Optimized reaction coordinates for analysis of enhanced sampling

TitleOptimized reaction coordinates for analysis of enhanced sampling
Publication TypeJournal Article
Year of Publication2023
AuthorsWidmer J., Langini C., Vitalis A., Caflisch A.
JournalThe Journal of Chemical Physics
Date Published2023 July 7
Type of ArticleResearch Article
Keywordsatomistic simulations, molecular binding, molecular dynamics, potential energy surfaces, reaction progress kinetic analysis, reaction rate constants

Atomistic simulations of biological processes offer insights at a high level of spatial and temporal resolution, but accelerated sampling is often required for probing timescales of biologically relevant processes. The resulting data need to be statistically reweighted and condensed in a concise yet faithful manner to facilitate interpretation. Here, we provide evidence that a recently proposed approach for the unsupervised determination of optimized reaction coordinate (RC) can be used for both analysis and reweighting of such data. We first show that for a peptide interconverting between helical and collapsed configurations, the optimal RC permits efficient reconstruction of equilibrium properties from enhanced sampling trajectories. Upon RC-reweighting, kinetic rate constants and free energy profiles are in good agreement with values obtained from equilibrium simulations. In a more challenging test, we apply the method to enhanced sampling simulations of the unbinding of an acetylated lysine-containing tripeptide from the bromodomain of ATAD2. The complexity of this system allows us to investigate the strengths and limitations of these RCs. Overall, the findings presented here underline the potential of the unsupervised determination of reaction coordinates and the synergy with orthogonal analysis methods, such as Markov state models and SAPPHIRE analysis.



Alternate JournalJ. Chem. Phys.
PubMed ID37403854