Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, 201203, China.
Phys Chem Chem Phys. 2019 Jun 5;21(22):11924-11936. doi: 10.1039/c8cp07524g.
A comprehensive understanding of protein folding includes the knowledge of the formation of individual secondary structures, tertiary structure, and the effects of non-native contacts on these folding events. The measurement of these microscopic events has been posing challenges for experiment and molecular simulation. In this work, we performed enhanced sampling MD simulations for three proteins (NTL9, NuG2b, and CspA) and analyzed minimum free energy paths on multi-dimensional free energy landscapes to explore the underlying folding mechanisms. Consistencies can be seen between the present simulations and the existing experiments as well as other MD simulations. Quantitative analysis reveals the nucleation-condensation folding mechanism indicating the concurrent build-up of secondary and tertiary structures for the three proteins and gives the detailed formation sequence of individual native secondary structure elements. More importantly, nonnative contacts are generally observed among the proteins, creating a nonnative environment to affect the folding of individual secondary structure elements. A general tendency is that the secondary structure element(s) where the maximal nonnative contacts are observed have the largest formation free-energy barrier(s), corresponding to the rate-limiting step(s) of the folding for proteins that follow the nucleation-condensation mechanism. In summary, while native contacts determine the folding mechanism and pathway, non-native contacts play an important role in determining the protein folding thermodynamics by influencing the free energies of individual secondary structure element formation.
全面了解蛋白质折叠包括形成单个二级结构、三级结构以及非天然接触对这些折叠事件的影响的知识。这些微观事件的测量一直对实验和分子模拟构成挑战。在这项工作中，我们对三种蛋白质（NTL9、NuG2b 和 CspA）进行了增强采样 MD 模拟，并在多维自由能景观上分析了最小自由能路径，以探索潜在的折叠机制。目前的模拟与现有的实验以及其他 MD 模拟之间存在一致性。定量分析揭示了成核-凝聚折叠机制，表明三种蛋白质的二级结构和三级结构同时构建，并给出了单个天然二级结构元件的详细形成序列。更重要的是，非天然接触通常在蛋白质之间观察到，形成非天然环境会影响单个二级结构元件的折叠。一般来说，观察到最大非天然接触的二级结构元件具有最大的形成自由能障碍，对应于遵循成核-凝聚机制的蛋白质的限速步骤。总之，虽然天然接触决定了折叠机制和途径，但非天然接触通过影响单个二级结构元件形成的自由能，在确定蛋白质折叠热力学方面起着重要作用。
