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Specific protein interactions are analytical for able cellular signaling, and bootless and altered protein interactions account signaling defects and adapt the fate of cells. Protein alternation is usually advised by protein alternation domains, a analytical allotment of proteins circuitous in the bounden of specific sequences to added proteins1,2.
Cell afterlife and congenital allowed signaling pathways are important aegis mechanisms adjoin assorted pathogens. These processes are advised by assorted complicated protein–protein interactions that about-face signals and ascendancy cellular signaling events. Abounding proteins accommodating in these cellular signaling contest accommodate baby protein alternation domains, such as the afterlife area (DD), afterlife effector area (DED), caspase-recruiting area (CARD), PYrin area (PYD), baculovirus IAP echo (BIR) domain, Bcl-2 affinity (BH) domain, and/or corpuscle death-inducing DFF45-like effector (CIDE) domain. These proteins collaborate with specific bounden partners3,4,5. Amid the protein alternation domains, DD, DED, CARD, and PYD accord to the afterlife area (DD) superfamily. This is one of the better protein alternation area families, administration arrangement affinity and a accumulation structural feature: a six-helix array fold3,6,7,8.
Apoptotic DNA breach is a authentication of apoptosis and is primarily advised by the CIDE domain-containing proteins DFF40 and DFF45 9. DFF40 is an endonuclease that digests chromosomal DNA and produces nucleosomal fragments, admitting DFF45 is an inhibitor of DFF40 10. Both DFF40 and DFF45 accommodate a CIDE area that can arbitrate the alternation amid two proteins, consistent in the inhibition of DFF40 nuclease action by DFF45 11,12. In accession to DFF40/DFF45, the CIDE-A, CIDE-B, and CIDE-3 proteins accept been articular as accepting CIDE domains11,13. Although anatomic studies accept apparent that these three CIDE domain-containing proteins are additionally circuitous in apoptosis regulation, contempo studies accept adumbrated their role in activity metabolism, accurately their captivation in authoritative the admeasurement of lipid droplets14,15,16.
Over contempo decades, the interprotein interactions in the corpuscle afterlife and congenital allowed signaling pathways advised by DD superfamily-containing and CIDE domain-containing proteins accept been assiduously studied. This absorption is based on their anatomic accent in biological systems and their links to abounding animal diseases, including cancer, obesity, and assorted allowed diseases7,17,18,19,20,21,22. Studies accept appear that assorted signaling molecules in corpuscle afterlife and congenital allowed signaling anatomy higher-order signaling complexes alleged supramolecular acclimation centers (SMOCs) via DD superfamily or CIDE domains23,24. In accession to SMOC formation, DD superfamily-containing proteins can be accumulated into assorted oligomerization structures. In this review, we abridge the bounden strategies of the DD superfamily and CIDE domains detected appropriately far. We additionally altercate the biological acceptation of these assemblies during corpuscle afterlife and congenital allowed signaling events.
In the aboriginal 1990s, an intracellular DD absolute ~90 amino acids was aboriginal articular and called during a cellular abstraction on bump afterlife agency receptor and Fas25,26,27. Since then, genetic, functional, and structural analyses accept appear agnate DD-like domains in assorted proteins, appointed DEDs28, CARDs29, and PYDs30,31. The subfamily allocation is mainly angled by arrangement homology6. In humans, 37 DD-containing proteins, 7 DED-containing proteins, 33 CARD-containing proteins, and 22 PYD-containing proteins accept been articular appropriately far and begin to be decidedly anatomic during corpuscle afterlife and congenital amnesty events4,6. DD superfamily-containing proteins accurately collaborate through their DDs with added after DD superfamily-containing proteins, appropriately appointment signals through cellular signaling. In addition, DD superfamily-mediated SMOC accumulation is analytical for activating assorted caspases and kinases, which are all-important for corpuscle afterlife and congenital amnesty processes32,33.
The six-helix array bend is the accepted affection of the DD superfamily (Fig. 1a). The anatomy of the Fas DD, with the six-helix array fold, was the aboriginal anatomy amid the DD superfamily-containing proteins to be identified25. Then, the structures of the Fas-associated DD protein (FADD) with a DED28; RIP-associated protein with DD (RAIDD) with a CARD34; and NACHT, leucine-rich echo and PYD-containing 1 (NLRP1) with a PYD35 were elucidated (Fig. 1a). Although they acquire a accepted structural fold, anniversary subfamily has altered structural features, including a adjustable and apparent third braid (H3) in DDs, an RxDL burden in DEDs, a angled aboriginal braid (H1) in CARDs, and a almost baby H3 and continued H2-H3 abutting bend in PYDs (Fig. 1a).
a The structural appearance of DD superfamily members. Ribbon diagrams for anniversary subfamily in the DD superfamily are shown. Adumbrative structures are provided assuming the Fas afterlife area as the DD, the FADD afterlife effector area (DED) as the DED, the RAIDD caspase application area (CARD) as the CARD, and the NLRP3 pyrin area (PYD) as the PYD. The audible structural appearance of anniversary superfamily are indicated. The structures in the N-terminus to the C-terminus are black dejected and red, respectively. Secondary structures, H1−H6, are adumbrated on the agnate structure. b The aboriginal circling anatomy apparent in the DD superfamily. The circling accumulation is formed by a heteromeric circuitous of RAIDD DD and PIDD DD. Top and ancillary angle of the circling anatomy are apparent in the high larboard panel. Electron microscopy angel of the abnormally decrepit RAIDD DD/PIDD DD circuitous is presented in the lower larboard panel. The basal band formed by bristles PIDD DDs, the average band formed by bristles RAIDD DDs, and the top band formed by two RAIDD DDs are adumbrated in the ancillary appearance of the circuitous structure. A schematic collapsed diagram assuming the action for the circling accumulation by alternating spiral rotations with up and bottomward interactions in a academic PR subcomplex is apparent in the appropriate panel; P and R announce PIDD DD and RAIDD DD, respectively. c The three altered alternation prototypes, types I, II, and III, formed by DD superfamily members. The alternation interface is apparent with a red circle. The helixes and loops circuitous in the alternation are indicated. d Ancestor of the heterodimeric anatomy of the DD superfamily formed by caspase-9 CARD and Apaf-1 CARD. Secondary structures, H1−H6, are adumbrated on the agnate structure. This heterodimer is formed by blazon I interactions. e Ancestor of the homodimeric anatomy of the DD superfamily formed by Pelle DD and Tube DD. Secondary structures, H1−H6, are adumbrated on the agnate structure. This heterodimer is formed by blazon II interactions. f, g Added cases of circling accumulation by DD superfamily members. f Adumbrative circling structures formed by heteromeric Fas DD and FADD DD and g by heteromeric IRAK2 DD, IRAK4 DD, and MyD88 DD are shown. Schematic collapsed diagrams are presented to appearance bounden action information; F and FD P announce Fas DD and FADD DD, respectively; I2, I4, and M announce IRAK2 DD, IRAK4 DD, and MyD88 DD, respectively.
Each affiliate of the DD superfamily interacts with associates of its own subfamily3,8,36,37,38. The accepted action of DD superfamily accumulation was appear via a structural abstraction of the PIDDosome amount complex, a atomic circuitous that activates caspase-2 and is composed of RAIDD DD and PIDD DD7. This structural abstraction showed that seven RAIDD DD and bristles PIDD DD molecules formed a circular, three-layer structure: two layers are formed by RAIDD DD and one is formed by PIDD DD (Fig. 1b). The capital two layers, the basal band and average layer, are formed by bristles PIDD DDs and bristles RAIDD DDs, respectively, admitting the top band is formed by two added RAIDD DDs (Fig. 1b). This annular anatomy is formed by the altered circling and adaptation action of DD molecules. A collapsed schematic showed that the annular circuitous is complete by bristles alternating spiral rotations of the DD molecules in the aforementioned band about the axial vertical axis. One spiral circling rotates about 84° and translates bottomward the axis, and the added rotates about 54° and translates up the axis. These segments can anatomy a annular anatomy with three 84° and two 54° rotations ((84 × 3) (54 × 2) = 360°) (Fig. 1b). This altered annular anatomy formed by DDs participates in three types of interactions, namely, types I, II, and III, which are now advised the ancestor interactions of the DD superfamily (Fig. 1b). In blazon I interactions, residues in the H1 and H4 helices of one DD collaborate with residues in the H2 and H3 helices of the apprenticed DD (Fig. 1c). In blazon II interactions, an interface is formed by residues in the H4 braid and the H4−H5 bend of one DD and the residues in the H5−H6 bend and H6 braid of the apprenticed DD (Fig. 1c). In blazon III interactions, residues in the H3 in one DD and the residues in the abutting loops, from H1−H2 and H3–H4, of the apprenticed DD. This alternation action formed by the hetero DD circuitous was additionally detected in associates of added subfamilies of the DD superfamily. The adumbrative heterodimeric CARD anatomy of the Apaf-1 CARD and caspase-9 CARD circuitous appear that the alternation is advised by the alternate acceptance of the biconcave apparent formed by H1 and H4 in the caspase-9 CARD and the arched apparent formed by H2 and H3 in the Apaf-1 CARD. These interactions announce that this heterodimeric CARD anatomy is complete via archetypal blazon I interactions (Fig. 1d)39. Blazon I-mediated homodimer CARD accumulation was additionally apparent via a structural abstraction of ARC CARD40. The homodimer interface of ARC CARD is created by alkali bridges and hydrogen bonds formed amid the residues in H1 and H4 of one ARC CARD and the residues in H2 and H3 of its counterpart. The blazon II-mediated dimeric DD anatomy was apparent by a structural abstraction of Pelle DD and Tube DD (Fig. 1e)41. In this case, H4 and the H4−H5 bend in Tube DD collaborate with the H5−H6 bend in Pelle DD. Added structural abstraction of the circuitous formed by DDs appear that a agnate accumulation strategy, based on ancestor blazon I, blazon II, and blazon III interactions, occurs during Fas DD/FADD DD circuitous accumulation (Fig. 1f)17,42, RIP1DD/FADD DD circuitous formation42, and MyD88 DD/IRAK4 DD/IRAK2 DD circuitous accumulation (Fig. 1g)20. This suggests that the blazon I-, blazon II-, and blazon III-mediated accumulation strategies are accepted amid DD superfamily members. However, aberant dimeric structures in associates of the DD superfamily were additionally begin in contempo structural studies43,44,45.
The ample atomic complexes formed by the circling accumulation of DD superfamily associates were difficult to actuate by their clear anatomy because it is absurd to accumulate a circling anatomy unless the circling aeon happens to be an integer. With the development of avant-garde cryo-electron microscopy (EM) technology, abounding circling fiber structures of the DD superfamily, important for SMOC formation, accept been determined18,19,21,46,47,48,49,50. These structural studies appear that associates of the DD superfamily use a accepted accumulation mechanism, detected during the structural abstraction of the RAIDD DD/PIDD DD complex, to anatomy the circling fiber anatomy in SMOCs. This apparatus is formed via blazon I, II, and III interactions.
DD superfamily-mediated SMOC accumulation has been advised best assiduously via structural studies of an inflammasome composed of Nod-like receptor (NLR), anarchic caspase-1, and the ASC adaptor molecule51,52,53,54,55. Anniversary NLRP ancestors protein and caspase-1 contains a PYD and CARD at their corresponding N-terminus. ASC is a bipartite adaptor absolute a PYD and CARD, which can articulation NLRP with caspase-1 by mediating the alternation of PYD–PYD through NLRP and the alternation of CARD–CARD through caspase-1. The after-effects of an assay based on cryo-EM adumbrated that all associates of the DD superfamily in the inflammasome anatomy a circling fiber structure19,21,48,56.
The ASC CARD forms a circling fiber with a bore of ~8 nm and a axial aperture of ~1 nm (Fig. 2a)19. The fiber architectonics is accumulated via awkward one-start circling agreement with about 3.6 subunits per turn. It is formed by three types of archetypal agee interactions and displays threefold agreement forth the circling arbor (Fig. 2a). Another CARD fiber is alien by caspase-1 to anatomy a circling fiber with a awkward one-start circling accumulation with about four subunits per turn. This anatomy is agnate to the fiber anatomy of ASC CARD (Fig. 2b)21. A caspase-1 CARD fiber is additionally complete application the three ahead authentic types of agee interactions and has a bore of 8 nm with an close aperture of about 1 nm, which is hardly beyond than that of the ASC CARD21. ASC PYD additionally forms a circling fiber application three types of approved alternation modes. The fiber is a right-handed circling fiber with threefold agreement forth the circling arbor (Fig. 2c)48. Although the bore of the ASC PYD fiber is agnate to that of ASC CARD and caspase-1 CARD, the admeasurement of its close aperture was abundant greater (Fig. 2c). Based on the fiber structures of the ASC CARD, caspase-1 CARD, ASC PYD, and NLRP PYD, the all-embracing anatomy of the inflammasome and the accumulation apparatus are proposed48,57,58. NLRP activation by a pathogen-associated atomic arrangement triggers NLRP PYD accumulation and fiber formation, appropriately mediating ASC fiber accumulation by confined as a nucleation belvedere via the PYD–PYD interaction. The circling fiber of ASC recruits procaspase-1 via the CARD–CARD interaction. The recruited procaspase-1 additionally forms a circling fiber in the inflammasome complex, which mediates proximity-induced self-activation48,57,58.
Helical fiber structures of a the ASC caspase application area (CARD), b caspase-1 CARD, c the ASC pyrin area (PYD), and d the caspase-8 afterlife effector area (DED) are represented. The apparent structures are apparent in the larboard console from a boarded view. A schematic collapsed diagram is apparent in the appropriate panel. The three altered types of interactions acclimated for circling fiber accumulation are appointed blazon I, blazon II, and blazon III. C and P in the schematic archetypal announce CARD (C) and PYD (P), respectively. The bike DEDs of caspase-8 that aftermath a circling fiber anatomy are alone adumbrated by D1 for the aboriginal DED and D2 for the additional DED in the schematic model.
The alone circling fiber anatomy of DED was appear via a structural abstraction of the bike DED in caspase-8, which is activated in the death-inducing signaling circuitous (DISC)18. The all-embracing anatomy and architecture strategies of the circling DED filament, formed by archetypal blazon I, II, and III interactions, are agnate to those of added subfamilies. However, the DED fiber bore of ~9 nm is hardly greater than that of added filaments, and the right-handed braid does not accept a audible agreement (Fig. 2d). In accession to these adumbrative circling fiber structures of the DD superfamily, assorted cases accept been appear to date and are abbreviated in Table 1.
Domain swapping is broadly acclimated by proteins for the anatomic interconversion of monomers, dimers, and college oligomers. It is additionally activated by DD superfamily associates for dimerization59,60,61,62,63,64. Domain-swapping-mediated dimerization has been empiric in all subfamilies of the DD superfamily, including Fas DD22, NLRP14 PYD65, caspase-8 DED66,67, and vPOP CARD68. Based on structural studies, it was appear that two altered domain-swapping mechanisms can be acclimated to anatomy a abiding DD superfamily dimer. The aboriginal apparatus involves axis braid (formed by affiliated H5 and H6)-mediated area swapping, during which structural changes action in the H5 and H6 regions. The axis braid is formed by H5 abutting to H6, which can collaborate with the axis braid through its bounden counterpart. The DD and PYD subfamily associates additionally use this apparatus for area swapping. The capacity of this axis helix-mediated oligomerization were declared in a structural abstraction on the amount of the DISC, which is composed of Fas DD/FADD DD (Fig. 3a)22. In this study, a structural about-face was empiric in the H5 and H6 regions of the Fas DD, which formed a axis braid and advised area swapping. This was the analytical footfall for Fas DD dimerization and for the bounden of Fas DD to FADD DD to anatomy the DISC core. This axis helix-mediated area swapping that leads to Fas DD dimerization was appropriate to be an important authoritative apparatus for DISC formation. Axis braid accumulation that leads to area swapping was additionally begin during a structural abstraction of NLRP14 PYD65. Agnate to the structural about-face of the Fas DD, NLRP14 PYD forms a accumulated H5−H6 axis helix, which mediates the dimerization of NLRP14 PYD (Fig. 3b). Although the interface of the axis braid during the dimerization of NLRP14 PYD is not accompanying to that of the Fas DD, the structural change-mediated dimerization action is agnate to that activated by Fas DD in the DISC. This affinity is based on the axis braid formed by H5 and H6, which is analytical for breeding the dimer interface. NOD1 CARD is additionally dimerized application this mechanism69.
Representative cases of a DD (Fas DD), b pyrin area (PYD) (NLRP14), c the caspase application area (CARD) (COP from frog virus 3), and d afterlife effector area (DED) (caspase-8) are shown. Axis helix-mediated dimerization was empiric for a DD and b PYD. The affiliation of H5 and H6, which serves as a dimerization axis helix, is labeled. A monomer (upper panel) and a axis loop-mediated dimer (lower panel) are apparent in a cartoon. Bounded domain-swapping-mediated dimerization is apparent for CARD (c) and DED (d). A monomer (upper panel) and bounded domain-swapping-mediated dimer (lower panel) are apparent application a cartoon. e Proposed activation archetypal of caspase-8 by domain-swapping-mediated dimerization of the caspase-8 prodomain (tandem DEDs). f Tentative archetypal of DISC alternation accumulation via the alternation of the trimeric afterlife receptor apprenticed to the afterlife ligand, adaptor FADD, and domain-swapping-mediated dimerized caspase-8.
Another domain-swapping apparatus acclimated by the DD superfamily is bounded structural alteration-mediated bounded area swapping, as approved via structural studies of the DED and CARD subfamilies. In these cases, ample structural changes involving the advance and addendum of the H3−H6 arena that acquiesce for area swapping were observed70,71. This dimerization action was apparent in a structural abstraction of viral CARD-only protein (vCOP)68. In this structure, H4, H5, and H6 in the archetypal six-helix vCOP array are displaced and amid amid H1, H2, and H3 in a atom adverse of vCOP. This admittance forms the archetypal six-helix array structure, arch to vCOP dimerization (Fig. 3c). Another case of huge structural change-mediated area swapping and dimerization in the DD superfamily was apparent during a structural abstraction of bike DEDs in caspase-866,67. This abstraction showed that the circling array of DED2 is abundant from H4 to H6 and translocated to a analogue atom area it interacts with the H1, H2, and H3 braid bundles in the aboriginal H4−H6-contributing molecule, basic a new six-helix array (Fig. 3d). Both DED1 and DED2 in the caspase-8 bike DEDs accept an FL motif; it has been accustomed that the FL burden in DED2 is analytical for dimerization, oligomerization, and the added activation of caspase-8, admitting the FL burden in DED1 is not associated with either oligomerization or caspase activation72,73,74. This aftereffect explains the acumen that the FL burden in DED2 is analytical for caspase-8 activation, assuming that it is the primary advocate for caspase-8 area swapping and dimerization (Fig. 3e). By celebratory the domain-swapping-mediated dimerization of caspase-8, a archetypal of DISC accumulation and caspase-8 activation was suggested66. DISC accumulation via the afterlife ligand alternation with the afterlife receptor, followed by FADD recruitment, mediates the accessibility of the FL burden in procaspase-8 DED2. This induced accessibility is followed by area swapping, dimerization, and the activation of caspase-8. Because the trimeric afterlife ligand and afterlife receptor frequently interact, the complete DISC circuitous is anticipation to anatomy a DISC array in lipid endless (Fig. 3f).
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