In silico modelling and characterization of Epstein–Barr virus LMP1 protein

Latent membrane protein 1 (LMP1) plays a crucial role in Epstein-Barr virus (EBV)’s ability to establish latency and is involved in the development and progression of EBV-associated cancers. Additionally, EBV-infected cells affect the immune responses, making it challenging for immune system to eliminate. Due to the aforementioned reasons, it is important to understand the structural features of LMP1 which is essential for the development of novel cancer therapies that target its signaling pathways. To date, there is no complete LMP1 protein structure therefore in our work, we modeled the full-length LMP1 containing the short cytoplasmic N-terminus, six transmembrane domains and a long-simulated C-terminus. Our model showed good stability and protein compactness evaluated through accelerated-Molecular Dynamics where the conformational ensemble exhibited compact folds, particularly in the transmembrane domains. Our results suggest that specific domains or motifs, predominantly in the C-terminus domain of LMP1 show promise as potential drug targets. As a whole, our work provides insights on key strucutral features of LMP1 that will allow the development of novel LMP1 therapies.