Large-Amplitude Conformational Changes in Self-Assembled Multi-Stranded Aromatic Sheets.
Ontology highlight
ABSTRACT:
SUBMITTER: Atcher J
PROVIDER: S-EPMC7898896 | biostudies-literature | 2021 Feb
REPOSITORIES: biostudies-literature
Publications
Large-Amplitude Conformational Changes in Self-Assembled Multi-Stranded Aromatic Sheets.
Atcher Joan J Mateus Pedro P Kauffmann Brice B Rosu Frédéric F Maurizot Victor V Huc Ivan I
Angewandte Chemie (International ed. in English) 20201130 5
The orchestration of ever larger conformational changes is made possible by the development of increasingly complex foldamers. Aromatic sheets, a rare motif in synthetic foldamer structures, have been designed so as to form discrete stacks of intercalated aromatic strands through the self-assembly of two identical subunits. Ion-mobility ESI-MS confirms the formation of compact dimers. X-ray crystallography reveals the existence of two distinct conformational dimeric states that require large cha ...[more]
Similar Datasets
Project description:Fibrin polymerizes into the fibrous network that is the major structural component of blood clots and thrombi. We demonstrate that fibrin from three different species can also spontaneously polymerize into extensive, molecularly thin, 2D sheets. Sheet assembly occurs in physiologic buffers on both hydrophobic and hydrophilic surfaces, but is routinely observed only when polymerized using very low concentrations of fibrinogen and thrombin. Sheets may have been missed in previous studies because they may be very short-lived at higher concentrations of fibrinogen and thrombin, and their thinness makes them very difficult to detect. We were able to distinguish fluorescently labeled fibrin sheets by polymerizing fibrin onto micro-patterned structured surfaces that suspended polymers 10 microm above and parallel to the cover-glass surface. We used a combined fluorescence/atomic force microscope system to determine that sheets were approximately 5 nm thick, flat, elastic and mechanically continuous. Video microscopy of assembling sheets showed that they could polymerize across 25-microm channels at hundreds of microm(2)/sec (approximately 10(13) subunits/s x M), an apparent rate constant many times greater than those of other protein polymers. Structural transitions from sheets to fibers were observed by fluorescence, transmission, and scanning electron microscopy. Sheets appeared to fold and roll up into larger fibers, and also to develop oval holes to form fiber networks that were "pre-attached" to the substrate and other fibers. We propose a model of fiber formation from sheets and compare it with current models of end-wise polymerization from protofibrils. Sheets could be an unanticipated factor in clot formation and adhesion in vivo, and are a unique material in their own right.
| S-EPMC2614779 | biostudies-literature
Project description:Programmed self-assembly of strands of nucleic acid has proved highly effective for creating a wide range of structures with desired shapes. A particularly successful implementation is DNA origami, in which a long scaffold strand is folded by hundreds of short auxiliary strands into a complex shape. Modular strategies are in principle simpler and more versatile and have been used to assemble DNA or RNA tiles into periodic and algorithmic two-dimensional lattices, extended ribbons and tubes, three-dimensional crystals, polyhedra and simple finite two-dimensional shapes. But creating finite yet complex shapes from a large number of uniquely addressable tiles remains challenging. Here we solve this problem with the simplest tile form, a 'single-stranded tile' (SST) that consists of a 42-base strand of DNA composed entirely of concatenated sticky ends and that binds to four local neighbours during self-assembly. Although ribbons and tubes with controlled circumferences have been created using the SST approach, we extend it to assemble complex two-dimensional shapes and tubes from hundreds (in some cases more than one thousand) distinct tiles. Our main design feature is a self-assembled rectangle that serves as a molecular canvas, with each of its constituent SST strands--folded into a 3 nm-by-7 nm tile and attached to four neighbouring tiles--acting as a pixel. A desired shape, drawn on the canvas, is then produced by one-pot annealing of all those strands that correspond to pixels covered by the target shape; the remaining strands are excluded. We implement the strategy with a master strand collection that corresponds to a 310-pixel canvas, and then use appropriate strand subsets to construct 107 distinct and complex two-dimensional shapes, thereby establishing SST assembly as a simple, modular and robust framework for constructing nanostructures with prescribed shapes from short synthetic DNA strands.
| S-EPMC4238960 | biostudies-literature
Project description:Amyloid fibrils are a hallmark of neurodegenerative diseases and exhibit a conformational diversity that governs their pathological functions. Despite recent findings concerning the pathological role of their conformational diversity, the way in which the heterogeneous conformations of amyloid fibrils can be formed has remained elusive. Here, we show that microwave-assisted chemistry affects the self-assembly process of amyloid fibril formation, which results in their conformational heterogeneity. In particular, microwave-assisted chemistry allows for delicate control of the thermodynamics of the self-assembly process, which enabled us to tune the molecular structure of β-lactoglobulin amyloid fibrils. The heterogeneous conformations of amyloid fibrils, which can be tuned with microwave-assisted chemistry, are attributed to the microwave-driven thermal energy affecting the electrostatic interaction during the self-assembly process. Our study demonstrates how microwave-assisted chemistry can be used to gain insight into the origin of conformational heterogeneity of amyloid fibrils as well as the design principles showing how the molecular structures of amyloid fibrils can be controlled.
| S-EPMC4655422 | biostudies-literature
Project description:Here we report the aromatic vapor sensing performance of bitter melon shaped nanoporous fullerene C60 crystals that are self-assembled at a liquid-liquid interface between isopropyl alcohol and C60 solution in dodecylbenzene at 25 °C. Average length and center diameter of the crystals were ca. 10 μm and ~2 μm, respectively. Powder X-ray diffraction pattern (pXRD) confirmed a face-centered cubic (fcc) structure with cell dimension ca. a = 1.4272 nm, and V = 2.907 nm³, which is similar to that of the pristine fullerene C60. Transmission electron microscopy (TEM) confirmed the presence of a nanoporous structure. Quartz crystal microbalance (QCM) results showed that the bitter melon shaped nanoporous C60 performs as an excellent sensing system, particularly for aromatic vapors, due to their easy diffusion through the porous architecture and strong π⁻π interactions with the sp²-carbon.
| S-EPMC6359261 | biostudies-literature
Project description:Self-assembly is a process of key importance in natural systems and in nanotechnology. Peptides are attractive building blocks due to their relative facile synthesis, biocompatibility, and other unique properties. Diphenylalanine (FF) and its derivatives are known to form nanostructures of various architectures and interesting and varied characteristics. The larger triphenylalanine peptide (FFF) was found to self-assemble as efficiently as FF, forming related but distinct architectures of plate-like and spherical nanostructures. Here, to understand the effect of triaromatic systems on the self-assembly process, we examined carboxybenzyl-protected diphenylalanine (z-FF) as a minimal model for such an arrangement. We explored different self-assembly conditions by changing solvent compositions and peptide concentrations, generating a phase diagram for the assemblies. We discovered that z-FF can form a variety of structures, including nanowires, fibers, nanospheres, and nanotoroids, the latter were previously observed only in considerably larger or co-assembly systems. Secondary structure analysis revealed that all assemblies possessed a β-sheet conformation. Additionally, in solvent combinations with high water ratios, z-FF formed rigid and self-healing hydrogels. X-ray crystallography revealed a "wishbone" structure, in which z-FF dimers are linked by hydrogen bonds mediated by methanol molecules, with a 2-fold screw symmetry along the c-axis. All-atom molecular dynamics (MD) simulations revealed conformations similar to the crystal structure. Coarse-grained MD simulated the assembly of the peptide into either fibers or spheres in different solvent systems, consistent with the experimental results. This work thus expands the building block library for the fabrication of nanostructures by peptide self-assembly.
| S-EPMC6333291 | biostudies-literature
Project description:Peptide self-assembly is a hierarchical process, often starting with the formation of ?-helices, ?-sheets or ?-hairpins. However, how the secondary structures undergo further assembly to form higher-order architectures remains largely unexplored. The polar zipper originally proposed by Perutz is formed between neighboring ?-strands of poly-glutamine via their side-chain hydrogen bonding and helps to stabilize the sheet. By rational design of short amphiphilic peptides and their self-assembly, here we demonstrate the formation of polar zippers between neighboring ?-sheets rather than between ?-strands within a sheet, which in turn intermesh the ?-sheets into wide and flat ribbons. Such a super-secondary structural template based on well-defined hydrogen bonds could offer an agile route for the construction of distinctive nanostructures and nanomaterials beyond ?-sheets.
| S-EPMC6269506 | biostudies-literature
Project description:It has been shown recently that atomically coherent superstructures of a nanocrystal monolayer in thickness can be prepared by self-assembly of monodisperse PbSe nanocrystals, followed by oriented attachment. Superstructures with a honeycomb nanogeometry are of special interest, as theory has shown that they are regular 2-D semiconductors, but with the highest valence and lowest conduction bands being Dirac-type, that is, with a linear energy-momentum relation around the K-points in the zone. Experimental validation will require cryogenic measurements on single sheets of these nanocrystal monolayer superstructures. Here, we show that we can incorporate these fragile superstructures into a transistor device with electrolyte gating, control the electron density, and measure the electron transport characteristics at room temperature. The electron mobility is 1.5 ± 0.5 cm2 V-1 s-1, similar to the mobility observed with terahertz spectroscopy on freestanding superstructures. The terahertz spectroscopic data point to pronounced carrier scattering on crystallographic imperfections in the superstructure, explaining the limited mobility.
| S-EPMC6559210 | biostudies-literature
Project description:Oligomeric porphyrin arrays with an alternating pyridyl-porphyrin sequence were synthesized to explore double-strand formation through self-complementary pyridyl-to-zinc axial coordination bonds. Competitive titration experiments revealed the thermodynamic aspects involved in the zipper effect within double-strand formation. Multiple axial coordination bonds defined the stacked conformation, despite a marginal contribution to the stability of the double-strands. Thus, the zipper cooperativity was the dominant factor for the remarkable stability. Moreover, the dimeric and trimeric porphyrin arrays were independently assembled into double-strands by self-sorting from a binary mixture. Double-strand formation engineered discretely stacked π-systems. Successive slipped-cofacial stacks of the porphyrin rings progressively extended the π-system via exciton coupling over the double-strand while keeping a relatively high fluorescence quantum yield.
| S-EPMC6054142 | biostudies-literature
Project description:Constructing polycyclic aromatics-based, highly emissive fluorophores with good solubility and tunable aggregated structures and properties is of great importance for film fabrication, solution processing, and relevant functionality studies. Herein, we describe a general strategy to endow conventional organic fluorophores with enhanced solubility and modulated fluorescent properties via their incorporation into coordination-driven self-assembled metallacycles. A widely used fluorophore, pyrene, was decorated with two pyridyl groups to yield functionalized pyrene 4. Mixing 4 with three aromatic dicarboxylates with different lengths and a 90° Pt(II) metal acceptor in a 2:2:4 stoichiometric ratio resulted in the formation of three metallacycles, 1, 2, and 3. The metallacycles display good solubility in polar organic solvents, highly aggregation-dependent fluorescence, and size-dependent emissions at higher concentrations. Moreover, metallacycle 2-based, silica-gel-supported film as fabricated not only is more emissive than the ligand 4-based one but also displays much improved sensing properties for amines in the vapor state, as demonstrated by significantly increased response speed and decreased recovery time. The enhanced solubility, unique fluorescence behavior, and multi-factor modulation character show that coordination-driven self-assembly can be utilized for the development of new fluorophores through simple modification of conventional fluorophores. The fluorophores synthesized this way possess not only complex topological structures but also good modularity and tunability in fluorescence behavior, which are important for grafting multi-stage energy-transfer systems necessary for the development of high-performance sensing materials.
| S-EPMC6396852 | biostudies-literature
Project description:Aromatic-aromatic interactions have long been believed to play key roles in protein structure, folding, and binding functions. However, we still lack full understanding of the contributions of aromatic-aromatic interactions to protein stability and the timing of their formation during folding. Here, using an aromatic ladder in the ?-barrel protein, cellular retinoic acid-binding protein 1 (CRABP1), as a case study, we find that aromatic ? stacking plays a greater role in the Phe65-Phe71 cross-strand pair, while in another pair, Phe50-Phe65, hydrophobic interactions are dominant. The Phe65-Phe71 pair spans ?-strands 4 and 5 in the ?-barrel, which lack interstrand hydrogen bonding, and we speculate that it compensates energetically for the absence of strand-strand backbone interactions. Using perturbation analysis, we find that both aromatic-aromatic pairs form after the transition state for folding of CRABP1, thus playing a role in the final stabilization of the ?-sheet rather than in its nucleation as had been earlier proposed. The aromatic interaction between strands 4 and 5 in CRABP1 is highly conserved in the intracellular lipid-binding protein (iLBP) family, and several lines of evidence combine to support a model wherein it acts to maintain barrel structure while allowing the dynamic opening that is necessary for ligand entry. Lastly, we carried out a bioinformatics analysis and found 51 examples of aromatic-aromatic interactions across non-hydrogen-bonded ?-strands outside the iLBPs, arguing for the generality of the role played by this structural motif.
| S-EPMC3778025 | biostudies-literature