Covalent capture: a natural complement to self-assembly

The utility of peptide self-assembly can be extended by covalent capture of these supramolecular materials. Disulfide bond formation, native chemical ligation, olefin metathesis, radical capture and oxidative lysine cross-linking have been used recently to help stabilize and characterize a variety of self-assembled peptides. These include natural peptides, proteins and protein mimics such as alpha-helical coiled coils, amyloid-like beta-sheet fibres, portions of p53, glutathione S-transferase and elastin as well as unnatural peptide constructs such as cyclic peptide nanotubes and cylindrical micelles of peptide amphiphiles.     

Self-assembled nucleolipids: from supramolecular structure to soft nucleic acid and drug delivery devices

This short review aims at presenting some recent illustrative examples of spontaneous nucleolipids self-assembly. High-resolution structural investigations reveal the diversity and complexity of assemblies formed by these bioinspired amphiphiles, resulting from the interplay between aggregation of the lipid chains and base-base interactions. Nucleolipids supramolecular assemblies are promising soft drug delivery systems, particularly for nucleic acids. Regarding prodrugs, squalenoylation is an innovative concept for improving efficacy and delivery of nucleosidic drugs.     

Supramolecular complexes for nanomedicine

Host-guest interactions studied in supramolecular chemistry have been inspired by interactions between enzymes and substrates. Furthermore, most of the interactions involved in the cells are based on non-covalent bonds between two or more molecules. The common aspects between supramolecular chemistry and medicine have led to the development of a “new” area called “supramolecular medicine”, in which non-covalent interactions and self-assembly processes are applied within several medical fields.The object of this Digest is to offer an account of how some macrocyclic hosts (e.g. cucurbiturils, cyclodextrins, pillararenes and calixarenes) are employed in supramolecular medicine creating new supramolecular hydrogels used as biomaterials for human tissue in regenerative medicine, and a diagnostic instrument, in-vitro and in-vivo, for the detection of diseases, as well as for the investigation of cell morphology.     

Origin of amphiphilic molecules and their role in primary structure formation

Attempts to solve two fundamental questions are described: the first concerns which mechanisms were responsible for the self-assembly of membrane structures on the prebiotic Earth, and the second concerns the routes by which considerable amounts of membrane amphiphiles formed from simpler hydrocarbons. The physicochemical properties of several amphiphilic compounds extracted from the Murchison carbonaceous chondrite were studied, using infra-red and fluorescent spectroscopy, measurements of surface activity, chromato-mass spectrometry, and polarization and electron microscopy. The results supported previous observations that amphiphilic and aromatic hydrocarbons were present in significant quantities, and the first demonstration of surface activity among a number of acidic derivatives of hydrocarbons is reported. In addition, one fraction of the surface-active compounds can form bilayer structures, showing that membranes could have self-assembled on the prebiotic Earth. Photochemical oxidation of hydrocarbons is shown to be a likely source of the amphiphilic molecules required for the self-assembly of primary membrane structures.     

Introducing a new Element - Fluorine -Into the Liposomal Membrane

Abstract

Amphiphiles with fluorinated hydrophobic tails constitute new, distinctively different components for membranes, liposomes, tubules and other self-aggregated supramolecular systems. Fluorinated liposomes (F-liposomes) can also be obtained from combinations of standard phospholipids with mixed fluorocarbon-hydrocarbon amphiphiles. The fluorinated moieties are considerably more hydrophobic than their hydrocarbon counterparts; they have also a larger cross section, are more rigid, and are lipophobic as well. As a result, fluorinated amphiphiles show enhanced propensity to self-assemble, lead to increased membrane ordering and stability, and their stacking creates a teflon-like repellent film within the liposomal membrane, which can significantly increase drug encapsulation stability. The fluorinated chains also impact on behavior in biological media and particle recognition, as exemplified by reduced hemolytic and detergent activity, prolonged intravascular persistence, or slower enzymatic hydrolysis of phospholipids.     

Molecular assemblies of diazafluorenone Schiff-base amphiphiles. I. Bilayer membrane and its electrochemical oscillations

A new kind of diazafluorenone Schiff base amphiphile has been synthesized from 1,10-phenanthroline. The superior self-assembling properties of the amphiphiles are advantageous for forming surface monolayer and bilayer membranes (BLMs). BLMs formed with these amphiphiles possess very good stability and electrochemical oscillations. The possibility is suggested of developing a new type of chemical sensor with the ability to distinguish various metal ions from the patterns of electrochemical oscillations.     

Chain-Length Heterogeneity Allows for the Assembly of Fatty Acid Vesicles in Dilute Solutions

A requirement for concentrated and chemically homogeneous pools of molecular building blocks would severely restrict plausible scenarios for the origin of life. In the case of membrane self-assembly, models of prebiotic lipid synthesis yield primarily short, single-chain amphiphiles that can form bilayer vesicles only at very high concentrations. These high critical aggregation concentrations (cacs) pose significant obstacles for the self-assembly of single-chain lipid membranes. Here, we examine membrane self-assembly in mixtures of fatty acids with varying chain lengths, an expected feature of any abiotic lipid synthesis. We derive theoretical predictions for the cac of mixtures by adapting thermodynamic models developed for the analogous phenomenon of mixed micelle self-assembly. We then use several complementary methods to characterize aggregation experimentally, and find cac values in close agreement with our theoretical predictions. These measurements establish that the cac of fatty acid mixtures is dramatically lowered by minor fractions of long-chain species, thereby providing a plausible route for protocell membrane assembly. Using an NMR-based approach to monitor aggregation of isotopically labeled samples, we demonstrate the incorporation of individual components into mixed vesicles. These experiments suggest that vesicles assembled in dilute, mixed solutions are depleted of the shorter-chain-length lipid species, a finding that carries implications for the composition of primitive cell membranes.     

Ricin antitoxins based on lyotropic mesophases containing galactose amphiphiles

Lyotropic mesophases of the inverse hexagonal or cubic type are nanostructured materials that result from the self-assembly of amphiphilic surfactant molecules in water. The extremely large area of the surfactant-water interface inherent within these structures makes them attractive media for sorbent or encapsulant systems. Here, we report on the development of a new class of polyvalent materials that are based on the incorporation of bioactive ligands within lyotropic mesophases. In particular, we have studied the potential for these materials to behave as polyvalent antitoxins by incorporating synthetic galactose amphiphiles, which mimic the natural cell surface ligand for the protein toxin ricin. The study demonstrates that cubic morphology lyotropic mesophases containing galactose amphiphiles exhibit high specificity ricin uptake, with favorably high dissociation constants and high capacities. We suggest that lyotropic mesophase polyvalent ligands are thus promising materials for the incorporation of a broad range of cell surface recognition moieties and hence may have wide applicability as materials capable of partaking in biological recognition processes.     

Chain-Length Heterogeneity Allows for the Assembly of Fatty Acid Vesicles in Dilute Solutions

A requirement for concentrated and chemically homogeneous pools of molecular building blocks would severely restrict plausible scenarios for the origin of life. In the case of membrane self-assembly, models of prebiotic lipid synthesis yield primarily short, single-chain amphiphiles that can form bilayer vesicles only at very high concentrations. These high critical aggregation concentrations (cacs) pose significant obstacles for the self-assembly of single-chain lipid membranes. Here, we examine membrane self-assembly in mixtures of fatty acids with varying chain lengths, an expected feature of any abiotic lipid synthesis. We derive theoretical predictions for the cac of mixtures by adapting thermodynamic models developed for the analogous phenomenon of mixed micelle self-assembly. We then use several complementary methods to characterize aggregation experimentally, and find cac values in close agreement with our theoretical predictions. These measurements establish that the cac of fatty acid mixtures is dramatically lowered by minor fractions of long-chain species, thereby providing a plausible route for protocell membrane assembly. Using an NMR-based approach to monitor aggregation of isotopically labeled samples, we demonstrate the incorporation of individual components into mixed vesicles. These experiments suggest that vesicles assembled in dilute, mixed solutions are depleted of the shorter-chain-length lipid species, a finding that carries implications for the composition of primitive cell membranes.     

Redox-responsive vesicles prepared from supramolecular cyclodextrin amphiphiles

Redox-responsive vesicles self-assembled by supramolecular cyclodextrin amphiphiles, consisting of the guest (N-1-decyl-ferrocenylmethylamine, 1) and the host (2-O-carboxymethyl-β-cyclodextrin, CM-β-CD), were prepared. The morphologies and sizes of these novel vesicles in an aqueous solution were observed by transmission electron microscopy (TEM) and were confirmed by atomic force microscopy (AFM) and dynamic light scattering (DLS) measurements. The effects of the host-guest ratio, the concentration and the solvent composition of water and methanol on vesicles were investigated in detail. The interactions between the host and the guest, the complex stoichiometry, the stability constant and conformations of 1·CM-β-CD in aqueous solution were investigated by cyclic voltammetry (CV), UV and nuclear magnetic resonance (NMR) measurements. According to the complex stoichiometry and ‘tadpole-like’ spatial conformations, the supramolecular cyclodextrin amphiphiles made from 1·CM-β-CD were proposed to form the membranes of the vesicles. This kind of vesicle system was responsive to an oxidizing agent, which could pave the way to combine supramolecular host-guest chemistry and membrane chemistry for potentially functional applications.     

Coarse-grained molecular simulation of self-assembly nanostructures of CTAB on nanoscale graphene

Coarse-grained molecular dynamics simulation has been performed to study the aggregated morphology of the cationic surfactant, cetyltrimethylammonium bromide (CTAB), adsorbed on nanoscale graphene surfaces. The CTAB surfactants can self-assemble on graphene to form various supramolecular morphologies and structures. The effect of packing density, thickness of graphene sheet and width of graphene nanoribbon on the CTAB–graphene self-assembly has been investigated. The buoyant densities of various graphene–CTAB assemblies were calculated, which increase with surfactant coverage and number of graphene layers. This result demonstrates that density gradient can be used to isolate graphenes with various layers. This simulation provides larger-scale microscopic insight into the supramolecular self-assembly nanostructures for the CTAB surfactants aggregated on graphene, which could be valuable to guide fabrication of graphene-based hybrid nanocomposites.     

An optimal degree of physical and chemical heterogeneity for the origin of life?

The accumulation of pure, concentrated chemical building blocks, from which the essential components of protocells could be assembled, has long been viewed as a necessary, but extremely difficult step on the pathway to the origin of life. However, recent experiments have shown that moderately increasing the complexity of a set of chemical inputs can in some cases lead to a dramatic simplification of the resulting reaction products. Similarly, model protocell membranes composed of certain mixtures of amphiphilic molecules have superior physical properties than membranes composed of single amphiphiles. Moreover, membrane self-assembly under simple and natural conditions gives rise to heterogeneous mixtures of large multi-lamellar vesicles, which are predisposed to a robust pathway of growth and division that simpler and more homogeneous small unilamellar vesicles cannot undergo. Might a similar relaxation of the constraints on building block purity and homogeneity actually facilitate the difficult process of nucleic acid replication? Several arguments suggest that mixtures of monomers and short oligonucleotides may enable the chemical copying of polynucleotides of sufficient length and sequence complexity to allow for the emergence of the first nucleic acid catalysts. The question of the origin of life may become less daunting once the constraints of overly well-defined laboratory experiments are appropriately relaxed.     

New amphiphiles for membrane protein structural biology

A challenging requirement for X-ray crystallography or NMR structure determination of membrane proteins (MPs), in contrast to soluble proteins, is the necessary use of amphiphiles to mimic the hydrophobic environment of membranes. A number of new detergents, lipids and non-detergent-like amphiphiles have been developed that stabilize MPs, and these have contributed to increased success in MP structural determinations in recent years. Despite some successes, currently available reagents are inadequate and there remains a pressing need for new amphiphiles. Literature examples and some new developments are selected here as a framework for discussing desirable properties of new amphiphiles for MP structural biology.     

Bioorthogonal noncovalent chemistry: Fluorous phases in chemical biology

Chemical entities designed to noncovalently interact with predetermined partners have fashioned a new paradigm in chemical biology. Fluorocarbons are extremely promising as supramolecular synthons toward these objectives. Bioorthogonal noncovalent interactions provide a way to modulate self-assembled systems in environments where such control has hitherto not been possible. Fluorocarbons have now found applications in self-assembly as well as proteomics, biomolecule purification and in the creation of microarray platforms. Other self-assembly motifs with similar attributes might be exploited using the same general approach.     

Membrane proteins: molecular dynamics simulations

Molecular dynamics simulations of membrane proteins are making rapid progress, because of new high-resolution structures, advances in computer hardware and atomistic simulation algorithms, and the recent introduction of coarse-grained models for membranes and proteins. In addition to several large ion channel simulations, recent studies have explored how individual amino acids interact with the bilayer or snorkel/anchor to the headgroup region, and it has been possible to calculate water/membrane partition free energies. This has resulted in a view of bilayers as being adaptive rather than purely hydrophobic solvents, with important implications, for example, for interaction between lipids and arginines in the charged S4 helix of voltage-gated ion channels. However, several studies indicate that the typical current simulations fall short of exhaustive sampling, and that even simple protein-membrane interactions require at least ca. 1mus to fully sample their dynamics. One new way this is being addressed is coarse-grained models that enable mesoscopic simulations on multi-mus scale. These have been used to model interactions, self-assembly and membrane perturbations induced by proteins. While they cannot replace all-atom simulations, they are a potentially useful technique for initial insertion, placement, and low-resolution refinement.     

Pyridinium and 4,4′-bipyridinium ylides of long-chain malonic esters as vesiculating pH indicators

Several synthetic amphiphiles with pyridinium ylide head-groups have been synthesized. The indicator groups are useful for microacidity measurement on inner and outer vesicular surfaces. Since the amphiphiles are water-insoluble, they constitute fully integrated parts of the vesicle membranes, Interfacial pH deviations on charged vesicle surfaces as compared to neutral surfaces are therefore much larger than with more water-soluble indicators.     

Self-assembly of double-stranded DNA molecules at nanomolar concentrations

Some proteins have the property of self-assembly, known to be an important mechanism in constructing supramolecular architectures for cellular functions. However, as yet, the ability of double-stranded (ds) DNA molecules to self-assemble has not been established. Here we report that dsDNA molecules also have a property of self-assembly in aqueous solutions containing physiological concentrations of Mg2+. We show that DNA molecules preferentially interact with molecules with an identical sequence and length even in a solution composed of heterogeneous DNA species. Curved DNA and DNA with an unusual conformation and property also exhibit this phenomenon, indicating that it is not specific to usual B-form DNA. Atomic force microscopy (AFM) directly reveals the assembled DNA molecules formed at concentrations of 10 nM but rarely at 1 nM. The self-assembly is concentration-dependent. We suggest that the attractive force causing DNA self-assembly may function in biological processes such as folding of repetitive DNA, recombination between homologous sequences, and synapsis in meiosis.     

Studies of Thermal Stability of Multivalent DNA Hybridization in a Nanostructured System

A fundamental understanding of molecular self-assembly processes is important for improving the design and construction of higher-order supramolecular structures. DNA tile based self-assembly has recently been used to generate periodic and aperiodic nanostructures of different geometries, but there have been very few studies that focus on the thermodynamic properties of the inter-tile interactions. Here we demonstrate that fluorescently-labeled multihelical DNA tiles can be used as a model platform to systematically investigate multivalent DNA hybridization. Real-time monitoring of DNA tile assembly using fluorescence resonance energy transfer revealed that both the number and the relative position of DNA sticky-ends play a significant role in the stability of the final assembly. As multivalent interactions are important factors in nature's delicate macromolecular systems, our quantitative analysis of the stability and cooperativity of a network of DNA sticky-end associations could lead to greater control over hierarchical nanostructure formation and algorithmic self-assembly.     

Controlling phospholipid self-assembly and film properties using highly fluorinated components--fluorinated monolayers, vesicles, emulsions and microbubbles

Use of fluorinated components instead or along with standard phospholipids in film, vesicle, bubble and emulsion engineering, can cause drastic modifications of the formation processes, structure and dynamics, and functional behavior of these systems. Perfluoroalkyl chains provide a powerful driving force for self-assembly and ordering. They allow, for example, obtainment of thermally stable vesicles from single-chain phosphocholine derivatives, tubules from non-chiral amphiphiles, faceted vesicles with fluid bilayer membranes, exceptionally stable and narrowly dispersed emulsions and microbubbles. Contact of a monolayer of DPPC with a fluorocarbon gas modifies the monolayer’s phase behavior, suppressing the liquid expanded/liquid condensed transition. Phospholipid absorption kinetics at an air/water interface can be substantially accelerated, and the equilibrium interfacial tension reduced by exposure to a fluorocarbon gas. Perfluoroalkyl chains induce nanocompartmentation in films and membranes, allowing, for example, polymerization within vesicular membranes. Vesicles involving highly fluorinated components generally exhibit stability, permeability, fusion and recognition characteristics, different from those of their hydrogenated analogues. Drastic stabilization can be gained for phospholipid-coated emulsions through a co-surfactant effect of (perfluoroalkyl)alkyl diblocks. Stable, size-controlled, narrowly dispersed populations of microbubbles have been obtained using fluorinated wall and/or internal gas components, allowing progress in the understanding of microbubble physics, and open new application perspectives.