One-dimensional self-assembly of a rational designed beta-structure peptide

Induced and Inversed Circularly Polarized Luminescence of Achiral Thioflavin T Assembled on Peptide Fibril

Chiroptical inversion of amyloid fibrils is a novel phenomenon and is of fundamental importance; however, the underlying structural basis remains poorly understood. Here, the co-assembly of Thioflavin T (ThT) with T1 amyloid fibril and the induced supramolecular chirality is investigated by induced circular dichroism (ICD) and circularly polarized luminescence (CPL), followed by direct morphological helicity observation of the fibril by an atomic force microscope (AFM). ThT exhibits negative ICD and CPL when assembled on the left-handed T1 fibril. Interestingly, when ThT dynamically interacts with the T1 fibril, the left-handed fibril partially converts into right-handed, accompanied with the inversion of CD and CPL signals. These results indicate that the morphological helicity of template fibril cannot be arbitrarily distinguished by the sign of chiroptical spectra of the dye/peptide assemblies.

Supramolecular assembly of protein building blocks: from folding to function

Several phenomena occurring throughout the life of living things start and end with proteins. Various proteins form one complex structure to control detailed reactions. In contrast, one protein forms various structures and implements other biological phenomena depending on the situation. The basic principle that forms these hierarchical structures is protein self-assembly. A single building block is sufficient to create homogeneous structures with complex shapes, such as rings, filaments, or containers. These assemblies are widely used in biology as they enable multivalent binding, ultra-sensitive regulation, and compartmentalization. Moreover, with advances in the computational design of protein folding and protein-protein interfaces, considerable progress has recently been made in the de novo design of protein assemblies. Our review presents a description of the components of supramolecular protein assembly and their application in understanding biological phenomena to therapeutics.

Influence of Hydrophobic Face Amino Acids on the Hydrogelation of β-Hairpin Peptide Amphiphiles

Hydrophobic residues provide much of the thermodynamic driving force for the folding, self-assembly, and consequent hydrogelation of amphiphilic β-hairpin peptides. We investigate how the identity of hydrophobic side chains displayed from the hydrophobic face of these amphiphilic peptides influences their behavior to expound on the design criteria important to gel formation. Six peptides were designed that globally incorporate valine, aminobutyric acid, norvaline, norleucine, phenylalanine, or isoleucine on the hydrophobic face of the hairpin to study how systematic changes in hydrophobic content, β-sheet propensity, and aromaticity affect gelation. Circular dichroism (CD) spectroscopy indicates that hydrophobic content, rather than β-sheet propensity, dictates the temperature- and pH-dependent folding and assembly behavior of these peptides. Transmission electron microscopy (TEM) and small-angle neutron scattering (SANS) show that the local morphology of the fibrils formed via self-assembly is little affected by amino acid type. However, residue type does influence the propensity of peptide fibrils to undergo higher order assembly events. Oscillatory rheology shows that the mechanical rigidity of the peptide gels is highly influenced by residue type, but there is no apparent correlation between rigidity and residue hydrophobicity nor β-sheet propensity. Lastly, the large planar aromatic side chain of phenylalanine supports hairpin folding and assembly, affording a gel characterized by a rate of formation and storage modulus similar to the parent valine-containing peptide.

The influence of amino acid sequence on structure and morphology of polydiacetylene containing peptide fibres

A systematic study was performed on the influence of charge and steric hindrance on the assembly into fibres of a series of pentameric peptides based on the well-known β-sheet forming sequence Gly-Ala-Gly-Ala-Gly, which were N-terminally acylated with pentacosadiynoic acid. To investigate the effect of steric hindrance and charge repulsion on the fibre structure, either the N-terminal or the C-terminal amino acid in the sequence was replaced by a glutamic acid or lysine residue. Furthermore, peptide amphiphiles (PAs) with an amide or a free acid group at the C-terminus were compared. Steric hindrance and charge repulsion were addressed individually by varying the pH during and after fibre preparation. The self-assembled structures were examined with circular dichroism (CD) spectroscopy and transmission electron microscopy (TEM). UV spectroscopy was used to probe the diacetylene packing in the hydrophobic tail, both by polymerisation behaviour and chromatic properties of the polymers. In brief, the assembly was hindered more if the modification was close to the alkyl tail, and glutamic acid brought about a larger effect than lysine. PAs with two charges yielded assemblies which after polymerisation were found to be the most susceptible towards changes in pH, behaving as a colour-based pH sensor. Typically, TEM and UV showed the same trends, indicating that a distorted morphology as observed with TEM is indicative of a poorer molecular packing of the peptide amphiphile fibres, probed via the changes in absorption of the polydiacetylene backbone.

Design of self-assembling peptide hydrogelators amenable to bacterial expression

Hydrogels formed from self-assembling peptides are finding use in tissue engineering and drug delivery applications. Given the notorious difficulties associated with producing self-assembling peptides by recombinant expression, most are typically prepared by chemical synthesis. Herein, we report the design of a family of self-assembling β-hairpin peptides amenable to efficient production using an optimized bacterial expression system. Expressing peptides, EX1, EX2 and EX3 contain identical eight-residue amphiphilic β-strands connected by varying turn sequences that are responsible for ensuring chain reversal and the proper intramolecular folding and consequent self-assembly of the peptide into a hydrogel network under physiological conditions. EX1 was initially used to establish and optimize the bacterial expression system by which all the peptides could be eventually individually expressed. Expression clones were designed to allow exploration of possible fusion partners and investigate both enzymatic and chemical cleavage as means to liberate the target peptide. A systematic analysis of possible expression systems followed by fermentation optimization lead to a system in which all three peptides could be expressed as fusions with BAD-BH3, the BH3 domain of the proapoptotic BAD (Bcl-2 Associated Death) Protein. CNBr cleavage followed by purification afforded 50, 31, and 15 mg/L yields of pure EX1, EX2 and EX3, respectively. CD spectroscopy, TEM, and rheological analysis indicate that these peptides fold and assembled into well-defined fibrils that constitute hydrogels having shear-thin/recovery properties.

Self-assembly of Arg-Phe nanostructures via the solid-vapor phase method

We report for the first time on the self-assembly of nanostructures composed exclusively of alternating positively charged and hydrophobic amino acids. A novel arginine/phenylalanine octapeptide, RF8, was synthesized. Because the low hydrophobicity of this sequence makes its spontaneous ordering through solution-based methods difficult, a recently proposed solid-vapor approach was used to obtain nanometric architectures on ITO/PET substrates. The formation of the nanostructures was investigated under different preparation conditions, specifically, under different gas-phase solvents (aniline, water, and dichloromethane), different peptide concentrations in the precursor solution, and different incubation times. The stability of the assemblies was experimentally studied by electron microscopy and thermogravimetric analysis coupled with mass spectrometry. The secondary structure was assessed by infrared and Raman spectroscopy, and the arrays were found to assume an antiparallel β-sheet conformation. FEG-SEM images clearly reveal the appearance of fibrillar structures that form extensive homogeneously distributed networks. A close relationship between the morphology and preparation parameters was found, and a concentration-triggered mechanism was suggested. Molecular dynamics simulations were performed to address the thermal stability and nature of intermolecular interactions of the putative assembly structure. Results obtained when water is considered as solvent shows that a stable lamellar structure is formed containing a thin layer of water in between the RF8 peptides that is stabilized by H-bonding.

Structure and hydrogel formation studies on homologs of a lactoglobulin-derived peptide

In order to study the impact of the amino acid sequence on the morphology of peptide-based nanostructures and their hydrogel formation, we designed a series of analogs of a milk-derived octapeptide (OP), mainly using strategic amino acid substitutions. Electronic transmission microscopy (TEM) and circular dichroism (CD) spectropolarimetry were used to analyze the nanostructures formed, and to characterize some structural features of the modified peptides. Further, the potential to form hydrogels was investigated for all of the analogous peptides. We learned that those able to undergo secondary structure transition to β-sheet conformation form strong gels. The results reported highlight some key structural properties that explain the self-assembly propensity of Peptide OP.

Nucleation and growth of elastin-like peptide fibril multilayers: an in situ atomic force microscopy study

Controlling how molecules assemble into complex supramolecular architectures requires careful consideration of the subtle inter- and intra-molecular interactions that control their association. This is particularly crucial in the context of assembly at interfaces, where both surface chemistry and structure can play a role in directing structure formation. We report here the results of a study into the self-assembly of the elastin-like peptide EP I on structurally modified highly ordered pyrolytic graphite, including the role of spatial confinement on fibril nucleation and the growth of oriented fibril multilayers. In situ atomic force microscopy performed in fluid and at elevated temperature provided direct evidence of frustrated fibril nuclei and oriented growth of independent fibril domains. These results portend the application of this in situ strategy for studies of the nucleation and growth mechanisms of other fibril- and amyloid-forming proteins.

Influence of amino acid specificities on the molecular and supramolecular organization of glycine-rich elastin-like polypeptides in water

Elastin-like polypeptides adopt complex supramolecular structures, showing either a hydrophobic or a hydrophilic surface, depending on their surrounding environment and the supporting substrate. The preferred organization is important in many situations ranging from biocompatibility to bio-function. Here we compare the n-repeat pentamer LeuGlyGlyValGly (n = 7) with the analogue ValGlyGlyValGly (n = 5), as water suspensions and as deposits on silicon substrates. These sequences contain the repeat XxxGlyGlyZzzGly (Xxx, Zzz = Val, Leu) motif belonging to the hydrophobic glycine-rich domain of elastin and represent a simplified model from which to obtain information on molecular interactions functional to elastin itself. The compounds studied differ only by the presence of the -CH(2)- spacer in the Leu moiety and thus the work was aimed at revealing the influence of this spacer element on self assembly. Both polypeptides were studied under identical conditions, using combined techniques, to identify differences in their conformational states both at molecular (CD, FTIR) and supramolecular (XPS, AFM) levels. By these means, together with a Congo Red spectroscopic assay of β-sheet formation in water, a clear correlation between amino acid sequences (sequence specificity) and their kinetics and ordering of aggregation has emerged. The novel outcomes of this work are from the supplementary measurements, made to augment the AFM and XPS studies, showing that the significant step in the self assembly of both polypeptides takes place in the liquid phase and from the finding that the substitution of Val by Leu in the first position of the pentapeptide effectively inhibits the formation of amyloidal fibers.

Formation and stability of nanofibers from a milk-derived peptide

The objective of the present work was to investigate the physicochemical conditions that trigger the self-assembly of peptide β-lg f1-8 and therefore lead to nanofibers and hydrogel formation. Nanostructures formed by self-assembly of peptide β-lg f1-8 in the pH range of 2.0-11.0 were studied by transmission electron microscopy (TEM). Hydrogel formation was studied as a function of pH and resulted in evidence of a link between hydrogel formation and the charge distribution carried by the peptide structure. Finally, circular dichroism (CD) spectroscopy was used to characterize the effects of peptide concentration (0.4-2.0 mg/mL), ionic strength (0-1 M NaCl), and temperature (20-80 °C) on the secondary structure of peptide β-lg f1-8. Hydrogels were obtained at peptide concentrations above 2.5 mg/mL. Peptide concentration and pH adjustment were shown to trigger self-assembly of β-lg f1-8, but increasing ionic strength had no effect. Heating to 80 °C induced a stronger CD signal intensity due to an increase in solubility of the peptide, whereas only slight changes in CD pattern were found upon cooling to 20 °C. Overall, results emphasize the role of particular molecular interactions in β-sheet self-assembly of peptide β-lg f1-8 and pH-dependent electrostatic interactions occurring between β-lg f1-8 units, which can explain its propensity to self-assembly.

Interfacial and emulsifying properties of designed β-strand peptides

The structural and surfactant properties of a series of amphipathic β-strand peptides have been studied as a function of pH. Each nine-residue peptide has a framework of hydrophobic proline and phenylalanine amino acid residues, alternating with acidic or basic amino acids to give a sequence closely related to known β-sheet formers. Surface activity, interfacial mechanical properties, electronic circular dichroism (ECD), droplet sizing and zeta potential measurements were used to gain an overview of the peptide behavior as the molecular charge varied from ±4 to 0 with pH. ECD data suggest that the peptides form polyproline-type helices in bulk aqueous solution when highly charged, but may fold to β-hairpins rather than β-sheets when uncharged. In the uncharged state, the peptides adsorb readily at a macroscopic fluid interface to form mechanically strong interfacial films, but tend to give large droplet sizes on emulsification, apparently due to flocculation at a low droplet zeta potential. In contrast, highly charged peptide states gave a low interfacial coverage, but retained good emulsifying activity as judged by droplet size. Best emulsification was generally seen for intermediate charged states of the peptides, possibly representing a compromise between droplet zeta potential and interfacial binding affinity. The emulsifying properties of β-strand peptides have not been previously reported. Understanding the interfacial properties of such peptides is important to their potential development as biosurfactants.

Folding, self-assembly, and bulk material properties of a de novo designed three-stranded beta-sheet hydrogel

A de novo designed three-stranded beta-sheet (TSS1) has been prepared that undergoes temperature-induced folding and self-assembly to afford a network of beta-sheet rich fibrils that constitutes a mechanically rigid hydrogel. Circular dichroism and infrared spectroscopies show that TSS1 folds and self-assembles into a beta-sheet secondary structure in response to temperature. Rheological measurements show that the resulting hydrogels are mechanically rigid [at pH 9, G' = 1750-9000 Pa, and at pH 7.4, G' = 8500 Pa] and that the storage modulus can be modulated by temperature and peptide concentration. Nanoscale structure analysis by transmission electron microscopy and small angle neutron scattering indicate that the hydrogel network is comprised of fibrils that are about 3 nm in width, consistent with the width of TSS1 in the folded state. A unique property of the TSS1 hydrogel is its ability to shear-thin into a low viscosity gel upon application of shear stress and immediately recover its mechanical rigidity upon termination of stress. This attribute allows the hydrogel to be delivered via syringe to a target site with spatial and temporal resolution. Finally, experiments employing C3H10t1/2 mesenchymal stem cells seeded onto the hydrogel and incubated for 24 h indicate that the TSS1 hydrogel surface is noncytotoxic, supports cell adhesion, and allows cell migration.

Isolation and characterization of an aggregating peptide from a tryptic hydrolysate of whey proteins

Spontaneous precipitation of a peptide mixture has been observed during the concentration by reverse osmosis of a tryptic hydrolysate of whey protein. The precipitated material collected by centrifugation could not be solubilized by urea, mercaptoethanol, or sodium dodecyl sulfate. However, a complete solubilization of the aggregates was observed when the pH of the solution was lowered to 2.0. Analysis of the insoluble fraction has allowed the identification of beta-lactoglobulin (beta-lg) fragment 1-8 as the major peptide involved in the formation of aggregates. Peptide beta-lg f1-8 accounted for >94% of the peptide content in the precipitate washed twice with distilled water. The investigation of the secondary structure using circular dichroism evidenced that the peptide beta-lg f1-8 isolated from the flocculated peptide mixture is under random coil conformation at acidic and neutral pH and tends to adopt a beta-sheet conformation at basic pH. The findings of this study provide evidence that peptide beta-lg f1-8 forms aggregates via an efficient self-assembly process.

Structure-function relationships of pre-fibrillar protein assemblies in Alzheimer's disease and related disorders

Several neurodegenerative diseases, including Alzheimer's, Parkinson's, Huntington's and prion diseases, are characterized pathognomonically by the presence of intra- and/or extracellular lesions containing proteinaceous aggregates, and by extensive neuronal loss in selective brain regions. Related non-neuropathic systemic diseases, e.g., light-chain and senile systemic amyloidoses, and other organ-specific diseases, such as dialysis-related amyloidosis and type-2 diabetes mellitus, also are characterized by deposition of aberrantly folded, insoluble proteins. It is debated whether the hallmark pathologic lesions are causative. Substantial evidence suggests that these aggregates are the end state of aberrant protein folding whereas the actual culprits likely are transient, pre-fibrillar assemblies preceding the aggregates. In the context of neurodegenerative amyloidoses, the proteinaceous aggregates may eventuate as potentially neuroprotective sinks for the neurotoxic, oligomeric protein assemblies. The pre-fibrillar, oligomeric assemblies are believed to initiate the pathogenic mechanisms that lead to synaptic dysfunction, neuronal loss, and disease-specific regional brain atrophy. The amyloid beta-protein (Abeta), which is believed to cause Alzheimer's disease (AD), is considered an archetypal amyloidogenic protein. Intense studies have led to nominal, functional, and structural descriptions of oligomeric Abeta assemblies. However, the dynamic and metastable nature of Abeta oligomers renders their study difficult. Different results generated using different methodologies under different experimental settings further complicate this complex area of research and identification of the exact pathogenic assemblies in vivo seems daunting. Here we review structural, functional, and biological experiments used to produce and study pre-fibrillar Abeta assemblies, and highlight similar studies of proteins involved in related diseases. We discuss challenges that contemporary researchers are facing and future research prospects in this demanding yet highly important field.

Elastic fibers and amyloid deposition in vascular tissue

Amyloid fibrils are associated with a large number of diseases, such as Alzheimer’s dementia and others. Evidence links Alzheimer’s dementia with vascular diseases and only few data connect amyloids and atherosclerosis and aging via deposits in the aortic intima. Recent results demonstrate that some elastin polypeptide sequences are also able to produce amyloid fibers. This finding could have useful implications in the study of amyloids in cardiovascular tissue whose main constituent is elastin. In this review, we have also outlined the main characterizing features regarding the structure of amyloid fibrils. Finally, we describe, as a future perspective, the design of proper inhibitors of amyloid deposition in vascular walls as potential therapeutic drugs.