Integrating Ultra-Coarse-Grained Protein Models into Accessible Workflows for Multiscale Molecular Dynamics

BY Chi and S Fulcar and J Ipe and O Schleifer and R Subramanian and C Vlases and N Matasci and K Georgouli and L Pottier and TM Hsu and TS Carpenter and DV Nissley and FC Lightstone and FH Streitz and HI Ingolfsson and F Aydin, ACS OMEGA, 10, 51726-51737 (2025).

DOI: 10.1021/acsomega.5c07601

To capture protein conformational transitions using molecular dynamics (MD), several simulation resolutions covering different spatial and temporal scales are typically needed. All-atom (AA) simulations provide fine resolution, but are computationally infeasible for large systems over longer durations. Coarse-grained (CG) and ultra-coarse-grained (UCG) models have a lower resolution and computational cost while still being able to conserve essential protein features. Prior work on a Multiscale Machine-learned Modeling Infrastructure (MuMMI) combined both AA and CG simulations to study RAS-RAF protein interactions, leveraging CG models for longer time scales and using AA to investigate unusual conformations in greater detail. However, MuMMI is still resource- intensive, and this study aims to maximize exploration of the protein conformational space while reducing computational cost. In this paper, we build on prior work that integrates UCG models based on heterogeneous elastic network modeling (hENM) into the MuMMI workflow. We demonstrate that UCG models enable accurate sampling of protein conformations, focusing on simulating RAS-RAF protein interactions. Using higher- resolution CG Martini simulation data, we can automatically refine intramolecular interactions in UCG models. We present a scalable Python package that uses fluctuations observed in higher-resolution CG Martini simulations to estimate bond coefficients of the UCG model. We built novel machine learning-based backmapping methods to recover more detailed CG Martini structures from UCG structures, using diffusion models to learn the mapping between scales. Finally, we present UCG- mini-MuMMI, an accessible and less compute-intensive version of MuMMI as a resource for the scientific community. Incorporating UCG models into MD studies is applicable to a broad range of systems and proteins, and our study offers insights into the advantages and limitations of these methods.

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