Parallel Temperature Replica-Exchange Molecular Dynamics Simulations Capture the Observed Impact of Stapling on Coiled-Coil Conformational Stability

Macrocyclization or stapling is an
important strategy for increasing
the conformational stability and target-binding affinity of peptides
and proteins, especially in therapeutic contexts. Atomistic simulations
of such stapled peptides and proteins could help rationalize existing
experimental data and provide predictive tools for the design of new
stapled peptides and proteins. Standard approaches exist for incorporating
nonstandard amino acids and functional groups into the force fields
required for MD simulations and have been used in the context of stapling
for more than a decade. However, enthusiasm for their use has been
limited by their time-intensive nature and concerns about whether
the resulting simulations would be physically realistic. Here, we
report the development of force field parameters for two unnatural
triazole staples, which we have incorporated into implicit-solvent
parallel temperature replica-exchange molecular dynamics simulations
of several stapled coiled-coil variants and their nonstapled counterparts.
We used these simulations to calculate melting temperatures (Tm) of each variant along with the impact of
stapling on the conformational stability of each variant relative
to its nonstapled counterpart (ΔΔG).
Trends among these simulated Tm and ΔΔG values closely match those observed in previous experiments,
suggesting that the parameters we developed for these staples are
sufficiently realistic to be useful in predicting the impact of stapling
on the protein/peptide conformational stability in other contexts.

大环化（macrocyclization）或肽链钉合（stapling）是提升肽类与蛋白质构象稳定性及靶标结合亲和力的关键策略，在治疗研究场景中尤为重要。
针对此类钉合肽与蛋白质的原子尺度模拟，可助力阐释现有实验数据，并为新型钉合肽与蛋白质的设计提供预测工具。
目前已有成熟方法可将非标准氨基酸（nonstandard amino acids）与官能团（functional groups）引入分子动力学（Molecular Dynamics, MD）模拟所需的力场（force fields）中，且该类方法应用于钉合体系已逾十载。
然而，此类方法的推广应用仍受限于其计算耗时过长的特性，以及所得模拟结果是否具备物理真实性的诸多质疑。
本文报道了两种非天然三唑类钉合结构（triazole staples）的力场参数开发工作，我们将其整合至多个钉合卷曲螺旋（coiled-coil）变体及其非钉合对应体的隐式溶剂（implicit-solvent）平行温度副本交换MD模拟中。
借此模拟，我们计算了各变体的解链温度（melting temperatures, Tm），以及相较于非钉合对应体，钉合对各变体构象稳定性的影响（ΔΔG）。
模拟所得的Tm与ΔΔG变化趋势与此前实验观测结果高度吻合，表明我们针对此类钉合结构开发的参数具备足够的物理真实性，可用于预测钉合对其他体系中蛋白质/肽类构象稳定性的影响。