Browse
Submit Data
Databases
API
Help

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bowl-shaped oligomeric structures on membranes as DegP's new functional forms in protein quality control.

ABSTRACT: In the periplasm of Escherichia coli, DegP (also known as HtrA), which has both chaperone-like and proteolytic activities, prevents the accumulation of toxic misfolded and unfolded polypeptides. In solution, upon binding to denatured proteins, DegP forms large cage-like structures. Here, we show that DegP forms a range of bowl-shaped structures, independent of substrate proteins, each with a 4-, 5-, or 6-fold symmetry and all with a DegP trimer as the structural unit, on lipid membranes. These membrane-bound DegP assemblies have the capacity to recruit and process substrates in the bowl chamber, and they exhibit higher proteolytic and lower chaperone-like activities than DegP in solution. Our findings imply that DegP might regulate its dual roles during protein quality control, depending on its assembly state in the narrow bacterial envelope.

SUBMITTER: Shen QT

PROVIDER: S-EPMC2660739 | biostudies-literature | 2009 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Bowl-shaped oligomeric structures on membranes as DegP's new functional forms in protein quality control.

Shen Qing-Tao QT Bai Xiao-Chen XC Chang Lei-Fu LF Wu Yi Y Wang Hong-Wei HW Sui Sen-Fang SF

Proceedings of the National Academy of Sciences of the United States of America 20090302 12

In the periplasm of Escherichia coli, DegP (also known as HtrA), which has both chaperone-like and proteolytic activities, prevents the accumulation of toxic misfolded and unfolded polypeptides. In solution, upon binding to denatured proteins, DegP forms large cage-like structures. Here, we show that DegP forms a range of bowl-shaped structures, independent of substrate proteins, each with a 4-, 5-, or 6-fold symmetry and all with a DegP trimer as the structural unit, on lipid membranes. These m ...[more]

PMID: 19255437

Similar Datasets

Mitsugumin 23 forms a massive bowl-shaped assembly and cation-conducting channel.

Project description:Mitsugumin 23 (MG23) is a 23 kDa transmembrane protein localized to the sarcoplasmic/endoplasmic reticulum and nuclear membranes in a wide variety of cells. Although the characteristics imply the participation in a fundamental function in intracellular membrane systems, the physiological role of MG23 is unknown. Here we report the biochemical and biophysical characterization of MG23. Hydropathicity profile and limited proteolytic analysis proposed three transmembrane segments in the MG23 primary structure. Chemical cross-linking analysis suggested a homo-oligomeric assembly of MG23. Ultrastructural observations detected a large symmetrical particle as the predominant component and a small asymmetric assembly as the second major component in highly purified MG23 preparations. Single-particle three-dimensional reconstruction revealed that MG23 forms a large bowl-shaped complex equipped with a putative central pore, which is considered an assembly of the small asymmetric subunit. After reconstitution into planar phospholipid bilayers, purified MG23 behaved as a voltage-dependent, cation-conducting channel, permeable to both K(+) and Ca(2+). A feature of MG23 gating was that multiple channels always appeared to be gating together in the bilayer. Our observations suggest that the bowl-shaped MG23 can transiently assemble and disassemble. These building transitions may underlie the unusual channel gating behavior of MG23 and allow rapid cationic flux across intracellular membrane systems.

| S-EPMC3065873 | biostudies-other

ULK1 forms distinct oligomeric states and nanoscopic structures during autophagy initiation.

Project description:Autophagy induction involves extensive molecular and membrane reorganization. Despite substantial progress, the mechanism underlying autophagy initiation remains poorly understood. Here, we used quantitative photoactivated localization microscopy with single-molecule sensitivity to analyze the nanoscopic distribution of endogenous ULK1, the kinase that triggers autophagy. Under amino acid starvation, ULK1 formed large clusters containing up to 161 molecules at the endoplasmic reticulum. Cross-correlation analysis revealed that ULK1 clusters engaging in autophagosome formation require 30 or more molecules. The ULK1 structures with more than the threshold number contained varying levels of Atg13, Atg14, Atg16, LC3B, GEC1, and WIPI2. We found that ULK1 activity is dispensable for the initial clustering of ULK1, but necessary for the subsequent expansion of the clusters, which involves interaction with Atg14, Atg16, and LC3B and relies on Vps34 activity. This quantitative analysis at the single-molecule level has provided unprecedented insights into the behavior of ULK1 during autophagy initiation.

| S-EPMC10541014 | biostudies-literature

Cylindrical macrocyclic compounds synthesized by connecting two bowl-shaped calix[3]aramide moieties: structures and chiroptical properties.

Project description:Calix[3]aramide-based macrocycles 1 were successfully synthesized by a Glaser coupling reaction of two meta-calix[3]aramide moieties that have three ethynyl groups. The obtained macrocycles have stereoisomers: an enantiomeric pair and a meso form based on a combination of amide bond directions in the calix[3]aramide moieties at both ends of the molecule. Characteristic absorption spectra derived from the 1,4-diphenylbutadiyne structure were observed, while their ECD spectra were mirror-images. Single-crystal X-ray analysis revealed that each stereoisomer had a cylindrical rigid shape, and the absolute structure of the chiral-form was also assigned by comparing the Flack parameters. Mirror-image VCD spectra were observed for the enantiomeric chiral forms, and a VCD signal pattern of one enantiomer corresponded to that predicted by the relationship between the dihedral angle of the pair of C[double bond, length as m-dash]O groups.

| S-EPMC9056864 | biostudies-literature

Self-Assembly of Bowl-Shaped Naphthalimide-Annulated Corannulene.

Project description:The self-assembly of a bowl-shaped naphthalimide-annulated corannulene of high solubility has been studied in a variety of solvents by NMR and UV/Vis spectroscopy. Evaluation by the anti-cooperative K 2-K model revealed the formation of supramolecular dimers of outstanding thermodynamic stability. Further structural proof for the almost exclusive formation of dimers over extended aggregates is demonstrated by atomic force microscopy (AFM) and diffusion ordered spectroscopy (DOSY) measurements as well as by theoretical calculations. Thus, herein we present the first report of a supramolecular dimer of an annulated corannulene derivative in solution and discuss its extraordinarily high thermodynamic stability with association constants up to >106?M-1 in methylcyclohexane, which is comparable to the association constants given for planar phthalocyanine and perylene bisimide dyes.

| S-EPMC6946951 | biostudies-literature

COMMD1 forms oligomeric complexes targeted to the endocytic membranes via specific interactions with phosphatidylinositol 4,5-bisphosphate.

Project description:Copper metabolism Murr1 domain 1 (COMMD1) is a 21-kDa protein involved in copper export from the liver, NF-kappaB signaling, HIV infection, and sodium transport. The precise function of COMMD and the mechanism through which COMMD1 performs its multiple roles are not understood. Recombinant COMMD1 is a soluble protein, yet in cells COMMD1 is largely seen as targeted to cellular membranes. Using co-localization with organelle markers and cell fractionation, we determined that COMMD1 is located in the vesicles of the endocytic pathway, whereas little COMMD1 is detected in either the trans-Golgi network or lysosomes. The mechanism of COMMD1 recruitment to cell membranes was investigated using lipid-spotted arrays and liposomes. COMMD1 specifically binds phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) in the absence of other proteins and does not bind structural lipids; the phosphorylation of PtdIns at position 4 is essential for COMMD1 binding. Proteolytic sensitivity and molecular modeling experiments identified two distinct domains in the structure of COMMD1. The C-terminal domain appears sufficient for lipid binding, because both the full-length and C-terminal domain proteins bind to PtdIns(4,5)P2. In native conditions, endogenous COMMD1 forms large oligomeric complexes both in the cytosol and at the membrane; interaction with PtdIns(4,5)P2 increases the stability of oligomers. Altogether, our results suggest that COMMD1 is a scaffold protein in a distinct sub-compartment of endocytic pathway and offer first clues to its role as a regulator of structurally unrelated membrane transporters.

| S-EPMC2610505 | biostudies-literature

Functional Properties of Oligomeric and Monomeric Forms of Helicobacter pylori VacA Toxin.

Project description:Helicobacter pylori VacA is a secreted toxin that assembles into water-soluble oligomeric structures and forms anion-selective membrane channels. Acidification of purified VacA enhances its activity in cell culture assays. Sites of protomer-protomer contact within VacA oligomers have been identified by cryoelectron microscopy, and in the current study, we validated several of these interactions by chemical cross-linking and mass spectrometry. We then mutated amino acids at these contact sites and analyzed the effects of the alterations on VacA oligomerization and activity. VacA proteins with amino acid charge reversals at interprotomer contact sites retained the capacity to assemble into water-soluble oligomers and retained cell-vacuolating activity. Introduction of paired cysteine substitutions at these sites resulted in formation of disulfide bonds between adjacent protomers. Negative-stain electron microscopy and single-particle two-dimensional class analysis revealed that wild-type VacA oligomers disassemble when exposed to acidic pH, whereas the mutant proteins with paired cysteine substitutions retain an oligomeric state at acidic pH. Acid-activated wild-type VacA caused vacuolation of cultured cells, whereas acid-activated mutant proteins with paired cysteine substitutions lacked cell-vacuolating activity. Treatment of these mutant proteins with both low pH and a reducing agent resulted in VacA binding to cells, VacA internalization, and cell vacuolation. Internalization of a nonoligomerizing mutant form of VacA by host cells was detected without a requirement for acid activation. Collectively, these results enhance our understanding of the molecular interactions required for VacA oligomerization and support a model in which toxin activity depends on interactions of monomeric VacA with host cells.

| S-EPMC8594603 | biostudies-literature

Self-Limited Formation of Bowl-Shaped Nanopores for Directional DNA Translocation.

Project description:Solid-state nanopores of on-demand dimensions and shape can facilitate desired sensor functions. However, reproducible fabrication of arrayed nanopores of predefined dimensions remains challenging despite numerous techniques explored. Here, bowl-shaped nanopores combining properties of ultrathin membrane and tapering geometry are manufactured using a self-limiting process developed on the basis of standard silicon technology. The upper opening of the bowl-nanopores is 60-120 nm in diameter, and the bottom orifice reaches sub-5 nm. Current-voltage characteristics of the fabricated bowl-nanopores display insignificant rectification indicating weak ionic selectivity, in accordance to numerical simulations showing minor differences in electric field and ionic velocity upon the reversal of bias voltages. Simulations reveal, concomitantly, high-momentum electroosmotic flow downward along the concave nanopore sidewall. Collisions between the left and right tributaries over the bottom orifice drive the electroosmotic flow both up into the nanopore and down out of the nanopore through the orifice. The resultant asymmetry in electrophoretic-electroosmotic force is considered the cause responsible for the experimentally observed strong directionality in λ-DNA translocation with larger amplitude, longer duration, and higher frequencies for the downward movements from the upper opening than the upward ones from the orifice. Thus, the resourceful silicon nanofabrication technology is shown to enable nanopore designs toward enriching sensor applications.

| S-EPMC8613906 | biostudies-literature

Structures of monomeric and oligomeric forms of the <i>Toxoplasma gondii</i> perforin-like protein 1.

Project description:Toxoplasma and Plasmodium are the parasitic agents of toxoplasmosis and malaria, respectively, and use perforin-like proteins (PLPs) to invade host organisms and complete their life cycles. The Toxoplasma gondii PLP1 (TgPLP1) is required for efficient exit from parasitophorous vacuoles in which proliferation occurs. We report structures of the membrane attack complex/perforin (MACPF) and Apicomplexan PLP C-terminal β-pleated sheet (APCβ) domains of TgPLP1. The MACPF domain forms hexameric assemblies, with ring and helix geometries, and the APCβ domain has a novel β-prism fold joined to the MACPF domain by a short linker. Molecular dynamics simulations suggest that the helical MACPF oligomer preserves a biologically important interface, whereas the APCβ domain binds preferentially through a hydrophobic loop to membrane phosphatidylethanolamine, enhanced by the additional presence of inositol phosphate lipids. This mode of membrane binding is supported by site-directed mutagenesis data from a liposome-based assay. Together, these structural and biophysical findings provide insights into the molecular mechanism of membrane targeting by TgPLP1.

| S-EPMC5943054 | biostudies-literature

Solvent Mixing To Induce Molecular Motor Aggregation into Bowl-Shaped Particles: Underlying Mechanism, Particle Nature, and Application To Control Motor Behavior.

Project description:Control over dynamic functions in larger assemblies is key to many molecular systems, ranging from responsive materials to molecular machines. Here we report a molecular motor that forms bowl-shaped particles in water and how confinement of the molecular motor affects rotary motion. Studying the aggregation process in a broader context, we provide evidence that, in the case of bowl-shaped particles, the structures are not the product of self-assembly, but a direct result of the mixing a good solvent and a (partial) non-solvent and highly independent of the molecular design. Under the influence of the non-solvent, droplets are formed, of which the exterior is hardened due to the increase in the glass transition temperature by the external medium, while the interior of the droplets remains plasticized by the solvent, resulting in the formation of stable bowl-shaped particles with a fluid interior, a glass-like exterior, and a very specific shape: dense spheres with a hole in their side. Applying this to a bulky first-generation molecular motor allowed us to change its isomerization behavior. Furthermore, the motor shows in situ photo-switchable aggregation-induced emission. Strong confinement prohibits the thermal helix inversion step while altering the energy barriers that determine the rotary motion, such that it introduces a reverse trans- cis isomerization upon heating. These studies show a remarkable control of forward and backward rotary motion by simply changing solvent ratios and extent of confinement.

| S-EPMC6026844 | biostudies-literature

New Class of Supramolecular Bowl-Shaped Columnar Mesogens Derived from Thiacalix[4]arene Exhibiting Gelation and Organic Light-Emitting Diodes Applications.

Project description:A new class of blue light-emitting bowl-shaped mesogens with the thiacalix[4]arene core appended with 1,3,4-thiadiazole derivatives having peripheral alkoxy side chains have been synthesized and well characterized. The liquid crystalline behavior of present synthesized derivatives was examined by optical polarizing microscopy, differential scanning calorimetry, and X-ray diffraction studies. It was observed that these thiacalix[4]arene derivatives were capable of stabilizing the observed Colh phase with a higher temperature range. The cone-shaped thiacalix[4]arene-based liquid crystals with peripheral alkoxy side chains able to pack into the columns with enriched intermolecular interactions and thermal behavior. All derivatives showed blue luminescence in solution, solid thin-film, and gelation state. The hexagonal columnar phase and emissive nature of thiadiazole-based thiacalixarene compounds having xerogel behavior make them favorable in the application of emissive electronic display devices. The electrochemical properties of these thiacalixarene-based compounds demonstrate the effect of alkyl side chain on the highest occupied molecular orbital-lowest unoccupied molecular orbital energy levels and also exhibited lower electron band gaps. The electroluminescence behavior of the compound 10c was examined as emissive layers in the fabrication of organic light-emitting diodes.

| S-EPMC6776968 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data