Salts drive controllable multilayered upright assembly of amyloid-like peptides at mica/water interface

Non-fibril amyloid aggregation at the air/water interface: self-adaptive pathway resulting in a 2D Janus nanofilm

The amyloid states of proteins are implicated in several neurodegenerative diseases and bioadhesion processes. However, the classical amyloid fibrillization mechanism fails to adequately explain the formation of polymorphic aggregates and their adhesion to various surfaces. Herein, we report a non-fibril amyloid aggregation pathway, with disulfide-bond-reduced lysozyme (R-Lyz) as a model protein under quasi-physiological conditions. Very different from classical fibrillization, this pathway begins with the air-water interface (AWI) accelerated oligomerization of unfolded full-length protein, resulting in unique plate-like oligomers with self-adaptive ability, which can adjust their conformations to match various interfaces such as the asymmetric AWI and amyloid-protein film surface. The pathway enables a stepwise packing of the plate-like oligomers into a 2D Janus nanofilm, exhibiting a divergent distribution of hydrophilic/hydrophobic residues on opposite sides of the nanofilm. The resulting Janus nanofilm possesses a top-level Young's modulus (8.3 ± 0.6 GPa) among amyloid-based materials and exhibits adhesive strength two times higher (145 ± 81 kPa) than that of barnacle cement. Furthermore, we found that such an interface-directed pathway exists in several amyloidogenic proteins with a similar self-adaptive 2D-aggregation process, including bovine serum albumin, insulin, fibrinogen, hemoglobin, lactoferrin, and ovalbumin. Thus, our findings on the non-fibril self-adaptive mechanism for amyloid aggregation may shed light on polymorphic amyloid assembly and their adhesions through an alternative pathway.

Multiscale Simulations to Discover Self-Assembled Oligopeptides: A Benchmarking Study

Peptide self-assembly is critical for biomedical and material discovery and production. While it is costly to experimentally test every possible peptide design, computational assessment provides an affordable solution to evaluate many designs and prioritize synthesis and characterization. Following a theoretical investigation, we present a systematic analysis of all-atom and coarse-grained simulations to predict peptide self-assembly. Benchmarking studies of two model dipeptides allow us to assess the impacts of intrinsic properties (such as amino acids and terminal modifications) and external environment (such as salinity) on the simulated aggregation. Further examination of 20 oligopeptides containing two to five amino acids shows good agreement among our theory, simulations, and prior experimental observations. The success rate of our prediction is 90%. Therefore, our theory, simulation, and analysis can be useful to identify peptide designs that can self-assemble and predict the potential nanostructures. These findings lay the ground for future virtual screening of peptide-assembled nanostructures and computer-aided biologics design.

Gel-to-Solution Transition of Sulfhydryl Self-Assembled Peptide Hydrogels Undergoing Oxidative Modulation

The design of self-assembling biomaterials needs to take into consideration the timing and location of the self-assembly process. In recent decades, the principal strategy has been to control the peptide self-assembly under specific conditions to enable its functional performance. However, few studies have explored the responsive elimination of functional self-assembled peptide hydrogels after their function has been performed. We designed peptide ECAFF (ECF-5), which under reductive conditions can self-assemble into a hydrogel. Upon exposure to oxidizing conditions, disulfide bonds form between the peptides, altering their molecular structure and impacting their self-assembly capability. As a result, the peptide hydrogels transition to a soluble state. This study investigates the utilization of oxidation to induce a gel-to-solution transition in peptide hydrogels and provides an explanation for their degradation following free radical treatment. Self-assembled peptide hydrogel materials can be designed from a fresh perspective by considering the degradation that takes place after functional execution.

Creating an Amyloid 'Kaleidoscope' Using Short Iodinated Peptides

Amyloid fibrils formed by peptides with different sequences exhibit diversified morphologies, material properties and activities, making them valuable for developing functional bionanomaterials. However, the molecular understanding underlying the structural diversity of peptide fibrillar assembly at atomic level is still lacking. In this study, by using cryogenic electron microscopy, we first revealed the structural basis underlying the highly reversible assembly of 1 GFGGNDNFG9 (referred to as hnRAC1) peptide fibril. Furthermore, by installing iodine at different sites of hnRAC1, we generated a collection of peptide fibrils with distinct thermostability. By determining the atomic structures of the iodinated fibrils, we discovered that iodination at different sites of the peptide facilitates the formation of diverse halogen bonds and triggers the assembly of entirely different structures of iodinated fibrils. Finally, based on this structural knowledge, we designed an iodinated peptide that assembles into new atomic structures of fibrils, exhibiting superior thermostability, that aligned with our design. Our work provides an in-depth understanding of the atomic-level processes underlying the formation of diverse peptide fibril structures, and paves the way for creating an amyloid "kaleidoscope" by employing various modifications and peptide sequences to fine-tune the atomic structure and properties of fibrillar nanostructures.

Direct Visualization of the Dynamic Process of Epsilon Toxin on Hemolysis

Hemolysis is the process of rupturing erythrocytes (red blood cells) by forming nanopores on their membranes using hemolysins, which then impede membrane permeability. However, the self-assembly process before the state of transmembrane pores and underlying mechanisms of conformational change are not fully understood. In this work, theoretical and experimental evidence of the pre-pore morphology of Clostridium perfringens epsilon toxin (ETX), a typical hemolysin, is provided using in situ atomic force microscopy (AFM) complemented by molecular dynamics (MD) simulations to detect the conformational distribution of different states in Mica. The AFM suggests that the ETX pore is formed in two stages: ETX monomers first attach to the membrane and form a pre-pore in no special conditions required, which then undergo a conformational change to form a transmembrane pore at temperatures above the critical point in the presence of receptors. The authors' MD simulations reveal that initial nucleation occurs when specific amino acids adsorb to negatively charged mica cavities. This work fills the knowledge gap in understanding the early stage of hemolysis and the oligomerization of hemolysins. Moreover, the newly identified pre-pore of ETX holds promise as a candidate for nanopore applications.

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.

Bottom-up supramolecular assembly in two dimensions

The self-assembly of molecules in two dimensions (2D) is gathering attention from all disciplines across the chemical sciences. Attracted by the interesting properties of two-dimensional inorganic analogues, monomers of different chemical natures are being explored for the assembly of dynamic 2D systems. Although many important discoveries have been already achieved, great challenges are still to be addressed in this field. Hierarchical multicomponent assembly, directional non-covalent growth and internal structural control are a just a few of the examples that will be discussed in this perspective about the exciting present and the bright future of two-dimensional supramolecular assemblies.

The self-assembly of molecules in two dimensions (2D) is gathering attention from all disciplines across the chemical sciences. This perspective discusses the main strategies to direct the supramolecular self-assembly of organic monomers in 2D.

Cosolvents Restrain Self-Assembly of a Fibroin-Like Peptide on Graphite

Controllable self-assembly of peptides on solid surfaces has been investigated for establishing functional bio/solid interfaces. In this work, we study the influence of organic solvents on the self-assembly of a fibroin-like peptide on a graphite surface. The peptide has been designed by mimicking fibroin proteins to have strong hydrogen bonds among peptides enabling their self-assembly. We have employed cosolvents of water and organic solvents with a wide range of dielectric constants to control peptide self-assembly on the surface. Atomic force microscopy has revealed that the peptides self-assemble into highly ordered monolayer-thick linear structures on graphite after incubation in pure water, where the coverage of peptides on the surface is more than 85%. When methanol is mixed, the peptide coverage becomes zero at a threshold concentration of 30% methanol on graphite and 25% methanol on MoS₂. The threshold concentration in ethanol, isopropanol, dimethyl sulfoxide, and acetone varies depending on the dielectric constant with restraining self-assembly of the peptides, and particularly low dielectric-constant protic solvents prevent the peptide self-assembly significantly. The observed phenomena are explained by competitive surface adsorption of the organic solvents and peptides and the solvation effect of the peptide assembly.

Effects of Dissolved Gases on the Amyloid Fibril Morphology

The onset or progression of numerous neurodegenerative diseases occurs due to aggregation of proteins that ultimately form fibrils. The assembly and morphology of fibrils are susceptible to environmental factors. In this work, we used atomic force microscopy (AFM) to investigate the effects of dissolved nitrogen and oxygen molecules on the morphology of fibrils formed by a hydrophobic amyloid peptide implicated in amyotrophic lateral sclerosis, 15 repeats of glycine-alanine, on a highly oriented pyrolytic graphite substrate. We started with preformed fibril solutions that were then diluted with buffers of different gas conditions, resulting in the aggregation of the fibrils into different morphologies that were revealed by AFM after adsorption on the substrate. Straight fibrils were observed in both degassed and ambient buffers, but a stronger lateral association was seen in degassed buffers. Smaller and softer fibrils were observed in O₂-supersaturated buffers, and plaque-like fibril aggregates of considerably large size were evident in N₂-supersaturated buffers. In overnight incubation experiments, we observed changes in both the morphology and height of the fibril aggregates, and their evolution varied with different gas conditions. These findings indicate that the gas type and concentration affect the aggregation of amyloid fibrils and may facilitate the development of biomaterial applications and treatments for amyloid-related diseases.

Effect of surface chemistry on islet amyloid polypeptide conformation

The formation of dense, linear arrays (fibrils) by biomolecules is the hallmark of a number of degenerative diseases, such as Alzheimer's and type-2 diabetes. Protein fibrils have also attracted interest as building blocks for new materials. It has long been recognized that surfaces can affect the fibrillation process. Recent work on the model fibril forming protein human islet amyloid polypeptide (hIAPP) has shown that while the protein concentration is highest at hydrophobic surfaces, the rate of fibril formation is lower than on other surfaces. To understand this, replica exchange molecular dynamics simulations were used to investigate the conformations that hIAPP adopts on surfaces of different hydrophobicities. The hydrophobic surface stabilizes α-helical structures which are significantly different to those found on the hydrophilic surface and in bulk solution. There is also a greatly reduced conformational ensemble on the hydrophobic surface due to long-lived contacts between hydrophobic residues on the protein and the surface. This new microscopic information will help us determine the mechanism of the enhancement of fibril formation on surfaces and provides new insight into the effect of nanointerfaces and protein conformation.

Multimodal spectroscopic investigation of the conformation and local environment of biomolecules at an electrified interface

The complex and dynamic interfacial regions between biological samples and electronic components pose many challenges for characterization, including their evolution over multiple temporal and spatial scales. Spectroscopic probes of buried interfaces employing mid-infrared plasmon resonances and time-resolved fluorescence detection in the visible range are used to study the properties of polypeptides adsorbed at the surface of a working electrode. Information from these complementary spectroscopic probes reveals the interplay of solvation, electric fields, and ion concentration on their resulting macromolecular conformations.

Unconventional Atomic Structure of Graphene Sheets on Solid Substrates

The atomic structure of free-standing graphene comprises flat hexagonal rings with a 2.5 Å period, which is conventionally considered the only atomic period and determines the unique properties of graphene. Here, an unexpected highly ordered orthorhombic structure of graphene is directly observed with a lattice constant of ≈5 Å, spontaneously formed on various substrates. First-principles computations show that this unconventional structure can be attributed to the dipole between the graphene surface and substrates, which produces an interfacial electric field and induces atomic rearrangement on the graphene surface. Further, the formation of the orthorhombic structure can be controlled by an artificially generated interfacial electric field. Importantly, the 5 Å crystal can be manipulated and transformed in a continuous and reversible manner. Notably, the orthorhombic lattice can control the epitaxial self-assembly of amyloids. The findings reveal new insights about the atomic structure of graphene, and open up new avenues to manipulate graphene lattices.

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.

Effect of Terminal Modifications on the Adsorption and Assembly of hIAPP(20-29)

The assembly of peptides and proteins into nanoscale amyloid fibrils via formation of intermolecular β-sheets not only plays an important role in the development of degenerative diseases but also represents a promising approach for the synthesis of functional nanomaterials. In many biological and technological settings, peptide assembly occurs in the presence of organic and inorganic interfaces with different physicochemical properties. In an attempt to dissect the relative contributions of the different molecular interactions governing amyloid assembly at interfaces, we here present a systematic study of the effects of terminal modifications on the adsorption and assembly of the human islet amyloid polypeptide fragment hIAPP(20-29) at organic self-assembled monolayers (SAMs) presenting different functional groups (cationic, anionic, polar, or hydrophobic). Using a selection of complementary in situ and ex situ analytical techniques, we find that even this well-defined and comparatively simple model system is governed by a rather complex interplay of electrostatic interactions, hydrophobic interactions, and hydrogen bonding, resulting in a plethora of observations and dependencies, some of which are rather counterintuitive. In particular, our results demonstrate that terminal modifications can have tremendous effects on peptide adsorption and assembly dynamics, as well as aggregate morphology and molecular structure. The effects exerted by the terminal modifications can furthermore be modulated in nontrivial ways by the physicochemical properties of the SAM surface. Therefore, terminal modifications are an important factor to consider when conducting and comparing peptide adsorption and aggregation studies and may represent an additional parameter for guiding the assembly of peptide-based nanomaterials.

Surface-Mediated Supramolecular Self-Assembly of Protein, Peptide, and Nucleoside Derivatives: From Surface Design to the Underlying Mechanism and Tailored Functions

Among the many parameters that have been explored to exercise control over self-assembly processes, the influence of surface properties on self-assembly has been recognized as important but has received considerably less attention than other factors. This is particularly true for biomolecule-derived self-assembling molecules such as protein, peptide, and nucleobase derivatives. Because of their relevance to biomaterial and drug delivery applications, interest in these materials is increasing. As the formation of supramolecular structures from these biomolecule derivatives inevitably brings them into contact with the surfaces of surrounding materials, understanding and controlling the impact of the properties of these surfaces on the self-assembly process are important. In this feature article, we present an overview of the different surface parameters that have been used and studied for the direction of the self-assembly of protein, peptide, and nucleoside-based molecules. The current mechanistic understanding of these processes will be discussed, and potential applications of surface-mediated self-assembly will be outlined.

Understanding the Interplay between Self-Assembling Peptides and Solution Ions for Tunable Protein Nanoparticle Formation

Protein-based nanomaterials are gaining importance in biomedical and biosensor applications where tunability of the protein particle size is highly desirable. Rationally designed proteins and peptides offer control over molecular interactions between monomeric protein units to modulate their self-assembly and thus particle formation. Here, using an example enzyme-peptide system produced as a single construct by bacterial expression, we explore how solution conditions affect the formation and size of protein nanoparticles. We found two independent routes to particle formation, one facilitated by charge interactions between protein-peptide and peptide-peptide exemplified by pH change or the presence of NO₃^- or NH₄⁺ and the second route via metal-ion coordination ( e.g., Mg²⁺) within peptides. We further demonstrate that the two independent factors of pH and Mg²⁺ ions can be combined to regulate nanoparticle size. Charge interactions between protein-peptide monomers play a key role in either promoting or suppressing protein assembly; the intermolecular contact points within protein-peptide monomers involved in nanoparticle formation were identified by chemical cross-linking mass spectrometry. Importantly, the protein nanoparticles retain their catalytic activities, suggesting that their native structures are unaffected. Once formed, protein nanoparticles remain stable over long periods of storage or with changed solution conditions. Nevertheless, formation of nanoparticles is also reversible-they can be disassembled by desalting the buffer to remove complexing agents ( e.g., Mg²⁺). This study defines the factors controlling formation of protein nanoparticles driven by self-assembly peptides and an understanding of complex ion-peptide interactions involved within, offering a convenient approach to tailor protein nanoparticles without changing amino acid sequence.

Force and time-dependent self-assembly, disruption and recovery of supramolecular peptide amphiphile nanofibers

Biological feedback mechanisms exert precise control over the initiation and termination of molecular self-assembly in response to environmental stimuli, while minimizing the formation and propagation of defects through self-repair processes. Peptide amphiphile (PA) molecules can self-assemble at physiological conditions to form supramolecular nanostructures that structurally and functionally resemble the nanofibrous proteins of the extracellular matrix, and their ability to reconfigure themselves in response to external stimuli is crucial for the design of intelligent biomaterials systems. Here, we investigated real-time self-assembly, deformation, and recovery of PA nanofibers in aqueous solution by using a force-stabilizing double-pass scanning atomic force microscopy imaging method to disrupt the self-assembled peptide nanofibers in a force-dependent manner. We demonstrate that nanofiber damage occurs at tip-sample interaction forces exceeding 1 nN, and the damaged fibers subsequently recover when the tip pressure is reduced. Nanofiber ends occasionally fail to reconnect following breakage and continue to grow as two individual nanofibers. Energy minimization calculations of nanofibers with increasing cross-sectional ellipticity (corresponding to varying levels of tip-induced fiber deformation) support our observations, with high-ellipticity nanofibers exhibiting lower stability compared to their non-deformed counterparts. Consequently, tip-mediated mechanical forces can provide an effective means of altering nanofiber integrity and visualizing the self-recovery of PA assemblies.

Rare Dissipative Transitions Punctuate the Initiation of Chemical Denaturation in Proteins

Protein unfolding dynamics are bound by their degree of entropy production, a quantity that relates the amount of heat dissipated by a nonequilibrium process to a system's forward and time-reversed trajectories. We here explore the statistics of heat dissipation that emerge in protein molecules subjected to a chemical denaturant. Coupling large molecular dynamics datasets and Markov state models with the theory of entropy production, we demonstrate that dissipative processes can be rigorously characterized over the course of the urea-induced unfolding of the protein chymotrypsin inhibitor 2. By enumerating full entropy production probability distributions as a function of time, we first illustrate that distinct passive and dissipative regimes are present in the denaturation dynamics. Within the dissipative dynamical region, we next find that chymotrypsin inhibitor 2 is strongly driven into unfolded states in which the protein's hydrophobic core has been penetrated by urea molecules and disintegrated. Detailed analyses reveal that urea's interruption of key hydrophobic contacts between core residues causes many of the protein's native structural features to dissolve.

Molecular mechanism of Gd@C82(OH)22 increasing collagen expression: Implication for encaging tumor

Gadolinium-containing fullerenol Gd@C₈₂(OH)₂₂ has demonstrated low-toxicity and highly therapeutic efficacy in inhibiting tumor growth and metastasis through new strategy of encaging cancer, however, little is known about the mechanisms how this nanoparticle regulates fibroblast cells to prison (instead of poison) cancer cells. Here, we report that Gd@C₈₂(OH)₂₂ promote the binding activity of tumor necrosis factor (TNFα) to tumor necrosis factor receptors 2 (TNFR2), activate TNFR2/p38 MAPK signaling pathway to increase cellular collagen expression in fibrosarcoma cells and human primary lung cancer associated fibroblasts isolated from patients. We also employ molecular dynamics simulations to study the atomic-scale mechanisms that dictate how Gd@C₈₂(OH)₂₂ mediates interactions between TNFα and TNFRs. Our data suggest that Gd@C₈₂(OH)₂₂ might enhance the association between TNFα and TNFR2 through a "bridge-like" mode of interaction; by contrast, the fullerenol appears to inhibit TNFα-TNFR1 association by binding to two of the receptor's cysteine-rich domains. In concert, our results uncover a sequential, systemic process by which Gd@C₈₂(OH)₂₂ acts to prison tumor cells, providing new insights into principles of designs of cancer therapeutics.

Graphene-Induced Pore Formation on Cell Membranes

Examining interactions between nanomaterials and cell membranes can expose underlying mechanisms of nanomaterial cytotoxicity and guide the design of safer nanomedical technologies. Recently, graphene has been shown to exhibit potential toxicity to cells; however, the molecular processes driving its lethal properties have yet to be fully characterized. We here demonstrate that graphene nanosheets (both pristine and oxidized) can produce holes (pores) in the membranes of A549 and Raw264.7 cells, substantially reducing cell viability. Electron micrographs offer clear evidence of pores created on cell membranes. Our molecular dynamics simulations reveal that multiple graphene nanosheets can cooperate to extract large numbers of phospholipids from the membrane bilayer. Strong dispersion interactions between graphene and lipid-tail carbons result in greatly depleted lipid density within confined regions of the membrane, ultimately leading to the formation of water-permeable pores. This cooperative lipid extraction mechanism for membrane perforation represents another distinct process that contributes to the molecular basis of graphene cytotoxicity.

Self-Assembly, Dynamics, and Polymorphism of hIAPP(20-29) Aggregates at Solid-Liquid Interfaces

The misfolding and subsequent assembly of proteins and peptides into insoluble amyloid structures play important roles in the development of numerous diseases. The dynamics of self-assembly and the morphology of the resulting aggregates critically depend on various environmental factors and especially on the presence of interfaces. Here, we show in detail how the presence of surfaces with different physicochemical properties influences the assembly dynamics and especially the aggregate morphology of hIAPP(20-29), an amyloidogenic fragment of the peptide hormone human islet amyloid polypeptide (hIAPP), which is involved in the development of type 2 diabetes. Time-lapse atomic force microscopy is employed to study the assembly dynamics of hIAPP(20-29) and the morphology of the resulting aggregates in bulk solution as well as at hydrophilic and hydrophobic model surfaces. We find that the presence of hydrophilic mica surfaces promotes fibrillation when compared with the assembly in bulk solution and results in a more pronounced polymorphism. Three fibrillar species are found to coexist on the mica surface, that is, straight, coiled, and ribbon-like fibrils, whereas only the straight and coiled fibrils are observed in bulk solution after comparable incubation times. In addition, the straight and coiled fibrils assembled at the mica surface have significantly different dimensions compared with those assembled in bulk solution. The three fibrillar species found on the mica surface most likely form independently by lateral association of arbitrary numbers of protofibrils with about 2 nm height. On hydrophobic hydrocarbon surfaces, fibrillation is retarded but not completely suppressed, in contrast to previous observations for full-length hIAPP(1-37). Our results show that peptide-surface interactions may induce diverse, peptide-specific alterations of amyloid assembly dynamics and fibrillar polymorphism. They may therefore contribute to a deeper understanding of the molecular processes that govern amyloid aggregation at different surfaces.

Dimensionality of carbon nanomaterial impacting on the modulation of amyloid peptide assembly

A wide variety of inorganic nanomaterials have been exploited so far for their great potential for biological applications. Some of these materials could be valid candidates to modulate the assembly of amyloid peptides, which is relevant to amyloid-related diseases. In this work, we reveal that a carbon nanomaterial can indeed modulate the assembly of amyloid peptides and, additionally, we show that this modulating effect is closely related to the dimensionality of the nanomaterials.

Surface-Directed Assembly of Sequence-Defined Synthetic Polymers into Networks of Hexagonally Patterned Nanoribbons with Controlled Functionalities

The exquisite self-assembly of proteins and peptides in nature into highly ordered functional materials has inspired innovative approaches to the design and synthesis of biomimetic materials. While sequence-defined polymers hold great promise to mimic proteins and peptides for functions, controlled assembly of them on surfaces still remains underdeveloped. Here, we report the assembly of 12-mer peptoids containing alternating acidic and aromatic monomers into networks of hexagonally patterned nanoribbons on mica surfaces. Ca(2+)-carboxylate coordination creates peptoid-peptoid and peptoid-mica interactions that control self-assembly. In situ atomic force microscopy (AFM) shows that peptoids first assemble into discrete nanoparticles; these particles then transform into hexagonally patterned nanoribbons on mica surfaces. AFM-based dynamic force spectroscopy studies show that peptoid-mica interactions are much stronger than peptoid-peptoid interactions, illuminating the driving forces for mica-directed peptoid assembly. We further demonstrate the display of functional domains at the N-terminus of assembling peptoids to produce extended networks with similar hierarchical structures. This research demonstrates that surface-directed peptoid assembly can be used as a robust platform to develop biomimetic coating materials for applications.

EGCG in Green Tea Induces Aggregation of HMGB1 Protein through Large Conformational Changes with Polarized Charge Redistribution

As a major effective component in green tea, (-)-epigallocatechin-3-gallate (EGCG)'s potential benefits to human health have been widely investigated. Recent experimental evidences indicate that EGCG can induce the aggregation of HMGB1 protein, a late mediator of inflammation, which subsequently stimulates the autophagic degradation and thus provides protection from lethal endotoxemia and sepsis. In this study, we use molecular dynamics (MD) simulations to explore the underlying molecular mechanism of this aggregation of HMGB1 facilitated by EGCG. Our simulation results reveal that EGCG firmly binds to HMGB1 near Cys106, which supports previous preliminary experimental evidence. A large HMGB1 conformational change is observed, where Box A and Box B, two homogenous domains of HMGB1, are repositioned and packed together by EGCG. This new HMGB1 conformation has large molecular polarity and distinctive electrostatic potential surface. We suggest that the highly polarized charge distribution leads to the aggregation of HMGB1, which differs from the previous hypothesis that two HMGB1 monomers are linked by the dimer of EGCG. Possible aggregating modes have also been investigated with potential of mean force (PMF) calculations. Finally, we conclude that the conformation induced by EGCG is more aggregation-prone with higher binding free energies as compared to those without EGCG.

Water stability of self-assembled peptide nanostructures for sequential formation of two-dimensional interstitial patterns on layered materials

Sequential-assembly of LEY and GrBP5 peptides on a graphite surface.

Protein corona mitigates the cytotoxicity of graphene oxide by reducing its physical interaction with cell membrane

Many recent studies have shown that the way nanoparticles interact with cells and biological molecules can vary greatly in the serum-containing or serum-free culture medium. However, the underlying molecular mechanisms of how the so-called "protein corona" formed in serum medium affects nanoparticles' biological responses are still largely unresolved. Thus, it is critical to understand how absorbed proteins on the surfaces of nanoparticles alter their biological effects. In this work, we have demonstrated with both experimental and theoretical approaches that protein BSA coating can mitigate the cytotoxicity of graphene oxide (GO) by reducing its cell membrane penetration. Our cell viability and cellular uptake experiments showed that protein corona decreased cellular uptake of GO, thus significantly mitigating the potential cytotoxicity of GO. The electron microscopy images also confirmed that protein corona reduced the cellular morphological damage by limiting GO penetration into the cell membrane. Further molecular dynamics (MD) simulations validated the experimental results and revealed that the adsorbed BSA in effect weakened the interaction between the phospholipids and graphene surface due to a reduction of the available surface area plus an unfavorable steric effect, thus significantly reducing the graphene penetration and lipid bilayer damaging. These findings provide new insights into the underlying molecular mechanism of this important graphene protein corona interaction with cell membranes, and should have implications in future development of graphene-based biomedical applications.

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.

Tunable assembly of amyloid-forming peptides into nanosheets as a retrovirus carrier

Using and engineering amyloid as nanomaterials are blossoming trends in bionanotechnology. Here, we show our discovery of an amyloid structure, termed "amyloid-like nanosheet," formed by a key amyloid-forming segment of Alzheimer's Aβ. Combining multiple biophysical and computational approaches, we proposed a structural model for the nanosheet that is formed by stacking the amyloid fibril spines perpendicular to the fibril axis. We further used the nanosheet for laboratorial retroviral transduction enhancement and directly visualized the presence of virus on the nanosheet surface by electron microscopy. Furthermore, based on our structural model, we designed nanosheet-forming peptides with different functionalities, elucidating the potential of rational design for amyloid-based materials with novel architecture and function.

Twist and turn: effect of stereoconfiguration on the interfacial assembly of polyelectrolytes

Understanding the conditions that promote the adsorption, assembly, and accumulation of charged macromolecules at the interface between aqueous and hydrophobic liquids is important to a multitude of biological, environmental, and industrial processes. Here, the oil-water interfacial behavior of stereoisomers of polymethacrylic acid (PMA), a model system for both naturally occurring and synthetic polyelectrolytes, is investigated with a combination of vibrational sum-frequency (VSF) spectroscopy, surface tension, and computations. Syndiotactic and isotactic isomers both show rapid adsorption to the oil-water interface with a net orientation indicative of a high degree of ordering. The stereoconfiguration is found to affect whether only a single layer or multiple layers assemble at the interface. Surface tension measurements show additional adsorption for syndiotactic PMA over time. The additional layers do not contribute to the VSF spectrum indicating disorder in all but the initial layer. The isotactic isomer shows no evidence of accumulation at the interface beyond the single ordered layer. Molecular dynamics calculations show marked differences between the two isomers in the orientation of their substituent groups at the interface. The hydrophilic and hydrophobic moieties in the isotactic isomer are easily partitioned to the water and oil phases, respectively, whereas a fair portion of hydrophobic groups remain in the water phase for the syndiotactic PMA. The available hydrophobic contacts in the water phase at the interface are credited with allowing further adsorption.

Interaction of amyloid inhibitor proteins with amyloid beta peptides: insight from molecular dynamics simulations

Knowledge of the detailed mechanism by which proteins such as human αB- crystallin and human lysozyme inhibit amyloid beta (Aβ) peptide aggregation is crucial for designing treatment for Alzheimer's disease. Thus, unconstrained, atomistic molecular dynamics simulations in explicit solvent have been performed to characterize the Aβ_17–42 assembly in presence of the αB-crystallin core domain and of lysozyme. Simulations reveal that both inhibitor proteins compete with inter-peptide interaction by binding to the peptides during the early stage of aggregation, which is consistent with their inhibitory action reported in experiments. However, the Aβ binding dynamics appear different for each inhibitor. The binding between crystallin and the peptide monomer, dominated by electrostatics, is relatively weak and transient due to the heterogeneous amino acid distribution of the inhibitor surface. The crystallin-bound Aβ oligomers are relatively long-lived, as they form more extensive contact surface with the inhibitor protein. In contrast, a high local density of arginines from lysozyme allows strong binding with Aβ peptide monomers, resulting in stable complexes. Our findings not only illustrate, in atomic detail, how the amyloid inhibitory mechanism of human αB-crystallin, a natural chaperone, is different from that of human lysozyme, but also may aid de novo design of amyloid inhibitors.

Direct observation of amyloid nucleation under nanomechanical stretching

Self-assembly of amyloid nanofiber is associated with both functional biological and pathological processes such as those in neurodegenerative diseases. Despite intensive studies, the stochastic nature of the process has made it difficult to elucidate a molecular mechanism for the key amyloid nucleation event. Here we investigated nucleation of the silk-elastin-like peptide (SELP) amyloid using time-lapse lateral force microscopy (LFM). By repeated scanning of a single line on a SELP-coated mica surface, we observed a sudden stepwise height increase. This corresponds to nucleation of an amyloid fiber, which subsequently grew perpendicular to the scanning direction. The lateral force profiles followed either a worm-like chain model or an exponential function, suggesting that the atomic force microscopy (AFM) tip stretches a single or multiple SELP molecules along the scanning direction. The probability of nucleation correlated with the maximum stretching force and extension, implying that stretching of SELP molecules is a key molecular event for amyloid nucleation. The mechanically induced nucleation allows for positional and directional control of amyloid assembly in vitro, which we demonstrate by generating single nanofibers at predetermined nucleation sites.