Discerning intersecting fusion‐activation pathways in the Nipah virus using machine learning

Abstract

The fusion of Nipah with host cells is facilitated by two of their glycoproteins, the G and the F proteins. The binding of cellular ephrins to the G head domain causes the G stalk domain to interact differently with F, which activates F to mediate virus-host fusion. To gain insight into how the ephrin-binding signal transduces from the head to the stalk domain of G, we examine quantitatively the differences between the conformational ensembles of the G head domain in its ephrin-bound and unbound states. We consider the human ephrins B2 and B3, and a double mutant of B2, all of which trigger fusion. The ensembles are generated using molecular dynamics, and the differences between them are quantified using a new machine learning method. We find that the portion of the G head domain whose conformational density is altered equivalently by the three ephrins is large, and comprises ∼25% of the residues in the G head domain. This subspace also includes the residues that are known to be important to F activation, which suggests that it contains at least one common signaling pathway. The spatial distribution of the residues constituting this subspace supports the model of signal transduction in which the signal transduces via the G head dimer interface. This study also adds to the growing list of examples where signaling does not depend solely on backbone deviations. In general, this study provides an approach to filter out conserved patterns in protein dynamics.

Stimulation of Nipah Fusion: Small Intradomain Changes Trigger Extensive Interdomain Rearrangements

“…In the case of the Nipah G RBD, the root mean square deviation (RMSD) between the x-ray structures of its apo and ephrin-bound states is <1 Å (25,26). A similar result also ensues from subjecting these x-ray structures to all-atom molecular dynamics (MD) simulations at physiological temperature (28,29). Commensurate with similar observations in many well-studied eukaryotic proteins, like GPCRs and PDZ domains, this implies a key role of thermal fluctuations in allosteric signaling (30)(31)(32).…”

“…Our previous MD studies of the RBD in its monomeric form suggested that the allosteric pathway common to three different fusion-inducing ephrins involves the RBD-RBD interface (28). This pathway was also implicated in another recent study based on cellular assays and monoclonal antibody binding experiments (33).…”

“…Firstly, x-ray structures are available for the isolated Nipah RBD as well as its complex with ephrin (25,26). Secondly, both the ephrin-free and ephrin-bound structures of Nipah RBD have been subjected to MD at physiological temperature, and have been found to be stable (28,29). Thirdly, Bowden et al (12) have proposed a RBD-RBD interface for the G protein of the Hendra virus (PDB: 2X9M).…”

“…To construct the initial model of the RBD-RBD interface in the ephrinfree state, we take the final snapshot (640 ns) from our earlier simulation of the monomeric form of Nipah's RBD (28), and geometrically fit two of its copies individually onto the two RBDs of Hendra's RBD-RBD dimer. Geometric fitting is conducted using the backbone C a atoms.…”

“…S3. We use the same protocol to construct the initial model of the RBD-RBD dimer in the ephrin-bound state, but in this case we take the final snapshot (460 ns) of our simulation of Nipah's ephrin-bound RBD monomer (28) (Fig. S3).…”