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

• Published in: Biophysical journal 2016-10, Vol.111 (8), p.1621-1630
• Main Authors: Dutta, Priyanka, Siddiqui, Ahnaf, Botlani, Mohsen, Varma, Sameer
• Format: Article
• Language: English
• Subjects: Binding sites; Biophysics; Computer simulation; Ephrins - metabolism; Membranes; Models, Molecular; Mutation; Nipah Virus - genetics; Nipah Virus - metabolism; Nipah Virus - physiology; Protein Binding; Protein Domains; Proteins; Viral Matrix Proteins - chemistry; Viral Matrix Proteins - genetics; Viral Matrix Proteins - metabolism; Virus Internalization
• ISSN: 0006-3495; 1542-0086
• DOI: 10.1016/j.bpj.2016.09.002

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, V209 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.