How Does an Ectodomain of Membrane-Associated Proteins Stand Upright and Exert Robust Signal?

Even after decades of research, a comprehensive mechanism that elucidates the underpinnings of signaling through the cell membrane is still elusive. Here, we address a simple question- “how does the ectodomain of a membrane-associated protein consisting of multiple domains and connected by flexible linkers stand ‘upright’ on the  membrane?”. Our analysis based on large amount of available functional and structural data, looking for a pattern of association of these molecules in the crystal structures and with the concept that ‘random things seldom repeat’ lead to a surprisingly interesting and consistent observation that (1) the weak cis-interaction mediated symmetric oligomerization of signaling molecules not only support their ‘upright’ orientation but often bury their ligand-binding surface to avoid spurious signaling (2) the linkers connecting the domains are probably not flexible as presumed. This analysis provides a model for pre-liganded receptor clustering that resolves some of the mysteries unanswered by hypothesis such as ‘lipid-rafts’ and ‘fence and pickets. With CD4, pMHCII, CD2 and TNFR1 as examples, we show that the observed cis-association of molecules also correlate well with their functional role and emphasise the need for considering these cis mediated physiological confirmations while designing the therapeutic agonist or antagonistic antibodies. Further, our analysis reconciles the long-standing controversies related to these molecules and appear to be generic enough to be applied to other signaling molecules. Finally, we also provide a new model for CD4:MHC:TCR signaling