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 (<i>T</i>_m) of each variant along with the impact of stapling on the conformational stability of each variant relative to its nonstapled counterpart (ΔΔ<i>G</i>). Trends among these simulated <i>T</i>_m and ΔΔ<i>G</i> 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.