Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109.
Biophysics Program, University of Michigan, Ann Arbor, Michigan, 48109.
Protein Sci. 2018 Nov;27(11):1910-1922. doi: 10.1002/pro.3500.
The estimation of changes in free energy upon mutation is central to the problem of protein design. Modern protein design methods have had remarkable success over a wide range of design targets, but are reaching their limits in ligand binding and enzyme design due to insufficient accuracy in mutational free energies. Alchemical free energy calculations have the potential to supplement modern design methods through more accurate molecular dynamics based prediction of free energy changes, but suffer from high computational cost. Multisite λ dynamics (MSλD) is a particularly efficient and scalable free energy method with potential to explore combinatorially large sequence spaces inaccessible with other free energy methods. This work aims to quantify the accuracy of MSλD and demonstrate its scalability. We apply MSλD to the classic problem of calculating folding free energies in T4 lysozyme, a system with a wealth of experimental measurements. Single site mutants considering 32 mutations show remarkable agreement with experiment with a Pearson correlation of 0.914 and mean unsigned error of 1.19 kcal/mol. Multisite mutants in systems with up to five concurrent mutations spanning 240 different sequences show comparable agreement with experiment. These results demonstrate the promise of MSλD in exploring large sequence spaces for protein design.
突变引起的自由能变化的估计是蛋白质设计问题的核心。现代蛋白质设计方法在广泛的设计目标上取得了显著的成功，但由于突变自由能的准确性不足，在配体结合和酶设计方面已经达到了极限。通过更准确的基于分子动力学的自由能变化预测，计算自由能可以补充现代设计方法，但存在计算成本高的问题。多位点 λ 动力学（MSλD）是一种特别高效和可扩展的自由能方法，具有探索其他自由能方法无法访问的组合大规模序列空间的潜力。这项工作旨在量化 MSλD 的准确性并证明其可扩展性。我们将 MSλD 应用于 T4 溶菌酶折叠自由能的经典问题计算，这是一个具有丰富实验测量的系统。考虑 32 个突变的单点突变与实验具有显著的一致性，Pearson 相关系数为 0.914，平均无符号误差为 1.19 kcal/mol。在多达五个并发突变的系统中，具有 240 个不同序列的多点突变与实验具有可比的一致性。这些结果表明 MSλD 在探索蛋白质设计的大序列空间方面具有广阔的前景。
