Peptide Diffusion and Self-Assembly in Ambient Water Nanofilm on Mica Surface

Empowering hydrophobic anticancer drugs by ultrashort peptides: General Co-assembly strategy for improved solubility, targeted efficacy, and clinical application

The current state of drug delivery systems allows for the resolution of specific issues like inadequate solubility, limited targeting capabilities, and complex preparation processes, requiring tailored designs for different drugs. Yet, the major challenge in clinical application lies in surmounting these obstacles with a universal carrier that is effective for a variety of anticancer drugs. Herein, with the help of computer simulation, we rationally design ultrashort peptides GY and CCYRGD, which can co-assemble with hydrophobic anticancer drugs into nanoparticles with enhanced solubility, targeting ability and anticancer efficacy. Taking 7-ethyl-10-hydroxy camptothecin (SN38) as a model anticancer drug, the co-assembled SN38-GY-CCYRGD nanoparticles significantly enhance the water solubility of SN38 by more than three orders of magnitude. The as-prepared nanoparticles can effectively kill cancer cells, e.g., human small cell lung cancer (A549) cells with a notable cell mortality rate of 71%. Mice experimental results demonstrate the nanoparticles' efficient targeting capability, marked reducing the toxicity to normal tissues while improving antitumor efficacy. This work presents a novel drug delivery method, integrating effective, targeted, and safe strategies into a comprehensive carrier system, designed for the administration of hydrophobic anticancer drugs.

Molecular Scale Structure and Kinetics of Layer-by-Layer Peptide Self-Organization at Atomically Flat Solid Surfaces

Understanding the mechanisms of self-organization of short peptides into two- and three-dimensional architectures are of great interest in the formation of crystalline biomolecular systems and their practical applications. Since the assembly is a dynamic process, the study of structural development is challenging at the submolecular dimensions continuously across an adequate time scale in the natural biological environment, in addition to the complexities stemming from the labile molecular structures of short peptides. Self-organization of solid binding peptides on surfaces offers prospects to overcome these challenges. Here we use a graphite binding dodecapeptide, GrBP5, and record its self-organization process of the first two layers on highly oriented pyrolytic graphite surface in an aqueous solution by using frequency modulation atomic force microscopy in situ. The observations suggest that the first layer forms homogeneously, generating self-organized crystals with a lattice structure in contact with the underlying graphite. The second layer formation is mostly heterogeneous, triggered by the crystalline defects on the first layer, growing row-by-row establishing nominally diverse biomolecular self-organized structures with transient crystalline phases. The assembly is highly dependent on the peptide concentration, with the nucleation being high in high molecular concentrations, e.g., >100 μM, while the domain size is small, with an increase in the growth rate that gradually slows down. Self-assembled peptide crystals are composed of either singlets or doublets establishing P1 and P2 oblique lattices, respectively, each commensurate with the underlying graphite lattice with chiral crystal relations. This work provides insights into the surface behavior of short peptides on solids and offers quantitative guidance toward elucidating molecular mechanisms of self-assembly helping in the scientific understanding and construction of coherent bio/nano hybrid interfaces.

Coacervates Forming Coexisting Phases on a Mineral Surface

Minerals played a crucial role in the chemical evolution of small molecules into biopolymers. Yet, it is still not clear how the minerals are related to the formation and the evolution of protocells on early Earth. In this work, using the coacervate formed by quaternized dextran (Q-dextran) and single-stranded oligonucleotides (ss-oligo) as the protocell model, we systematically studied the phase separation of Q-dextran and ss-oligo on the muscovite surface. Serving as rigid and 2D polyelectrolytes, the muscovite surface can be treated by Q-dextran to become negatively charged, neutral, or positively charged. We observed that Q-dextran and ss-oligo form uniform coacervates on naked and neutral muscovite surfaces, while they form biphasic coacervates containing Q-dextran-rich phases and ss-oligo-rich phases on positively or negatively charged muscovite surfaces that were pretreated by Q-dextran. The evolution of the phases is caused by the redistribution of the components as the coacervate touches the surface. Our study indicates that the mineral surface could be a potential driving force for the formation of protocells with hierarchical structures and desirable functions on prebiotic Earth.

Creating de novo peptide-based bioactivities: from assembly to origami

DNA origami has created complex structures of various spatial dimensions. However, their versatility in terms of function is limited due to the lower number of the intrinsic building blocks, i.e. nucleotides, compared with the number of amino acids. Therefore, protein origami has been proposed and demonstrated to precisely fabricate artificial functional nanostructures. Despite their hierarchical folded structures, chain-like peptides and DNA share obvious similarities in both structures and properties, especially in terms of chain hybridization; therefore, replacing DNA with peptides to create bioactivities not only has high theoretical feasibility but also provides a new bottom-up synthetic strategy. However, designing functionalities with tens to hundreds of peptide chains using the similar principle of DNA origami has not been reported, although the origami strategy holds great potential to generate more complex bioactivities. In this perspective review, we have reviewed the recent progress in and highlighted the advantages of peptide assembly and origami on the orientation of artificially created bioactivities. With the great potential of peptide origami, we appeal to develop user-friendly softwares in combination with artificial intelligence.

Self-assembly of colloidal single-layer carbon nitride

We introduce a new concept of a "bottom-to-top" design of intercalate carbon nitride compounds based on the effects of self-assembly of colloidal single-layer carbon nitride (SLCN) sheets stabilized by tetraethylammonium hydroxide NEt₄OH upon ambient drying of the water solvent. These effects include (i) formation of stage-1 intercalates of NEt₄OH during the ambient drying of SLCN colloids on glass substrates and (ii) the spontaneous formation of layered hexagonally-shaped networks of SLCN sheets on freshly-cleaved mica surfaces. The dynamics of the intercalate formation was followed by in situ X-ray diffraction allowing different stages to be identified, including the deposition of a primary "wet" intercalate of hydrated NEt₄OH and the gradual elimination of excessive water during its ambient drying. The intercalated NEt₄⁺ cations show a specific "flattened" conformation allowing the dynamics of formation and structure of the intercalate to be probed by vibrational spectroscopies. The two-dimensional self-assembly on mica is assumed to be driven both by the internal hexagonal symmetry of heptazine units and by a templating effect of the mica surface.

Chiral Recognition of Self-Assembled Peptides on MoS2 via Lattice Matching

Chiral recognition of peptides on solid surfaces has been studied for a better understanding of their assembly mechanism toward its applications in stereochemistry and enantioselective catalysis. However, moving from small peptides such as dipeptides, understanding the chiral recognition of larger biomolecules such as oligopeptides or peptides with a larger sequence is challenging. Furthermore, their intrinsic mechanism for chiral recognition in liquid conditions was poorly investigated experimentally. Here, we used in/ex situ atomic force microscopy (AFM) to investigate the chiral recognition of self-assembled structures of l/d-type peptides on molybdenum disulfide (MoS₂). We chose single-layer MoS₂ with a triangular shape as a substrate for the self-assembly of peptides. The facet edges of MoS₂ were utilized as a landmark to identify the crystallographic orientation of their ordered structures. We found both peptide enantiomers formed nanowires on MoS₂ with a mirror symmetry according to the facet edges of MoS₂. From in situ AFM measurements, we found a dimension of a unit cell in the self-assembled structure and proposed a model of lattice matching between peptides and MoS₂ lattice. The lattice matching for chiral recognition was further investigated by changing peptide sequences and surface lattice from MoS₂ to graphite. This work further deepened the understanding of biomolecular chiral recognition and will lead us to rationally design specific morphologies and conformations of chiral self-assembled structures of peptides with expected functions in the future.

Assembly of peptides in mica-graphene nanocapillaries controlled by confined water

Water in nanoscale-confined geometries has unique physicochemical properties in contrast to bulk water, and is believed to play important roles in biological processes although there is less direct information available in the literature. Here, we report the self-assembly behaviors of a neurodegenerative disease related peptide termed GAV-9 encapsulated in mica-graphene nanocapillaries interacting with water nanofilms condensed under ambient conditions, based on atomic force microscopy (AFM) imaging and molecular dynamics (MD) simulations. The results revealed that, upon increase in the humidity, the GAV-9 peptide monomers adsorbed the confined water molecules and transitioned to unexpected hydrogel-like structures. Our MD simulations also suggested that in the confined mica-graphene nanocapillaries, the GAV-9 peptide monomers would indeed form water-rich hydrogel structures instead of highly ordered nanofilaments. The interfacial water confined in the mica-graphene nanocapillary is found to be crucial for such a transition. Moreover, the distribution of confined water layers largely depended on the locations of the preformed peptide nanofilaments, and the peptide nanofilaments further assembled into nanosheets with the water layer increasing, but depolymerized to amorphous peptide assemblies with the water layer decreasing. The polymerization and depolymerization of the peptide nanofilaments could be controlled in a reversible manner. Our results have supplied a simplified model system to uncover the effects of the confined interfacial water on the biological process at the molecular level.

Thick Two-Dimensional Water Film Confined between the Atomically Thin Mica Nanosheet and Hydrophilic Substrate

The interesting properties of water molecules confined in a two-dimensional (2D) environment have aroused great attention. However, the study of 2D-confined water at the hydrophilic-hydrophilic interface is largely unexplored due to the lack of appropriate system. In this work, the behavior of water molecules confined between an atomically thin mica nanosheet and a hydrophilic SiO₂/Si substrate was investigated using an atomic force microscope in detail at ambient conditions. The confined water molecules aggregated as droplets when the relative humidity (RH) of the environment was 11%. A large-area 2D water film with a uniform thickness of ∼2 nm was observed when the mica flake was incubated at 33% RH for 1 h before being mechanically exfoliated on a SiO₂/Si substrate. Interestingly, the water film showed ordered edges with a predominant angle of 120°, which was the same with the lattice orientation of the mica nanosheet on top of it. The water film showed a fluidic behavior at the early stage and reached a stable state after 48 h under ambient conditions. The surface properties of the upper mica nanosheet and the underlying substrate played a crucial role in manipulating the behavior of confined water molecules. When the surface of the upper mica nanosheet was modified by Na⁺, Ni²⁺_, and aminopropyltriethoxysilane (APS), only some small water droplets were observed instead of a water film. The surface of the underlying SiO₂/Si substrate was functionalized by hydrophilic APS and hydrophobic octadecyltrimethoxysiliane (OTS). The small water droplets were imaged on a hydrophobic OTS-SiO₂/Si substrate, while the water film with regular edges was maintained on a hydrophilic APS-SiO₂/Si substrate. Our results might provide an alternative molecular view for investigating structures and properties of confined water molecules in 2D environments.

Mineral Surface-Templated Self-Assembling Systems: Case Studies from Nanoscience and Surface Science towards Origins of Life Research

An increasing body of evidence relates the wide range of benefits mineral surfaces offer for the development of early living systems, including adsorption of small molecules from the aqueous phase, formation of monomeric subunits and their subsequent polymerization, and supramolecular assembly of biopolymers and other biomolecules. Each of these processes was likely a necessary stage in the emergence of life on Earth. Here, we compile evidence that templating and enhancement of prebiotically-relevant self-assembling systems by mineral surfaces offers a route to increased structural, functional, and/or chemical complexity. This increase in complexity could have been achieved by early living systems before the advent of evolvable systems and would not have required the generally energetically unfavorable formation of covalent bonds such as phosphodiester or peptide bonds. In this review we will focus on various case studies of prebiotically-relevant mineral-templated self-assembling systems, including supramolecular assemblies of peptides and nucleic acids, from nanoscience and surface science. These fields contain valuable information that is not yet fully being utilized by the origins of life and astrobiology research communities. Some of the self-assemblies that we present can promote the formation of new mineral surfaces, similar to biomineralization, which can then catalyze more essential prebiotic reactions; this could have resulted in a symbiotic feedback loop by which geology and primitive pre-living systems were closely linked to one another even before life’s origin. We hope that the ideas presented herein will seed some interesting discussions and new collaborations between nanoscience/surface science researchers and origins of life/astrobiology researchers.

Inorganic salt transition states: a stable and highly stretchable elastomer-like phase (ELP) of phosphate salts at the air–solid interface

An ultra-high stable elastomer-like phase (ELP) of phosphate salts was formed at the air–solid interface of a specially designed substrate, possessing multilayered structures, elasticity and self-healing abilities.

Morphology and aggregation of RADA-16-I peptide Studied by AFM, NMR and molecular dynamics simulations

RADA-16-I is a self-assembling peptide which forms biocompatible fibrils and hydrogels. We used molecular dynamics simulations, atomic-force microscopy, NMR spectroscopy, and thioflavin T binding assay to examine size, structure, and morphology of RADA-16-I aggregates. We used the native form of RADA-16-I (H-(ArgAlaAspAla)4 -OH) rather than the acetylated one commonly used in the previous studies. At neutral pH, RADA-16-I is mainly in the fibrillar form, the fibrils consist of an even number of stacked β-sheets. At acidic pH, RADA-16-I fibrils disassemble into monomers, which form an amorphous monolayer on graphite and monolayer lamellae on mica. RADA-16-I fibrils were compared with the fibrils of a similar peptide RLDL-16-I. Thickness of β-sheets measured by AFM was in excellent agreement with the molecular dynamics simulations. A pair of RLDL-16-I β-sheets was thicker (2.3 ± 0.4 nm) than a pair of RADA-16-I β-sheets (1.9 ± 0.1 nm) due to the volume difference between alanine and leucine residues.

Large scale anomalous patterns of muscovite mica discovered by atomic force microscopy

Muscovite mica is a widely used substrate because of its flatness. The large scale anomalous patterns of muscovite have been discovered by atomic force microscopy (AFM). These patterns distribute around the defects of the muscovite surface. By using different imaging modes and analyzing functions of AFM, these extraordinary patterns are thoroughly characterized, and it was revealed that some selected regularly aligned patterns mimic 2-D orthorhombic crystal systems surrounding the regular structure. However, such patterned nanostructures have no effects on the template-assisted self-assembly (or epitaxial growth) of a disease-related peptide GAV-9.

Universality in the morphology and mechanics of coarsening amyloid fibril networks

Peptide hydrogels have important applications as biomaterials and in nanotechnology, but utilization often depends on their mechanical properties for which we currently have no predictive capability. Here we use a peptide model to simulate the formation of percolating amyloid fibril networks and couple these to the elastic network theory to determine their mechanical properties. We find that the time variation of network length scales can be collapsed onto master curves by using a time scaling function that depends on the peptide interaction anisotropy. The same scaling applies to network mechanics, revealing a nonmonotonic dependence of the shear modulus with time. Our structure-function relationship between the peptide building blocks, network morphology, and network mechanical properties can aid in the design of amyloid fibril networks with tailored mechanical properties.

An ion diffusion method for visualising a solid-like water nanofilm

A nano-thick solid-like water film on solid surfaces plays an important role in various fields, including biology, materials science, atmospheric chemistry, catalysis and astrophysics. Visualising the water nanofilm has been a challenge due to its dynamic nature and nanoscale thickness. Here we report an ion diffusion method to address this problem using a membrane formed with a BSA-Na2CO3 (BSA, bovine serum albumin) mixture. After a solid-like water nanofilm deposits onto the membrane, Na(+) and CO3(2-) ions diffuse into the film to form a solid Na2CO3 phase in its place. Consequently, the morphology of the nanofilm can be visualised by the space filled by the Na2CO3. Using this method, we successfully observed polygon-like, ribbon-like and spot-like nanofilms at 193 K, 253 K and room temperature, respectively. Our method may provide a tool for characterising confined water films ranging from a few nanometres to hundreds of nanometres in thickness.

Hierarchical ordering of amyloid fibrils on the mica surface

The aggregation of amyloid peptides into ordered fibrils is closely associated with many neurodegenerative diseases. The surfaces of cell membranes and biomolecules are believed to play important roles in modulation of peptide aggregation under physiological conditions. Experimental studies of fibrillogenesis at the molecular level in vivo, however, are inherently challenging, and the molecular mechanisms of how surface affects the structure and ordering of amyloid fibrils still remain elusive. Herein we have investigated the aggregation behavior of insulin peptides within water films adsorbed on the mica surface. AFM measurements revealed that the structure and orientation of fibrils were significantly affected by the mica lattice and the peptide concentration. At low peptide concentration (~0.05 mg mL(-1)), there appeared a single layer of short and well oriented fibrils with a mean height of 1.6 nm. With an increase of concentration to a range of 0.2-2.0 mg mL(-1), a different type of fibrils with a mean height of 3.8 nm was present. Interestingly, when the concentration was above 2.0 mg mL(-1), the thicker fibrils exhibited two-dimensional liquid-crystal-like ordering probably caused by the combination of entropic and electrostatic forces. These results could help us gain better insight into the effects of the substrate on amyloid fibrillation.

High-resolution visualization of fibrinogen molecules and fibrin fibers with atomic force microscopy

We report an atomic force microscopy (AFM) study of fibrinogen molecules and fibrin fibers with resolution previously achieved only in few electron microscopy images. Not only are all objects triads, but the peripheral D regions are resolved into the two subdomains, apparently corresponding to the βC and γC domains. The conformational analysis of a large population of fibrinogen molecules on mica revealed the two most energetically favorable conformations characterized by bending angles of ∼100 and 160 degrees. Computer modeling of the experimental images of fibrinogen molecules showed that the AFM patterns are in good agreement with the molecular dimensions and shapes detected by other methods. Imaging in different environments supports the expected hydration of the fibrinogen molecules in buffer, whereas imaging in humid air suggests the 2D spreading of fibrinogen on mica induced by an adsorbed water layer. Visualization of intact hydrated fibrin fibers showed cross-striations with an axial period of 24.0 ± 1.6 nm, in agreement with a pattern detected earlier with electron microscopy and small-angle X-ray diffraction. However, this order is clearly detected on the surface of thin fibers and becomes less discernible with the fiber's growth. This structural change is consistent with the proposal that thinner fibers are denser than thicker ones, that is, that the molecule packing decreases with the increasing of the fibers' diameter.

Mechanical manipulation assisted self-assembly to achieve defect repair and guided epitaxial growth of individual peptide nanofilaments

We have succeeded in the production of defect-free and spatially organized individual one-dimensional peptide nanofilaments by real-time control of the self-assembly process on a solid substrate. Using a unique mechanical manipulation method based on atomic force microscopy, we are able to introduce mechanical stimuli to generate active ends at designated positions on an existing peptide nanofilament previously formed. By doing so, defects in the filament were removed, and self-repairing occurred when the active ends extended along the direction of the supporting lattice, resulting in the closure of the broken filament. Furthermore, new active ends of the nanofilaments can be specifically generated to guide the self-assembly of new filaments at designated positions with selected orientations. The mechanism of defect repair and guided epitaxial growth is also discussed.