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.