Molecular Self-assembly Mechanism Research Articles

Self-Assembly of Rhein and Matrine Nanoparticles for Enhanced Wound Healing.

Carrier-free self-assembly has gradually shifted the focus of research on natural products, which effectively improve the bioavailability and the drug-loading rate. However, in spite of the existing studies, the development of self-assembled natural phytochemicals that possess pharmacological effects still has scope for further exploration and enhancement. Herein, a nano-delivery system was fabricated through the direct self-assembly of Rhein and Matrine and was identified as a self-assembled Rhein-Matrine nanoparticles (RM NPs). The morphology of RM NPs was characterized by TEM. The molecular mechanisms of self-assembly were explored using FT-IR, 1H NMR, and molecular dynamics simulation analysis. Gelatin methacryloyl (GelMA) hydrogel was used as a drug carrier for controlled release and targeted delivery of RM NPs. The potential wound repair properties of RM NPs were evaluated on a skin wound-healing model. TEM and dynamic light scattering study demonstrated that the RM NPs were close to spherical, and the average size was approximately 75 nm. 1H NMR of RM NPs demonstrated strong and weak changes in the interaction energies during self-assembly. Further molecular dynamics simulation analysis predicted the self-assembly behavior. An in vivo skin wound-healing model demonstrated that RM NPs present better protection effect against skin damages. Taken together, RM NPs are a new self-assembly system; this may provide new directions for natural product applications.

Resolution of trans-1,2-cyclohexanedicarboxylic acid containing two carboxylic groups by forming diastereomeric salts based on feeding molar ratio control.

To investigate the thermodynamic and molecular self-assembly mechanism of trans-1,2-cyclohexane dicarboxylic acid containing two carboxylic acid groups in the chiral resolution process, (S)-phenylethylamine was used as the chiral resolving agent. Two stoichiometric salts were formed when the raw materials were fed at different molar ratios: cyclohexane dicarboxylate monophenylethylamine salt and cyclohexane dicarboxylate diphenylethylamine salt. When the molar ratio of the (S)-phenylethylamine to trans-1,2-cyclohexane dicarboxylic acid was less than 3:1, trans-(1S,2S)-cyclohexane dicarboxylic acid was obtained with 97 e.e% purity. But when the molar ratio exceeded 3:1, the product was the racemic trans-(1,2)-cyclohexane dicarboxylic acid. In addition, single crystal structures of more soluble mono-salt, less soluble mono-salt, and less soluble di-salt were obtained. The weak intermolecular interactions and the way of the molecules packing in the crystals were analyzed. The hydrogen bond was stronger in the less soluble salt than that in the more soluble salt. And a "lock-and-key" structure in the hydrophobic layers makes it more tightly packed through the van der Waals interaction, which is responsible for the stability of less soluble salts.

Hierarchical self-assembly of a reflectin-derived peptide.

Reflectins are a family of intrinsically disordered proteins involved in cephalopod camouflage, making them an interesting source for bioinspired optical materials. Understanding reflectin assembly into higher-order structures by standard biophysical methods enables the rational design of new materials, but it is difficult due to their low solubility. To address this challenge, we aim to understand the molecular self-assembly mechanism of reflectin's basic unit-the protopeptide sequence YMDMSGYQ-as a means to understand reflectin's assembly phenomena. Protopeptide self-assembly was triggered by different environmental cues, yielding supramolecular hydrogels, and characterized by experimental and theoretical methods. Protopeptide films were also prepared to assess optical properties. Our results support the hypothesis for the protopeptide aggregation model at an atomistic level, led by hydrophilic and hydrophobic interactions mediated by tyrosine residues. Protopeptide-derived films were optically active, presenting diffuse reflectance in the visible region of the light spectrum. Hence, these results contribute to a better understanding of the protopeptide structural assembly, crucial for the design of peptide- and reflectin-based functional materials.

Self-assembled short peptides: Recent advances and strategies for potential pharmaceutical applications.

Self-assembled short peptides have intrigued scientists due to the convenience of synthesis, good biocompatibility, low toxicity, inherent biodegradability and fast response to change in the physiological environment. Therefore, it is necessary to present a comprehensive summary of the recent advances in the last decade regarding the construction, route of administration and application of self-assembled short peptides based on the knowledge on their unique and specific ability of self-assembly. Herein, we firstly explored the molecular mechanisms of self-assembly of short peptides, such as non-modified amino acids, as well as Fmoc-modified, N-functionalized, and C-functionalized peptides. Next, cell penetration, fusion, and peptide targeting in peptide-based drug delivery were characterized. Then, the common administration routes and the potential pharmaceutical applications (drug delivery, antibacterial activity, stabilizers, imaging agents, and applications in bioengineering) of peptide drugs were respectively summarized. Last but not least, some general conclusions and future perspectives in the relevant fields were briefly listed. Although with certain challenges, great opportunities are offered by self-assembled short peptides to the fascinating area of drug development.

Thermodynamic and Molecular Recognition Mechanism of Diastereomeric Salt/Cocrystal-Induced Chiral Separation

To better understand the thermodynamics and molecular self-assembly mechanism of diastereomeric salt/cocrystal-induced chiral separation, a series of 1:1 cocrystals and salts consisting of chiral valines (VAL) and tartaric acid derivatives were synthesized via different methods. Powders of these as-screened cocrystals/salts were characterized by PXRD, TGA, DSC, FT-IR, and Raman spectroscopy. The crystal structures of the five cocrystals/salts were determined and analyzed. It was found that both DBTA and DTTA form diastereomeric salt pairs with VAL enantiomers. Interestingly, l-DMTA cocrystallizes with d-VAL and l-VAL via hydrogen bonding and proton transfer, respectively. Considering this particularity, the differential isothermal (10 °C) ternary phase diagrams (TPDs) of d-DMTA and l-VAL (d-VAL) cocrystals (salt) were constructed in the mixed solvent of MeOH/H2O. Moreover, a pure l-VAL:d-DMTA cocrystal and d-VAL:d-DMTA:0.5CH4O:0.25H2O salt were prepared via equimolar slurry conversion at 10 °C. In situ Raman spectroscopy was applied to monitor the molecular assembly process during the incubation of the cocrystal/salt. Molecular dynamics simulation was employed to rationalize the molecular recognition mechanism, demonstrating the excellent chirality preference of l-DMTA toward l-VAL instead of d-VAL. Calculations of density functional theory approved the synergistic instead of antagonistic effects of binding energy and solvation free energy toward chiral separation.

Probing Molecular Mechanisms during the Oscillatory Adsorption of Propyl Chain Functionalized Organosilane Films with Sum Frequency Generation Spectroscopy.

The selectivity rules of sum frequency generation spectroscopy were exploited to determine propyl chain order during the time-dependent oscillatory adsorption of propyltrimethoxysilane (PTMS) and Langmuir-type growth of propyldimethylmethoxysilane (PDMMS). During the early stages of film growth, molecular packing density determines the extent of propyl chain defects within both films with high surface coverage resulting in a film with fewer defects. Following this, an ordered monolayer-like film stabilizes on the Al2O3 substrate for both silanes. Although this result is intuitive for the Langmuir-type growth of PDMMS, the stabilization of molecular ordering despite the continuing oscillation in PTMS surface coverage indicates the presence of a stable monolayer, while it is the oligomerized PTMS dendrimers which continue to desorb and readsorb to the substrate. We also reveal for the first time, the formation of a physisorbed bilayer during the self-assembly process of PTMS. The presence of this ordered, physisorbed bilayer on top of the covalently bound PTMS film plays a key role in the process of the molecular self-assembly mechanism and is proposed to enable further condensation of the covalently bound film.

Navigated Self-Assembly of a Pd2L4 Cage by Modulation of an Energy Landscape under Kinetic Control.

Kinetic control of molecular self-assembly remains difficult because of insufficient understanding of molecular self-assembly mechanisms. Here we report the formation of a metastable [Pd2L4]4+ cage structure composed of naphthalene-based ditopic ligands (L) and Pd(II) ions in very high yield (99%) under kinetic control by modulating the energy landscape. When self-assembly occurs with anionic guests in weakly cooordinating solvent then suitable intermedites and the metastable cage is formed. These conditions also prevent further transformation into the thermodynamically decomposed state. The cage formation pathways under kinetic control and the effect of the anions encapsulated on the self-assembly processes were investigated by QASAP (quantitative analysis of self-assembly process) and NASAP (numerical analysis of self-assembly process). It was found that the self-assembly with a preferred guest (BF4-) proceeds through intermediates composed of no more components than the cage ([PdaLbXc]2a+ (a ≤ 2, b ≤ 4, X indicates a leaving ligand)) and that the final intramolecular cage-closure step is the rate-determining step. In contrast, a weaker guest (OTf-) causes the transient formation of intermediates composed of more components than the cage ([PdaLbXc]2a+ (a > 2, b > 4)), which are finally converted into the cage.

To pursue FexCoy-PANI/CNT catalysts for oxygen reduction reaction in acid medium with controlled molecular self-assembly method

The mainstream of pyrolyzed transitional metal-nitrogen-carbon (M-N-C) catalysts for ORR still confront difficulty in PEMFC application. To pursue M-N-C structure from wet chemistry at ambient temperature, this paper prepares FexCoy-PANI/CNT porous structures composed of amorphous Fe and Co NPs into PANI layer on CNT surface, supported by the controlled molecular self-assembly mechanism (MS). For their ORR behaviors in acid medium, all FexCoy-PANI/CNT catalysts demonstrate similar features as Pt-based catalyst in low current density region, and 4e pathway and active sites in pore utilization in high current density region. Specifically, we disclosed nitrogen in PANI matrix dominates specific activity for ORR, and a little transitional metal attain mass activity at maximum. The active sites mounted into PANI matrix and 4e pathway help catalysts to achieve high durability. Thus, we extend a new type of platinum-free catalyst and develop a bottom-up approach for preparation-structure-activity, expecting to drive PEMFC remarkably.

Molecular Mechanism of Self-Assembly of Aromatic Oligoamides into Interlocked Double-Helix Foldamers.

Foldamer, inspired by the structures and functions of biopolymers, is defined as an artificial molecular architecture that can fold into a three-dimensional structure in solution and has been a growing and active field in supramolecular chemistry. The central issue in foldamer science is to understand how the primary sequence of oligomer folds into conformationally ordered structures as well as how individual subunits self-associate into assembly. For duplex structures, these two issues are always interrelated and inseparable with each other. Although the emergence of new foldamer keeps growing, the detailed mechanism remains elusive. On the basis of an artificially synthesized arylamide oligoamide foldamer with its crystal structure available, we constructed a set of four foldamers with a similar backbone but different substituents and aimed at dissecting the folding and self-association mechanisms of a double-helical foldamer with computations. Using molecular simulations at a microsecond time scale, we observed very consistent processes of the spontaneous self-assembly of two single-helical motifs into an entwined complex. Our results reveal that aggregation of two single-helical motifs driven by extensive π-π interactions is energetically favorable and that this spontaneous self-assembly proceeds through an "unwinding-threading-rewinding" mechanism. The detailed mechanisms about the folding and self-assembly in an aromatic oligoamide foldamer we present here disclose how the sequence is associated with a well-ordered three-dimensional structure at atomic level and therefore may have implications for designing new foldamers with versatile functions.

Molecular mechanism and characterization of self-assembly of feather keratin gelation

Protein gels with controlled viscoelastic properties could find numerous material and biomedical applications. Feather keratin is naturally abundant protein while its gelation property has not been explored. In this study hydrogel from fully reduced feather keratin was prepared by dialysis. The objectives of this work were to study the molecular mechanism of self-assembly of feather keratin gel and to characterize the structural and viscoelastic properties of hydrogels prepared under various pHs (3–9) and temperatures (50–90°C). Re-oxidation of free cysteine thiols and formation of hydrophobic interactions and hydrogen bond were determined as the main stabilizing forces in self-assembly of feather keratin gel. Adding thiol blocking agent of N-ethylmaleimide leads to reduced storage modulus of keratin gel; gelation was completely inhibited at 82% blockage of free thiols. Increasing temperature decreased storage modulus, while gelation at pH 3 resulted in stiffer gels compared to pHs of 5, 7 and 9. Feather keratin gels with tunable viscoelastic properties could find applications as engineered scaffolds for different tissues.

Synthesis of Infectious Bacteriophages in an <em>E. coli-</em>based Cell-free Expression System

A new generation of cell-free transcription-translation (TXTL) systems, engineered to have a greater versatility and modularity, provide novel capabilities to perform basic and applied sciences in test tube reactions. Over the past decade, cell-free TXTL has become a powerful technique for a broad range of novel multidisciplinary research areas related to quantitative and synthetic biology. The new TXTL platforms are particularly useful to construct and interrogate biochemical systems through the execution of synthetic or natural gene circuits. In vitro TXTL has proven convenient to rapidly prototype regulatory elements and biological networks as well as to recapitulate molecular self-assembly mechanisms found in living systems. In this article, we describe how infectious bacteriophages, such as MS2 (RNA), ΦΧ174 (ssDNA), and T7 (dsDNA), are entirely synthesized from their genome in one-pot reactions using an all Escherichia coli, cell-free TXTL system. Synthesis of the three coliphages is quantified using the plaque assay. We show how the yield of synthesized phage depends on the biochemical settings of the reactions. Molecular crowding, emulated through a controlled concentration of PEG 8000, affects the amount of synthesized phages by orders of magnitudes. We also describe how to amplify the phages and how to purify their genomes. The set of protocols and results presented in this work should be of interest to multidisciplinary researchers involved in cell-free synthetic biology and bioengineering.

Synthesis of Infectious Bacteriophages in an E. coli-based Cell-free Expression System.

A new generation of cell-free transcription-translation (TXTL) systems, engineered to have a greater versatility and modularity, provide novel capabilities to perform basic and applied sciences in test tube reactions. Over the past decade, cell-free TXTL has become a powerful technique for a broad range of novel multidisciplinary research areas related to quantitative and synthetic biology. The new TXTL platforms are particularly useful to construct and interrogate biochemical systems through the execution of synthetic or natural gene circuits. In vitro TXTL has proven convenient to rapidly prototype regulatory elements and biological networks as well as to recapitulate molecular self-assembly mechanisms found in living systems. In this article, we describe how infectious bacteriophages, such as MS2 (RNA), ΦΧ174 (ssDNA), and T7 (dsDNA), are entirely synthesized from their genome in one-pot reactions using an all Escherichia coli, cell-free TXTL system. Synthesis of the three coliphages is quantified using the plaque assay. We show how the yield of synthesized phage depends on the biochemical settings of the reactions. Molecular crowding, emulated through a controlled concentration of PEG 8000, affects the amount of synthesized phages by orders of magnitudes. We also describe how to amplify the phages and how to purify their genomes. The set of protocols and results presented in this work should be of interest to multidisciplinary researchers involved in cell-free synthetic biology and bioengineering.

Probing Molecular Mechanisms of Self-Assembly in Metal-Organic Frameworks.

Metal-organic framework materials (MOFs) are a class of nanoporous materials, important to many applications (e.g., gas storage, separation), and their synthesis has received considerable attention. Yet, very little is known about the mechanisms of self-assembly of MOFs. Here, we provide molecular-level insights into the previously unexplored behavior of the self-assembly process, through molecular dynamics simulations, for an archetypal Zn-carboxylate MOF system exhibiting complex vertex topologies (e.g., paddle-wheel clusters). A key finding of this study is the characterization of a stochastic and multistage ordering process intrinsic to self-assembly of the Zn-carboxylate MOF system. A variety of transient intermediate structures consisting of various types of Zn-ion clusters and carboxylate-ligand coordination, and featuring a range of geometric arrangements, are observed during structural evolution. The general features deduced here for the mechanism of the self-assembly of this archetypal MOF system expose the complexities of the various molecular-level events that can occur during the early stages of this process spanning time scales of nano- to microseconds. More generally, we provide fundamental insights that elucidate key aspects of the early stages of the self-assembly mechanism for an important class of nanoporous materials, and of experimental studies exploring nucleation and growth processes in such materials.

Adsorption behavior of mixed cationic/anionic surfactants and their depression mechanism on the flotation of quartz

Mixed cationic/anionic surfactants are generating increasing attention as effective collectors during the flotation of muscovite, feldspar and spodumene ores. Many papers have been published focusing on the flotation mechanisms of these valuable minerals. However, the depression mechanisms on gangue minerals such as quartz have rarely been reported. In this study, mixed dodecylamine (DDA)/sodium oleate (NaOL) surfactants were used in the flotation separation of muscovite and quartz, and their depression mechanisms on quartz were investigated. Compared to DDA alone, the use of mixed surfactants resulted in a significantly higher adsorption amount of surfactants on the quartz but a lower flotation recovery and contact angle with the quartz. This is attributed to the different molecular self-assembly mechanisms between solely DDA and mixed surfactants at the quartz/water interface, as revealed by molecular dynamics simulations. A hydrophobic monolayer coating forms for solely DDA, with the head groups adsorbing on the quartz via electrostatic interactions. In the case of mixed surfactants, DDA preferentially interacts with NaOL via electrostatic interaction through the oppositely charged head groups and hydrophobic interactions between their carbon chains. As a result, most DDA and NaOL molecules form hydrophilic spherical-like micelles near quartz, whereas only a few DDA molecules adsorb directly on the quartz via hydrogen bonding. These act as a bridge linking the rest of the surfactants, leading to a relatively lower flotation recovery and contact angle for the quartz. This study is beneficial for complementing the flotation theories and mechanisms of mixed cationic/anionic surfactants on minerals.

The Structure of Misfolded Amyloidogenic Dimers: Computational Analysis of Force Spectroscopy Data

Progress in understanding the molecular mechanism of self-assembly of amyloidogenic proteins and peptides requires knowledge about their structure in misfolded states. Structural studies of amyloid aggregates formed during the early aggregation stage are very limited. Atomic force microscopy (AFM) spectroscopy is widely used to analyze misfolded proteins and peptides, but the structural characterization of transiently formed misfolded dimers is limited by the lack of computational approaches that allow direct comparison with AFM experiments. Steered molecular dynamics (SMD) simulation is capable of modeling force spectroscopy experiments, but the modeling requires pulling rates 107 times higher than those used in AFM experiments. In this study, we describe a computational all-atom Monte Carlo pulling (MCP) approach that enables us to model results at pulling rates comparable to those used in AFM pulling experiments. We tested the approach by modeling pulling experimental data for I91 from titin I-band (PDB ID: 1TIT) and ubiquitin (PDB ID: 1UBQ). We then used MCP to analyze AFM spectroscopy experiments that probed the interaction of the peptides [Q6C] Sup35 (6–13) and [H13C] Aβ (13–23). A comparison of experimental results with the computational data for the Sup35 dimer with out-of-register and in-register arrangements of β-sheets suggests that Sup35 monomers adopt an out-of-register arrangement in the dimer. A similar analysis performed for Aβ peptide demonstrates that the out-of-register antiparallel β-sheet arrangement of monomers also occurs in this peptide. Although the rupture of hydrogen bonds is the major contributor to dimer dissociation, the aromatic-aromatic interaction also contributes to the dimer rupture process.

Creating new supramolecular materials by architecture of three-dimensional nanocrystal fiber networks.

The architecture of three-dimensional interconnecting self-organized nanofiber networks from separate needlelike crystals of L-DHL (lanosta-8,24-dien-3beta-ol:24,25-dihydrolanosterol = 56:44) in di-isooctylphthalate has been achieved for the first time, on the basis of the completely new concept of branching creation by additives (branching promoters). [In this work, an additive, ethylene/vinyl acetate copolymer (EVACP), is used at a concentration of several 10 ppm.] We demonstrate that this novel technique enables us to produce previously unknown self-supporting supramolecular functional materials with tailormade micro- or nanostructures, possessing significantly modified macroscopic properties, by utilizing materials thus far considered to be "useless". In addition, both the self-organized structure and the properties of the new materials can be fine-tuned by altering the processing conditions. Our results show that the formation of the interconnecting 3D self-organized network structure is controlled by a new mechanism, so-called crystallographic mismatch branching mechanism, as opposed to the conventionally adopted molecular self-assembly mechanism. The principles and criteria for the selection of branching promoters are also discussed from the point of view of molecular structures.

Molecular Mechanisms of Self-Assembly and Polymorphic Switching of the Bacterial Flagellum

Bacterial flagellum is a helical filament by means of which bacteria swim. Each filament rotated by the motor at its base works as a screw that propels the cell, but it is not simply a rigid propeller. The filament is normally in a left-handed supercoiled form and several of them form a bundle when bacteria swim. Upon quick reversal of the motor rotation, which occurs every few seconds, the filament switches into a right-handed supercoil, making the filament bundle fall apart and enabling the cell to tumble for its tactic behavior. The filament is a tubular structure formed by helical assembly of single protein, flagellin, whose molecular mass is 51.5 kDa in the case of Salmonella typhimurium, which we study. The supercoiling of the filament is thought to involve two distinct subunit conformations and/or packing, whose mechanism is interesting in terms of conformational distinctness and adaptability of flagellin.To understand the mechanisms of self-assembly and polymorphism of the filament, electron cryomicroscopy (EM) and X-ray fiber diffraction have been used to analyze the structures of two straight filaments with distinct helical symmetries.

Ｘ線と電子線による細菌べん毛フィラメントの構造解析

Bacterial flagellum consists of a rotary motor and a helical filament as a screw, and works for bacterial motility and taxis. The filament is built by a self-assembly process and has a polymorphic ability to be various forms of supercoils. Here, we describe a complementary use of X-ray diffraction and electron cryomicroscopy for structure analysis of this large helical complex. The structure reveals the molecular mechanism of self assembly and polymorphism.

Processing and microstructural control: lessons from natural materials

Renewable natural materials have been exploited for several millennia. Within the past two decades, it has become apparent that materials science can benefit from a detailed knowledge of the synthetic pathways and molecular self-assembly mechanisms by which natural materials are produced. This review describes the most significant classes of macromolecule used in the synthesis of biological materials. It explains how the techniques of genetic engineering can be employed to modify the structure or quantitative yield of these materials. The role of the liquid crystalline state in materials self-assembly, and the effects of hierachical molecular order on the properties of natural materials, are emphasized. The wide range of contexts in which biological principles have impacted materials science is illustrated with several specific examples.