Abstract A015: Dynamics and lipid interactions of the RAS-RBD-CRD protein complex

Abstract

Abstract The high-resolution structure of the RAS G-domain complexed to the RBD and CRD domains of RAF provides critical insights into the assembly and conformation of the RAS-RAF signaling complex[1]. The influence and impact of the membrane on both the RAS and RAF proteins is a factor that we are just beginning to understand and appreciate. Molecular simulation is an ideal methodology to further study the complicated relationship between the membrane and associated proteins. Our recent work, using MuMMI[2] (Multiscale Machine-learned Modeling Infrastructure), investigated the different lipid compositions around KRAS4b and the interplay between the protein behavior and these membrane environments[3]. MuMMI uses machine learning to couple adjacent simulation scales and can be effectively scaled across some of the world’s largest high performance computing systems. The MuMMI multi-resolution framework has been expanded to include the RAF RBD-CRD domains. Here we present the overall simulation results from this latest MuMMI campaign. Tens of thousands of coarse-grained molecular dynamics simulations were completed, sampled from a variety of protein/lipid composition configurations. The orientations of the RAS-RBD-CRD complex on the membrane occupies distinct configurational states. Furthermore, the spatial patterns of lipid arrangements around these different protein states are also unique to each state. Interactions of the CRD with the membrane indicate the enrichment of very specific lipids in precise locations act to stabilize the complex. The extent, and size of the lipid ‘fingerprint’ imposed on the membrane by the RAS-RBD-CRD protein complex is significantly larger than observed for just the RAS protein on its own. We do not observe any statistically significant defined protein-protein orientations within the simulation ensemble. These observations indicate that spatial co-localize the RAS-RBD-CRD proteins in the same vicinity may be assisted by specific membrane environments. [1] Tran, Timothy H., et al. "KRAS interaction with RAF1 RAS-binding domain and cysteine-rich domain provides insights into RAS-mediated RAF activation." Nature communications 12.1 (2021): 1-16. [2] Di Natale, Francesco, et al. "A massively parallel infrastructure for adaptive multiscale simulations: modeling RAS initiation pathway for cancer." Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis. 2019. [3] Ingólfsson, Helgi I., et al. "Machine learning–driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins." Proceedings of the National Academy of Sciences 119.1 (2022): e2113297119. Citation Format: Felice C. Lightstone, Timothy S. Carpenter. Dynamics and lipid interactions of the RAS-RBD-CRD protein complex [abstract]. In: Proceedings of the AACR Special Conference: Targeting RAS; 2023 Mar 5-8; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Res 2023;21(5_Suppl):Abstract nr A015.