Enhanced Exploration of Protein Conformational Space through Integration of Ultra-Coarse-Grained Models to Multiscale Workflows.
Journal:
The journal of physical chemistry. B
Published Date:
May 22, 2025
Abstract
Computational techniques such as all-atom (AA) molecular dynamics (MD) simulations and coarse-grained (CG) models have been essential to study various biological problems over a wide range of scales. While AA simulations provide detailed insights, they are computationally expensive for capturing dynamics over longer length and time scales. CG approaches, particularly ultra-coarse-grained (UCG) models as considered in this study, have addressed this limitation by simplifying molecular representations, enabling the study of larger systems and longer time scales. This work focuses on the development of UCG models of proteins and their integration into the Multiscale Machine-Learned Modeling Infrastructure (MuMMI) to efficiently sample protein conformations, exemplified by the RAS-RBDCRD protein complex. By employing a combination of essential dynamics coarse graining (EDCG) and heterogeneous elastic network modeling (hENM) with anharmonic modifications, we developed UCG models based on the fluctuations observed in the higher resolution Martini CG simulations. These models allow the accurate sampling of protein configurations and long-range conformational changes. The incorporation of an implicit membrane model further enhanced the exploration of protein-membrane dynamics. Additionally, a novel machine-learning-based backmapping approach was developed to convert UCG structures to Martini CG representations, resulting in improved prediction accuracy. Finally, the integration of UCG models into MuMMI significantly enhances the exploration of protein configurations, offering critical insights into the role of protein dynamics in biological processes.
