Designing Multifunctional Biomaterials via Protein Self-Assembly

Protein self-assembly is a fundamental biological process where proteins spontaneously organize into complex and functional structures without external direction. This process is crucial for the formation of various biological functionalities. However, when protein self-assembly fails, it can trigger the development of multiple disorders, thus making understanding this phenomenon extremely important. Up until recently, protein self-assembly has been solely linked either to biological function or malfunction; however, in the past decade or two it has also been found to hold promising potential as an alternative route for fabricating materials for biomedical applications. It is therefore necessary and timely to summarize the key aspects of protein self-assembly: how the protein structure and self-assembly conditions (chemical environments, kinetics, and the physicochemical characteristics of protein complexes) can be utilized to design biomaterials. This minireview focuses on the basic concepts of forming supramolecular structures, and the existing routes for modifications. We then compare the applicability of different approaches, including compartmentalization and self-assembly monitoring. Finally, based on the cutting-edge progress made during the last years, we summarize the current knowledge about tailoring a final function by introducing changes in self-assembly and link it to biomaterials' performance.

An AIE-Active NIR Fluorescent Probe with Good Water Solubility for the Detection of Aβ1-42 Aggregates in Alzheimer's Disease

Alzheimer's disease (AD), an amyloid-related disease, seriously endangers the health of elderly individuals. According to current research, its main pathogenic factor is the amyloid protein, which is a kind of fibrillar aggregate formed by noncovalent self-assembly of proteins. Based on the characteristics of aggregation-induced emission (AIE), a bislactosyl-decorated tetraphenylethylene (TPE) molecule TMNL (TPE + malononitrile + lactose), bearing two malononitrile substituents, was designed and synthesized in this work. The amphiphilic TMNL could self-assemble into fluorescent organic nanoparticles (FONs) with near-infrared (NIR) fluorescence emission in physiological PBS (phosphate buffered saline), achieving excellent fluorescent enhancement (47-fold) upon its combination with Aβ_1-42 fibrils. TMNL was successfully applied to image Aβ_1-42 plaques in the brain tissue of AD transgenic mice, and due to the AIE properties of TMNL, no additional rinsing process was necessary. It is believed that the probe reported in this work should be useful for the sensitive detection and accurate localization mapping of Aβ_1-42 aggregates related to Alzheimer's disease.

Designer, Programmable DNA-peptide hybrid materials with emergent properties to probe and modulate biological systems

The chemistry of DNA endows it with certain functional properties that facilitate the generation of self-assembled nanostructures, offering precise control over their geometry and morphology, that can be exploited for advanced biological applications. Despite the structural promise of these materials, their applications are limited owing to lack of functional capability to interact favourably with biological systems, which has been achieved by functional proteins or peptides. Herein, we outline a strategy for functionalizing DNA structures with short-peptides, leading to the formation of DNA-peptide hybrid materials. This proposition offers the opportunity to leverage the unique advantages of each of these bio-molecules, that have far reaching emergent properties in terms of better cellular interactions and uptake, better stability in biological media, an acceptable and programmable immune response and high bioactive molecule loading capacities. We discuss the synthetic strategies for the formation of these materials, namely, solid-phase functionalization and solution-coupling functionalization. We then proceed to highlight selected biological applications of these materials in the domains of cell instruction & molecular recognition, gene delivery, drug delivery and bone & tissue regeneration. We conclude with discussions shedding light on the challenges that these materials pose and offer our insights on future directions of peptide-DNA research for targeted biomedical applications.

Inhibitory effects of fluorinated benzenesulfonamides on insulin fibrillation

Amyloid fibrils are protein aggregates formed by protein assembly through cross β structures. Inhibition of amyloid fibril formation may contribute to therapy against amyloid-related disorders like Parkinson's, Alzheimer's, and type 2 diabetes. Here we report that several fluorinated sulfonamide compounds, previously shown to inhibit human carbonic anhydrase, also inhibit the fibrillation of different proteins. Using a range of spectroscopic, microscopic and chromatographic techniques, we found that the two fluorinated sulfonamide compounds completely inhibit insulin fibrillation over a period of 16 h and moderately suppress α-synuclein and Aβ fibrillation. In addition, these compounds decreased cell toxicity of insulin incubated under fibrillation-inducing conditions. We ascribe these effects to their ability to maintain insulin in the native monomeric state. Molecular dynamic simulations suggest that these compounds inhibit insulin self-association by interacting with residues at the dimer interface. This highlights the general anti-aggregative properties of aromatic sulfonamides and suggests that sulfonamide compounds which inhibit carbonic anhydrase activity may have potential as therapeutic agents against amyloid-related disorders.

Preparation and Characterization of an Electrospun Whey Protein/Polycaprolactone Nanofiber Membrane for Chromium Removal from Water

Chromium pollution represents a worldwide concern due to its high toxicity and bioaccumulation in organisms and ecosystems. An interesting material to remove metal ions from water is a whey-protein-based material elaborated by electrospinning, which is an emerging method to produce adsorbent membranes with diverse applications. The aim of this study was to prepare an adsorbent membrane of whey protein isolate (WPI) and polycaprolactone (PCL) by electrospinning to remove chromium ions from water. The adsorbent membrane was synthesized by a central composed design denaturing WPI using 2-Mercaptoethanol and mixing it with PCL to produce electrospun nanofibers. The adsorbent membrane was characterized by denaturation, Scanning Electron Microscope, Fourier-Transform Infrared Spectroscopy, Contact Angle, Thermogravimetric Analysis, and X-ray Photoelectron Spectrometry. The adsorption properties of this membrane were assessed in the removal of chromium. The removal performance of the membrane was enhanced by an increase in temperature showing an endothermic adsorption process. The adsorption process of chromium ions onto the nanofiber membrane followed the Sips adsorption isotherm, while the adsorption kinetics followed a pseudo-second kinetics where the maximum adsorption capacity was 31.0 mg/g at 30 °C and pH 2. This work provides a novel method to fabricate a hybrid membrane with amyloid-type fibrils of WPI and PCL, which is a promising adsorbent to remove heavy metal ions from water.

Biopolymeric composite hydrogel loaded with silver NPs and epigallocatechin gallate (EGCG) effectively manages ROS for rapid wound healing in type II diabetic wounds

Delayed wound healing in patients having type-II diabetes mellitus (T2DM) often results in a high rate of amputation. We report an innovative Guar Gum-based macroporous hydrogel (HG) infused with an antibacterial agent (Ag NPs), and antioxidant, epigallocatechin gallate (EGCG) to address rapid wound healing and interestingly could inhibit the associated pathophysical bone infection in a high-fat-diet-induced T2DM C57BL/6 mice model. The HG-Ag-EGCG elicits scar-free wound healing in subcutaneous wounds and histopathological evidence confirmed HG-Ag-EGCG hydrogel patch elicits better wound healing through enhanced cell proliferation, mature connecting tissue fiber formation, minimum void spaces formation, and better re-epithelialization when compared with a market available hydrogel patch material (Luofucon®). Supportive of the in vivo outcomes, in vitro experiments delineated better-wound closure due to improved management of ROS by the HG-Ag-EGCG. Additionally, a favorable non-toxicity outcome assessed through both in vitro and in vivo conditions confirmed its potential applicability in clinical wound care management.

Amyloid and Hydrogel Formation of a Peptide Sequence from a Coronavirus Spike Protein

We demonstrate that a conserved coronavirus spike protein peptide forms amyloid structures, differing from the native helical conformation and not predicted by amyloid aggregation algorithms. We investigate the conformation and aggregation of peptide RSAIEDLLFDKV, which is a sequence common to many animal and human coronavirus spike proteins. This sequence is part of a native α-helical S2 glycoprotein domain, close to and partly spanning the fusion sequence. This peptide aggregates into β-sheet amyloid nanotape structures close to the calculated pI = 4.2, but forms disordered monomers at high and low pH. The β-sheet conformation revealed by FTIR and circular dichroism (CD) spectroscopy leads to peptide nanotape structures, imaged using transmission electron microscopy (TEM) and probed by small-angle X-ray scattering (SAXS). The nanotapes comprise arginine-coated bilayers. A Congo red dye UV–vis assay is used to probe the aggregation of the peptide into amyloid structures, which enabled the determination of a critical aggregation concentration (CAC). This peptide also forms hydrogels under precisely defined conditions of pH and concentration, the rheological properties of which were probed. The observation of amyloid formation by a coronavirus spike has relevance to the stability of the spike protein conformation (or its destabilization via pH change), and the peptide may have potential utility as a functional material. Hydrogels formed by coronavirus peptides may also be of future interest in the development of slow-release systems, among other applications.

Dual Functional Amphiphilic Sugar-Coated AIE-Active Fluorescent Organic Nanoparticles for the Monitoring and Inhibition of Insulin Amyloid Fibrillation Based on Carbohydrate-Protein Interactions

Amyloid-related diseases, such as Alzheimer's disease, are all considered to be related to the deposition of amyloid fibrils in the body. Insulin is a protein hormone that easily undergoes aggregation...

Tuning Chain Relaxation from an Amorphous Biopolymer Film to Crystals by Removing Air/Water Interface Limitations

A promising route to the synthesis of protein-mimetic materials that are capable of strong mechanics and complex functions is provided by intermolecular β-sheet stacking. An understanding of the assembly mechanism on β-sheet stacking at molecular-level and the related influencing factors determine the potential to design polymorphs of such biomaterials towards broad applications. Herein, we quantitatively reveal the air/water interface (AWI) parameters regulating the transformation from crowding amorphous aggregates to ordered phase and show that the polymorph diversity of β-sheet stacking is regulated by the chain relaxation-crystallization mechanism. An amorphous macroscale amyloid-like nanofilm is formed at the AWI, in which unfolded protein chains are aligned in a short-range manner to form randomly packed β-sheets. The subsequent biopolymer chain relaxation-crystallization to form nanocrystals is further triggered by removing the limitations of energy and space at the AWI.

A near-infrared fluorescent probe quinaldine red lights up the β-sheet structure of amyloid proteins in mouse brain

In this report, we describe a near-infrared fluorescent probe called quinaldine red (QR) which lights up the β-sheet structure of amyloid fibrils. The photochemical and biophysical properties of QR along with other canonical amyloid probes in the presence of protein fibrils were investigated by using fluorescence spectroscopy, confocal fluorescent microscopy and isothermal titration calorimetry. Moreover, the binding sites and interaction mode between QR and insulin fibrils were calculated based on molecule docking. Among these amyloid probes, QR showed several advantages including strong supramolecular force, near-infrared emission, high sensitivity and resistance to bleaching. A linear response of the fluorescence intensity of QR towards fibril samples in the presence of sera was visualized in the range of 1-30 μM, with the limit of detection (LOD) of 2.31 μM. The recovery and relative standard deviation (RSD) of the proposed method for the determination of protein fibrils was 90.4%-99.2% and 3.05%-3.47%, respectively. Finally, QR can be fluorescently lighted up when meeting the aberrant protein aggregates of pathogenic mice. We recommend QR as a novel and excellent alternative tool for monitoring conformational transition of amyloid proteins.

Small-angle X-ray scattering characterization of a β -amyloid model in phantoms

OBJECTIVE

We present a method to prepare an amyloid model at scalable quantities for phantom studies to evaluate small-angle x-ray scattering systems for amyloid detection. Two amyloid models were made from a plasma protein with and without heating. Both models mimic theβ -sheet structure of theβ -amyloid (β A ) plaques in Alzheimer's disease. Amyloid detection is based on the distinct peaks in the scattering signature of theβ -sheet structure. We characterized the amyloid models using a spectral small-angle x-ray scattering (sSAXS) prototype with samples in a plastic syringe and within a cylindrical polymethyl methacrylate (PMMA) phantom.

RESULTS

sSAXS data show that we can detect the scattering peaks characteristic of amyloidβ -sheet structure in both models around 6 and 13nm − 1 . Theβ A model prepared without heating provides a stronger signal in the PMMA phantom. The methods described can be used to prepare models in sufficiently large quantities and used in samples with different packing density to assess the performance ofβ A quantification systems.

The biofilm adhesion protein Aap from Staphylococcus epidermidis forms zinc-dependent amyloid fibers

The skin-colonizing commensal bacterium Staphylococcus epidermidis is a leading cause of hospital-acquired and device-related infections. Its pathogenicity in humans is largely due to its propensity to form biofilms, surface-adherent bacterial accumulations that are remarkably resistant to chemical and physical stresses. Accumulation-associated protein (Aap) from S. epidermidis has been shown to be necessary and sufficient for mature biofilm formation and catheter infection. Aap contains up to 17 tandem B-repeat domains, capable of zinc-dependent assembly into twisted, rope-like intercellular filaments in the biofilm. Using microscopic and biophysical techniques, we show here that Aap B-repeat constructs assemble further into zinc-dependent functional amyloid fibers. We observed such amyloid fibers by confocal microscopy during both early and late stages of S. epidermidis biofilm formation, and we confirmed that extracellular fibrils from these biofilms contain Aap. Unlike what has been observed for amyloidogenic biofilm proteins from other bacteria, which typically use chaperones or initiator proteins to initiate amyloid assembly, our findings indicate that Aap from S. epidermidis requires Zn²⁺ as a catalyst that drives amyloid fiber formation, similar to many mammalian amyloid-forming proteins that require metals for assembly. This work provides detailed insights into S. epidermidis biofilm formation and architecture that improve our understanding of persistent staphylococcal infections.

Identifying the Coiled-Coil Triple Helix Structure of β-Peptide Nanofibers at Atomic Resolution

Peptide self-assembly represents a powerful bottom-up approach to the fabrication of nanomaterials. β³-Peptides are non-natural peptides composed entirely of β-amino acids, which have an extra methylene in the backbone, and we reported fibers derived from the self-assembly of β³-peptides that adopt 14-helical structures. β³-Peptide assemblies represent a class of stable nanomaterials that can be used to generate bio- and magneto-responsive materials with proteolytic stability. However, the three-dimensional structure of many of these materials remains unknown. To develop structure-based criteria for the design of β³-peptide-based biomaterials with tailored function, we investigated the structure of a tri-β³-peptide nanoassembly by molecular dynamics simulations and X-ray fiber diffraction analysis. Diffraction data was collected from aligned fibrils formed by Ac-β³[LIA] in water and used to inform and validate the model structure. Models with 3-fold radial symmetry resulted in stable fibers with a triple-helical coiled-coil motif and measurable helical pitch and periodicity. The fiber models revealed a hydrophobic core and twist along the fiber axis arising from a maximization of contacts between hydrophobic groups of adjacent tripeptides on the solvent-exposed fiber surface. These atomic structures of macroscale fibers derived from β³-peptide-based materials provide valuable insight into the effects of the geometric placement of the side chains and the influence of solvent on the core fiber structure which is perpetuated in the superstructure morphology.

The protofilament architecture of a de novo designed coiled coil-based amyloidogenic peptide

Amyloid fibrils are polymers formed by proteins under specific conditions and in many cases they are related to pathogenesis, such as Parkinson's and Alzheimer's diseases. Their hallmark is the presence of a β-sheet structure. High resolution structural data on these systems as well as information gathered from multiple complementary analytical techniques is needed, from both a fundamental and a pharmaceutical perspective. Here, a previously reported de novo designed, pH-switchable coiled coil-based peptide that undergoes structural transitions resulting in fibril formation under physiological conditions has been exhaustively characterized by transmission electron microscopy (TEM), cryo-TEM, atomic force microscopy (AFM), wide-angle X-ray scattering (WAXS) and solid-state NMR (ssNMR). Overall, a unique 2-dimensional carpet-like assembly composed of large coexisiting ribbon-like, tubular and funnel-like structures with a clearly resolved protofilament substructure is observed. Whereas electron microscopy and scattering data point somewhat more to a hairpin model of β-fibrils, ssNMR data obtained from samples with selectively labelled peptides are in agreement with both, hairpin structures and linear arrangements.

Solid-State NMR Structural Characterization of Self-Assembled Peptides with Selective 13C and 15N Isotopic Labels

For the structural characterization methods discussed here, information on molecular conformation and intermolecular organization within nanostructured peptide assemblies is discerned through analysis of solid-state NMR spectral features. This chapter reviews general NMR methodologies, requirements for sample preparation, and specific descriptions of key experiments. An attempt is made to explain choices of solid-state NMR experiments and interpretation of results in a way that is approachable to a nonspecialist. Measurements are designed to determine precise NMR peak positions and line widths, which are correlated with secondary structures, and probe nuclear spin-spin interactions that report on three-dimensional organization of atoms. The formulation of molecular structural models requires rationalization of data sets obtained from multiple NMR experiments on samples with carefully chosen 13C and 15N isotopic labels. The information content of solid-state NMR data has been illustrated mostly through the use of simulated data sets and references to recent structural work on amyloid fibril-forming peptides and designer self-assembling peptides.

Methods to Characterize the Nanostructure and Molecular Organization of Amphiphilic Peptide Assemblies

Methods to characterize the nanostructure and molecular organization of aggregates of peptides such as amyloid or amphiphilic peptide assemblies are reviewed. We discuss techniques to characterize conformation and secondary structure including circular and linear dichroism and FTIR and Raman spectroscopies, as well as fluorescence methods to detect aggregation. NMR spectroscopy methods, especially solid-state NMR measurements to probe beta-sheet packing motifs, are also briefly outlined. Also discussed are scattering methods including X-ray diffraction and small-angle scattering techniques including SAXS (small-angle X-ray scattering) and SANS (small-angle neutron scattering) and dynamic light scattering. Imaging methods are direct methods to uncover features of peptide nanostructures, and we provide a summary of electron microscopy and atomic force microscopy techniques. Selected examples are highlighted showing data obtained using these techniques, which provide a powerful suite of methods to probe ordering from the molecular scale to the aggregate superstructure.

Shape-specific nanostructured protein mimics from de novo designed chimeric peptides

We experimentally and theoretically demonstrated the formation of well-defined trigonal-bipyramidal protein-mimics through self-assembly of “simple” de novo designed chimeric peptides.

Detecting the Formation and Transformation of Oligomers during Insulin Fibrillation by a Dendrimer Conjugated with Aggregation-Induced Emission Molecule

The fibrillation of protein is harmful and impedes the use of protein drugs. It also relates to various debilitating diseases such as Alzheimer's diseases. Thus, investigating the protein fibrillation process is necessary. In this study, poly(amido amine) dendrimers (PAMAM) of generation 3 (G3) and generation 4 (G4) were synthesized and conjugated with 4-aminobiphenyl, an aggregation-induced emission (AIE) moiety, at varied grafting ratios. Among them, one fluorescence probe named G3-biph-3 that was grafted average 3.25 4-aminobiphenyl to the G3, can detect the transformations both from native insulin to oligomers and from oligomers to fibrils. The size difference of native insulin, oligomers, and fibrils was proposed to be the main factor leading to the detection of the above transformations. Different molecular weights of sodium polyacrylate (PAAS) were also applied as a model to interact with G3-biph-3 to further reveal the mechanism. The results indicated that PAMAM with a certain generation and grafted with appropriate AIE groups can detect the oligomer formation and transformation during the insulin fibrillation process.

Light induced construction of porous covalent organic polymeric networks for significant enhancement of CO2 gas sorption

Porous covalent organic polymers were prepared from self-assembled fibers using a topochemical polymerization reaction and their four times higher CO₂ sorption behaviour is demonstrated.

Secondary Structure Adopted by the Gly-Gly-X Repetitive Regions of Dragline Spider Silk

Solid-state NMR and molecular dynamics (MD) simulations are presented to help elucidate the molecular secondary structure of poly(Gly-Gly-X), which is one of the most common structural repetitive motifs found in orb-weaving dragline spider silk proteins. The combination of NMR and computational experiments provides insight into the molecular secondary structure of poly(Gly-Gly-X) segments and provides further support that these regions are disordered and primarily non-β-sheet. Furthermore, the combination of NMR and MD simulations illustrate the possibility for several secondary structural elements in the poly(Gly-Gly-X) regions of dragline silks, including β-turns, 310-helicies, and coil structures with a negligible population of α-helix observed.

Self-assembly of PEGylated tetra-phenylalanine derivatives: structural insights from solution and solid state studies

Water soluble fibers of PEGylated tetra-phenylalanine (F4), chemically modified at the N-terminus with the DOTA chelating agent, have been proposed as innovative contrast agent (CA) in Magnetic Resonance Imaging (MRI) upon complexation of the gadolinium ion. An in-depth structural characterization of PEGylated F4-fibers, in presence (DOTA-L6-F4) and in absence of DOTA (L6-F4), is reported in solution and at the solid state, by a multiplicity of techniques including CD, FTIR, NMR, DLS, WAXS and SAXS. This study aims to better understand how the aggregation process influences the performance of nanostructures as MRI CAs. Critical aggregation concentrations for L6-F4 (43 μM) and DOTA-L6-F4 (75 μM) indicate that self-aggregation process occurs in the same concentration range, independently of the presence of the CA. The driving force for the aggregation is the π-stacking between the side chains of the aromatic framework. CD, FTIR and WAXS measurements indicate an antiparallel β-sheet organization of the monomers in the resulting fibers. Moreover, WAXS and FTIR experiments point out that in solution the nanomaterials retain the same morphology and monomer organizations of the solid state, although the addition of the DOTA chelating agent affects the size and the degree of order of the fibers.

Substituent Effects on the Self-Assembly/Coassembly and Hydrogelation of Phenylalanine Derivatives

Supramolecular hydrogels derived from the self-assembly of organic molecules have been exploited for applications ranging from drug delivery to tissue engineering. The relationship between the structure of the assembly motif and the emergent properties of the resulting materials is often poorly understood, impeding rational approaches for the creation of next-generation materials. Aromatic π-π interactions play a significant role in the self-assembly of many supramolecular hydrogelators, but the exact nature of these interactions lacks definition. Conventional models that describe π-π interactions rely on quadrupolar electrostatic interactions between neighboring aryl groups in the π-system. However, recent experimental and computational studies reveal the potential importance of local dipolar interactions between elements of neighboring aromatic rings in stabilizing π-π interactions. Herein, we examine the nature of π-π interactions in the self- and coassembly of Fmoc-Phe-derived hydrogelators by systematically varying the electron-donating or electron-withdrawing nature of the side chain benzyl substituents and correlating these effects to the emergent assembly and gelation properties of the systems. These studies indicate a significant role for stabilizing dipolar interactions between neighboring benzyl groups in the assembled materials. Additional evidence for specific dipolar interactions is provided by high-resolution crystal structures obtained from dynamic transition of gel fibrils to crystals for several of the self-assembled/coassembled Fmoc-Phe derivatives. In addition to electronic effects, steric properties also have a significant effect on the interaction between neighboring benzyl groups in these assembled systems. These findings provide significant insight into the structure-function relationship for Fmoc-Phe-derived hydrogelators and give cues for the design of next-generation materials with desired emergent properties.

Amino acid sequence controls the self-assembled superstructure morphology of N-acetylated tri-β3-peptides

Peptides based on unnatural β3-amino acids offer a versatile platform for the design of self-assembling nanostructures due to the folding stability of the 14-helix and the high symmetry of the side chains inherent in this geometry. We have previously described that N-terminal acetylation (Ac-) forms a supramolecular self-assembly motif that allows β3-peptides to assemble head-to-tail into a helical nanorod which then further bundles into hierarchical superstructures. Here we investigate the effect of the topography of the 14-helical nanorod on lateral self-assembly. Specifically, we report on the variations in the superstructure of three isomeric peptides comprising the same three β3-amino acid residues: β3-leucine (L), β3-isoleucine (I) β3-alanine (A) to give peptides Ac-β3[LIA], Ac-β3[IAL] and Ac-β3[ALI]. AFM imaging shows markedly different superstructures for the three peptides. Well defined synchrotron far-infrared spectra reveal uniform geometries with a high degree of similarity between the isomeric peptides in the amide modes of the 400–650 wavenumber range. Far-IR also confirms that the C-terminal carboxyl group is free in the assemblies, thus it is solvated in the dispersant. Hence, the differences in the superstructures formed by the fibers are defined primarily by van der Waals energy minimization between the varied cross sectional morphologies of the core nanorods.

Copper(II)-Mediated Self-Assembly of Hairpin Peptides and Templated Synthesis of CuS Nanowires

The self-assembly of peptides and proteins under well-controlled conditions underlies important nanostructuring processes that could be harnessed in practical applications. Herein, the synthesis of a new hairpin peptide containing four histidine residues is reported and the self-assembly process mediated by metal ions is explored. The work involves the combined use of circular dichroism, NMR spectroscopy, UV/Vis spectroscopy, AFM, and TEM to follow the structural and morphological details of the metal-coordination-mediated folding and self-assembly of the peptide. The results indicate that by forming a tetragonal coordination geometry with four histidine residues, copper(II) ions selectively trigger the peptide to fold and then self-assemble into nanofibrils. Furthermore, the copper(II)-bound nanofibrils template the synthesis of CuS nanowires, which display a near-infrared laser-induced thermal effect.

Hydrogels formed from Fmoc amino acids

A number of Fmoc amino acids can be effective low molecular weight hydrogelators; we compare single crystal structures to fibre X-ray diffraction data.

Amyloid structure

Amyloid fibrils are formed by numerous proteins and peptides that share little sequence homology. The structures formed are highly ordered and extremely stable, being composed of β-sheet structure and stabilized along their length by hydrogen bonding. The fibrils are formed by several protofilaments that wind around one another in rope-like structures, lending further strength and stability to the resulting fibres. The fact that so many proteins and peptides form amyloid structures under suitable conditions, seems to suggest that the sequence of the precursor is unimportant. However, it is now clear that side chains play a central role in forming interactions between several β-sheets to further stabilize and regulate the structures. The primary sequence plays a central role in determining the rate of fibril formation, the stability of the resulting structure to degradation and the final morphology of the fibrils. The side chains regulate the elongation and growth, and also the lateral association of the protofilament and fibrils, having a significant impact on the final architecture.

Effects of hydrophobic interaction strength on the self-assembled structures of model peptides

Stable and ordered self-assembled peptide nanostructures are formed as a result of cooperative effects of various relatively weak intermolecular interactions. We systematically studied the influence of hydrophobic interaction strength and temperature on the self-assembly of peptides with a coarse-grained model by Monte Carlo simulations. The simulation results show a rich phase behavior of peptide self-assembly, indicating that the formation and morphology of peptide assemblies may be tuned by varying the temperature and the strength of hydrophobic interactions. There exist optimal combinations of temperature and hydrophobic interaction strength where ordered fibrillar nanostructures are readily formed. Our simulation results not only facilitate the understanding of the self-assembly behavior of peptides at the molecular level, but also provide useful insights into the development of fabrication strategies for high-quality peptide fibrils.

Modulating materials by orthogonally oriented β-strands: composites of amyloid and silk fibroin fibrils

Amyloid fibrils and silk fibroin (SF) fibrils are proteinaceous aggregates occurring either naturally or as artificially reconstituted fibrous systems, in which the constituent β-strands are aligned either orthogonally or parallel to the fibril main axis, conferring complementary physical properties. Here, it is shown how the combination of these two classes of protein fibrils with orthogonally oriented β-strands results in composite materials with controllable physical properties at the molecular, mesoscopic, and continuum length scales.

Length-dependent β-sheet growth mechanisms of polyalanine peptides in water and on hydrophobic surfaces

Fibrillar assemblies by peptides are becoming one of the most promising nanomaterials due to their exceptional properties. The self-assembly of peptides into β sheets is a critical step in the fibrillization pathway. We investigated the length-dependent β-sheet growth mechanisms of polyalanine [poly(A)] peptides consisting of 6 to 24 alanines (A6 to A24) in water and on the hydrophobic surface, respectively, by molecular dynamics simulations. β-sheet growth behavior in water fits negative exponential growth model, showing that β-sheet growth rate decays exponentially with time. Meanwhile, increasing chain length leads to an accelerated decay of the β-sheet growth rate. By contrast, β-sheet growth on the surface from A6 to A18 occurs in two consecutive stages, both of which fit linear growth models. β-sheet growth rate in the first stage increases as chain length is increased, while the intermediate length peptide A12 has the highest β-sheet growth rate in the second stage. β-sheet growth behavior of A24 on the surface still fits negative exponential model. Overall, the hydrophobic surface accelerates β-sheet growth by enhancing local concentration and reducing conformational entropy of poly(A) peptide, and the β-sheet growth of the intermediate length peptide A12 is the fastest on the surface. Our simulation results shed light on understanding the accelerated peptide fibrillization on the hydrophobic surface.

Using cell structures to develop functional nanomaterials and nanostructures – case studies of actin filaments and microtubules

Actin filaments and microtubules are utilized as building blocks to create functional nanomaterials and nanostructures for nature-inspired small-scale devices and systems.

Inhibition of human and bovine insulin fibril formation by designed peptide conjugates

The aggregation of insulin, to afford amyloidogenic fibers, is a well-studied phenomenon, which has interesting biological ramifications and pharmaceutical implications. These fibers have been ascribed an intriguing role in certain disease states and stability of pharmaceutical formulations of this hormone. The present study describes the design and inhibitory effects of novel peptide conjugates toward fibrillation of insulin as investigated by thioflavin T assay, circular dichroism (CD), and atomic force microscopy (AFM). Possible interaction of insulin with peptide-based fibrillation inhibitors is also probed by other solution phase studies, which reveal an important role of aromatic π-π interactions in the inhibition process. CD studies suggest that a freshly prepared solution of insulin, rich in α-helices, transforms into a β-sheet structure upon aggregation, which gets perturbed in the presence of synthesized inhibitors. Therefore, these newly designed peptides could serve as potential leads as inhibitors of insulin aggregation.

Modelling amyloid fibril formation kinetics: mechanisms of nucleation and growth

Amyloid and amyloid-like fibrils are self-assembling protein nanostructures, of interest for their robust material properties and inherent biological compatibility as well as their putative role in a number of debilitating mammalian disorders. Understanding fibril formation is essential to the development of strategies to control, manipulate or prevent fibril growth. As such, this area of research has attracted significant attention over the last half century. This review describes a number of different models that have been formulated to describe the kinetics of fibril assembly. We describe the macroscopic implications of mechanisms in which secondary processes such as secondary nucleation, fragmentation or branching dominate the assembly pathway, compared to mechanisms dominated by the influence of primary nucleation. We further describe how experimental data can be analysed with respect to the predictions of kinetic models.

Exploring the sequence-structure relationship for amyloid peptides

Amyloid fibril formation is associated with misfolding diseases, as well as fulfilling a functional role. The cross-β molecular architecture has been reported in increasing numbers of amyloid-like fibrillar systems. The Waltz algorithm is able to predict ordered self-assembly of amyloidogenic peptides by taking into account the residue type and position. This algorithm has expanded the amyloid sequence space, and in the present study we characterize the structures of amyloid-like fibrils formed by three peptides identified by Waltz that form fibrils but not crystals. The structural challenge is met by combining electron microscopy, linear dichroism, CD and X-ray fibre diffraction. We propose structures that reveal a cross-β conformation with 'steric-zipper' features, giving insights into the role for side chains in peptide packing and stability within fibrils. The amenity of these peptides to structural characterization makes them compelling model systems to use for understanding the relationship between sequence, self-assembly, stability and structure of amyloid fibrils.

Cross-β-sheet supersecondary structure in amyloid folds: techniques for detection and characterization

The formation of protein aggregates is linked to the onset of several human disorders of increasing prevalence, ranging from dementia to diabetes. In most of these diseases, the toxic effect is exerted by the self-assembly of initially soluble proteins into insoluble amyloid-like fibrils. Independently of the protein origin, all these macromolecular assemblies share a common supersecondary structure: the cross-β-sheet conformation, in which a core of β-strands is aligned perpendicularly to the fibril axis forming extended regular β-sheets. Due to this ubiquity, the presence of cross-β-sheet conformational signatures is usually exploited to detect, characterize, and screen for amyloid fibrils in protein samples. Here we describe in detail some of the most commonly used methods to analyze such supersecondary structure.

Self-assembly of amphipathic β-sheet peptides: insights and applications

Amphipathic peptides composed of alternating polar and nonpolar residues have a strong tendency to self-assemble into one-dimensional, amyloid-like fibril structures. Fibrils derived from peptides of general (XZXZ)(n) sequence in which X is hydrophobic and Z is hydrophilic adopt a putative β-sheet bilayer. The bilayer configuration allows burial of the hydrophobic X side chain groups in the core of the fibril and leaves the polar Z side chains exposed to solvent. This architectural arrangement provides fibrils that maintain high solubility in water and has facilitated the recent exploitation of self-assembled amphipathic peptide fibrils as functional biomaterials. This article is a critical review of the development and application of self-assembling amphipathic peptides with a focus on the fundamental insight these types of peptides provide into peptide self-assembly phenomena.