In Silico Modeling and Characterization of Epstein-Barr Virus Latent Membrane Protein 1 Protein

Abstract

Latent membrane protein 1 (LMP1) plays a crucial role in Epstein-Barr virus (EBV)'s ability to establish latency and is involved in developing and progressing EBV-associated cancers. Additionally, EBV-infected cells affect the immune responses, making it challenging for the immune system to eliminate them. Due to the aforementioned reasons, it is crucial to understand the structural features of LMP1, which are essential for the development of novel cancer therapies that target its signaling pathways. To date, there is yet to be a complete LMP1 protein structure; therefore, in our work, we modeled the full-length LMP1 containing the short cytoplasmic N-terminus, six transmembrane domains (TMDs), 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 TMDs. Our results suggest that specific domains or motifs, predominantly in the C-terminal domain of LMP1, show promise as potential drug targets. As a whole, our work provides insights into key structural features of LMP1 that will allow the development of novel LMP1 therapies.

Figure 1

(a) pLDDT score per position for the 10 predicted models generated by Alphafold2. (b) Ramachandran plot for predicted protein model 3 of Alphafold2. (c) Ramachandran plot for our predicted LMP1 protein structure. The Ramachandran plot showing two core regions (blue color) and three allowed regions in the three separate boxes (green color). The beta-sheet region occupies the left-top box, the α helix at the lower-left box, and the left-handed helix at the top-right box.

Figure 2

Behavior of N-terminal regions of LMP1 in MD simulations showing values around 25 Å or lesser for all the three graphs. Replicate 1 is in blue, replicate 2 is in orange, replicate 3 is in black. (a) RMSD graph. (b) RMSF graph. (c) Radius of gyration (Rg) plot.

Figure 3

Behavior of TMD of LMP1 in MD simulations showing replicate 1 RMSD has a lower threshold compared to replicates 2 and 3. Replicate 1 is in blue, replicate 2 is in orange, and replicate 3 is in black. (a) RMSD graph. (b) RMSF graph. (c) Radius of gyration (Rg) plot.

Figure 4

Behavior of C-terminal region of LMP1 in MD simulations with replicate 2 (RMSD and Rg) has a higher threshold from replicates 1 and 3. Replicate 1 is in blue, replicate 2 is in orange, and replicate 3 is in black. (a) RMSD graph. (b) RMSF graph. (c) Radius of gyration (Rg) plot.

Figure 5

Behavior of LMP1 bilayer in MD simulations, showing replicate 2 (RMSD) has a lower threshold from the other two replicates. Replicate 1 is in blue, replicate 2 is in orange, and replicate 3 is in black. (a) RMSD graph. (b) RMSF graph. (c) Radius of gyration (Rg) plot.

Figure 6

Intramolecular hydrogen bonding analysis for LMP1 bilayer triplicate data runs with a cutoff limit of 60%. (a) Replicate 1. (b) Replicate 2. (c) Replicate 3.

Figure 7

Combined FEL plot with the corresponding conformations of the three basins and the time evolution of LMP1 from replicate 1 that showed the steepest basin. (a) Combined FEL plot showed 3 basins which are conformation 1 (replicate 1), conformation 2 (replicate 2), and conformation 3 (replicate 3). (b) Time evolution of LMP1 from replicate 1 that showed the steepest free-energy basin. The TMD, NTER, and CTAR domains are shown in green, red, and blue, respectively.