Structural basis of TIR-domain-assembly formation in MAL- and MyD88-dependent TLR4 signaling

Ve, Thomas; Vajjhala, Parimala R.; Hedger, Andrew; Croll, Tristan I.; DiMaio, Frank; Horsefield, S.; Xiong, Yong; Lavrencic, Peter; Hassan, Zurina; Morgan, Garry; Mansell, Ashley; Mobli, Mehdi; O’Carroll, Ailís; Chauvin, Brieuc; Gambin, Yann; Sierecki, Emma; Landsberg, Michael J.; Stacey, Katryn J.; Egelman, Edward H.; Kobe, Boštjan

doi:10.1038/nsmb.3444

Cited by 138 publications

(217 citation statements)

References 75 publications

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“…This behaviour was consistent no matter what concentrations of the protein were expressed ( Figure 1B). The absence of large events is consistent with the findings by Ve et al that MyD88 TIR alone does not spontaneously polymerise 12 . Similarly, comparisons of the brightness profiles, PCH and FCS and purified GFP-foldon data obtained when the MyD88 DD alone is expressed, demonstrates that it too consistently forms small oligomers, more specifically octamers based on PCH analysis (Figure 2A-C).…”

Section: At Low Concentrations Both the Tir And Death Domains Are Resupporting

confidence: 92%

“…For many years, TIR domain associations, which are weak and transient, have been seen to contribute little to the oligomerisation status of signalling proteins 27,28 . However, the recent cryoEM structure of Mal TIR domain in filamentous form, as well as novel studies 12 ,demonstrated that upon specific ligand binding TIR-containing proteins cooperatively assemble into large multiprotein complexes 12,23 . The TIR domain of MyD88 was also demonstrated to polymerise but only upon seeding by Mal filaments.…”

Section: Full-length Myd88 Biophysical Behaviour and Its Link To Signmentioning

confidence: 99%

“…In parallel, recent studies demonstrate the role of the TIR domain in the self-assembly of MyD88. Ve et al discovered that the recombinant TIR domains of Mal and MyD88 alone can self-organize into helical filaments and have solved the structure of the assembly by cryo-electron microscopy 12 . These TIR filaments of both Mal and MyD88 have self-replicating propensity, joining the growing list of "prion-like" polymers found within the proteins of the immune system, namely RIPK1, RIPK3 13 , MAVS (mitochondrial antiviralsignalling protein) and ASC (Apoptosis-Associated Speck-Like Protein Containing CARD 9, 10, 12, .…”

Section: Introductionmentioning

confidence: 99%

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Effects of Pathological Mutations on the Prion-Like Polymerisation of MyD88

O’Carroll

Chauvin

Brown

et al. 2018

Preprint

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A novel concept has emerged whereby the higher-order self-assembly of proteins provides a simple and robust mechanism for signal amplification. This appears to be a universal signalling mechanism within the innate immune system, where the recognition of pathogens or danger-associated molecular patterns need to trigger a strong, binary response within cells. Previously, multiple structural studies have been limited to single domains, expressed and assembled at high protein concentrations. We therefore set out to develop new in vitro strategies to characterise the behaviour of full-length proteins at physiological levels. In this study we focus on the adaptor protein MyD88, which contains two domains with different self-assembly properties: a TIR domain that can polymerise similarly to the TIR domain of Mal, and a Death Domain that has been shown to oligomerise with helical symmetry in the Myddosome complex. To visualize the behaviour of fulllength MyD88 without purification steps, we use single-molecule fluorescence coupled to eukaryotic cell-free protein expression. These experiments demonstrate that at low protein concentration, only full-length MyD88 forms prion-like polymers. We also demonstrate that the metastability of MyD88 polymerisation creates the perfect binary response required in innate signalling: the system is silenced at normal concentrations but upstream signalling creates a "seed" that triggers polymerisation and amplification of the response. These findings pushed us to re-interpret the role of polymerisation in MyD88-related diseases and we studied the impact of disease-associated point mutations L93P, R196C and L252P/L265P at the molecular level. We discovered that all mutations completely block the ability of MyD88 to polymerise. We also confirm that L252P, a gain-of-function mutation, allows the MyD88 mutant to form extremely stable oligomers, even when expressed at low nanomolar concentrations. Thus, our results are consistent with and greatly add to the findings on the Myddosomes digital 'all-or-none' responses and the behaviour of the oncogenic mutation of MyD88.

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Section: At Low Concentrations Both the Tir And Death Domains Are Resupporting

confidence: 92%

Section: Full-length Myd88 Biophysical Behaviour and Its Link To Signmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Effects of Pathological Mutations on the Prion-Like Polymerisation of MyD88

O’Carroll

Chauvin

Brown

et al. 2018

Preprint

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“…TIR domains function as a homotypic interaction motif, and the molecular basis of interactions has recently been characterized for TLR4 signalling assembly with MyD88 and MAL (Ve et al, 2017). The TIR domains from the mammalian protein SARM1 and some bacterial proteins have also been shown to have NAD + -cleavage activity (Essuman et al, 2017(Essuman et al, , 2018; this finding suggests there may be evolutionary, rather than merely structural links with bacterial enzymes such as the CMP hydrolase MilB.…”

Section: Secondary Structure-based Phylogenetic Inferencementioning

confidence: 99%

Evolutionary model of protein secondary structure capable of revealing new biological relationships

Lai

Rost

Kobe

et al. 2019

Preprint

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AbstractAncestral sequence reconstruction has had recent success in decoding the origins and the determinants of complex protein functions. However, phylogenetic analyses of remote homologues must handle extreme amino-acid sequence diversity resulting from extended periods of evolutionary change. We exploited the wealth of protein structures to develop an evolutionary model based on protein secondary structure. The approach follows the differences between discrete secondary structure states observed in modern proteins and those hypothesised in their immediate ancestors. We implemented maximum likelihood-based phylogenetic inference to reconstruct ancestral secondary structure. The predictive accuracy from the use of the evolutionary model surpasses that of comparative modelling and sequence-based prediction; the reconstruction extracts information not available from modern structures or the ancestral sequences alone. Based on a phylogenetic analysis of multiple protein families, we showed that the model can highlight relationships that are evolutionarily rooted in structure and not evident in amino acid-based analysis.

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“…3). In fact, several structures of the TLR4/Adaptor/LPS complex and the TIR domain have been resolved separately (e.g., PDB codes: 3FXI [15] and 5UZB [16], respectively). Furthermore, the structure of the TLR4 transmembrane domain was recently solved by nuclear magnetic resonance (PDB code: 5NAM [17]) completing the atomistic modular description of the entire receptor.…”

Section: Lipid-stimulated Prrs (Tlr4)mentioning

confidence: 99%