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Abstract
The Tumor Necrosis Factor (TNF) and the TNF receptor (TNFR) superfamilies are composed of 19 ligands and 30 receptors, respectively. The oligomeric properties of ligands, both membrane bound and soluble, has been studied most. However, less is known about the oligomeric properties of TNFRs. Earlier reports identified the extracellular, membrane-distal, cysteine-rich domain as a pre-ligand assembly domain which stabilizes receptor dimers and/or trimers in the absence of ligand. Nevertheless, recent reports based on structural nuclear magnetic resonance (NMR) highlight the intrinsic role of the transmembrane domains to form dimers (p75NTR), trimers (Fas), or dimers of trimers (DR5). Thus, understanding the structural basis of transmembrane oligomerization may shed light on the mechanism for signal transduction and the impact of disease-associated mutations in this region. To this end, here we used an in silico coarse grained molecular dynamics approach with Martini force field to study TNFR transmembrane homotypic interactions. We have first validated this approach studying the three TNFR described by NMR (p75NTR, Fas, and DR5). We have simulated membrane patches composed of 36 helices of the same receptor equidistantly distributed in order to get unbiassed information on spontaneous proteins assemblies. Good agreement was found in the specific residues involved in homotypic interactions and we were able to observe dimers, trimers, and higher-order oligomers corresponding to those reported in NMR experiments. We have, applied this approach to study the assembly of disease-related mutations being able to assess their impact on oligomerization stability. In conclusion, our results showed the usefulness of coarse grained simulations with Martini force field to study in an unbiased manner higher order transmembrane oligomerization.
Highlights
Since the report of the first structure of the extracellular domain of the unliganded tumor necrosis factor receptor (Naismith et al, 1995), the Tumor Necrosis Factor (TNF)-related scientific community is interested in understanding the role of ligand independent receptor assembly in signal transduction
Naismith and colleagues showed that the soluble extracellular domain of TNFRSF1A was able to form homodimers in the absence of ligand and opened the discussion of whether these dimers restrain the receptor in an inactive ligand-free state or if they persist following ligand binding to extend an activating network (Naismith et al, 1996)
Such a model cannot be extended to small TNF receptor (TNFR) superfamily (TNFRSF) members which do not possess a pre-ligand assembly domain, and it does not explain the impact of pathogenic mutations located in the transmembrane region of several TNFRSF members
Summary
Several reports have shown the importance of pre-ligand assembly of different TNF receptor (TNFR) family members for proper ligand responses (Chan et al, 2000; Siegel et al, 2000; Clancy et al, 2005; Smulski et al, 2013, 2017; Pieper et al, 2014). Afterwards, two reports published back to back showed the importance of this region for proper ligand responses for TNFR1 and Fas (Chan et al, 2000; Siegel et al, 2000) and coined the term PLAD for pre-ligand assembly domain Other reports confirmed these observations and extended it to other TNFR family members (Clancy et al, 2005; Smulski et al, 2013; Pieper et al, 2014). In this report we used coarse grained molecular dynamics simulations using the Martini force field to study the transmembrane domain of all available NMR structures of TNFR superfamily (SF) members: p75NTR wt and C257A (TNFRSF16), Fas (TNFRSF6), and DR5 (TNFRSF10B) Each one of these structures showed different association levels such as dimers (Nadezhdin et al, 2016), trimers (Fu et al, 2016), and dimer of trimers (Pan et al, 2019), respectively. This method has proven to be reproducible and robust when compared to NMR data and set the bases for studying other TNFR family members, the impact of pathogenic mutations, different lipid compositions, and/or heteromeric associations
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