Supermolecular Assemblies Research Articles

Chiral Self‐Assembly and Enantioselective Photocatalysis of Tetra‐(4‐carboxyphenyl) Porphyrin‐diphenylalanine

AbstractInspired by the photosynthesis and protein structure of green plants in nature, TCPP‐(FF)4, a porphyrin‐dipeptide derivative with chiral and optical properties, was synthesized by chemical coupling. The experimental results show that the optical properties and structural morphology of TCPP‐(FF)4 supermolecular assemblies can be precisely controlled by adjusting the types of solvents and pH. Moreover, the TCPP‐(FF)4 can self‐assemble into nanohelix with photocatalytic activity, which can be used as a catalyst for enantioselective photocatalysis of tyrosine (Tyr) into di‐tyrosine (di‐Tyr), which provides a promising strategy for the development of enantioselective photocatalysts.

Molecular design, gel properties, and anti-settling ability with natural rosin-based sulfonamide compounds regulated by conjugation

The design of compounds with excellent controllable weak forces is of great significance to solve current industrial problems. Herein, three natural rosin-based sulfonamide compounds (i.e., dehydroabietyl-based benzene sulfonamide (DBS-1); dehydroabietyl-based benzyl sulfonamide (DBS-2), and dehydrofiranic acid-based p-toluene sulfonamide (DBS-3)) were designed and synthesized by regulating the conjugation of sulfamide, carbonamide, and benzene. Organogels with rod-like, spherical, and layered morphologies were formed by π–π stacking and one-dimensional hydrogen bonding in the absence of an external driving force. Rheological studies emphasized the mechanical strength of these organogels, and gel three-dimensional networks at the nano- and micron-scales can effectively capture six volatile organic solvents. Notably, the presence of conjugation can effectively regulate the dynamic and static equilibrium of organogels to construct stable supermolecular assemblies. DBS-1, which contained abundant conjugated structures and weak intermolecular forces, exhibited amazing anti-settling ability in synthetic oil-based drilling fluids, with a static sedimentation factor of 0.512. Thus, industrial problems such as barite settlement can be solved by using DBS-1 as an additive agent. This report provides inspiration for the effective design of natural anti-settling agents.

Эко-генетическая стресс-устойчивость растений, как стратегия и тактика: супер- молекулярно-протеомного, морфо-динамического дизайна физико-химической природы биологии развития

From the standpoint of eco-genetic adaptation of plants, from the position of interdisciplinary science – supramolecular physical chemistry, the dynamics of supramolecular topologically associated structures of the total chromatin matrix (TChrM) is considered: Np-nucleoplasm, ChrI-eu-, ChrII-heterochromatin and nuclear matrix. On the interface of which, the proteo-supermolecular reorganization of ensembles is presented: "linker", "core" histones and non-histones, the macrokinetics of which is important for understanding the features of biochemical processes in the genetic subsystems of a plant (root → mesocotyl → coleoptile) of the transition period from heterotrophic to autotrophic plant development. An algorithm for the features of the biological specificity of morphogenesis and structural stability of the genetic and proteomic basis of the TChrM model system, collection germs of wheat seeds, in the process of their organ-specific, coordinated-regular growth when switching development subprograms is shown where an experimental analysis of proteomic positioning in supermolecular assemblies was carried out: “linker”, "core" and "non-histone" proteins in different genetic subsystems (mesocotyl → root → highly differentiated embryo), respectively: donor (spring) → transferred to winter (donor winter-phenotype) → transferred back to spring-phenotype. Based on the distribution of nucleosomal arginine-rich “core” histone (H3-H4)'' on the TChM interface: donor (spring) Np=ChrI (mesocotyl) → transferred to winter (donor winter-phenotype) Np˃ChrII≥NM (root)→transferred again into the spring phenotype Np˃ChrI˃NM˃ChrII) (highly differentiated embryo); possible switching of genetic subroutines of development in the genetic subsystems of the whole organism is assumed, which is carried out due to the combinatorial principle of proteomic ensembles, potential epigenetic networks of the "histone code", in the conditions of environmental ecosystems.

Design of surface nanostructures for chirality sensing based on quartz crystal microbalance.

Quartz crystal microbalance (QCM) has been widely used for various sensing applications, including chirality detection due to the high sensitivity to nanogram or picogram mass changes, fast response, real-time detection, easy operation, suitability in different media, and low experimental cost. The sensing performance of QCM is dependent on the surface design of the recognition layers. Various strategies have been employed for studying the relationship between the structural features and the specific detection of chiral isomers. This review provides an overview of the construction of chiral sensing layers by various nanostructures and materials in the QCM system, which include organic molecules, supermolecular assemblies, inorganic nanostructures, and metal surfaces. The sensing mechanisms based on these surface nanostructures and the related potentials for chiral detection by the QCM system are also summarized.

Buckling and Torsional Instabilities of a Nanoscale Biological Rope Bound to an Elastic Substrate.

Rope-like structures are ubiquitous in Nature. They are supermolecular assemblies of macromolecules responsible for the structural and mechanical integrity of plant and animal tissues. Collagen fibrils with diameters between 50 and 500 nm and their helical supermolecular structure are good examples of such nanoscale biological ropes. Like man-made laid ropes, fibrils are typically loaded in tension, and due to their large aspect ratio, they are, in principle, prone to buckling and torsional instabilities. One way to study buckling of a rigid rod is to attach it to a stretched elastic substrate that is then returned to its original length. In the case of single collagen fibrils, the observed behavior depends on the degree of hydration. By going from buckling in ambient conditions to immersed in a buffer, fibrils go from the well-known sine wave response to a localized behavior reminiscent of the bird-caging of laid ropes. In addition, in ambient conditions, the sine wave response coexists with the formation of loops along the length of the fibrils, as observed for the torsional instability of a twisted filament when tension is decreased. This work provides direct evidence that single collagen fibrils are highly susceptible to axial compression because of their helical supermolecular structure. As a result, mammals that use collagen fibrils as their main load-bearing element in many tissues have evolved mitigating strategies that protect single fibrils from axial compression damage.

Simulation of small-angle scattering patterns using a CPU-efficient algorithm

Small-angle scattering (of neutrons, x-ray or light; SAS) is a well-established experimental technique for structural analysis of disordered systems at nano and micro scales. For complex systems, such as super-molecular assemblies or protein molecules, analytic solutions of SAS intensity are generally not available. Thus, a frequent approach to simulate the corresponding patterns is to use a CPU-efficient version of the Debye formula. For this purpose, in this paper we implement the well-known DALAI algorithm in Mathematica software. We present calculations for a series of 2D Sierpinski gaskets and respectively of pentaflakes, obtained from chaos game representation.

Enhancing in vitro dissolution and in vivo bioavailability of fenofibrate by solid self-emulsifying matrix combined with SBA-15 mesoporous silica

Mesoporous silica Santa Barbara amorphous-15 (SBA-15), derived from supermolecular assemblies of surfactant Pluronic® P123 with well-ordered 2-D hexagonal pores, was investigated as a reservoir to construct a novel solid self-emulsifying matrix for enhancing the oral bioavailability of fenofibrate (FNB). The emulsification rate and droplet size of a liquid self-emulsifying delivery system (SEDDS) were analyzed for optimization. SBA-15 was then added to the ethanol solution containing liquid SEDDS, and the obtained suspension changed into solid SEDDS matrix via solvent evaporation. The characterizations by SEM and XRD revealed that the solid matrix consisted of particles with smooth surface and FNB was completely transformed into molecular or amorphous state in the formulation. When introduced to aqueous media under gentle agitation, the solid matrix exhibited excellent self-emulsification properties and formed a uniform microemulsion with mean diameter of 117.35±2.33nm. The solid SEDDS matrix showed faster in vitro release rate than the raw powder and commercial capsule. The absorption of FNB delivered by solid SEDDS matrix was significantly improved in beagle dogs, and its Cmax and AUC values were about 8- and 4-fold greater than those of commercial products, respectively. In conclusion, SBA-15 emerged as a promising reservoir for SEDDS to enhance the bioavailability of poorly water-soluble drugs, which may provide a new strategy for advanced therapies.

Comprehensive structure–function correlation of photoactive ionic π-conjugated supermolecular assemblies: an experimental and computational study

Experimental and computational structure–function study of an organic crystalline photoconductor composed of oppositely charged ionic porphyrins.

A novel mechanism for small heat shock proteins to function as molecular chaperones.

Small heat shock proteins (sHSPs) are molecular chaperones ubiquitously present in all forms of life, but their function mechanisms remain controversial. Here we show by cryo-electron microscopy and single particle 3D reconstruction that, at the low temperatures (4–25°C), CeHSP17 (a sHSP from Caenorhabditis elegans) exists as a 24-subunit spherical oligomer with tetrahedral symmetry. Our studies demonstrate that CeHSP17 forms large sheet-like super-molecular assemblies (SMAs) at the high temperatures (45–60°C), and such SMAs are apparently the form that exhibits chaperone-like activity. Our findings suggest a novel molecular mechanism for sHSPs to function as molecular chaperones.

Supramolecular Structure and Renaturation of a (1→3)-β-d-Glucan Compared with Curdlan and Scleroglucan

A (1→3)-β-d-Glucan produced by Lactobacillus suebicus CUPV221 strain was investigated by tapping mode atomic force microscopy (TM-AFM), to compare its supramolecular structure and conformation with two commercial polysaccharides: curdlan and scleroglucan. It was found that the β-d-Glucan was a (1→3)(1→2)-β-d-Glucan and at room temperature formed three-dimensional networks by entanglements between strands, as does scleroglucan. However, (1→3)(1→2)-β-d-Glucan strands seemed to be more stiff than those of scleroglucan. It was also observed that curdlan samples deposited from 5 mM NaOH aqueous solution showed supermolecular assemblies, recognized in the literature as micelles, which are controlled by hydrophobic hydration. The (1→3)(1→2)-β-d-Glucan in alkaline aqueous solutions produced different supramolecular structures depending on pH, and at 0.4 M NaOH (pH 13.16), denaturation took place. After neutralizing the alkaline solution with HCl, the formation of short linear, circular, and hairpin structures was observed.

Competing hydrogen bonding and halogen bonding interactions in crystal engineering: A case study of bi-functional donor molecules

Based on the recent determined co-crystals of a set of bi-functional donor molecules with two isomeric symmetric acceptors, the competition between hydrogen bonding and halogen bonding interactions in crystal engineering was investigated in this work using the M06-2x and ωB97XD methods. The preference of the occurrence of secondary weak interactions was observed in hydrogen-bonded complexes. Hydrogen bonding interactions are predicted to be much stronger than corresponding halogen bonding interactions. No obvious difference was found between the systems of the two acceptors under study. The model complexes, in which hydrogen bonds and halogen bonds coexist, show additivity. Finally, a comparison between theoretical results and experimental observations was presented, and the implications of the calculations on the supermolecular assemblies based on the two interactions were also discussed.

Hydrogen-Bond-Induced Supermolecular Assemblies in a Nanoconfined Tertiary Alcohol

Tert-butanol is the molecular archetype of a variety of H-bonded systems that form micelle-like supermolecular clusters in the liquid state. This self-association process is characterized by a prepeak in the static structure factor. Recently, it has been shown by neutron scattering that this prepeak is totally suppressed in a nanoconfined geometry [Morineau, D.; Alba-Simionesco, C.J. Phys. Chem. Lett. 2010, 1, 7155.]. The authors have shown that excluded volume effects was one main ingredient of this suppression, but the question of the survival of H-bonded self-association in nanochannels has remained unresolved experimentally. From molecular dynamics simulations, we prove that self-association survives under confinement despite the absence of the prepeak. Furthermore, we show that its apparent suppression is due to a negative contribution arising from the liquid–porous solid correlations, which cannot be disentangled experimentally. Strikingly, the stability of micelle-like clusters surpasses the putati...

Amyloid Fibril Recognition with the Conformational B10 Antibody Fragment Depends on Electrostatic Interactions

Amyloid fibrils are naturally occurring polypeptide scaffolds with considerable importance for human health and disease. These supermolecular assemblies are β-sheet rich and characterized by a high structural order. Clinical diagnosis and emerging therapeutic strategies of amyloid-dependent diseases, such as Alzheimer's, rely on the specific recognition of amyloid structures by other molecules. Recently, we generated the B10 antibody fragment, which selectively binds to Alzheimer's Aβ(1–40) amyloid fibrils but does not explicitly recognize other protein conformers, such as oligomers and disaggregated Aβ peptide. B10 presents poly-amyloid specific binding and interacts with fibrillar structures consisting of different polypeptide chains. To determine the molecular basis behind its specificity, we have analyzed the molecular properties of B10 with a battery of biochemical and biophysical techniques, ranging from X-ray crystallography to chemical modification studies. We find that fibril recognition depends on positively charged residues within the B10 antigen binding site. Mutation of these basic residues into alanine potently impairs fibril binding, and reduced B10–fibril interactions are also observed when the fibril carboxyl groups are covalently masked by a chemical modification approach. These data imply that the B10 conformational specificity for amyloid fibrils depends upon specific electrostatic interactions with an acidic moiety, which is common to different amyloid fibrils.

Branched silica nanostructures oriented by dynamic G-quadruplex transformation

Polymorphic G-quadruplexes including stacked G-quartet planes are potentially promising DNA templates beyond Watson-Crick duplexes to construct inorganic nanostructures. In this work, a novel G-rich oligonucleotide that can be modulated from the antiparallel G-quadruplex to multi-stranded supermolecular assemblies was designed. Based on this dynamic G-quadruplex transformation, an interesting leaf-vein silica nanostructure with regular branched intervals was constructed. The G-quadruplex assembly structure was found to play a significant role in the organization of the silica structures.

Does Molecular Self-Association Survive in Nanochannels?

tert-Butanol spontaneously forms supermolecular clusters in the liquid state. This phenomenon results from the balance between hydrogen(H)-bonded self-association and steric repulsion, which is ubiquitous in complex supermolecular assemblies. Neutron scattering provides direct insight into this mesoscopic order through a distinct signature (prepeak) in the structure factor. Using MCM-41 molecular sieves, we show that the spatial correlations associated with micelle-like clusters are totally suppressed in nanoconfined geometry. This is direct evidence of a considerable variation of the structure at the mescoscopic scale of an associated liquid during its manipulation in nanostructured materials and illustrates to what extent nanoconfinement affects the formation of the highly directional hydrogen-bonded systems and the properties of confined liquids in general.

Characterization of self-assembly of Euplotes octocarinatus centrin

Centrin, an EF-hand calcium-binding protein with high homology to calmodulin (CaM), is an essential component for microtubule-organizing center (MTOC) in organisms ranging from algae and yeast to human. It plays an important structural role by contributing to the formation of Ca 2+-sensitive contractile filaments and some super-molecular assemblies. Previous work suggests that the N-terminal domain of centrin especially its first 20-residue fragment, is required for the self-assembly of protein. Native polyacrylamide gel electrophoresis (native-PAGE), pull-down assay, fluorescence resonance light scattering (RLS) and yeast two-hybrid assay indicate that the C-terminal domain of Euplotes octocarinatus centrin (EoCen) also contributes to the centrin self-assembly besides its N-terminal domain in vivo and in vitro. On the basis of our results, a self-assembly mode of centrin, which is C-to-C as well as N-to-N (between C- and C-terminal domains as well as between N- and N-terminal domains), is put forward providing maybe some insights into the molecular mechanism of centrin functions in the cell.

Enzyme Nanorings

We have demonstrated that nanostructures, and in particular nanorings incorporating a homodimeric enzyme, can be prepared by chemically induced self-assembly of dihydrofolate reductase (DHFR)-histidine triad nucleotide binding 1 (Hint1) fusion proteins. The dimensions of the nanorings were found by static light scattering and atomic force microscopy studies to be dependent on the length and composition of the peptide linking the fusion proteins, ranging in size from 10 to 70 nm in diameter and 64 to 740 kDa. The catalytic efficiency of the nanorings was found to be dependent on ring size, thus suggesting that the arrangement of supermolecular assemblies of enzymes may be used to control their catalytic parameters.

Rheological Behavior of Poly(vinylpyrrolidone)/Fullerene C60 Complexes in Aqueous Medium

Aqueous solutions of complexes formed between poly(vinylpyrrolidone) (PVP), as a matrix polymer, and fullerene C60 were investigated. The effect of the external hydrodynamic field on the supermolecular assemblies formed by the complexes was analyzed. Despite the low content in the complexes (1.5 mass%), fullerene significantly modified the viscosity of aqueous PVP. Thus, the dynamic viscosity of the PVP/C60 complexes grew faster than that of the pure PVP upon increasing the PVP/C60 concentration. The difference in viscosities is especially pronounced for semidilute solutions. As a possible explanation, it is assumed that fullerenes act as crosslinks, in addition to the physical entanglements of the PVP macromolecules, which appear in the vicinity of the crossover concentration. Shear flow corresponding to the high shear rates destroyed fullerene‐induced intermolecular crosslinks in PVP/C60 solutions.

Induction of chirality into a fully sulfonated poly(methoxyaniline) via acid–base interactions with chiral amines

A wide range of chiral amines and amino alcohols associate with poly(2-methoxyaniline-5-sulfonic acid) (PMAS) in aqueous solution, from which optically active PMAS·(amine) films can be cast. The chiral induction is believed to be initiated by acid–base interactions with “free” sulfonic acid groups on the PMAS chains. Chiral amine:PMAS dimer molar ratios as low as 1:4 give PMAS·(amine) films with similar optical activity to those cast from 1:1 molar mixtures, indicating that only one in four of the “free” sulfonate groups on the PMAS chains need to be electrostatically bound by chiral ammonium ions to achieve optimal chiral induction. Circular dichroism studies show that the enantiomeric amines ( R)-(+)- and (S)-(−)-1-phenylethylamine induce the opposite helical hands for the supermolecular assemblies of PMAS chains. However, there is no clear correlation between the sign of the CD signals for the PMAS·(amine) films and the configuration of structurally diverse amines.

Conformation of curdlan as observed by tapping mode atomic force microscopy

Tapping mode atomic force microscopy was used to study the bacterial polysaccharide curdlan deposited from dimethyl sulfoxide (Me2SO) and NaOH aqueous solutions. For curdlan in Me2SO, flexible single chains corresponding to a disordered conformation were observed at a concentration of 5 mg/l, and the chain diameter was measured to be 0.65±0.05 nm, which showed good agreement with the expected value of the single polysaccharide chain. Because the concentration of curdlan increased, the chains became more rigid and aggregated, subsequently, the network structures of curdlan appeared. However, curdlan samples deposited from a 5 mM NaOH solution showed entirely different conformations. The chains observed were almost in the form of micelles of several nanometers, which were supermolecular assemblies. The heterogeneously dense zones were observed as the curdlan concentration increased to 40 mg/l. When the concentration of curdlan was above 100 mg/l, which might cause the real concentration of curdlan on the mica substrate after drying treatment exceeding some critical value of gelation, gel network structures were formed. Keeping on increasing the concentration of curdlan, the image showed a more homogeneous fibrous network.