Self-assembly and bioactivity of a polymer/peptide conjugate containing the RGD cell adhesion motif and PEG

The self-assembly and bioactivity of the peptide–polymer conjugate DGRFFF–PEG3000 containing the RGD cell adhesion motif has been examined, in aqueous solution. The conjugate is designed to be amphiphilic by incorporation of three hydrophobic phenylalanine residues as well as the RGD unit and a short poly(ethylene glycol) (PEG) chain of molar mass 3000 kg mol⁻¹. Above a critical aggregation concentration, determined by fluorescence measurements, signals of β-sheet structure are revealed by spectroscopic measurements, as well as X-ray diffraction. At high concentration, a self-assembled fibril nanostructure is revealed by electron microscopy. The fibrils are observed despite PEG crystallization which occurs on drying. This suggests that DGRFFF has an aggregation tendency that is sufficiently strong not to be prevented by PEG crystallization. The adhesion, viability and proliferation of human corneal fibroblasts was examined for films of the conjugate on tissue culture plates (TCPs) as well as low attachment plates. On TCP, DGRFFF–PEG3000 films prepared at sufficiently low concentration are viable, and cell proliferation is observed. However, on low attachment surfaces, neither cell adhesion nor proliferation was observed, indicating that the RGD motif was not available to enhance cell adhesion. This was ascribed to the core–shell architecture of the self-assembled fibrils with a peptide core surrounded by a PEG shell which hinders access to the RGD unit.     

Design of peptides that form amyloid-like fibrils capturing amyloid beta1-42 peptides

Amyloid beta-peptide (Abeta) plays a critical role in Alzheimer's disease (AD). The monomeric state of Abeta can self-assemble into oligomers, protofibrils, and amyloid fibrils. Since the fibrils and soluble oligomers are believed to be responsible for AD, the construction of molecules capable of capturing these species could prove valuable as a means of detecting these potentially toxic species and of providing information pertinent for designing drugs effective against AD. To this aim, we have designed short peptides with various hydrophobicities based on the sequence of Abeta14-23, which is a critical region for amyloid fibril formation. The binding of the designed peptides to Abeta and the amplification of the formation of peptide amyloid-like fibrils coassembled with Abeta are elucidated. A fluorescence assay utilizing thioflavin T, known to bind specifically to amyloid fibrils, revealed that two designed peptides (LF and VF, with the leucine and valine residues, respectively, in the hydrophobic core region) could form amyloid-like fibrils effectively by using mature Abeta1-42 fibrils as nuclei. Peptide LF also coassembled with soluble Abeta oligomers into peptide fibrils. Various analyses, including immunostaining with gold nanoparticles, enzyme-linked immunosorbent assays, and size-exclusion chromatography, confirmed that the LF and VF peptides formed amyloid-like fibrils by capturing and incorporating Abeta1-42 aggregates into their peptide fibrils. In this system, small amounts of mature Abeta1-42 fibrils or soluble oligomers could be transformed into peptide fibrils and detected by amplifying the amyloid-like fibrils with the designed peptides.     

Light and heat control over secondary structure and amyloid-like fiber formation in an overcrowded-alkene-modified Trp zipper

The external photocontrol over peptide folding, by the incorporation of molecular photoswitches into their structure, provides a powerful tool to study biological processes. However, it is limited so far to switches that exhibit only a rather limited geometrical change upon photoisomerization and that show thermal instability of the photoisomer. Here we describe the use of an overcrowded alkene photoswitch to control a model β-hairpin peptide. This photoresponsive unit undergoes a large conformational change and has two thermally stable isomers which has major influence on the secondary structure and the aggregation of the peptide, permitting the phototriggered formation of amyloid-like fibrils.     

Structural insights into the polymorphism of amyloid-like fibrils formed by region 20-29 of amylin revealed by solid-state NMR and X-ray fiber diffraction

Many unrelated proteins and peptides can assemble into amyloid or amyloid-like nanostructures, all of which share the cross-beta motif of repeat arrays of beta-strands hydrogen-bonded along the fibril axis. Yet, paradoxically, structurally polymorphic fibrils may derive from the same initial polypeptide sequence. Here, solid-state nuclear magnetic resonance (SSNMR) analysis of amyloid-like fibrils of the peptide hIAPP 20-29, corresponding to the region S (20)NNFGAILSS (29) of the human islet amyloid polypeptide amylin, reveals that the peptide assembles into two amyloid-like forms, (1) and (2), which have distinct structures at the molecular level. Rotational resonance SSNMR measurements of (13)C dipolar couplings between backbone F23 and I26 of hIAPP 20-29 fibrils are consistent with form (1) having parallel beta-strands and form (2) having antiparallel strands within the beta-sheet layers of the protofilament units. Seeding hIAPP 20-29 with structurally homogeneous fibrils from a 30-residue amylin fragment (hIAPP 8-37) produces morphologically homogeneous fibrils with similar NMR properties to form (1). A model for the architecture of the seeded fibrils is presented, based on the analysis of X-ray fiber diffraction data, combined with an extensive range of SSNMR constraints including chemical shifts, torsional angles, and interatomic distances. The model features a cross-beta spine comprising two beta-sheets with an interface defined by residues F23, A25, and L27, which form a hydrophobic zipper. We suggest that the energies of formation for fibril form containing antiparallel and parallel beta-strands are similar when both configurations can be stabilized by a core of hydrophobic contacts, which has implications for the relationship between amino acid sequence and amyloid polymorphism in general.     

Genetic engineering combined with deep UV resonance Raman spectroscopy for structural characterization of amyloid-like fibrils

Elucidating the structure of the cross-beta core in large amyloid fibrils is a challenging problem in modern structural biology. For the first time, a set of de novo polypeptides was genetically engineered to form amyloid-like fibrils with similar morphology and yet different strand length. Differential ultraviolet Raman spectroscopy allowed for separation of the spectroscopic signatures of the highly ordered beta-sheet strands and turns of the fibril core. The relationship between Raman frequencies and Ramachandran dihedral angles of the polypeptide backbone indicates the nature of the beta-sheet and turn structural elements.     

Laminated morphology of nontwisting beta-sheet fibrils constructed via peptide self-assembly

A synthetic peptide has been de novo designed that self-assembles into beta-sheet fibrils exhibiting a nontwisted, stacked morphology. The stacked morphology is constituted by 2.5 nm wide filaments that laterally associate to form flat fibril laminates exceeding 50 nm in width and micrometers in length. The height of each fibril is limited to the length of exactly one peptide monomer in an extended beta-strand conformation, approximately 7 nm. Once assembled, these highly ordered, 2-D structures are stable over a wide range of pH and temperature and exhibit characteristics similar to those of amyloid fibrils. Furthermore, the rate of assembly and degree of fibril lamination can be controlled with kinetic parameters of pH and temperature. Finally, the presence of a diproline peptide between two beta-sheet-forming strands in the peptide sequence is demonstrated to be an important factor in promoting the nontwisting, laminated fibril morphology.     

Vibrational circular dichroism as a probe of fibrillogenesis: the origin of the anomalous intensity enhancement of amyloid-like fibrils

Amyloid fibrils are affiliated with various human pathologies. Knowledge of their molecular architecture is necessary for a detailed understanding of the mechanism of fibril formation. Vibrational circular dichroism (VCD) spectroscopy has recently shown sensitivity to amyloid fibrils [Ma et al. J. Am. Chem. Soc. 2007, 129, 12364 and Measey et al. J. Am. Chem. Soc. 2009, 131, 18218]. In particular, amyloid fibrils give rise to an intensity enhanced signal in the amide I band region of the corresponding VCD spectrum, offering promise of utilizing such a method for probing fibrillogenesis and the chiral structure of fibrils. Herein, we further investigate this phenomenon and demonstrate the use of VCD to probe the fibril formation kinetics of a short alanine-rich peptide. To elucidate the origin of the anomalous VCD intensity enhancement, we use an excitonic coupling model to simulate the VCD spectrum of stacked β-sheets containing one (Ising-like model) and two amide I oscillators per strand, as models for the underlying amyloid-fibril secondary structure. With this simple model, we show that the VCD intensity enhancement of amyloid-like fibrils results from intrasheet and, to a more limited extent, also from intersheet vibrational coupling between stacked β-sheets. The enhancement requires helically twisted sheets and is most pronounced for arrangements with parallel-oriented strands. Both the intersheet distance and the orientation of the amide I transition dipole moments of neighboring sheets are found to modulate the intensity enhancement of the amide I VCD signal. Moreover, our simulations suggest that, depending on the three-dimensional arrangement of the β-strands, the sign of the VCD signal of amyloid-like fibrils can be used to distinguish between right- and left-handed helical twists of parallel-oriented β-sheets. We compare the results of our simulation to experimental spectra of two short peptides, GNNQQNY, the N-terminal peptide fragment of the yeast prion protein Sup35, and an amyloidogenic alanine-rich peptide, AKY8. Our results demonstrate the advantages of using VCD spectroscopy to probe the kinetics of peptide and protein aggregation as well as the chirality of the resulting supramolecular structure.     

The role of the disulfide bond in amyloid-like fibrillogenesis in a model peptide system

Three terminally protected short peptides Bis[Boc-D-Leu1-Cys2-OMe] 1, Bis[Boc-Leu1-Cys2-OMe] and Bis[Boc-Val1-Cys2-OMe] 3 exhibit amyloid-like fibrillar morphology. Single crystal X-ray diffraction analysis of peptide 1 clearly demonstrates that it adopts an overall extended backbone molecular conformation that self-assembles to form an intermolecular hydrogen-bonded antiparallel supramolecular beta-sheet structure in crystals. Scanning electron microscopic (SEM) images, transmission electron microscopic (TEM) images and Congo red binding studies vividly demonstrate the amyloid-like fibril formation of peptides 1, 2 and 3. However, after reduction of the disulfide bridge of peptides 1, 2 and 3, three newly generated peptides Boc-D-Leu1-Cys2-OMe 4, Boc-Leu1-Cys2-OMe 5 and Boc-Val1-Cys2-OMe 6 are formed and all of them failed to form any kind of fibril under the same conditions, indicating the important role of the disulfide bond in amyloid-like fibrillogenesis in a peptide model system.     

Patterning amyloid peptide fibrils by AFM charge writing

Surface charge patterns generated by atomic force microscopy-based charge writing were used to pattern amyloid-like peptide fibrils on a solid substrate. Fibrils of the short peptide TTR105-115 were encapsulated inside water droplets of a water-in-perfluorocarbon oil emulsion and retained their rod morphology. They were observed to deposit selectively with a lateral resolution of approximately 1 microm onto negatively charged patterns on a polymethyl-methacrylate substrate.     

Photoswitched Cell Adhesion on Azobenzene‐Containing Self‐Assembled Films

Stimuli‐responsive surfaces that can regulate and control cell adhesion have attracted much attention for their great potential in diverse biomedical applications. Unlike for pH‐ and temperature‐responsive surfaces, the process of photoswitching requires no additional input of chemicals or thermal energy. In this work, two different photoresponsive azobenzene films are synthesized by chemisorption and electrostatic layer‐by‐layer (LbL) assembly techniques. The LbL film exhibits a relatively loose packing of azobenzene chromophores compared with the chemisorbed film. The changes in trans/cis isomer ratio of the azobenzene moiety and the corresponding wettability of the LbL films are larger than those of the chemisorbed films under UV light irradiation. The tendency for cell adhesion on the LbL films decreases markedly after UV light irradiation, whereas adhesion on the chemisorbed films decreases only slightly, because the azobenzene chromophores stay densely packed. Interestingly, the tendency for cell adhesion can be considerably increased on rough substrates, the roughness being introduced by use of photolithography and inductively coupled plasma deep etching techniques. For the chemisorbed films on rough substrates, the amount of cells that adhere also changes slightly after UV light irradiation, whereas, the amount of cells that adhere to LbL films on rough substrates decreases significantly.     

Peptide Self-Assembly into Amyloid Fibrils at Hard and Soft Interfaces—From Corona Formation to Membrane Activity

Peptides and proteins are exposed to a variety of interfaces in a physiological environment, such as cell membranes, protein nanoparticles (NPs), or viruses. These interfaces have a significant impact on the interaction, self-assembly, and aggregation mechanisms of biomolecular systems. Peptide self-assembly, particularly amyloid fibril formation, is associated with a wide range of functions; however, there is a link with neurodegenerative diseases, such as Alzheimer's disease. This review highlights how interfaces affect peptide structure and the kinetics of aggregation leading to fibril formation. In nature, many surfaces are nanostructures, such as liposomes, viruses, or synthetic NPs. Once exposed to a biological medium, nanostructures are coated with a corona, which then determines their activity. Both accelerating and inhibiting effects on peptide self-assembly have been observed. When amyloid peptides adsorb to a surface, they typically concentrate locally, which promotes aggregation into insoluble fibrils. Starting from a combined experimental and theoretical approach, models that allow for a better understanding of peptide self-assembly near hard and soft matter interfaces are introduced and reviewed. Research results from recent years are presented and relationships between biological interfaces, such as membranes and viruses, and amyloid fibril formation are proposed.     

Spatially controlled cell adhesion via micropatterned surface modification of poly(dimethylsiloxane)

Spatial control of cell growth on surfaces can be achieved by the selective deposition of molecules that influence cell adhesion. The fabrication of such substrates often relies upon photolithography and requires complex surface chemistry to anchor adhesive and inhibitory molecules. The production of simple, cost-effective substrates for cell patterning would benefit numerous areas of bioanalytical research including tissue engineering and biosensor development. Poly(dimethylsiloxane) (PDMS) is routinely used as a biomedical implant material and as a substrate for microfluidic device fabrication; however, the low surface energy and hydrophobic nature of PDMS inhibits its bioactivity. We present a method for the surface modification of PDMS to promote localized cell adhesion and proliferation. Thin metal films are deposited onto PDMS through a physical mask in the presence of a gaseous plasma. This treatment generates topographical and chemical modifications of the polymer surface. Removal of the deposited metal exposes roughened PDMS regions enriched with hydrophilic oxygen-containing species. The morphology and chemical composition of the patterned substrates were assessed by optical and atomic force microscopies as well as X-ray photoelectron spectroscopy. We observed a direct correlation between the surface modification of PDMS and the micropatterned adhesion of fibroblast cells. This simple protocol generates inexpensive, single-component substrates capable of directing cell attachment and growth.     

A Mobile Precursor Determines Amyloid-β Peptide Fibril Formation at Interfaces

The aggregation of peptides into amyloid fibrils plays a crucial role in various neurodegenerative diseases. While it has been generally recognized that fibril formation in vivo may be greatly assisted or accelerated by molecular surfaces, such as cell membranes, little is known about the mechanism of surface-mediated fibrillation. Here we study the role of adsorbed Alzheimer's amyloid-β peptide (Aβ42) on surface-mediated fibrillation using polymer coatings of varying hydrophobicity as well a supported lipid bilayer membrane. Using single molecule fluorescent tracking and atomic force microscopy imaging, we show that weakly adsorbed peptides with two-dimensional diffusivity are critical precursors to fibril growth on surfaces. This growth mechanism is inhibited on the highly hydrophilic surface where the surface coverage of adsorbed peptides is negligible or on the highly hydrophobic surface where the diffusion constant of the majority of adsorbed peptides is too low. Physical properties that favor weakly adsorbed peptides with sufficient translational mobility can locally concentrate peptide molecules on the surface and promote inter-peptide interaction via two-dimensional confinement, leading to fibrillation at Aβ peptide concentration many orders of magnitude below the critical concentration for fibrillation in the bulk solution.     

Direct Observation of Aggregation‐Induced Backbone Conformational Changes in Tau Peptides

In tau proteins, the hexapeptides in the R2 and R3 repeats are known to initiate tau fibril formation, which causes a class of neurodegenerative diseases called the taupathies. We show that in R3, in addition to the presence of the hexapeptides, the correct turn conformation upstream to it is also essential for producing prion‐like fibrils that are capable of propagation. A time‐dependent NMR aggregation assay of a slow fibril forming R3‐S316P peptide revealed a trans to cis equilibrium shift in the peptide‐bond conformation preceding P316 during the growth phase of the aggregation process. S316 was identified as the key residue in the turn that confers templating capacity on R3 fibrils to accelerate the aggregation of the R3‐S316P peptide. These results on the specific interactions and conformational changes responsible for tau aggregation could prove useful for developing an efficient therapeutic intervention in Alzheimer's disease.     

The Prenucleation Equilibrium of the Parathyroid Hormone Determines the Critical Aggregation Concentration and Amyloid Fibril Nucleation

Nucleation and growth of amyloid fibrils were found to only occur in supersaturated solutions above a critical concentration (c_crit). The biophysical meaning of c_crit remained mostly obscure, since typical low values of c_crit in the sub-μM range hamper investigations of potential oligomeric states and their structure. Here, we investigate the parathyroid hormone PTH₈₄ as an example of a functional amyloid fibril forming peptide with a comparably high c_crit of 67±21 μM. We describe a complex concentration dependent prenucleation ensemble of oligomers of different sizes and secondary structure compositions and highlight the occurrence of a trimer and tetramer at c_crit as possible precursors for primary fibril nucleation. Furthermore, the soluble state found in equilibrium with fibrils adopts to the prenucleation state present at c_crit. Our study sheds light onto early events of amyloid formation directly related to the critical concentration and underlines oligomer formation as a key feature of fibril nucleation. Our results contribute to a deeper understanding of the determinants of supersaturated peptide solutions. In the current study we present a biophysical approach to investigate c_crit of amyloid fibril formation of PTH₈₄ in terms of secondary structure, cluster size and residue resolved intermolecular interactions during oligomer formation. Throughout the investigated range of concentrations (1 μM to 500 μM) we found different states of oligomerization with varying ability to contribute to primary fibril nucleation and with a concentration dependent equilibrium. In this context, we identified the previously described c_crit of PTH₈₄ to mark a minimum concentration for the formation of homo-trimers/tetramers. These investigations allowed us to characterize molecular interactions of various oligomeric states that are further converted into elongation competent fibril nuclei during the lag phase of a functional amyloid forming peptide.     

Peptides derived from two dynamically disordered proteins self-assemble into amyloid-like fibrils

Short peptides derived from p14ARF and Hdm2 (14 and 15 amino acids in length, respectively), two cancer associated proteins, have been found to co-assemble into amyloid-like structures. Larger protein domains containing these peptide segments interact in cells and also undergo a disorder-to-order transition upon binding in vitro. In contrast to the association of beta-strand assemblies with amyloid diseases, the system described herein utilizes the formation of binary, extended beta-strands as a novel mechanism of biomolecular assembly. The beta-strand-containing fibrils formed from these peptides may allow the directed assembly of decorated fibrils with applications as biological nanostructures.     

Self-assembly of short amyloidogenic peptides at the air-water interface

Short peptide stretches in amyloidogenic proteins can form amyloid fibrils in vitro and have served as good models for studying amyloid fibril formation. Recently, these amyloidogenic peptides have gained considerable attention, as non-amyloid ordered structures can be obtained from these peptides by carefully tuning the conditions of self-assembly, especially pH, temperature and presence of organic solvents. We have examined the effect of surface pressure on the self-assembled structures of two amyloidogenic peptides, Pβ(2)m (Ac-DWSFYLLYYTEFT-am) and AcPHF6 (Ac-VQIVYK-am) at the air-water interface when deposited from different solvents. Both the peptides are surface-active and form Thioflavin T (ThT) positive structures at the air-water interface. There is considerable hysteresis in the compression and expansion isotherms, suggesting the occurrence of structural rearrangements during compression. Preformed Pβ(2)m fibrillar structures at the air-water interface are disrupted as peptide is compressed to lower molecular areas but restored if the film is expanded, suggesting that the process is reversible. AcPHF6, on the other hand, shows largely sheet-like structures at lower molecular areas. The solvents used for dissolution of the peptides appear to influence the nature of the aggregates formed. Our results show that like hydrostatic pressure, surface pressure can also be utilized for modulating the self-assembly of the amyloidogenic and self-assembling peptides.     

A Detailed Analysis of the Morphology of Fibrils of Selectively Mutated Amyloid β (1–40)

A small library of rationally designed amyloid β [Aβ(1–40)] peptide variants is generated, and the morphology of their fibrils is studied. In these molecules, the structurally important hydrophobic contact between phenylalanine 19 (F19) and leucine 34 (L34) is systematically mutated to introduce defined physical forces to act as specific internal constraints on amyloid formation. This Aβ(1–40) peptide library is used to study the fibril morphology of these variants by employing a comprehensive set of biophysical techniques including solution and solid‐state NMR spectroscopy, AFM, fluorescence correlation spectroscopy, and XRD. Overall, the findings demonstrate that the introduction of significant local physical perturbations of a crucial early folding contact of Aβ(1–40) only results in minor alterations of the fibrillar morphology. The thermodynamically stable structure of mature Aβ fibrils proves to be relatively robust against the introduction of significantly altered molecular interaction patterns due to point mutations. This underlines that amyloid fibril formation is a highly generic process in protein misfolding that results in the formation of the thermodynamically most stable cross‐β structure.     

Understanding the crystallization process of a diketopyrrolopyrrole-based conjugated polymer in blend films

The film morphology of fullerene and diketopyrrolopyrrole-based conjugated polymers (PDPPs) blends largely influences the device performance in organic solar cells. It is critical to control the morphology of blend films, which usually requires investigations of the crystallization of PDPP-based thin films. Here, we study the influence of marginal solvent additive 1,2-dichlorobenzene (ODCB) and non-solvent additive 1,8-diiodooctane (DIO) on the crystallization of poly[2,5-bis(2-octyldodecyl)pyrrolo-[3,4-c]pyrrole-1,4(2H,5H)-dione-alt-2,2′: 5′,2″: 5″,2″′-quaterthiophene] (PDQT). The blends formed fibril structures in thin films, as revealed by transmission electron microscopy. The fibril density increased and the width decreased with the ODCB amount. The critical ODCB content to achieve constant fibril width is almost proportional to the concentration of PDQT. Higher ODCB content also results in higher fibril density in pure PDQT films. In contrast, the amount of DIO has a negligible influence on the fibril width and density of thin films. Moreover, novel dendritic fibrils were formed in PDQT films upon addition of ODCB. A model based on nucleation and growth is proposed to explain these findings. The heterogeneous nucleation was dominant with the presence of ODCB, while the homogeneous nucleation was prevailing when DIO was used. The results show that initial nucleation density and growth direction are key factors determining the fibril width.     

Effect of the self-assembly of collagen on crystallisation of calcium carbonate in aqueous solution

In order to investigate how the self-assembly of organic matrix influences crystallisation and growth of inorganic minerals, we selected collagen as the matrix and conducted three experiments of crystallisation of CaCO₃ in different reaction systems: H₂O system, as-assembled collagen fibrils system and self-assembling of collagen system. It is found that (i) the self-assembly process of organic matrix had a remarkable effect on the morphology of inorganic minerals: CaCO₃ crystals formed in the as-assembled collagen fibrils system were global clusters and those formed in the self-assembling of collagen system appeared as interlaced networks and (ii) the organic matrix decided the polymorph of crystals: CaCO₃ crystals were calcite in the H₂O system and appeared vaterite in the collagen system. From this study, we can conclude that the self-assembly of collagen fibrils greatly affect the crystallisation and growth of CaCO₃. Such results are significant in understanding the mechanism of biomineralisation in calcified tissues in general, and useful in the synthesis of biominerals.

(a)?CaCO₃ formed in the as-assembled collagen fibrils system. (b)?CaCO₃ formed in the self-assembling of collagen monomer system.The TEM images of samples obtained in the as-assembled collagen fibrils and self-assembling of collagen monomer system, were observed, respectively. The result shows that crystals CaCO₃ formed in the as-assembled collagen fibrils system were global clusters; crystals CaCO₃ formed in the self-assembling of collagen monomer system appeared interlaced networks.