Implementing and Assessing an Alchemical Method for Calculating Protein–Protein Binding Free Energy

Protein–protein
binding is fundamental to most biological
processes. It is important to be able to use computation to accurately
estimate the change in protein–protein binding free energy
due to mutations in order to answer biological questions that would
be experimentally challenging, laborious, or time-consuming. Although
nonrigorous free-energy methods are faster, rigorous alchemical molecular
dynamics-based methods are considerably more accurate and are becoming
more feasible with the advancement of computer hardware and molecular
simulation software. Even with sufficient computational resources,
there are still major challenges to using alchemical free-energy methods
for protein–protein complexes, such as generating hybrid structures
and topologies, maintaining a neutral net charge of the system when
there is a charge-changing mutation, and setting up the simulation.
In the current study, we have used the pmx package
to generate hybrid structures and topologies, and a double-system/single-box
approach to maintain the net charge of the system. To test the approach,
we predicted relative binding affinities for two protein–protein
complexes using a nonequilibrium alchemical method based on the Crooks
fluctuation theorem and compared the results with experimental values.
The method correctly identified stabilizing from destabilizing mutations
for a small protein–protein complex, and a larger, more challenging
antibody complex. Strong correlations were obtained between predicted
and experimental relative binding affinities for both protein–protein
systems.

蛋白质-蛋白质结合（Protein–protein binding）是绝大多数生物学过程的核心基础。借助计算手段准确估算因突变引发的蛋白质-蛋白质结合自由能变化，对于解答那些实验操作极具挑战性、费力且耗时的生物学问题至关重要。尽管非严格自由能方法运算速度更快，但基于严格化学映射分子动力学的方法精度显著更高，且随着计算机硬件与分子模拟软件的发展，其应用可行性正不断提升。即便拥有充足的计算资源，将化学映射自由能方法应用于蛋白质-蛋白质复合物仍面临诸多重大挑战，例如生成杂合结构与拓扑文件、在发生电荷改变的突变时维持体系净电荷为中性，以及模拟体系的搭建工作。在本研究中，我们使用pmx工具包（pmx package）生成杂合结构与拓扑文件，并采用双体系单盒方法（double-system/single-box approach）维持体系的净电荷。为验证该方法的有效性，我们基于克鲁克斯涨落定理（Crooks fluctuation theorem）提出的非平衡化学映射方法，对两种蛋白质-蛋白质复合物的相对结合亲和力进行了预测，并将预测结果与实验值进行了对比。针对小型蛋白质-蛋白质复合物以及规模更大、更具挑战性的抗体复合物，该方法均能正确区分稳定型与去稳定型突变。两种蛋白质-蛋白质体系的预测相对结合亲和力与实验值均呈现出较强的相关性。