Higher-order assemblies in immune signaling: supramolecular complexes and phase separation.
Ontology highlight
ABSTRACT:
SUBMITTER: Xia S
PROVIDER: S-EPMC8403095 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Dipyrrolyldiketones are essential building units of anion-responsive π-electronic molecules and ion-pairing assemblies. Here, we demonstrated that they form complexes with CuII characterized by planar geometries. The solid-state stacking assembled structures, as revealed by single-crystal X-ray analysis, were modulated by the substitution of pyrrole units. The rectangular shapes of the CuII complexes resulted in the formation of mesophases upon introduction of aliphatic chains.
| S-EPMC7914842 | biostudies-literature
Project description:Selective autophagy is the mechanism by which large cargos are specifically sequestered for degradation. The structural details of cargo and receptor assembly giving rise to autophagic vesicles remain to be elucidated. We utilize the yeast cytoplasm-to-vacuole targeting (Cvt) pathway, a prototype of selective autophagy, together with a multi-scale analysis approach to study the molecular structure of Cvt vesicles. We report the oligomeric nature of the major Cvt cargo Ape1 with a combined 2.8 Å X-ray and negative stain EM structure, as well as the secondary cargo Ams1 with a 6.3 Å cryo-EM structure. We show that the major dodecameric cargo prApe1 exhibits a tendency to form higher-order chain structures that are broken upon interaction with the receptor Atg19 in vitro The stoichiometry of these cargo-receptor complexes is key to maintaining the size of the Cvt aggregate in vivo Using correlative light and electron microscopy, we further visualize key stages of Cvt vesicle biogenesis. Our findings suggest that Atg19 interaction limits Ape1 aggregate size while serving as a vehicle for vacuolar delivery of tetrameric Ams1.
| S-EPMC4931565 | biostudies-literature
Project description:The centrosome is a unique membraneless organelle that plays a pivotal role in the orderly progression of the cell cycle in animal cells. It has been shown that two pericentriolar scaffold proteins, Cep63 and Cep152, generate a heterotetrameric complex to self-assemble into a higher-order cylindrical architecture around a centriole. However, the mechanisms underlying how they reach their threshold concentrations in the vast intracellular space and generate a self-assembled architecture remain mysterious. Here we demonstrate that, like liquid-like assemblies, Cep63 and Cep152 cooperatively generate amorphous aggregates capable of undergoing dynamic turnover and inter-aggregate fusion in vivo and a significant level of internal rearrangemefnt within a condensate in vitro. Consistently, 1,6-hexanediol, a liquid-liquid phase separation disruptor, greatly diminished the ability of endogenous Cep63 and Cep152 to localize to centrosomes. Interestingly, a purified Cep63•Cep152 complex generated either a cylindrical structure or a vesicle-like hollow sphere in a spatially controlled manner. It also formed condensate-like solid spheres in the presence of a macromolecular crowder. At the molecular level, two hydrophobic motifs, one each from Cep63 and Cep152, were required for generating phase-separating condensates and a high molecular-weight assembly. Thus, we propose that the self-assembly of the Cep63•Cep152 complex is triggered by an intrinsic property of the complex undergoing density transition through the hydrophobic-motif-mediated phase separation. Abbreviations: PCM, pericentriolar material; LLPS, liquid-liquid phase separation; MW, molecular-weight; CLEM, correlative light and electron microscopy; WT, wild-type; CMV, cytomegalovirus; FRAP, fluorescence recovery after photobleaching; FITC, fluorescein isothiocyanate; PCR, polymerase chain reaction; 3D-SIM, three-dimensional structured illumination microscopy; DMEM, Dulbecco's Modified Eagle Medium; PEI Max, Polyethylenimine Max; PBS, phosphate-buffered saline; RT, room temperature; DAPI, 4', 6-diamidino-2-phenylindole; AOTF, acousto-optic tunable filter; LB, Luria broth; OD, optical density; IPTG, isopropyl β-D-1-thiogalactopyranoside; SDS-PAGE, sodium dodecyl sulfate-polyacrylamide gel electrophoresis.
| S-EPMC7781590 | biostudies-literature
Project description:Five zinc(II) coordination compounds, [ZnCl2(isn)2] (1), [ZnBr2(isn)2] (2), [Zn(NO3)2(H2O)(isn)2] (3), [Zn(CH3COO)2(isn)]2 (4) and [Zn(isn)4(H2O)2](ClO4)2 (5) (isn = isonicotinamide), were prepared by the reactions of the isonicotinamide (pyridine-4-carboxamide, isn) and corresponding zinc(II) salts. Their crystal structures were determined by the single-crystal X-ray diffraction method. The coordination environment of zinc(II) is tetrahedral in the compounds containing small halide anions (chloride, bromide), 1 and 2. An expansion of the zinc(II) coordination environment to the octahedral is observed in the presence of the monodentate and bridging nitrate ions in 3. The coordination environments of both zinc(II) ions in dimeric acetate complex 4 is also enlarged in the comparison with 1 and 2, one zinc(II) ion being octahedrally coordinated and the other being pentacoordinated. The zinc(II) ion in 5 also reaches higher coordination environment (octahedral), which is enabled by binding of additional water molecules, since the perchlorate ion is uncoordinated. The supramolecular amide-amide homosynthon R22(8) is preserved in the presence of halide, nitrate and acetate ions (1-4), but it is completely disrupted in the crystal packing of 5 due to the presence of the bulky perchlorate anion. Spectroscopic analysis of compounds 1-5 was performed by IR spectroscopy in the solid state and by 13C NMR spectroscopy in the DMSO solutions. The NMR data support a complete decomposition of 3 in the DMSO solution, but 1, 2, 4 and 5 remain unchanged in the solution. Thermal properties of the coordination compounds were also investigated by TGA and DSC methods.
| S-EPMC9307440 | biostudies-literature
Project description:Cell death-inducing DFF45-like effector (CIDE) domains, initially identified in apoptotic nucleases, form a family with diverse functions ranging from cell death to lipid homeostasis. Here we show that the CIDE domains of Drosophila and human apoptotic nucleases Drep2, Drep4, and DFF40 all form head-to-tail helical filaments. Opposing positively and negatively charged interfaces mediate the helical structures, and mutations on these surfaces abolish nuclease activation for apoptotic DNA fragmentation. Conserved filamentous structures are observed in CIDE family members involved in lipid homeostasis, and mutations on the charged interfaces compromise lipid droplet fusion, suggesting that CIDE domains represent a scaffold for higher-order assembly in DNA fragmentation and other biological processes such as lipid homeostasis.
| S-EPMC5514754 | biostudies-literature
Project description:Lanthanoid ions exhibit extremely large anomalous X-ray scattering at their L(III) absorption edge. They are thus well suited for anomalous diffraction experiments. A novel class of lanthanoid complexes has been developed that combines the physical properties of lanthanoid atoms with functional chemical groups that allow non-covalent binding to proteins. Two structures of large multimeric proteins have already been determined by using such complexes. Here the use of the luminescent europium tris-dipicolinate complex [Eu(DPA)(3)](3-) to solve the low-resolution structure of a 444 kDa homododecameric aminopeptidase, called PhTET1-12s from the archaea Pyrococcus horikoshii, is reported. Surprisingly, considering the low resolution of the data, the experimental electron density map is very well defined. Experimental phases obtained by using the lanthanoid complex lead to maps displaying particular structural features usually observed in higher-resolution maps. Such complexes open a new way for solving the structure of large molecular assemblies, even with low-resolution data.
| S-EPMC3004260 | biostudies-literature
Project description:The Hippo pathway was originally discovered to control tissue growth in Drosophila and includes the Hippo kinase (Hpo; MST1/2 in mammals), scaffold protein Salvador (Sav; SAV1 in mammals), and the Warts kinase (Wts; LATS1/2 in mammals). The Hpo kinase is activated by binding to Crumbs-Expanded (Crb-Ex) and/or Merlin-Kibra (Mer-Kib) proteins at the apical domain of epithelial cells. Here we show that activation of Hpo also involves formation of supramolecular complexes with properties of a biomolecular condensate, including concentration dependence and sensitivity to starvation, macromolecular crowding, or 1,6-hexanediol treatment. Overexpressing Ex or Kib induces formation of micron-scale Hpo condensates in the cytoplasm, rather than at the apical membrane. Several Hippo pathway components contain unstructured low-complexity domains and purified Hpo-Sav complexes undergo phase separation in vitro. Formation of Hpo condensates is conserved in human cells. We propose that apical Hpo kinase activation occurs in phase separated 'signalosomes' induced by clustering of upstream pathway components.
| S-SCDT-10_15252-EMBJ_2022112863 | biostudies-other
Project description:Singularities ubiquitously exist in different fields and play a pivotal role in probing the fundamental laws of physics and developing highly sensitive sensors. Nevertheless, achieving higher-order (≥3) singularities, which exhibit superior performance, typically necessitates meticulous tuning of multiple (≥3) coupled degrees of freedom or additional introduction of nonlinear potential energies. Here we propose theoretically and confirm using mechanics experiments, the existence of an unexplored cusp singularity in the phase-tracked (PhT) steady states of a pair of coherently coupled mechanical modes without the need for multiple (≥3) coupled modes or nonlinear potential energies. By manipulating the PhT singularities in an electrostatically tunable micromechanical system, we demonstrate an enhanced cubic-root response to frequency perturbations. This study introduces a new phase-tracking method for studying interacting systems and sheds new light on building and engineering advanced singular devices with simple and well-controllable elements, with potential applications in precision metrology, portable nonreciprocal devices, and on-chip mechanical computing.
| S-EPMC10692225 | biostudies-literature
Project description:Fractionaion of nuclear periphery and core, followed by DDA in primary HFFs at 1 hour post infection with ICP0-RF HSV-1; IP-PRM of IFI16 in primary HFFs at 1 hpi; in vitro kinase assay with IFI16 and select kinases and quantification on phosphorlyated peptides by PRM.
2023-05-22 | PXD034348 | Pride
Project description:The importance of phosphate in biology and chemistry has long motivated investigation of its recognition. Despite this interest, phosphate's facile oligomerization is only now being examined following the discovery of complexes of anion-anion dimers of hydroxyanions. Here we address how oligomerization dictates phosphate's recognition properties when engaged with planar cyanostar macrocycles that can also oligomerize by stacking. The crystal structure of cyanostar with phosphate shows an unprecedented tetrameric stack of cyanostar macrocycles threaded by a phosphate trimer, [H2PO4···H2PO4···H2PO4]3-. The solution behaviour, studied as a function of solvent quality, highlights how dimers and trimers of phosphate drive formation of higher order stacks of cyanostar into dimer, trimer and tetramer co-assemblies. Solution behaviors differ significantly from simpler complexes of bisulfate hydroxyanion dimers. Phosphate oligomerization is: (1) preferred over ion pairing with tetrabutylammonium cations, (2) inhibits disassembly of the complexes upon dilution, and (3) resists interference from competitive anion solvation. The phosphate oligomers also appear critical for stability; complexation of just one phosphate with cyanostars is unfavored. The cyanostar's ability to self-assemble is found to create a tubular, highly electropositive cavity that complements the size and shape of the phosphate oligomers as well as their higher charge. When given the opportunity, phosphate will cooperate with the receptor to form co-assembled architectures.
| S-EPMC5941797 | biostudies-other