Computational simulations in biophysics describe the dynamics and functions of biological macromolecules at the atomic level. Among motions particularly important for life are the transport processes in heterogeneous media. The process of ligand diffusion inside proteins is an example of a complex rare event that can be modeled using molecular dynamics simulations. The study of physical interactions between a ligand and its biological target is of paramount importance for the design of novel drugs and enzymes. Unfortunately, the process of ligand diffusion is difficult to study experimentally. The need for identifying the ligand egress pathways and understanding how ligands migrate through protein tunnels has spurred the development of several methodological approaches to this problem. The complex topology of protein channels and the transient nature of the ligand passage pose difficulties in the modeling of the ligand entry/escape pathways by canonical molecular dynamics simulations. In this review, we report a methodology involving a reconstruction of the ligand diffusion reaction coordinates and the free-energy profiles along these reaction coordinates using enhanced sampling of conformational space. We illustrate the above methods on several ligand–protein systems, including cytochromes and G-protein-coupled receptors. The methods are general and may be adopted to other transport processes in living matter.

生物物理学中的计算模拟在原子水平上描述了生物大分子的动力学和功能。在生命中特别重要的运动是异质媒体中的传输过程。蛋白质内部配体扩散的过程是一个复杂的稀有事件的例子，可以使用分子动力学模拟对其进行建模。配体与其生物学靶标之间的物理相互作用的研究对于新型药物和酶的设计至关重要。不幸的是，配体扩散的过程很难进行实验研究。对鉴定配体流出途径和理解配体如何通过蛋白质通道迁移的需求刺激了针对该问题的几种方法学方法的发展。蛋白质通道的复杂拓扑结构和配体通道的瞬态性质在通过规范的分子动力学模拟对配体进入/逃逸途径进行建模时遇到了困难。在这篇综述中，我们报告了一种方法，该方法涉及使用构象空间的增强采样来重建配体扩散反应坐标和沿着这些反应坐标的自由能分布。我们在几种配体-蛋白质系统（包括细胞色素和G蛋白偶联受体）上说明了上述方法。这些方法是通用的，并且可以用于生物的其他运输过程。我们报告了一种方法，该方法涉及使用构象空间的增强采样来重建配体扩散反应坐标和沿着这些反应坐标的自由能分布。我们在几种配体-蛋白质系统（包括细胞色素和G蛋白偶联受体）上说明了上述方法。这些方法是通用的，并且可以用于生物的其他运输过程。我们报告了一种方法，该方法涉及使用构象空间的增强采样来重建配体扩散反应坐标和沿着这些反应坐标的自由能分布。我们在几种配体-蛋白质系统（包括细胞色素和G蛋白偶联受体）上说明了上述方法。这些方法是通用的，并且可以用于生物的其他运输过程。