分子，要实现收敛的自由能曲线是一个艰巨的挑战。这个问题主要是由于在自由能计算中忽略了正交自由度。然而，自由驱动的元动力学方法导致了明显有利的结果。此外，还讨论了所有三种溶质的迁移机制的原子见解。
