Keep It Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS

We describe a versatile method to enforce the rotation of subsets of atoms, e.g., a protein subunit, in molecular dynamics (MD) simulations. In particular, we introduce a “flexible axis” technique that allows realistic flexible adaptions of both the rotary subunit as well as the local rotation axis during the simulation. A variety of useful rotation potentials were implemented for the GROMACS 4.5 MD package. Application to the molecular motor F1-ATP synthase demonstrates the advantages of the flexible axis approach over the established fixed axis rotation technique.

我们提出了一种通用方法，可在分子动力学（MD）模拟中对原子子集（例如蛋白质亚基）施加旋转约束。具体而言，我们引入了一种“柔性轴”技术，能够在模拟过程中对旋转亚基与局部旋转轴同时实现贴合实际的柔性适配。我们已为GROMACS 4.5分子动力学软件包实现了多种实用的旋转势能函数。针对分子马达F1-ATP合酶的应用验证表明，相较于已成熟的固定轴旋转技术，柔性轴方法具备显著优势。