Limits...
The Architecture of the TIR Domain Signalosome in the Toll-like Receptor-4 Signaling Pathway.

Guven-Maiorov E, Keskin O, Gursoy A, VanWaes C, Chen Z, Tsai CJ, Nussinov R - Sci Rep (2015)

Bottom Line: The architecture that we obtain with 8 MyD88 molecules provides the structural basis for the MyD88-templated myddosome helical assembly and receptor clustering; it also provides clues to pro- and anti-inflammatory signaling pathways branching at the signalosome level to Mal/MyD88 and TRAM/TRIF pro- and anti-inflammatory pathways.The assembly of MyD88 death domain (DD) with TRAF3 (anti-viral/anti-inflammatory) and TRAF6 (pro-inflammatory) suggest that TRAF3/TRAF6 binding sites on MyD88 DD partially overlap, as do IRAK4 and FADD.Significantly, the organization illuminates mechanisms of oncogenic mutations, demonstrates that almost all TLR4 parallel pathways are competitive and clarifies decisions at pathway branching points.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey.

ABSTRACT
Activated Toll-like receptors (TLRs) cluster in lipid rafts and induce pro- and anti-tumor responses. The organization of the assembly is critical to the understanding of how these key receptors control major signaling pathways in the cell. Although several models for individual interactions were proposed, the entire TIR-domain signalosome architecture has not been worked out, possibly due to its complexity. We employ a powerful algorithm, crystal structures and experimental data to model the TLR4 and its cluster. The architecture that we obtain with 8 MyD88 molecules provides the structural basis for the MyD88-templated myddosome helical assembly and receptor clustering; it also provides clues to pro- and anti-inflammatory signaling pathways branching at the signalosome level to Mal/MyD88 and TRAM/TRIF pro- and anti-inflammatory pathways. The assembly of MyD88 death domain (DD) with TRAF3 (anti-viral/anti-inflammatory) and TRAF6 (pro-inflammatory) suggest that TRAF3/TRAF6 binding sites on MyD88 DD partially overlap, as do IRAK4 and FADD. Significantly, the organization illuminates mechanisms of oncogenic mutations, demonstrates that almost all TLR4 parallel pathways are competitive and clarifies decisions at pathway branching points. The architectures are compatible with the currently-available experimental data and provide compelling insights into signaling in cancer and inflammation pathways.

No MeSH data available.


Related in: MedlinePlus

MyD88 interaction models with the downstream orchestrators reveal that the three parallel downstream paths are competitive.(a) TRAF6 (1lb5:A) and TRAF3 (1fll:A) binds to almost completely overlapping interfaces on MyD88 DD (3mop:F), thus they are mutually exclusive. (b) IRAK4 (3mop:J) and FADD (2gf5:A) bind to overlapping interfaces on MyD88 DD (3mop:F), thus they compete to bind to MyD88. MyD88-IRAK4 interaction is not PRISM prediction, where the crystal structure of the complex is available (3mop:FJ). Red box indicates the location of steric clash.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4544004&req=5

f7: MyD88 interaction models with the downstream orchestrators reveal that the three parallel downstream paths are competitive.(a) TRAF6 (1lb5:A) and TRAF3 (1fll:A) binds to almost completely overlapping interfaces on MyD88 DD (3mop:F), thus they are mutually exclusive. (b) IRAK4 (3mop:J) and FADD (2gf5:A) bind to overlapping interfaces on MyD88 DD (3mop:F), thus they compete to bind to MyD88. MyD88-IRAK4 interaction is not PRISM prediction, where the crystal structure of the complex is available (3mop:FJ). Red box indicates the location of steric clash.

Mentions: Clustering of MyD88 DDs initiates the oligomerization of the myddosome complex. Besides IRAK4 and IRAK2, MyD88 DDs also associate with TRAF646, TRAF311, and FADD4748. Schematic representations suggested that downstream proteins, like TRAF6, interact with IRAK1/2, but not with MyD881526. However, a recent study revealed that there is also a direct interaction between MyD88 and TRAF6 and abrogation of this interaction inhibits NF-κB activation46. In line with this, we observed that TRAF6 prefers to bind to MyD88 when the whole myddosome is given as a target instead of monomeric MyD88 or IRAK2. That is, although there are favorable interactions of TRAF6 with both monomeric MyD88 and monomeric IRAK2 (Supplementary Figure S7), when the whole myddosome is taken into consideration, TRAF6 selects MyD88. As we stated before, higher order oligomerization is important for function and should be considered in modeling. We select the myddosome-TRAF6 interaction, with TRAF6 bound to MyD88, instead of the monomeric IRAK2-TRAF6. Figure 7 illustrates the interaction of TRAF6 with MyD88; the detailed supplementary Fig. S8 shows that the myddosome-TRAF6 organization in which the TRAF-C domain of TRAF6 is in contact with DDs of two MyD88 molecules (two layers of MyD88), one interaction is major, with hotspots and the other further stabilizing the complex. The interface is similar to the concave TRAF binding site with peptides as observed in TRAF6-CD40 (1lb6.pdb)49, TRAF2-TRADD (1f3v.pdb)50, and TRAF2-OX40 (1d0a.pdb)51. The TRAF-C region of TRAF6 needs to trimerize to function25 and TRAF6 trimerization is possible with this myddosome-TRAF6 architecture (Supplementary Figure S8). Previous studies showed that TRAF3 also associates with MyD88-IRAK4-IRAK1 complex52. Similar to TRAF6, TRAF3 also associates with two MyD88 proteins (two layers of MyD88) in the myddosome (Supplementary Figure S8). MyD88 binds to the concave site on the TRAF-C region of TRAF3, as previously observed in other interactions such as TRAF3-CD40 (1fll.pdb)53, TRAF3-BAFFR (2gkw.pdb)54, TRAF3-LMP1 (1zms.pdb)55, and TRAF3-Cardif (4ghu.pdb)56.


The Architecture of the TIR Domain Signalosome in the Toll-like Receptor-4 Signaling Pathway.

Guven-Maiorov E, Keskin O, Gursoy A, VanWaes C, Chen Z, Tsai CJ, Nussinov R - Sci Rep (2015)

MyD88 interaction models with the downstream orchestrators reveal that the three parallel downstream paths are competitive.(a) TRAF6 (1lb5:A) and TRAF3 (1fll:A) binds to almost completely overlapping interfaces on MyD88 DD (3mop:F), thus they are mutually exclusive. (b) IRAK4 (3mop:J) and FADD (2gf5:A) bind to overlapping interfaces on MyD88 DD (3mop:F), thus they compete to bind to MyD88. MyD88-IRAK4 interaction is not PRISM prediction, where the crystal structure of the complex is available (3mop:FJ). Red box indicates the location of steric clash.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4544004&req=5

f7: MyD88 interaction models with the downstream orchestrators reveal that the three parallel downstream paths are competitive.(a) TRAF6 (1lb5:A) and TRAF3 (1fll:A) binds to almost completely overlapping interfaces on MyD88 DD (3mop:F), thus they are mutually exclusive. (b) IRAK4 (3mop:J) and FADD (2gf5:A) bind to overlapping interfaces on MyD88 DD (3mop:F), thus they compete to bind to MyD88. MyD88-IRAK4 interaction is not PRISM prediction, where the crystal structure of the complex is available (3mop:FJ). Red box indicates the location of steric clash.
Mentions: Clustering of MyD88 DDs initiates the oligomerization of the myddosome complex. Besides IRAK4 and IRAK2, MyD88 DDs also associate with TRAF646, TRAF311, and FADD4748. Schematic representations suggested that downstream proteins, like TRAF6, interact with IRAK1/2, but not with MyD881526. However, a recent study revealed that there is also a direct interaction between MyD88 and TRAF6 and abrogation of this interaction inhibits NF-κB activation46. In line with this, we observed that TRAF6 prefers to bind to MyD88 when the whole myddosome is given as a target instead of monomeric MyD88 or IRAK2. That is, although there are favorable interactions of TRAF6 with both monomeric MyD88 and monomeric IRAK2 (Supplementary Figure S7), when the whole myddosome is taken into consideration, TRAF6 selects MyD88. As we stated before, higher order oligomerization is important for function and should be considered in modeling. We select the myddosome-TRAF6 interaction, with TRAF6 bound to MyD88, instead of the monomeric IRAK2-TRAF6. Figure 7 illustrates the interaction of TRAF6 with MyD88; the detailed supplementary Fig. S8 shows that the myddosome-TRAF6 organization in which the TRAF-C domain of TRAF6 is in contact with DDs of two MyD88 molecules (two layers of MyD88), one interaction is major, with hotspots and the other further stabilizing the complex. The interface is similar to the concave TRAF binding site with peptides as observed in TRAF6-CD40 (1lb6.pdb)49, TRAF2-TRADD (1f3v.pdb)50, and TRAF2-OX40 (1d0a.pdb)51. The TRAF-C region of TRAF6 needs to trimerize to function25 and TRAF6 trimerization is possible with this myddosome-TRAF6 architecture (Supplementary Figure S8). Previous studies showed that TRAF3 also associates with MyD88-IRAK4-IRAK1 complex52. Similar to TRAF6, TRAF3 also associates with two MyD88 proteins (two layers of MyD88) in the myddosome (Supplementary Figure S8). MyD88 binds to the concave site on the TRAF-C region of TRAF3, as previously observed in other interactions such as TRAF3-CD40 (1fll.pdb)53, TRAF3-BAFFR (2gkw.pdb)54, TRAF3-LMP1 (1zms.pdb)55, and TRAF3-Cardif (4ghu.pdb)56.

Bottom Line: The architecture that we obtain with 8 MyD88 molecules provides the structural basis for the MyD88-templated myddosome helical assembly and receptor clustering; it also provides clues to pro- and anti-inflammatory signaling pathways branching at the signalosome level to Mal/MyD88 and TRAM/TRIF pro- and anti-inflammatory pathways.The assembly of MyD88 death domain (DD) with TRAF3 (anti-viral/anti-inflammatory) and TRAF6 (pro-inflammatory) suggest that TRAF3/TRAF6 binding sites on MyD88 DD partially overlap, as do IRAK4 and FADD.Significantly, the organization illuminates mechanisms of oncogenic mutations, demonstrates that almost all TLR4 parallel pathways are competitive and clarifies decisions at pathway branching points.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey.

ABSTRACT
Activated Toll-like receptors (TLRs) cluster in lipid rafts and induce pro- and anti-tumor responses. The organization of the assembly is critical to the understanding of how these key receptors control major signaling pathways in the cell. Although several models for individual interactions were proposed, the entire TIR-domain signalosome architecture has not been worked out, possibly due to its complexity. We employ a powerful algorithm, crystal structures and experimental data to model the TLR4 and its cluster. The architecture that we obtain with 8 MyD88 molecules provides the structural basis for the MyD88-templated myddosome helical assembly and receptor clustering; it also provides clues to pro- and anti-inflammatory signaling pathways branching at the signalosome level to Mal/MyD88 and TRAM/TRIF pro- and anti-inflammatory pathways. The assembly of MyD88 death domain (DD) with TRAF3 (anti-viral/anti-inflammatory) and TRAF6 (pro-inflammatory) suggest that TRAF3/TRAF6 binding sites on MyD88 DD partially overlap, as do IRAK4 and FADD. Significantly, the organization illuminates mechanisms of oncogenic mutations, demonstrates that almost all TLR4 parallel pathways are competitive and clarifies decisions at pathway branching points. The architectures are compatible with the currently-available experimental data and provide compelling insights into signaling in cancer and inflammation pathways.

No MeSH data available.


Related in: MedlinePlus