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

Abstract

Nipah is an emerging paramyxovirus that is of serious concern to human health. It invades host cells using two of its membrane proteins-G and F. G binds to host ephrins and this stimulates G to activate F. Upon activation, F mediates virus-host membrane fusion. Here we focus on mechanisms that underlie the stimulation of G by ephrins. Experiments show that G interacts with ephrin and F through separate sites located on two different domains, the receptor binding domain (RBD) and the F activation domain (FAD). No models explain this allosteric coupling. In fact, the analogous mechanisms in other paramyxoviruses also remain undetermined. The structural organization of G is such that allosteric coupling must involve at least one of the two interfaces-the RBD-FAD interface and/or the RBD-RBD interface. Here we examine using molecular dynamics the effect of ephrin binding on the RBD-RBD interface. We find that despite inducing small changes in individual RBDs, ephrin reorients the RBD-RBD interface extensively, and in a manner that will enhance solvent exposure of the FAD. While this finding supports a proposed model of G stimulation, we also find from additional simulations that ephrin induces a similar RBD-RBD reorientation in a stimulation-deficient G mutant, V 209 VG / AAA. Together, our simulations suggest that while inter-RBD reorientation may be important, it is not, by itself, a sufficient condition for G stimulation. Additionally, we find that the mutation affects the conformational ensemble of RBD globally, including the RBD-FAD interface, suggesting the latter's role in G stimulation. Because ephrin induces small changes in individual RBDs, a proper analysis of conformational ensembles required that they are compared directly-we employ a method we developed recently, which we now release at SimTK, and show that it also performs excellently for non-Gaussian distributions.

Monomeric ephrinB2 binding induces allosteric changes in Nipah virus G that precede its full activation

“…8a ). Molecular dynamics simulations of ephrinB2 binding to the crystallographic NiV G dimer resulted in significant reorientation of the dimer 43 . It is interesting to note the correlation in solvent accessibility of key peptides in these simulations with the H/D exchange rates in our study.…”

Molecular basis for SARS-CoV-2 spike affinity for human ACE2 receptor

“…Given existing evidence on the general reliability of employed MD methods [13,[18][19][20], and our recent work [21] that yielded validated predictions on virus-host protein-protein interactions [22], we consider our qualitative conclusions to be robust. Nevertheless, from the perspective of intermolecular interaction theory, the underlying potential energy functions that we employ do rely on describing interactions using point charges, no polarization, and only pairwise vdW interactions.…”

Therapeutic potential of targeting the Eph/ephrin signaling complex

“…In short, HeV and NiV attach and infect cells through the coordinated functions of the receptor-binding G-protein and the fusion-mediating F-protein on the viral envelope (Bossart et al, 2013; Dutch, 2010). After ephrin engagement, there’s a conformational or other alteration in the G-protein that either releases the F-protein towards a fusion-active state or induces conformational changes in the F-protein, eventually leading to membrane fusion (Dutta et al, 2016; Steffen et al, 2012). …”