Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Modulating the Nucleated Self-Assembly of Tri-?(3) -Peptides Using Cucurbit[n]urils.

ABSTRACT: The modulation of the hierarchical nucleated self-assembly of tri-?(3) -peptides has been studied. ?(3) -Tyrosine provided a handle to control the assembly process through host-guest interactions with CB[7] and CB[8]. By varying the cavity size from CB[7] to CB[8] distinct phases of assembling tri-?(3) -peptides were arrested. Given the limited size of the CB[7] cavity, only one aromatic ?(3) -tyrosine can be simultaneously hosted and, hence, CB[7] was primarily acting as an inhibitor of self-assembly. In strong contrast, the larger CB[8] can form a ternary complex with two aromatic amino acids and hence CB[8] was acting primarily as cross-linker of multiple fibers and promoting the formation of larger aggregates. General insights on modulating supramolecular assembly can lead to new ways to introduce functionality in supramolecular polymers.

SUBMITTER: Satav T

PROVIDER: S-EPMC6680354 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Modulating the Nucleated Self-Assembly of Tri-β(3) -Peptides Using Cucurbit[n]urils.

Satav Tushar T Korevaar Peter P de Greef Tom F A TF Huskens Jurriaan J Jonkheijm Pascal P

Chemistry (Weinheim an der Bergstrasse, Germany) 20160729 36

The modulation of the hierarchical nucleated self-assembly of tri-β(3) -peptides has been studied. β(3) -Tyrosine provided a handle to control the assembly process through host-guest interactions with CB[7] and CB[8]. By varying the cavity size from CB[7] to CB[8] distinct phases of assembling tri-β(3) -peptides were arrested. Given the limited size of the CB[7] cavity, only one aromatic β(3) -tyrosine can be simultaneously hosted and, hence, CB[7] was primarily acting as an inhibitor of self-as ...[more]

PMID: 27434777

Similar Datasets

Broad-Spectrum Extracellular Antiviral Properties of Cucurbit[<i>n</i>]urils.

Project description:Viruses are microscopic pathogens capable of causing disease and are responsible for a range of human mortalities and morbidities worldwide. They can be rendered harmless or destroyed with a range of antiviral chemical compounds. Cucurbit[n]urils (CB[n]s) are a family of macrocycle chemical compounds existing as a range of homologues; due to their structure, they can bind to biological materials, acting as supramolecular "hosts" to "guests", such as amino acids. Due to the increasing need for a nontoxic antiviral compound, we investigated whether cucurbit[n]urils could act in an antiviral manner. We have found that certain cucurbit[n]uril homologues do indeed have an antiviral effect against a range of viruses, including herpes simplex virus 2 (HSV-2), respiratory syncytial virus (RSV) and SARS-CoV-2. In particular, we demonstrate that CB[7] is the active homologue of CB[n], having an antiviral effect against enveloped and nonenveloped species. High levels of efficacy were observed with 5 min contact times across different viruses. We also demonstrate that CB[7] acts with an extracellular virucidal mode of action via host-guest supramolecular interactions between viral surface proteins and the CB[n] cavity, rather than via cell internalization or a virustatic mechanism. This finding demonstrates that CB[7] acts as a supramolecular virucidal antiviral (a mechanism distinct from other current extracellular antivirals), demonstrating the potential of supramolecular interactions for future antiviral disinfectants.

| S-EPMC9578052 | biostudies-literature

Surface effects mediate self-assembly of amyloid-β peptides.

Project description:Here we present a label-free method for studying the mechanism of surface effects on amyloid aggregation. In this method, spin-coating is used to rapidly dry samples, in a homogeneous manner, after various incubation times. This technique allows the control of important parameters for self-assembly, such as the surface concentration. Atomic force microscopy is then used to obtain high-resolution images of the morphology. While imaging under dry conditions, we show that the morphologies of self-assembled aggregates of a model amyloid-β peptide, Aβ(12-28), are strongly influenced by the local surface concentration. On mica surfaces, where the peptides can freely diffuse, homogeneous, self-assembled protofibrils formed spontaneously and grew longer with longer subsequent incubation. The surface fibrillization rate was much faster than the rates of fibril formation observed in solution, with initiation occurring at much lower concentrations. These data suggest an alternative pathway for amyloid formation on surfaces where the nucleation stage is either bypassed entirely or too fast to measure. This simple preparation procedure for high-resolution atomic force microscopy imaging of amyloid oligomers and protofibrils should be applicable to any amyloidogenic protein species.

| S-EPMC4212779 | biostudies-literature

Synthesis and self-assembly processes of monofunctionalized cucurbit[7]uril.

Project description:We present a building-block approach toward functionalized CB[7] derivatives by the condensation of methylene-bridged glycoluril hexamer 1 and glycoluril bis(cyclic ethers) 2 and 12. The CB[7] derivatives Me2CB[7] and CyCB[7] are highly soluble in water (264 mM and 181 mM, respectively). As a result of the high intrinsic solubility of Me2CB[7], it is able to solubilize the insoluble benzimidazole drug albendazole. The reaction of hexamer 1 with glycoluril derivative 12, which bears a primary alkyl chloride group, gives CB[7] derivative 18 in 16% isolated yield. Compound 18 reacts with NaN3 to yield azide-substituted CB[7] 19 in 81% yield, which subsequently undergoes click reaction with propargylammonium chloride (21) to yield CB[7] derivative 20 in 95% yield, which bears a covalently attached triazolyl ammonium group along its equator. The results of NMR spectroscopy ((1)H, variable-temperature, and DOSY) and electrospray mass spectrometry establish that 20 undergoes self-assembly to form a cyclic tetrameric assembly (204) in aqueous solution. CB[7] derivatives bearing reactive functional groups (e.g., N3, Cl) are now available for incorporation into more complex functional systems.

| S-EPMC3510339 | biostudies-literature

Energetics and geometry of FtsZ polymers: nucleated self-assembly of single protofilaments.

Project description:Essential cell division protein FtsZ is an assembling GTPase which directs the cytokinetic ring formation in dividing bacterial cells. FtsZ shares the structural fold of eukaryotic tubulin and assembles forming tubulin-like protofilaments, but does not form microtubules. Two puzzling problems in FtsZ assembly are the nature of protofilament association and a possible mechanism for nucleated self-assembly of single-stranded protofilaments above a critical FtsZ concentration. We assembled two-dimensional arrays of FtsZ on carbon supports, studied linear polymers of FtsZ with cryo-electron microscopy of vitrified unsupported solutions, and formulated possible polymerization models. Nucleated self-assembly of FtsZ from Escherichia coli with GTP and magnesium produces flexible filaments 4-6 nm-wide, only compatible with a single protofilament. This agrees with previous scanning transmission electron microscopy results and is supported by recent cryo-electron tomography studies of two bacterial cells. Observations of double-stranded FtsZ filaments in negative stain may come from protofilament accretion on the carbon support. Preferential protofilament cyclization does not apply to FtsZ assembly. The apparently cooperative polymerization of a single protofilament with identical intermonomer contacts is explained by the switching of one inactive monomer into the active structure preceding association of the next, creating a dimer nucleus. FtsZ behaves as a cooperative linear assembly machine.

| S-EPMC2242775 | biostudies-literature

Controllable Synthesis and Catalytic Performance of Gold Nanoparticles with Cucurbit[n]urils (n = 5?8).

Project description:A series of gold nanoparticles (AuNPs) was prepared in situ with different cucurbit[n]urils (CB[n]s) in an alkaline aqueous solution. The nanoparticle sizes can be well controlled by CB[n]s (n = 5, 6, 7, 8) with different ring sizes. The packing densities of CB[5?8] and free surface area on AuNPs were determined. A direct relationship was found between the ring size and packing density of CB[n]s with respect to the AuNP-catalyzed reduction of 4-nitrophenol in the presence of NaBH?. The larger particle size and higher surface coverage of bigger CB[n]-capped AuNPs significantly decreased the catalytic activity. Furthermore, this work could lead to new applications that utilize AuNPs under an overlayer of CB[n]s for catalysis, sensing, and drug delivery.

| S-EPMC6316165 | biostudies-literature

Self-Assembly of Chiral Cyclohexanohemicucurbit[n]urils with Bis(Zn Porphyrin): Size, Shape, and Time-Dependent Binding.

Project description:In order to investigate the ability of bis(zinc octaethylporphyrin) (bis-ZnOEP) to discriminate cyclohexanohemicucurbit[n]urils (cycHC[n]) of different shapes and sizes, the self-assembly of barrel-shaped chiral cycHC[n] with bis-ZnOEP was studied by various spectroscopic methods (absorption, fluorescence, circular dichroism (CD), and NMR). While the binding of 6-membered cycHC[6] induced a tweezer-like conformation followed by the formation of anti-form of bis-ZnOEP upon further addition of cycHC[6], the interaction of 8-membered cycHC[8] is more complex and proceeds through the featured syn-to-anti conformational change of bis-ZnOEP and further intermolecular self-assembly via multiple noncovalent associations between cycHC[8] and bis-ZnOEP. Whilst bis-porphyrins are known to be effective chemical sensors able to differentiate various guests based on their chirality via induced CD, their ability to sense small differences in the shape and size of relatively large macrocycles, such as chiral cycHC[6] and cycHC[8], is scarcely examined. Both studied complexes exhibited characteristic induced CD signals in the region of porphyrin absorption upon complexation.

| S-EPMC8839860 | biostudies-literature

Thermally-nucleated self-assembly of water and alcohol into stable structures at hydrophobic interfaces.

Project description:At the interface with solids, the mobility of liquid molecules tends to be reduced compared with bulk, often resulting in increased local order due to interactions with the surface of the solid. At room temperature, liquids such as water and methanol can form solvation structures, but the molecules remain highly mobile, thus preventing the formation of long-lived supramolecular assemblies. Here we show that mixtures of water with methanol can form a novel type of interfaces with hydrophobic solids. Combining in situ atomic force microscopy and multiscale molecular dynamics simulations, we identify solid-like two-dimensional interfacial structures that nucleate thermally, and are held together by an extended network of hydrogen bonds. On graphite, nucleation occurs above ∼35 °C, resulting in robust, multilayered nanoscopic patterns. Our findings could have an impact on many fields where water-alcohol mixtures play an important role such as fuel cells, chemical synthesis, self-assembly, catalysis and surface treatments.

| S-EPMC5059760 | biostudies-literature

Controlling self-assembly of diphenylalanine peptides at high pH using heterocyclic capping groups.

Project description:Using small angle neutron scattering (SANS), it is shown that the existence of pre-assembled structures at high pH for a capped diphenylalanine hydrogel is controlled by the selection of N-terminal heterocyclic capping group, namely indole or carbazole. At high pH, changing from a somewhat hydrophilic indole capping group to a more hydrophobic carbazole capping group results in a shift from a high proportion of monomers to self-assembled fibers or wormlike micelles. The presence of these different self-assembled structures at high pH is confirmed through NMR and circular dichroism spectroscopy, scanning probe microscopy and cryogenic transmission electron microscopy.

| S-EPMC5341053 | biostudies-literature

Self-Assembly of Catenanes from Lasso Peptides.

Project description:Lasso peptides exist naturally in a threaded state as [1]rotaxanes, and we reasoned that lasso peptides cleaved in their loop region could serve as building blocks for catenanes. Mutagenesis of the lasso peptide microcin J25 (MccJ25) with two cysteine residues followed by cleavage of the peptide with trypsin led to a [2]rotaxane structure that self-assembled into a [3]catenane and [4]catenanes at room temperature in aqueous solution. The [3]catenane represents the smallest ring size of a catenane composed solely of polypeptide segments. The NMR structure of the [3]catenane was determined, suggesting that burial of hydrophobic residues may be a driving force for assembly of the catenane structure.

| S-EPMC5245162 | biostudies-literature

Self-assembly of cucurbit[7]uril based triangular [4]molecular necklaces and their fluorescence properties.

Project description:Self-assembly of rigid-rod dipyridine ligand 1 with M(en)(NO3)2 (M = Pd, Pt) affords triangular (3, 5) and square (4, 6) supramolecular coordination complexes (SCCs). The binding affinity of 1 toward CB[n]-type containers results in the formation of triangular [4]molecular necklaces ([4]MNs, 7-10) by either one-pot or post complexation approaches as evidenced by 1H NMR, diffusion ordered spectroscopy, and ESI-MS.

| S-EPMC5382929 | 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