Xanthene[n]arenes: Exceptionally Large, Bowl-Shaped Macrocyclic Building Blocks Suitable for Self-Assembly.
Ontology highlight
ABSTRACT:
SUBMITTER: Pfeuffer-Rooschuz J
PROVIDER: S-EPMC8611668 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
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
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
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
Project description:Self-assembling molecular building blocks able to dynamically change their shapes, is a concept that would offer a route to reconfigurable systems. Although simulation studies predict novel properties useful for applications in diverse fields, such kinds of building blocks, have not been implemented thus far with molecules. Here, we report shape-variable building blocks fabricated by DNA self-assembly. Blocks are movable enough to undergo shape transitions along geometrical ranges. Blocks connect to each other and assemble into polymorphic ring-shaped clusters via the stacking of DNA blunt-ends. Reconfiguration of the polymorphic clusters is achieved by the surface diffusion on mica substrate in response to a monovalent salt concentration. This work could inspire novel reconfigurable self-assembling systems for applications in molecular robotics.
| S-EPMC5312864 | biostudies-literature
Project description:A chiral perylene diimide building block has been prepared based on an amine derivative of the amino acid L-phenylalanine. Detailed studies were carried out into the self-assembly behaviour of the material in solution and the solid state using UV/Vis, circular dichroism (CD) and fluorescence spectroscopy. For the charged building block BTPPP, the molecular chirality of the side chains is translated into the chiral supramolecular structure in the form of right-handed helical aggregates in aqueous solution. Temperature-dependent UV/Vis studies of BTPPP in aqueous solution showed that the self-assembly behaviour of this dye can be well described by an isodesmic model in which aggregation occurs to generate short stacks in a reversible manner. Wide-angle X-ray diffraction studies (WXRD) revealed that this material self-organises into aggregates with ?-? stacking distances typical for ?-conjugated materials. TEM investigations revealed the formation of self-assembled structures of low order and with no expression of chirality evident. Differential scanning calorimetry (DSC) and polarised optical microscopy (POM) were used to investigate the mesophase properties. Optical textures representative of columnar liquid-crystalline phases were observed for solvent-annealed samples of BTPPP. The high solubility, tunable self-assembly and chiral ordering of these materials demonstrate their potential as new molecular building blocks for use in the construction of chiro-optical structures and devices.
| S-EPMC4973615 | biostudies-literature
Project description:The spontaneous assembly of chiral structures from building blocks that lack chirality is fundamentally important for colloidal chemistry and has implications for the formation of advanced optical materials. Here, we find that purified achiral gold tetrahedron-shaped nanoparticles assemble into two-dimensional superlattices that exhibit planar chirality under a balance of repulsive electrostatic and attractive van der Waals and depletion forces. A model accounting for these interactions shows that the growth of planar structures is kinetically preferred over similar three-dimensional products, explaining their selective formation. Exploration and mapping of different packing symmetries demonstrates that the hexagonal chiral phase forms exclusively because of geometric constraints imposed by the presence of constituent tetrahedra with sharp tips. A formation mechanism is proposed in which the chiral phase nucleates from within a related 2D achiral phase by clockwise or counterclockwise rotation of tetrahedra about their central axis. These results lay the scientific foundation for the high-throughput assembly of planar chiral metamaterials.
| S-EPMC9304327 | biostudies-literature
Project description:Show me the way: protein building blocks are programmed to assemble hierarchically and yield a defined fiber morphology of micrometric length and precise nanometric diameter. The key step of this method is to align the building blocks with an AC field prior to assembly. The resulting protein nanofibers are straightforwardly integrated with the circuitry for potential applications in bionanotechnology.
| S-EPMC5412948 | biostudies-literature
Project description:Combining proteins or their defined domains offers new enhanced functions. Conventionally, two proteins are either fused into a single polypeptide chain by recombinant means or chemically cross-linked. However, these strategies can have drawbacks such as poor expression (recombinant fusions) or aggregation and inactivation (chemical cross-linking), especially in the case of large multifunctional proteins. We developed a new linking method which allows site-oriented, noncovalent, yet irreversible stapling of modified proteins at neutral pH and ambient temperature. This method is based on two distinct polypeptide linkers which self-assemble in the presence of a specific peptide staple allowing on-demand and irreversible combination of protein domains. Here we show that linkers can either be expressed or be chemically conjugated to proteins of interest, depending on the source of the proteins. We also show that the peptide staple can be shortened to 24 amino acids still permitting an irreversible combination of functional proteins. The versatility of this modular technique is demonstrated by stapling a variety of proteins either in solution or to surfaces.
| S-EPMC3309608 | biostudies-literature
Project description:Enzyme-promoted assembly: The construction of a hetero-bifunctional protein building block, HaloTag-cutinase, that reacts rapidly and selectively with a small-molecule linker is described. The step-wise combination of these building blocks generates a 300 kDa "megamolecule" with precisely defined domain orientation, connectivity, and composition.
| S-EPMC3804166 | biostudies-literature
Project description:Utilizing concepts of protein building blocks, we propose a de novo computational algorithm that is similar to combinatorial shuffling experiments. Our goal is to engineer new naturally occurring folds with low homology to existing proteins. A selected protein is first partitioned into its building blocks based on their compactness, degree of isolation from the rest of the structure, and hydrophobicity. Next, the protein building blocks are substituted by fragments taken from other proteins with overall low sequence identity, but with a similar hydrophobic/hydrophilic pattern and a high structural similarity. These criteria ensure that the designed protein has a similar fold, low sequence identity, and a good hydrophobic core compared with its native counterpart. Here, we have selected two proteins for engineering, protein G B1 domain and ubiquitin. The two engineered proteins share approximately 20% and approximately 25% amino acid sequence identities with their native counterparts, respectively. The stabilities of the engineered proteins are tested by explicit water molecular dynamics simulations. The algorithm implements a strategy of designing a protein using relatively stable fragments, with a high population time. Here, we have selected the fragments by searching for local minima along the polypeptide chain using the protein building block model. Such an approach provides a new method for engineering new proteins with similar folds and low homology.
| S-EPMC2286547 | biostudies-literature