Large Supramolecular Structures Research Articles

The heterogeneity of aqueous solutions: the current situation in the context of experiment and theory.

The advancement of experimental methods has provided new information about the structure and structural fluctuations of water. Despite the appearance of numerous models, which aim to describe a wide range of thermodynamic and electrical characteristics of water, there is a deficit in systemic understanding of structuring in aqueous solutions. A particular challenge is the fact that even pure water is a heterogeneous, multicomponent system composed of molecular and supramolecular structures. The possibility of the existence of such structures and their nature are of fundamental importance for various fields of science. However, great difficulties arise in modeling relatively large supramolecular structures (e.g. extended hydration shells), where the bonds between molecules are characterized by low energy. Generally, such structures may be non-equilibrium but relatively long-lived. Evidently, the short times of water microstructure exchanges do not mean short lifetimes of macrostructures, just as the instability of individual parts does not mean the instability of the entire structure. To explain this paradox, we review the data from experimental and theoretical research. Today, only some of the experimental results on the lifetime of water structures have been confirmed by modeling, so there is not a complete theoretical picture of the structure of water yet. We propose a new hierarchical water macrostructure model to resolve the issue of the stability of water structures. In this model, the structure of water is presented as consisting of many hierarchically related levels (the stratification model). The stratification mechanism is associated with symmetry breaking at the formation of the next level, even with minimal changes in the properties of the previous level. Such a hierarchical relationship can determine the unique physico-chemical properties of water systems and, in the future, provide a complete description of them.

Attractive acceptor-acceptor interactions in self-complementary quadruple hydrogen bonds for molecular self-assembly.

Molecular self-assembly provides the means for creating large supramolecular structures, extending beyond the capability of standard chemical synthesis. To harness the power of self-assembly, it is necessary to understand its driving forces. A potent method is to exploit self-complementary hydrogen bonding, where a molecule interacts with its own copy by suitable positions of hydrogen-bond donor (D) and acceptor (A) groups. With four hydrogen bonds, there are two possible self complementary patterns: the DDAA/AADD and the DADA/ADAD motifs. Of these, the DDAA pattern is usually more stable. The traditional explanation assumes that the secondary interactions between equal groups, that is, between donors (D⋯D) or acceptors (A⋯A), are repulsive. DDAA arrays would then have two, and DADA arrays six repulsive interactions. Here, using high-end quantum chemical analysis, we show that contrary to the traditional explanation, the secondary A⋯A interactions are, in fact, attractive. We revise the model of secondary interactions accordingly.

Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). The NSP15 endoribonuclease enzyme, known as NendoU, is highly conserved and plays a critical role in the ability of the virus to evade the immune system. NendoU is a promising target for the development of new antiviral drugs. However, the complexity of the enzyme's structure and kinetics, along with the broad range of recognition sequences and lack of structural complexes, hampers the development of inhibitors. Here, we performed enzymatic characterization of NendoU in its monomeric and hexameric form, showing that hexamers are allosteric enzymes with a positive cooperative index, and with no influence of manganese on enzymatic activity. Through combining cryo-electron microscopy at different pHs, X-ray crystallography and biochemical and structural analysis, we showed that NendoU can shift between open and closed forms, which probably correspond to active and inactive states, respectively. We also explored the possibility of NendoU assembling into larger supramolecular structures and proposed a mechanism for allosteric regulation. In addition, we conducted a large fragment screening campaign against NendoU and identified several new allosteric sites that could be targeted for the development of new inhibitors. Overall, our findings provide insights into the complex structure and function of NendoU and offer new opportunities for the development of inhibitors.

Parallel Functionalization of DNA Origami.

DNA origami enables the creation of large supramolecular structures, with precisely defined features at the nanoscale. The concept thus naturally lends itself to the concept of molecular patterning, i.e., the positioning of molecular moieties and functional features. Creation of nanoscale patterns was already disseminated by Rothemund in 2006, in which DNA hairpins were used to produce nanoscale patterns on the flat origami canvases (Rothemund PWK, Nature 440(7082):297-302, 2006). For this type of application, it is often desired to produce multiple different patterns using the same origami canvas by reusing existing origami staple strands, rather than ordering new, custom oligonucleotides for each unique pattern. This chapter presents a method where the enzyme terminal deoxynucleotidyl transferase (TdT) is used in a parallelized reaction to add functional moieties to the end of a selected pool of unmodified staple strand oligonucleotides, which are then incorporated at precisely defined positions in the DNA origami canvas. Introducing arrays of functional features using this enzymatic functionalization of origami staple strands offers a very high degree of flexibility, versatility, and ease of use and can often be obtained faster than custom synthesis. For small synthesis scales, typically employed during initial functional screening of many different molecular patterns, the method also offers a significant advantage in terms of cost. During the past years, we have utilized this to incorporate a large variety of molecules including bulky proteins (Sørensen RS, Okholm AH, Schaffert D, Kodal ALB, Gothelf KV, Kjems J, ACS Nano 7:8098-8104, 2013) in designed patterns from modified nucleotide triphosphate (NTP) building blocks (Jahn K, Tørring T, Voigt NV, Sørensen RS, Kodal ALB, Andersen ES, Bioconjug Chem 22:819-823, 2011). The near-quantitative yields obtained by enzymatic functionalization allow synthesis of a large set of oligonucleotides in a one-pot reaction from commercial starting materials without the need for individual post-purification. Based on the chosen subset of staple strand, it is possible to create any designed functionality, array, or pattern. Here we describe the process going from an idea/design of a DNA origami-specific molecular pattern to nucleotide synthesis and subsequent parallel functionalization of the DNA origami, assembly, and the final characterization.

Observation of Rare Tri6Di9 Imine Cages Using Highly Fluorinated Building Blocks

The first synthesis of organic Tri 6 Di 9 cages is presented. Two structurally distinct Tri 6 Di 9 cages were synthesised by combining a highly fluorinated aldehyde with two ditopic amines. Although the pure compounds could not be isolated despite many attempts, the information obtained is critical for the future design of large supramolecular structures. Computational and experimental methods indicate that the addition of perfluorinated aromatic linkers in the assembly of porous organic cages opens up new possibilities for influencing the reaction pathway towards rare and unknown structures.

Self-assembly of an MRI responsive agent under physiological conditions provides an extended time window for in vivo imaging.

An MRI-responsive agent that spontaneously self-assembles to a large supramolecular structure under physiological conditions was designed. The obtained assembly provides an extended time window for in vivo studies, as demonstrated for a fluorine-19 probe constructed to sense Zn2+ with 19F-iCEST MRI, in the future.

Complex supramolecular fiber formed by coordination-induced self-assembly of benzene-1,3,5-tricarboxamide (BTA)

HypothesisIn the quest for large but well-controlled supramolecular structures, the discotic benzene-1,3,5-tricarboxamide (BTA) has received quite some attention, because it can form hydrogen-bonded stacks that can be regarded as supramolecular polymers of which the single BTA molecule is the monomer. In this report, we consider a more complex BTA-based supramolecular polymer, namely one that is built up from supramolecular ‘monomers’. ExperimentsWe design a tris-ligand L3 consisting of a BTA core carrying three dipicolinic acid (DPA) groups. L3 itself is too small to form polymers, but in the presence of appropriate metal ions, each L3 can form three coordination bonds and so form (L3)n clusters that are large enough to stack successfully: at an appropriate metal dose, long and stable filaments with a cross-sectional diameter of 12 nm appear. We monitor the growth process by UV–vis spectroscopy and light scattering, and use small angle X-ray scattering (SAXS), TEM as well as molecular simulation to confirm the filamentous structure of the fibers and determine their dimensions. FindingsThe formation and structure of the fiber are very similar for various transition metal ions, which enables introducing different functionalities, e.g., magnetic relaxivity, by proper choice of the metal ions. Hence, we obtain a doubly supramolecular polymer, connected axially by hydrogen bonds, and radially by coordination bonds. Not only does this realize a higher level of complexity, but it also allows to easily introduce and vary metal-derived functionalities.

Structural characterization of hexameric shell proteins from two types of choline-utilization bacterial microcompartments.

Bacterial microcompartments are large supramolecular structures comprising an outer proteinaceous shell that encapsulates various enzymes in order to optimize metabolic processes. The outer shells of bacterial microcompartments are made of several thousand protein subunits, generally forming hexameric building blocks based on the canonical bacterial microcompartment (BMC) domain. Among the diverse metabolic types of bacterial microcompartments, the structures of those that use glycyl radical enzymes to metabolize choline have not been adequately characterized. Here, six structures of hexameric shell proteins from type I and type II choline-utilization microcompartments are reported. Sequence and structure analysis reveals electrostatic surface properties that are shared between the four types of shell proteins described here.

Dynamics of Ion Pairing in Dilute Aqueous HCl Solutions by Spectroscopic Measurements of Hydroxyl Radical Conversion into Dichloride Radical Anions.

The rate of formation of dichloride anions (Cl2•–) in dilute aqueous solutions of HCl (2–100 mmol·kg–1) was measured by the technique of pulse radiolysis over the temperature range of 288–373 K. The obtained Arrhenius dependence shows a concentration averaged activation energy of 7.3 ± 1.8 kJ·mol–1, being half of that expected from the mechanism assuming the •OHCl– intermediate and supporting the ionic equilibrium-based mechanism, i.e., the formation of Cl2•– in the reaction of •OH with a hydronium–chloride (Cl–·H3O+) contact ion pair. Assuming diffusion-controlled encounter of the hydronium and chloride ions and including the effect of the ionic atmosphere, we showed that the reciprocal of τ, the lifetime of (Cl–·H3O+), follows an Arrhenius dependence with an activation energy of 23 ± 4 kJ·mol–1, independent of the acid concentration. This result indicates that the contact pair is stabilized by hydrogen bonding interaction of the solvent molecules. We also found that at a fixed temperature, τ is noticeably increased in less-concentrated solutions (mHCl < 0.01 m). Since this concentration effect is particularly pronounced at near ambient temperatures, the increasing pair lifetime may result from the solvent cage effect enhanced by the presence of large supramolecular structures (patches) formed by continuously connected four-bonded water molecules.

Pepsin Digest of Gliadin Forms Spontaneously Amyloid-Like Nanostructures Influencing the Expression of Selected Pro-Inflammatory, Chemoattractant, and Apoptotic Genes in Caco-2 Cells: Implications for Gluten-Related Disorders.

Proteolysis-resistant gliadin peptides are intensely investigated in biomedical research relates to celiac disease and gluten-related disorders. Herein, the first integrated supramolecular investigation of pepsin-digested gliadin peptides (p-gliadin) is presented in combination with its functional behavior in the Caco-2 cell line. First, gliadins are degraded by pepsin at pH 3, and the physicochemical properties of p-gliadin are compared with gliadin. An integrated approach using interfacial, spectroscopic, and microscopic techniques reveals that the p-gliadin forms spontaneously soluble large supramolecular structures, mainly oligomers and fibrils, capable of binding amyloid-sensitive dyes. The self-assembly of p-gliadin starts at a concentration of 0.40 µg mL-1 . Second, the stimulation of Caco-2 cells with the p-gliadin supramolecular system is performed, and the mRNA expression levels of a panel of genes are tested. The experiments show that p-gliadin composed of supramolecular structures triggers significant mRNA up-regulation (p < 0.05) of pro-apoptotic biomarkers (ratio Bcl2/Bak-1), chemokines (CCL2, CCL3, CCL4, CCL5, CXCL8), and the chemokine receptor CXCR3. This work demonstrates that p-gliadin is interfacial active, forming spontaneously amyloid-type structures that trigger genes in the Caco-2 cell line involved in recruiting specialized immune cells.

Catalytic Systems Based on the Metal Complexes of 1-Alkyl-4-Aza-1-Azoniabicyclo[2.2.2]Octane Bromides

The catalytic activity of supramolecular systems based on the complexes of 1-alkyl-4-aza-1-azoniabicyclo[2.2.2]octane bromide (Alk = CnH2n+ 1, n = 16, 18) with lanthanum nitrate in the reaction of hydrolytic decomposition of 4-nitrophenyl-O-alkylchloromethylphosphonates (Alk = CnH2n+ 1, n = 4, 6) was demonstrated. It was found that the reaction was accelerated due to the formation of nanoscale aggregates of various sizes and types (small micelles and larger supramolecular structures), which effectively bind the reagents. The binding constants of phosphonates with aggregates are greater than three or four orders of magnitude. The catalytic activity of the metal complex systems manifested itself at a lower amphiphile concentration in solution, as compared with that of ligands.

Tuning the Aggregation of GHG by Changing Sample Concentration and pH

Self-assembly of peptides is an important issue explored in biomedical, biophysical, and biomaterial research. Small peptides have been heavily researched due to their inherent biodegradability. Low molecular weight di- and tripeptides with aromatic residues and terminal groups have been found to self-assemble into gels. However, despite their aromatic character, short histidine-containing peptides were predicted to exhibit a low aggregation propensity. Contrary to this expectation, we discovered that unblocked GHG forms a hydrogel upon deprotonation of the imidazole side chain. Concomitantly, its apparent pK decreases due to a gelation induced stabilization of its deprotonated state. The apparent pK decreases further with increasing concentration. The sub-millimeter fibril length differs significantly from those of other hydrogel-forming peptides, which are generally on the sub-micrometer scale. We utilized rheology, circular dichroism, and vibrational spectroscopy to study the gelation process and the thermal stability of the gel. Rheology measurements yielded G’ values on the order of 105 kPa. As we increase the pH past the initial point of gelation, the rate of formation and the final G’ value increase. The enhanced circular dichroism of the amide I’ band is diagnostic of long and stable fibrils. The circular dichroism signal indicates anisotropy of the sample. Corresponding IR band profiles indicate a complex mixture of β-sheet and amorphous aggregate structures. Our results show that histidine can be used as a switch for the formation of large supramolecular structures even in very short peptides and that the properties of the gel can be tuned by altering the concentration and pH of the sample.

Correlation Between the Adsorption and the Nanotribological Performance of Fatty Acid-Based Organic Friction Modifiers on Stainless Steel

Surface adsorption of amphiphilic molecules is a vital mechanism of boundary lubrication on stainless steel surfaces. The self-assembly of four fatty acid-based organic friction modifiers in two alkane solvents and their adsorption onto stainless steel surfaces was investigated using Dynamic Light Scattering and Quartz Crystal Balance with Dissipation, respectively. These properties were related to the friction force between a sharp tip and the steel surface measured using Lateral Force Microscopy. The molecular structures of the organic friction modifiers were chosen in order to study the effects of unsaturation and number of alkyl chains as well as the composition of the polar head groups on their assembly in solution, adsorption, and nanotribological behavior. Sorbitan monooleate and dioleate adsorb as monolayers with their alkyl chains either in the upright or tilted configuration, depending on their concentration. If large supramolecular structures were present in the solvent, i.e., for sorbitan monolaurate and glycerol monooleate, micelle adsorption and rearrangement on the surface and multilayer formation took place, respectively. A correlation between the adsorption rate constant and the coefficient of friction of the organic friction modifiers was revealed in these studies, with the coefficient of friction decreasing with an increase in the adsorption rate.

Alzheimer's disease - history of failures - a short opinion on the contemporary status of research

Over 110 years have passed since first description of Alzheimer's disease (AD). Despite intensive research, AD remains incurable. The vast majority of clinical trials on new therapies aimed at suppressing undesirable aggregation of β-amyloid have failed. This requires rethinking of the strategy to fight AD. A lot of evidence supports the maintenance of β-amyloid as the central object of AD pathology, however, its aggregation into larger supramolecular structures is probably an intermediate stage and not the cause of the disease. In the early stages of life, cellular stresses lead to epigenetic changes resulting in later amyloidogenesis and subsequent neurodegeneration. This process takes decades of life trajectory. Therefore, possible therapies should take into account this fact and be applied early in the life and prolonged later. Diagnosis of epigenetic changes leading to AD should be a research priority. If this concept is true, it may give hope to reverse these changes.

Behavior of metal complexes of polyacrylic acid in solutions

Metal complexes of polyacrylic acid containing Li, Li, and Cu, or Li and Zn have been studied in saline aqueous solutions using molecular hydrodynamics and light scattering methods. Intrinsic viscosities, weight-average molar masses, hydrodynamic radii, and radii of gyration were obtained. It was shown that the macromolecules of polymetalloacrylates containing divalent metals form small and large supramolecular structures, their dimensions, and composition being dependent on the ionic strength of the solution.

Substrate Preferences Establish the Order of Cell Wall Assembly in Staphylococcus aureus.

The Gram-positive bacterial cell wall is a large supramolecular structure and its assembly requires coordination of complex biosynthetic pathways. In the step that merges the two major biosynthetic pathways in Staphylococcus aureus cell wall assembly, conserved protein ligases attach wall teichoic acids to peptidoglycan, but the order of biosynthetic events is a longstanding question. Here, we use a chemical approach to define which of the possible peptidoglycan intermediates are substrates for wall-teichoic acid ligases, thereby establishing the order of cell wall assembly. We have developed a strategy to make defined glycan chain-length polymers of either un-cross-linked or cross-linked peptidoglycan, and we find that wall teichoic acid ligases cannot transfer wall teichoic acid precursors to the cross-linked substrates. A 1.9 Å crystal structure of a LytR-CpsA-Psr (LCP) family ligase in complex with a wall teichoic acid precursor defines the location of the peptidoglycan binding site as a long, narrow groove, and suggests that the basis for selectivity is steric exclusion of cross-linked peptidoglycan. Consistent with this hypothesis, we have found that chitin oligomers are good substrates for transfer, showing that LCPs do not discriminate cross-linked from un-cross-linked peptidoglycan substrates by recognizing features of the un-cross-linked stem peptide. We conclude that wall teichoic acids are coupled to un-cross-linked peptidoglycan chains at an early stage of peptidoglycan synthesis and may create marks that define the proper spacing of subsequent cross-links.

Exploring the Unexpected Gelation of Tripeptides in a Binary Mixture of Water and Ethanol

Hydrogels formed by peptides of different length are a special class of materials that have been heavily researched in the past due to their inherent biodegradability. In this context, some low molecular weight di- or tripeptides with aromatic residues and terminal groups have been shown to form gels after self-assembling into large supramolecular structures above critical concentrations in the centimolar range. Contrary to expectations, our group recently discovered that cationic glycylanalylglycine (GAG), a tripeptide of rather limited hydrophobicity, forms a gel in 55 mol% ethanol/45 mol% water at room temperature if the concentration exceeds 200 mM.

Thermoresponsive Corannulene

We demonstrate herein that corannulene, a bowl‐shaped polycyclic aromatic hydrocarbon, can assemble into larger supramolecular structures in water through a change in the solution temperature. This property is invoked through a simple five‐fold symmetric substitution of the corannulene nucleus with triethylene glycol units. Interestingly, an increase in the solution temperature, which triggers the assembly process, also enhances the fluorescence emission properties of the assembled materials. Although the emission remains very weak in solution, bright green luminescence can be observed in the fibrilar form. This unexpected and interesting behavior indicates that the corannulene nucleus presents a new motif for the design of aggregation‐induced emission (AIE) based luminogens. To the best of our knowledge, this is the first report of a thermoresponsive nonplanar polycyclic hydrocarbon derivative that can respond to a thermal trigger and assemble into larger emissive structures.

In situ conversion of porphyrin microbubbles to nanoparticles for multimodality imaging.

Converting nanoparticles or monomeric compounds into larger supramolecular structures by endogenous or external stimuli is increasingly popular because these materials are useful for imaging and treating diseases. However, conversion of microstructures to nanostructures is less common. Here, we show the conversion of microbubbles to nanoparticles using low-frequency ultrasound. The microbubble consists of a bacteriochlorophyll-lipid shell around a perfluoropropane gas. The encapsulated gas provides ultrasound imaging contrast and the porphyrins in the shell confer photoacoustic and fluorescent properties. On exposure to ultrasound, the microbubbles burst and form smaller nanoparticles that possess the same optical properties as the original microbubble. We show that this conversion is possible in tumour-bearing mice and could be validated using photoacoustic imaging. With this conversion, our microbubble can potentially be used to bypass the enhanced permeability and retention effect when delivering drugs to tumours.

2D Chiral Structures in Quinoline Mixed Langmuir Monolayers

Chirality at interfaces is a relevant topic in nanoscience, as well as a key point for prebiotic chemistry. Mixed Langmuir monolayers, composed of the anionic phospholipid dimyristoyl phosphatidic acid (DMPA) and the cationic amphiphilic quinoline derivative 2-methyl-1-octadecylquinoline (MQ) have been built at the air–water interface. Both DMPA and MQ molecules are miscible, thus the equimolar mixture yields homogeneous monolayers completely. Chiral domains have been formed by this monolayer and observed in situ by Brewster angle microscopy (BAM). These chiral domains display a large array of shapes and sizes. The chirality of the monolayers has been confirmed by circular dichroism spectroscopy. The ordered aggregation of the quinoline group into large chiral supramolecular structures is proposed as the molecular origin of the observed chirality. Theoretical simulations using molecular mechanics confirm the strong trend of the quinoline group to form chiral aggregates. The great diversity in the size and shape of the chiral domains has been found to be strongly influenced by the competition between two nuclei growth mechanisms. An experimental procedure allowing a minimized growth through one of these mechanism is proposed, achieving a homogeneous distribution of ring-shaped domains. An overshoot in the π–A isotherms of this mixed monolayer appears at an intermediate surface pressure. This overshoot is interpreted as being due to the large difference between the surface pressure which starts the nuclei formation, πcrit, and the superficial pressure in which the nuclei can grow, πe. The rather small πe value compared to πcrit observed for this system must be attributed to the molecular interactions involved in the mixed monolayer, which facilitate the incorporation of molecules in preformed nuclei.