Relation between Serum Amyloid A Truncated Peptides and Their Suprastructure Chirality

Key charged residues influence the amyloidogenic propensity of the helix-1 region of serum amyloid A

Increased plasma levels of serum amyloid A (SAA), an acute-phase protein that is secreted in response to inflammation, may lead to the accumulation of amyloid in various organs thereby obstructing their functions. Severe cases can lead to a systemic disorder called AA amyloidosis. Previous studies suggest that the N-terminal helix is the most amyloidogenic region of SAA. Moreover, computational studies implicated a significant role for Arg-1 and the residue-specific interactions formed during the fibrillization process. With a focus on the N-terminal region of helix-1, SAA1-13, mutational analysis was employed to interrogate the roles of the amino acid residues, Arg-1, Ser-5, Glu-9, and Asp-12. The truncated SAA1-13 fragment was systematically modified by substituting the key residues with alanine or uncharged but structurally similar amino acids. We monitored the changes in the amyloidogenic propensities, associated conformational markers, and morphology of the amyloids resulting from the mutation of SAA1-13. Mutating out Arg-1 resulted in much reduced aggregation propensity and a lack of detectable β-structures alluding to the importance of salt-bridge interactions involving Arg-1. Our data revealed that by systematically mutating the key amino acid residues, we can modulate the amyloidogenic propensity and alter the time-dependent conformational variation of the peptide. When the behaviors of each mutant peptide were analyzed, they provided evidence consistent with the aggregation pathway predicted by MD simulation studies. Here, we detail the important temporal molecular interactions formed by Arg-1 with Ser-5, Glu-9, and Asp-12 and discuss its mechanistic implications on the self-assembly of the helix-1 region of SAA.

Chiral inversion induced by aromatic interactions in short peptide assembly

Although hydrophobic interactions provide the main driving force for initial peptide aggregation, their role in regulating suprastructure handedness of higher-order architectures remains largely unknown. We here interrogate the effects of hydrophobic amino acids on handedness at various assembly stages of peptide amphiphiles. Our studies reveal that relative to aliphatic side chains, aromatic side chains set the twisting directions of single β-strands due to their strong steric repulsion to the backbone, and upon packing into multi-stranded β-sheets, the side-chain aromatic interactions between strands form the aromatic ladders with a directional preference. This ordering not only leads to parallel β-sheet arrangements but also induces the chiral flipping over of single β-strands within a β-sheet. In contrast, the lack of orientational hydrophobic interactions in the assembly of aliphatic peptides implies no chiral inversion upon packing into β-sheets. This study opens an avenue to harness peptide aggregates with targeted handedness via aromatic side-chain interactions.

Chiral nanomaterial-based approaches for diagnosis and treatment of protein-aggregated neurodiseases: current status and future opportunities

Protein misfolding and its aggregation, known as amyloid aggregates (Aβ), are some of the major causes of more than 20 diseases such as Parkinson's disease, Alzheimer's disease, and type 2 diabetes. The process of Aβ formation involves an energy-driven oligomerization of Aβ monomers, leading to polymerization and eventual aggregation into fibrils. Aβ fibrils exhibit multilevel chirality arising from its amino acid residues and the arrangement of folded polypeptide chains; thus, a chirality-driven approach can be utilized for the detection and inhibition of Aβ fibrils. In this regard, chiral nanomaterials have recently opened new possibilities for various biomedical applications owing to their stereoselective interaction with biological systems. Leveraging this chirality-driven approach with chiral nanomaterials against protein-aggregated diseases could yield promising results, particularly in the early detection of Aβ forms and the inhibition of Aβ aggregate formation via specific and strong "chiral-chiral interaction." Despite the advantages, the development of advanced theranostic systems using chiral nanomaterials against protein-aggregated diseases has received limited attention so far because of considerably limited formulations for chiral nanomaterials and lack of information of their chiroptical behavior. This review aims to present the current status of chiral nanomaterials explored for detecting and inhibiting Aβ forms. This review covers the origin of chirality in amyloid fibrils and nanomaterials and different chiral detection methods; furthermore, different chiral nanosystems such as chiral plasmonic nanomaterials, chiral carbon-based nanomaterials, and chiral nanosurfaces, which have been used so far for different therapeutic applications against protein-aggregated diseases, are discussed in detail. The findings from this review may pave the way for the development of novel approaches using chiral nanomaterials to combat diseases resulting from protein misfolding and can further be extended to other disease forms.

Twisted Structures in Natural and Bioinspired Molecules: Self-Assembly and Propagation of Chirality Across Multiple Length Scales

Several biomolecules can form dynamic aggregates in water, whose nanometric structures often reflect the chirality of the monomers in unexpected ways. Their twisted organization can be further propagated to the mesoscale, in chiral liquid crystalline phases, and even to the macroscale, where chiral, layered architectures contribute to the chromatic and mechanical properties of various plant, insect, and animal tissues. At all scales, the resulting organization is determined by a subtle balance among chiral and nonchiral interactions, whose understanding and fine-tuning is fundamental also for applications. We present recent advances in the chiral self-assembly and mesoscale ordering of biological and bioinspired molecules in water, focusing on systems based on nucleic acids or related aromatic molecules, oligopeptides, and their hybrid stuctures. We highlight the common features and key mechanisms governing this wide range of phenomena, together with novel characterization approaches.

Signal peptide stabilizes folding and inhibits misfolding of serum amyloid A

Signal peptide (SP) plays an important role in membrane targeting for insertion of secretory and membrane proteins during translocation processes in prokaryotes and eukaryotes. Beside the targeting functions, SP has also been found to affect the stability and folding of several proteins. Serum amyloid A (SAA) proteins are apolipoproteins responding to acute-phase inflammation. The fibrillization of SAA results in a protein misfolding disease named amyloid A (AA) amyloidosis. The main disease-associated isoform of human SAA, SAA1.1, is expressed as a precursor protein with an N-terminal signal peptide composed of 18 residues. The cleavage of the SP generates mature SAA1.1. To investigate whether the SP affects properties of SAA1.1, we systematically examined the structure, protein stability, and fibrillization propensity of pre-SAA1.1, which possesses the SP, and Ser-SAA1.1 without the SP but containing with an additional N-terminal serine residue. We found that the presence of the SP did not significantly affect the predominant helical structure but changed the tertiary conformation as evidenced by intrinsic fluorescence and exposed hydrophobic surfaces. Pre-SAA1.1 and Ser-SAA1.1 formed distinct oligomeric assemblies in which pre-SAA1.1 populated as tetramer and octamer, whereas Ser-SAA1.1 existed as a predominant hexamer. Pre-SAA1.1 was found significantly more stable than Ser-SAA1.1 upon thermal and chemical unfolding. Ser-SAA1.1, but not pre-SAA1.1, is capable of forming amyloid fibrils in protein misfolding study, indicating a protective role of the SP. Altogether, our results demonstrated a novel role of the SP in SAA folding and misfolding and provided a novel direction for therapeutic development of AA amyloidosis.

Hydrogels from the Assembly of SAA/Elastin-Inspired Peptides Reveal Non-Canonical Nanotopologies

Peptide-based hydrogels are of great interest in the biomedical field according to their biocompatibility, simple structure and tunable properties via sequence modification. In recent years, multicomponent assembly of peptides have expanded the possibilities to produce more versatile hydrogels, by blending gelating peptides with different type of peptides to add new features. In the present study, the assembly of gelating P5 peptide SFFSF blended with P21 peptide, SFFSFGVPGVGVPGVGSFFSF, an elastin-inspired peptides or, alternatively, with FF dipeptide, was investigated by oscillatory rheology and different microscopy techniques in order to shed light on the nanotopologies formed by the self-assembled peptide mixtures. Our data show that, depending on the added peptides, cooperative or disruptive assembly can be observed giving rise to distinct nanotopologies to which correspond different mechanical properties that could be exploited to fabricate materials with desired properties.

Ordered Packing of β-Sheet Nanofibrils into Nanotubes: Multi-hierarchical Assembly of Designed Short Peptides

Although it is well-known proteins and their complexes are hierarchically organized and highly ordered structures, it remains a major challenge to replicate their hierarchical self-assembly process and to fabricate multihierarchical architectures with well-defined shapes and monodisperse characteristic sizes via peptide self-assembly. Here we describe an amphiphilic short peptide Ac-I₃GGHK-NH₂ that first preassembles into thin, left-handed β-sheet nanofibrils, followed by their ordered packing into right-handed nanotubes. The key intermediate morphology and structures featuring the hierarchical process are simultaneously demonstrated. Further mechanistic exploration with the variants Ac-I₃GGGK-NH₂, Ac-I₃GGFK-NH₂, and Ac-I₃GG^DH^DK-NH₂ reveals the vital role of multiple His-His side chain interactions between nanofibrils in mediating higher-order assembly and architectures. Altogether, our findings not only advance current understanding of hierarchical assembly of peptides and proteins but also afford a paradigm of how to take advantage of side chain interactions to construct higher-order assemblies with enhanced complexities.

Supramolecular Interactions and Morphology of Self-Assembling Peptide Amphiphile Nanostructures

The morphology of supramolecular peptide nanostructures is difficult to predict given their complex energy landscapes. We investigated peptide amphiphiles containing β-sheet forming domains that form twisted nanoribbons in water. We explained the morphology based on a balance between the energetically favorable packing of molecules in the center of the nanostructures, the unfavorable packing at the edges, and the deformations due to packing of twisted β-sheets. We find that morphological polydispersity of PA nanostructures is determined by peptide sequences, and the twisting of their internal β-sheets. We also observed a change in the supramolecular chirality of the nanostructures as the peptide sequence was modified, although only amino acids with l-configuration were used. Upon increasing charge repulsion between molecules, we observed a change in morphology to long cylinders and then rodlike fragments and spherical micelles. Understanding the self-assembly mechanisms of peptide amphiphiles into nanostructures should be useful to optimize their well-known functions.

Chirality Effects in Peptide Assembly Structures

Peptide assembly structures have been widely exploited in fabricating biomaterials that are promising for medical applications. Peptides can self-organize into various highly ordered supramolecular architectures, such as nanofibril, nanobelt, nanotube, nanowire, and vesicle. Detailed studies of the molecular mechanism by which these versatile building blocks assemble can guide the design of peptide architectures with desired structure and functionality. It has been revealed that peptide assembly structures are highly sequence-dependent and sensitive to amino acid composition, the chirality of peptide and amino acid residues, and external factors, such as solvent, pH, and temperature. This mini-review focuses on the regulatory effects of chirality alteration on the structure and bioactivity of linear and cyclic peptide assemblies. In addition, chiral self-sorting and co-assembly of racemic peptide mixtures were discussed.

Unexpected Role of Achiral Glycine in Determining the Suprastructural Handedness of Peptide Nanofibrils

Helical supramolecular architectures play important structural and functional roles in biological systems. Although their occurrence is widely perceived to correlate to fundamental chiral units including l-amino acids and d-sugars, the detailed relationship between molecular and supramolecular handedness is still unclear. At the same time, although achiral units are practically always in close proximity to chiral ones by covalent linkage along a polymeric chain, their effect on supramolecular handedness has received relatively less attention. Here, we designed a set of short amphiphilic peptides, in which an achiral glycine residue was incorporated at the interface between the hydrophobic and hydrophilic segments. We observed that glycine incorporation caused dramatic variations in suprastructural handedness in self-assembled peptide nanofibrils, and the effect of the hydrophilic charged residue at the C-terminus on supramolecular handedness was demolished, leading to chiral truncation. Furthermore, molecular dynamics simulations and quantum chemistry calculations revealed that the unanticipated role of the glycine residue in regulating supramolecular handedness originated from its effect on the conformational preference of single β-strands. Importantly, reduced density gradient analyses on single β-strands indicated that, due to the lack of a side chain in glycine, intricate noncovalent interactions were produced among the neighboring amino acid side chains of the incorporated glycine and its local backbone, resulting in diverse β-strand conformations.

Chiral structure fluctuations predicted by a coarse-grained model of peptide aggregation

This work reports on the chiral structure fluctuations of peptide clusters at the early stages of aggregation in a coarse-grained peptide model. Our model reproduces a variety of aggregate structures, from disordered to crystal-like, that are observed experimentally. Unexpectedly, our molecular dynamics simulations showed that the small peptide cluster undergoes chiral structure fluctuations although the underlying implicit solvent model does not assume the chirality of peptides. The chiral fluctuations are quantified through a cluster twist parameter. A simple model is presented where the twist parameter undergoes a stochastic diffusion on a 1D potential surface. The shape of the potential surface changes with the cluster size. The model shows semi-quantitative agreement with the simulations. We hypothesize that the chiral fluctuations at the early stages of peptide aggregation can contribute to the selection of the final fibril structures.

Labeling of Nanofiber-Forming Peptides by Site-Directed Bioconjugation: Effect of Spacer Length on Self-Assembly

BACKGROUND

The conjugation of small organic molecules to self-assembling peptides is a versatile tool to decorate nanostructures with original functionalities. Labeling with chromophores or fluorophores, for example, creates optically active fibers with potential interest in photonic devices.

AIM AND OBJECTIVE

In this work, we present a rapid and effective labeling procedure for a self-assembling peptide able to form nanofibers. Rapid periodate oxidation of the N-terminal serine residue of the peptide and subsequent conjugation with dansyl moiety generated fluorophore-decorated peptides.

RESULTS

Three dansyl-conjugated self-assembling peptides with variable spacer-length were synthesized and characterized and the role of the size of the linker between fluorophore and peptide in self-assembling was investigated. Our results show that a short linker can alter the self-assembly in nanofibers of the peptide.

CONCLUSIONS

Herein we report on an alternative strategy for creating functionalized nanofibrils, able to expand the toolkit of chemoselective bioconjugation strategies to be used in site-specific decoration of self-assembling peptides.

Peptide interdigitation-induced twisted nanoribbons as chiral scaffolds for supramolecular nanozymes

Establishing reliable strategies for rationally manipulating the organization of peptide building blocks and thereby precisely creating chiral nanostructures is challenging, while meaningful toward development of advanced functional materials. Here we report on a peptide-interdigitating mechanism for the reliable self-assembly of lipid-inspired amphiphiles (LIPIAs) into robust twisted nanoribbons by grafting domains to one alkyl tail of lipids as an extended element. Peptide interdigitation promoted the self-assembly of LIPIAs into twisted or flat nanoribbons driven by antiparallel or parallel β-sheet hydrogen bonds, respectively, strongly associated with the connecting direction of the incorporated domains. We found that the LIPIAs containing N-terminus-connected domains with either bulky or small side chain groups formed twisted nanoribbons in a broad pH range, thus implying a sequence- and pH-independent strategy for creation of robust chiral nanostructures. Integrating the resulting twisted nanoribbons with gold nanoparticles led to supramolecular nanozymes exhibiting the excellent catalytic activity and enantioselectivity of asymmetric oxidation of 3,4-dihyroxy-phenylalanine molecules. Our finding demonstrates that the peptide-interdigitating mechanism is a reliable strategy for precise creation of chiral nanostructures serving as chiral matrices for supramolecular nanozymes with improved catalytic performance, thus potentially paving the way towards advanced biomimetic systems resembling natural systems.

Functional differentiation of three phosphatidylinositol 3-kinase catalytic subunit alpha (PIK3CA) in response to Vibrio anguillarum infection in turbot (Scophthalmus maximus)

PIK3CA has been extensively investigated from its molecular mechanism perspective and association with its mutations in different types of cancers. However, little has been reported regarding the pathological significance of PIK3CA expression in teleost. Here, in our present study, three PIK3CA genes termed SmPIK3CAa, SmPIK3CAb and SmPIK3CA-like were firstly identified in the genome of turbot S. maximus. Although these three genes located in different chromosomes, all of them share the same five domains. Phylogenetic and synteny analysis indicated that SmPIK3CAa, SmPIK3CAb and SmPIK3CA-like were three paralogs that may originate from duplication of the same ancestral PIK3CA gene. Subcellular localization analysis confirmed the cytoplasm distribution of these three paralogs. All three SmPIK3CA were ubiquitously expressed in examined tissues in turbot, with the higher expression levels in immune-related tissues such as blood, spleen, kidney, gills and intestines. Upon Vibrio anguillarum challenge, SmPIK3CAa and SmPIK3CA-like transcripts were significantly induced in spleen, intestine and blood despite of differential expression levels and responsive time points. Additionally, individuals in resistant group showed significantly higher expression level of both two genes than in the susceptible group. Moreover, four SNPs (102, 2530, 3027 and 3060) and one haplotype (Hap2) located in exon region of SmPIK3CA-like were identified and confirmed to be associated with V. anguillarum resistance in turbot by association analysis in different populations. Taken together, these results suggested that functional differentiation occurred in three SmPIK3CA paralogs with Vibrio anguillarum resistance and SmPIK3CAa and SmPIK3CA-like probable play potential roles in innate immune response to pathogenic invasions in turbot.

Tuning of hydrogel stiffness using a two-component peptide system for mammalian cell culture

Self-assembling peptide hydrogels (SAPHs) represent emerging cell cultures systems in several biomedical applications. The advantages of SAPHs are mainly ascribed to the absence of toxic chemical cross-linkers, the presence of ECM-like fibrillar structures and the possibility to produce hydrogels with a large range of different mechanical properties. We will present a two-component peptide system with tuneable mechanical properties, consisting of a small pentapeptide (SFFSF-NH2 , SA5N) that acts as a gelator and a larger 21-mer peptide (SFFSF-GVPGVGVPGVG-SFFSF, SA21) designed as a physical cross-linker. The hydrogels formed by different mixtures of the two peptides are made up mainly of antiparallel β-sheet nanofibers entangling in an intricate network. The effect of the addition of SA21 on the morphology of the hydrogels was investigated by atomic force microscopy and transmission electron microscopy and correlated to the mechanical properties of the hydrogel. Finally, the biocompatibility of the hydrogels using 2D cell cultures was tested. © 2018 The Authors. journal Of Biomedical Materials Research Part A Published By Wiley Periodicals, Inc. J Biomed Mater Res Part A: 107A: 535-544, 2019.

Construction of supramolecular hydrogels using photo-generated nitric oxide radicals

Photo-generated nitric oxide radicals (NO˙) derived from sodium nitroprusside dihydrate (SNP) are employed for the construction of supramolecular hydrogels based on an amino acid derivative precursor, N-fluorenylmethyloxycarbonyl tyrosine phosphate (FYP), which through dephosphorylation produces the gelator, N-fluorenylmethyloxycarbonyl tyrosine (FY). Self-assembly of the amphiphilic gelator yields high-aspect ratio nanofilaments that entangle to form self-supporting, viscoelastic hydrogels. The presence of photolyzed SNP yields periodically twisted nanofilaments with opposite chirality to filaments formed through conventional hydrogelation routes.

Implications of peptide assemblies in amyloid diseases

Neurodegenerative disorders and type 2 diabetes are global epidemics compromising the quality of life of millions worldwide, with profound social and economic implications. Despite the significant differences in pathology - much of which are poorly understood - these diseases are commonly characterized by the presence of cross-β amyloid fibrils as well as the loss of neuronal or pancreatic β-cells. In this review, we document research progress on the molecular and mesoscopic self-assembly of amyloid-beta, alpha synuclein, human islet amyloid polypeptide and prions, the peptides and proteins associated with Alzheimer's, Parkinson's, type 2 diabetes and prion diseases. In addition, we discuss the toxicities of these amyloid proteins based on their self-assembly as well as their interactions with membranes, metal ions, small molecules and engineered nanoparticles. Through this presentation we show the remarkable similarities and differences in the structural transitions of the amyloid proteins through primary and secondary nucleation, the common evolution from disordered monomers to alpha-helices and then to β-sheets when the proteins encounter the cell membrane, and, the consensus (with a few exceptions) that off-pathway oligomers, rather than amyloid fibrils, are the toxic species regardless of the pathogenic protein sequence or physicochemical properties. In addition, we highlight the crucial role of molecular self-assembly in eliciting the biological and pathological consequences of the amyloid proteins within the context of their cellular environments and their spreading between cells and organs. Exploiting such structure-function-toxicity relationship may prove pivotal for the detection and mitigation of amyloid diseases.

Influence of C-terminal truncation of murine Serum amyloid A on fibril structure

Amyloid A (AA) amyloidosis is a systemic protein misfolding disease affecting humans and other vertebrates. While the protein precursor in humans and mice is the acute-phase reactant serum amyloid A (SAA) 1.1, the deposited fibrils consist mainly of C-terminally truncated SAA fragments, termed AA proteins. For yet unknown reasons, phenotypic variations in the AA amyloid distribution pattern are clearly associated with specific AA proteins. Here we describe a bacterial expression system and chromatographic strategies to obtain significant amounts of C-terminally truncated fragments of murine SAA1.1 that correspond in truncation position to relevant pathological AA proteins found in humans. This enables us to investigate systematically structural features of derived fibrils. All fragments form fibrils under nearly physiological conditions that show similar morphological appearance and amyloid-like properties as evident from amyloid-specific dye binding, transmission electron microscopy and infrared spectroscopy. However, infrared spectroscopy suggests variations in the structural organization of the amyloid fibrils that might be derived from a modulating role of the C-terminus for the fibril structure. These results provide insights, which can help to get a better understanding of the molecular mechanisms underlying the different clinical phenotypes of AA amyloidosis.

Left or Right: How Does Amino Acid Chirality Affect the Handedness of Nanostructures Self-Assembled from Short Amphiphilic Peptides?

Peptide and protein fibrils have attracted an enormous amount of interests due to their relevance to many neurodegenerative diseases and their potential applications in nanotechnology. Although twisted fibrils are regarded as the key intermediate structures of thick fibrils or bundles of fibrils, the factors determining their twisting tendency and their handedness development from the molecular to the supramolecular level are still poorly understood. In this study, we have designed three pairs of enantiomeric short amphiphilic peptides: ^LI₃^LK and ^DI₃^DK, ^LI₃^DK and ^DI₃^LK, and ^LaI₃^LK and ^DaI₃^DK, and investigated the chirality of their self-assembled nanofibrils through the combined use of atomic force microscopy (AFM), circular dichroism (CD) spectroscopy, scanning electron microscopy (SEM), and molecular dynamic (MD) simulations. The results indicated that the twisted handedness of the supramolecular nanofibrils was dictated by the chirality of the hydrophilic Lys head at the C-terminal, while their characteristic CD signals were determined by the chirality of hydrophobic Ile residues. MD simulations delineated the handedness development from molecular chirality to supramolecular handedness by showing that the β-sheets formed by ^LI₃^LK, ^LaI₃^LK, and ^DI₃^LK exhibited a propensity to twist in a left-handed direction, while the ones of ^DI₃^DK, ^DaI₃^DK, and ^LI₃^DK in a right-handed twisting orientation.

Electrostatic Interactions at N- and C-Termini Determine Fibril Polymorphism in Serum Amyloid A Fragments

Amyloid polymorphism presents a challenge to physical theories of amyloid formation and stability. The amyloidogenic protein serum amyloid A (SAA) exhibits complex and unexplained structural polymorphism in its N-terminal fragments: the N-terminal 11-residue peptide (SAA1-11) forms left-handed helical fibrils, while extension by one residue (SAA1-12) produces a rare right-handed amyloid. In this study, we use a combination of vibrational spectroscopy and ultramicroscopy to examine fibrils of these peptides and their terminally acetylated and amidated variants, in an effort to uncover the physical basis for this effect. Raman spectroscopy and atomic force microscopy provide evidence that SAA1-12 forms a β-helical fibril architecture, while SAA1-11 forms more typical stacked β-sheets. Importantly, N-terminal acetylation blocks fibril formation by SAA1-12 with no effect on SAA1-11, while C-terminal amidation has nearly the opposite effect. Together, these data suggest distinct electrostatic interactions at the N- and C-termini stabilize the two fibril structures; we propose model fibril structures in which C-terminal extension changes the favored intermolecular interaction between peptide monomers from an Arg1-C-terminus charge pair to an N-terminus-C-terminus charge pair. This model suggests a general mechanism for charge-mediated amyloid polymorphism and may inform strategies for design of peptide-based nanomaterials stabilized by engineered intermolecular contacts.

Designing peptidic inhibitors of serum amyloid A aggregation process

Amyloid A amyloidosis is a life-threatening complication of a wide range of chronic inflammatory, infectious and neoplastic diseases, and the most common form of systemic amyloidosis worldwide. It is characterized by extracellular tissue deposition of fibrils that are composed of fragments of serum amyloid A protein (SAA), a major acute-phase reactant protein, produced predominantly by hepatocytes. Currently, there are no approved therapeutic agents directed against the formation of fibrillar SAA assemblies. We attempted to develop peptidic inhibitors based on their similarity and complementarity to the regions critical for SAA self-association, which they should interact with and block their assembly into amyloid fibrils. Inh1 and inh4 which are comprised of the residues from the amyloidogenic region of SAA1.1 protein and Aβ peptide, respectively, were found by us as capable to significantly suppress aggregation of the SAA1-12 peptide. It was chosen as an aggregation model that mimicks the amyloidogenic nucleus of SAA protein. We suppose that aromatic interactions may be responsible for inhibitory activity of both compounds. We also recognized that aromatic residues are involved in self-association of SAA1-12.

Supramolecular chirality in peptide microcrystals

The vibrational circular dichroism (VCD) spectra of microcrystals of fibril-forming peptides have been measured for the first time. VCD spectra were measured and compared for microcrystals and fibrils formed from the same peptide, human islet amyloid polypeptide (IAPP, amylin). Structural information related to the supramolecular chirality of both the microcrystals and the fibrils, as well as the VCD enhancement mechanisms in fibrils and microcrystals, is obtained from these spectral comparisons. It is concluded that strongly enhanced VCD does not require braiding of two or more filaments that is permitted in fibrils but not microcrystals.

Identification of a Serum amyloid A gene and the association of SNPs with Vibrio-resistance and growth traits in the clam Meretrix meretrix

Serum amyloid A (SAA), an acute response protein as well as an apolipoprotein, is considered to play crucial roles in both innate immunity and lipid metabolism. In this study, a SAA gene (MmSAA) was identified in the clam Meretrix meretrix. The full length DNA of MmSAA was 1407bp, consisting of three exons and two introns. The distribution of MmSAA in clam tissues was examined with the highest expression in hepatopancreas. In response to the Vibrio parahaemolyticus challenge, MmSAA mRNA showed significantly higher expression at 24 h post-challenge in experimental clams (P < 0.05). Forty-eight single nucleotide polymorphisms (SNPs) in the DNA partial sequence of MmSAA were discovered and examined for their association with Vibrio-resistance and growth traits, respectively. The single SNP association analysis indicated that five single SNPs (g.42, g.72, g.82, g.147 and g.165) were significantly associated with Vibrio-resistance (P < 0.05). Haplotype analysis produced additional support for association with the Chi-square values 6.393 (P = 0.012). Among the five selected SNPs, the effect of a missense mutation (g.82, A → G) was detected by site-directed mutagenesis with fusion expression of protein assay, and the result showed that the recombinant plasmids containing wild-type pET30a-MmSAA had more inhibition effect than the mutant ones on the growth rate of the host bacteria. In addition, four growth traits of the clams in 09G3SPSB population were recorded and the SNP g.176 was found to be significantly associated with the growth traits with the Global score value 0.790 (P = 0.015). Our findings suggested that common genetic variation in MmSAA might contribute to the risk of susceptibility to Vibrio infection and might be associated with the growth traits in the clams M. meretrix, and more works are still needed to validate these SNPs as potential markers for actual selective breeding.

Nanospheres from the self-assembly of an elastin-inspired triblock peptide

The self-assembly of an elastin-inspired triblock peptide into nanospheres highlights the important role of conformational flexibility and π–π stacking.

Is supramolecular filament chirality the underlying cause of major morphology differences in amyloid fibrils?

The unique enhanced sensitivity of vibrational circular dichroism (VCD) to the formation and development of amyloid fibrils in solution is extended to four additional fibril-forming proteins or peptides where it is shown that the sign of the fibril VCD pattern correlates with the sense of supramolecular filament chirality and, without exception, to the dominant fibril morphology as observed in AFM or SEM images. Previously for insulin, it has been demonstrated that the sign of the VCD band pattern from filament chirality can be controlled by adjusting the pH of the incubating solution, above pH 2 for “normal” left-hand-helical filaments and below pH 2 for “reversed” right-hand-helical filaments. From AFM or SEM images, left-helical filaments form multifilament braids of left-twisted fibrils while the right-helical filaments form parallel filament rows of fibrils with a flat tape-like morphology, the two major classes of fibril morphology that from deep UV resonance Raman scattering exhibit the same cross-β-core secondary structure. Here we investigate whether fibril supramolecular chirality is the underlying cause of the major morphology differences in all amyloid fibrils by showing that the morphology (twisted versus flat) of fibrils of lysozyme, apo-α-lactalbumin, HET-s (218–289) prion, and a short polypeptide fragment of transthyretin, TTR (105–115), directly correlates to their supramolecular chirality as revealed by VCD. The result is strong evidence that the chiral supramolecular organization of filaments is the principal underlying cause of the morphological heterogeneity of amyloid fibrils. Because fibril morphology is linked to cell toxicity, the chirality of amyloid aggregates should be explored in the widely used in vitro models of amyloid-associated diseases.

A clear view of polymorphism, twist, and chirality in amyloid fibril formation

The self-assembly of protein molecules into highly ordered linear aggregates, known as amyloid fibrils, is a phenomenon receiving increasing attention because of its biological roles in health and disease and the potential of these structures to form artificial proteinaceous scaffolds for biomaterials applications. A particularly powerful approach to probe the key physical properties of fibrillar structures is atomic force microscopy, which was used by Usov et al. in this issue of ACS Nano to reveal the polymorphic transitions and chirality inversions of amyloid fibrils in unprecedented detail. Starting from this study, this Perspective highlights recent progress in understanding the dynamic polymorphism, twisting behavior, and handedness of amyloid fibrils and discusses the promising future of these self-assembling structures as advanced functional materials with applications in nanotechnology and related fields.

Local frustration determines molecular and macroscopic helix structures

Decorative domains force amyloid fibers to adopt spiral ribbon morphologies, as opposed to the more common twisted ribbon. We model the effect of decorating domains as a perturbation to the relative orientation of β strands in a bilayered extended β-sheet. The model consists of minimal energy assemblies of rigid building blocks containing two anisotropic interacting ellipsoids. The relative orientation of the ellipsoids dictates the morphology of the resulting assembly. Amyloid structures derived from experiment are consistent with our model, and we use magnets to demonstrate that the frustration principle is scale and system independent. In contrast to other models of amyloid, our model isolates the effect of frustration from the fundamental interactions between building blocks to reveal the frustration rather than dependence of morphology on the physical interactions. Consequently, amyloid is viewed as a discrete molecular version of the more general macroscopic frustrated bilayer that is exemplified by Bauhinia seedpods. The model supports the idea that the interactions arising from an arbitrary peptide sequence can support an amyloid structure if a bilayer can form first, which suggests that supplementary protein sequences, such as chaperones or decorative domains, could play a significant role in stabilizing such bilayers and therefore in selecting morphology during nucleation. Our model provides a foundation for exploring the effects of frustration on higher-order superstructural polymorphic assemblies that may exhibit complex functional behavior. Two outstanding examples are the systematic kinking of decorated fibers and the nested frustration of the Bauhinia seedpod.

Levels of supramolecular chirality of polyglutamine aggregates revealed by vibrational circular dichroism

Polyglutamine (PolyQ) aggregates are a hallmark of several severe neurodegenerative diseases, expanded CAG-repeat diseases in which inheritance of an expanded polyQ sequence above a pathological threshold is associated with a high risk of disease. Application of vibrational circular dichroism (VCD) reveals that these PolyQ fibril aggregates exhibit a chiral supramolecular organization that is distinct from the supramolecular organization of previously observed amyloid fibrils. PolyQ fibrils grown from monomers with Q repeats 35 and above (Q≥35) exhibit approximately 10-fold enhancement of the same VCD spectrum compared to the already enhanced VCD of fibrils formed from Q repeats 30 and below (Q≤30).

Normal and reversed supramolecular chirality of insulin fibrils probed by vibrational circular dichroism at the protofilament level of fibril structure

Fibrils are β-sheet-rich aggregates that are generally composed of several protofibrils and may adopt variable morphologies, such as twisted ribbons or flat-like sheets. This polymorphism is observed for many different amyloid associated proteins and polypeptides. In a previous study we proposed the existence of another level of amyloid polymorphism, namely, that associated with fibril supramolecular chirality. Two chiral polymorphs of insulin, which can be controllably grown by means of small pH variations, exhibit opposite signs of vibrational circular dichroism (VCD) spectra. Herein, using atomic force microscopy (AFM) and scanning electron microscopy (SEM), we demonstrate that indeed VCD supramolecular chirality is correlated not only by the apparent fibril handedness but also by the sense of supramolecular chirality from a deeper level of chiral organization at the protofilament level of fibril structure. Our microscopic examination indicates that normal VCD fibrils have a left-handed twist, whereas reversed VCD fibrils are flat-like aggregates with no obvious helical twist as imaged by atomic force microscopy or scanning electron microscopy. A scheme is proposed consistent with observed data that features a dynamic equilibrium controlled by pH at the protofilament level between left- and right-twist fibril structures with distinctly different aggregation pathways for left- and right-twisted protofilaments.

A stereochemical switch in the aDrs model system, a candidate for a functional amyloid

Amyloid fibrils are commonly observed to adopt multiple distinct morphologies, which eventually can have significantly different neurotoxicities, as e.g. demonstrated in case of the Alzheimer peptide. The architecture of amyloid deposits is apparently also determined by the stereochemistry of amino acids. Post-translational changes of the chirality of certain residues may thus be a factor in controlling the formation of functional or disease-related amyloids. Anionic dermaseptin (aDrs), an unusual peptide from the skin secretions of the frog Pachymedusa dacnicolor, assembles to amyloid-like fibrils in a pH-dependent manner, which could play a functional role in defense. aDrs can be enzymatically converted into the diastereomer [d-Leu2]-aDrs by an l/d-isomerase. EM and AFM on fibrils formed by these isomers have shown that their predominant morphology is controlled by the stereochemistry of residue 2, whereas kinetic and thermodynamic parameters of aggregation are barely affected. When fibrils were grown from preformed seeds, backbone stereochemistry rather than templating-effects apparently dominated the superstructural organization of the isomers. Interestingly, MD indicated small differences in the conformational propensities between the isomers. Our results demonstrate how d-amino acid substitutions could take active part in the formation of functional or disease-related amyloid. Moreover, these findings contribute to the development of amyloid-based nanomaterials.

Spontaneous inter-conversion of insulin fibril chirality

Amyloid fibrils are associated with many neurodegenerative diseases and are considered to be the energetically most favorable form of proteins. Here we report that a small pH change initiates spontaneous transformation of insulin fibrils from one polymorph to another. As a result, fibril supramolecular chirality overturns both accompanying morphological and structural changes.

Identification of regions responsible for heparin-induced amyloidogenesis of human serum amyloid A using its fragment peptides

Human serum amyloid A (SAA) is a precursor protein of amyloid fibrils. Although several studies have been performed, a detailed understanding of the molecular mechanism for SAA fibrillation remains elusive. Glycosaminoglycans such as heparin are suggested to serve as scaffolds in amyloid fibril formation in some cases. In the present study, amyloidogenic properties of synthetic fragment peptides corresponding to the N-terminal (residues 1-27), central (residues 43-63), and C-terminal (residues 77-104) regions of SAA molecule induced by heparin were examined using fluorescence, circular dichroism (CD), and electron microscopy. Fluorescence and CD measurements demonstrated that SAA (1-27) peptide is evidently involved in heparin-induced amyloidogenesis. Correspondingly, relatively minor changes in fluorescence and a quite different pattern in the CD spectrum were observed in SAA (43-63) peptide. In contrast, SAA (77-104) peptide did not show any changes induced by heparin. Transmission electron microscopy indicated that SAA (1-27) peptide forms short and straight fibrils, whereas SAA (43-63) peptide forms much longer and seemingly elastic fibrils. These results suggest that the N-terminal region plays a crucial role as a rigid core and the central region facilitates the elongation of fibrils in heparin-induced amyloidogenesis of SAA molecule.

Unraveling the mechanism of nanotube formation by chiral self-assembly of amphiphiles

The self-assembly of nanotubes from chiral amphiphiles and peptide mimics is still poorly understood. Here, we present the first complete path to nanotubes by chiral self-assembly studied with C(12)-β(12) (N-α-lauryl-lysyl-aminolauryl-lysyl-amide), a molecule designed to have unique hybrid architecture. Using the technique of direct-imaging cryo-transmission electron microscopy (cryo-TEM), we show the time-evolution from micelles of C(12)-β(12) to closed nanotubes, passing through several types of one-dimensional (1-D) intermediates such as elongated fibrils, twisted ribbons, and coiled helical ribbons. Scattering and diffraction techniques confirm that the fundamental unit is a monolayer lamella of C(12)-β(12), with the hydrophobic tails in the gel state and β-sheet arrangement. The lamellae are held together by a combination of hydrophobic interactions, and two sets of hydrogen-bonding networks, supporting C(12)-β(12) monomers assembly into fibrils and associating fibrils into ribbons. We further show that neither the "growing width" model nor the "closing pitch" model accurately describe the process of nanotube formation, and both ribbon width and pitch grow with maturation. Additionally, our data exclusively indicate that twisted ribbons are the precursors for coiled ribbons, and the latter structures give rise to nanotubes, and we show chirality is a key requirement for nanotube formation.