Biophys J. 2025 Aug 22:S0006-3495(25)00532-6. doi: 10.1016/j.bpj.2025.08.020. Online ahead of print.
ABSTRACT
To gain molecular and mechanistic insights into initiation of the RAS-RAF signaling cascade we developed and used a combination of multiscale simulation and experimental approaches. The influence and impact of the membrane on RAS and RAF proteins is a factor we are just beginning to understand and appreciate in more detail. Molecular simulation is an ideal methodology to further study this complicated relationship between the membrane and associated proteins. Our previous work using MuMMI (Multiscale Machine-learned Modeling Infrastructure) investigated different lipid compositions solely around the KRAS4b protein and the interplay between protein behavior and these membrane environments. MuMMI uses machine learning to couple adjacent simulation scales and has been efficiently scaled across some of the world’s largest high-performance computers. Recently, we have expanded this multi-resolution framework to include the all-atom simulation scale, and to incorporate the RAF RBDCRD domains. Here we present the overall analysis results from this new simulation campaign comprising a mixture of RAS and RAF RBDCRD proteins. Approximately 35,000 coarse-grained, and 10,000 all-atom molecular dynamics simulations were completed, sampled from a variety of protein/lipid composition configurations that were generated from a micron-scale continuum simulation containing hundreds of copies of the proteins. Our studies suggest that orientations of the RAS-RBDCRD complex on the membrane occupy distinct configurational states and the spatial patterns of lipid arrangements around these different protein states are unique to each state. The extent, and size of lipid ‘fingerprints’ imposed on the membrane by the RAS-RBDCRD protein complex is significantly larger than observed for just the RAS protein on its own. These protein complexes strongly associate but we do not observe statistically significant preferred protein-protein orientations. These observations indicate that spatial co-localization of RAS-RBDCRD proteins in the same vicinity may be assisted by specific membrane environments, acting to increase the probability of signaling complex formation.
PMID:40849684 | DOI:10.1016/j.bpj.2025.08.020
