通过使用蛋白质工程优化的酶加速化学反应代表了生物技术对可持续性的贡献的关键支柱之一。具有埋藏活性位点的酶的隧道和通道能够交换配体，离子,以及外部环境和活性位点口袋之间的水分子。配体的有效交换是生物催化的基本过程。因此,酶已经进化出一系列重复构象变化的机制，这些机制能够实现周期性的打开和关闭。蛋白质-配体相互作用传统上通过分子对接来研究，而分子动力学是研究构象变化和配体转运的首选方法。然而,计算需求使分子动力学无法用于筛选目的。因此，最近已经开发了几种近似方法来研究配体运输过程中蛋白质和配体之间的相互作用。除了确定最佳的绑定模式，这些方法还提供了有关运输的能量学的信息，并确定了限制配体通过的有问题的区域。这些方法使用近似值来快速模拟结合或非结合事件(计算时间从几分钟到几小时),并提供可用于对配体或途径进行排序的能量曲线。在这里，我们提供了可用方法的关键比较，在样本系统上展示他们的结果，讨论它们在分子生物学技术中的实际应用，并概述未来可能的发展。
Acceleration of chemical reactions by the enzymes optimized using protein engineering represents one of the key pillars of the contribution of biotechnology towards sustainability. Tunnels and channels of enzymes with buried active sites enable the exchange of ligands, ions, and water molecules between the outer environment and active site pockets. The efficient exchange of ligands is a fundamental process of biocatalysis. Therefore, enzymes have evolved a wide range of mechanisms for repetitive conformational changes that enable periodic opening and closing. Protein-ligand interactions are traditionally studied by molecular docking, whereas molecular dynamics is the method of choice for studying conformational changes and ligand transport. However, computational demands make molecular dynamics impractical for screening purposes. Thus, several approximative methods have been recently developed to
study interactions between a protein and ligand during the ligand transport process. Apart from identifying the best binding modes, these methods also provide information on the energetics of the transport and identify problematic regions limiting the ligand passage. These methods use approximations to simulate binding or unbinding events rapidly (calculation times from minutes to hours) and provide energy profiles that can be used to rank ligands or pathways. Here we provide a critical comparison of available methods, showcase their results on sample systems, discuss their practical applications in molecular biotechnologies and outline possible future developments.
