Adaptive Resolution Force Probe Simulations: Coarse Graining in the Ideal Gas Approximation

TL;DR

This paper demonstrates that adaptive resolution force probe simulations can accurately model the mechanical unfolding of biomolecules, even with simplified solvent models, matching fully atomistic results in various unfolding scenarios.

Contribution

It introduces the application of the adaptive resolution scheme with an ideal gas approximation for coarse graining in force probe molecular dynamics simulations, showing accurate results for complex unfolding pathways.

Findings

Excellent agreement between atomistic and AdResS simulations in unfolding pathways

Method accurately reproduces force distributions and hydrogen-bond sequences

Applicable to systems with protic solvents and complex conformational changes

Abstract

The unfolding of molecular complexes or biomolecules under the influence of external mechanical forces can routinely be simulated with atomistic resolution. To obtain a match of the characteristic time scales with those of experimental force spectroscopy, often coarse graining procedures are employed. Here, building on a previous study, we apply the adaptice resolution scheme (AdResS) to force probe molecular dynamics (FPMD) simulations using two model systems as examples. One system is the previously investigated calix[4]arene dimer that shows reversible one-step unfolding and the other example is provided by a small peptide, a $\beta$-alanine octamer in methanol solvent. The mechanical unfolding of this peptide proceeds via a metastable intermediate and therefore represents a first step towards a complex unfolding pathway. In addition to increasing the complexity of the relevant conformational changes we study the impact of the methodology used for coarse graining. Apart from a standard technique, the iterative Boltzmann inversion method, we apply an ideal gas approximation and therefore we replace the solvent by a non-interacting system of spherical particles. In all cases we find excellent agreement between the results of FPMD simulations performed fully atomistically and the AdResS simulations also in the case of fast pulling. This holds for all details of the unfolding pathways like the distributions of the characteristic forces and also the sequence of hydrogen-bond opening in case of the $\beta$-alanine octamer. Therefore, the methodology is very well suited to simulate the mechanical unfolding of systems of experimental relevance also in the presence of protic solvents.