An infrared spectroscopy approach to follow β-sheet formation in peptide amyloid assemblies

Understanding the structural dynamics of human islet amyloid polypeptide: Advancements in and applications of ion-mobility mass spectrometry

Human islet amyloid polypeptide (hIAPP) forms amyloid deposits that contribute to β-cell death in pancreatic islets and are considered a hallmark of Type II diabetes Mellitus (T2DM). Evidence suggests that the early oligomers of hIAPP formed during the aggregation process are the primary pathological agent in islet amyloid induced β-cell death. The self-assembly mechanism of hIAPP, however, remains elusive, largely due to limitations in conventional biophysical techniques for probing the distribution or capturing detailed structures of the early, structurally dynamic oligomers. The advent of Ion-mobility Mass Spectrometry (IM-MS) has enabled the characterisation of hIAPP early oligomers in the gas phase, paving the way towards a deeper understanding of the oligomerisation mechanism and the correlation of structural information with the cytotoxicity of the oligomers. The sensitivity and the rapid structural characterisation provided by IM-MS also show promise in screening hIAPP inhibitors, categorising their modes of inhibition through "spectral fingerprints". This review delves into the application of IM-MS to the dissection of the complex steps of hIAPP oligomerisation, examining the inhibitory influence of metal ions, and exploring the characterisation of hetero-oligomerisation with different hIAPP variants. We highlight the potential of IM-MS as a tool for the high-throughput screening of hIAPP inhibitors, and for providing insights into their modes of action. Finally, we discuss advances afforded by recent advancements in tandem IM-MS and the combination of gas phase spectroscopy with IM-MS, which promise to deliver a more sensitive and higher-resolution structural portrait of hIAPP oligomers. Such information may help facilitate a new era of targeted therapeutic strategies for islet amyloidosis in T2DM.

Probing High-Order Transient Oligomers Using Ion Mobility Mass Spectrometry Coupled with Infrared Action Spectroscopy

Understanding and controlling peptide aggregation are critical due to its neurotoxic implications. However, structural information about the key intermediates, the oligomers, is obscured by a cascade of coinciding events occurring at various time and energy scales, which results in complex and heterogeneous mixtures of oligomers. To address this challenge, we have developed the Photo-Synapt, a novel, multidimensional spectrometer that integrates ion mobility mass spectrometry with infrared (IR) action spectroscopy within a single experiment. By combining three different orthogonal analytical dimensions, we can select and isolate individual oligomers by mass, charge, size, and shape and provide a unique molecular fingerprint for each oligomer. The broad application of this technology is demonstrated by its application to oligosaccharide analysis from glycoproteins, which are challenging to analyze due to the minute differences between isomers. By integration of IR action spectroscopy with ion mobility mass spectrometry, this approach adds an analytical dimension that effectively addresses this limitation, offering a unique molecular fingerprint for each isomer.

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.

Chemically fueled dynamic switching between assembly-encoded emissions

Self-assembly provides access to non-covalently synthesized supramolecular materials with distinct properties from a single building block. However, dynamic switching between functional states still remains challenging, but holds enormous potential in material chemistry to design smart materials. Herein, we demonstrate a chemical fuel-mediated strategy to dynamically switch between two distinctly emissive aggregates, originating from the self-assembly of a naphthalimide-appended peptide building block. A molecularly dissolved building block shows very weak blue emission, whereas, in the assembled state (Agg-1), it shows cyan emission through π stacking-mediated excimer emission. The addition of a chemical fuel, ethyl-3-(3-(dimethylamino)propyl)carbodiimide (EDC), converts the terminal aspartic acid present in the building block to an intra-molecularly cyclized anhydride in situ forming a second aggregated state, Agg-2, by changing the molecular packing, thereby transforming the emission to strong blue. Interestingly, the anhydride gets hydrolyzed gradually to reform Agg-1 and the initial cyan emission is restored. The kinetic stability of the strong blue emissive aggregate, Agg-2, can be regulated by the added concentration of the chemical fuel. Moreover, we expand the scope of this system within an agarose gel matrix, which allows us to gain spatiotemporal control over the properties, thereby producing a self-erasable writing system where the chemical fuel acts as the ink.

1-Naphthylacetic acid appended amino acids-based hydrogels: probing of the supramolecular catalysis of ester hydrolysis reaction

A 1-naphthaleneacetic acid-appended phenylalanine-derivative (Nap-F) forms a stable hydrogel with a minimum gelation concentration (MGC) of 0.7% w/v (21 mM) in phosphate buffer of pH 7.4. Interestingly, Nap-F produces two-component [Nap-F + H = Nap-FH, Nap-F + K = Nap-FK and Nap-F + R = Nap-FR], three-component [Nap-F + H + K = Nap-FH-K, Nap-F + H + R = Nap-FH-R and Nap-F + K + R = Nap-FK-R] and four-component [Nap-F + H + K + R = Nap-FH-K-R] hydrogels in water with all three natural basic amino acids (H = histidine, K = lysine and R = arginine) at various combinations below its MGC. Nap-F-hydrogel forms a nice entangled nanofibrillar network structure as evidenced by field emission scanning electron microscopy (FE-SEM). Interestingly, lysine-based co-assembled two- (Nap-FK), three- (Nap-FH-K and Nap-FK-R) and four-component (Nap-FH-K-R) xerogels exhibit helical nanofibrillar morphology, which was confirmed by circular dichroism spectroscopy, FE-SEM and TEM imaging. However, histidine and arginine-based two-component (Nap-FH and Nap-FR) and three-component (Nap-FH-R) co-assembled xerogels exhibiting straight nanofibrillar morphology. In their co-assembled states, these two-, three- and four-component supramolecular hydrogels show promising esterase-like activity below their MGCs. The enhanced catalytic activity of helical fibers compared to obtained straight fibers (other than lysine-based assembled systems) suggests that the helical fibrillar nanostructure is involved in ordering the esterase-like although all supramolecular assemblies are chemically different from one another.

Hierarchical Protofilament Intertwining Rules the Formation of Mixed-Curvature Amyloid Polymorphs

Amyloid polymorphism is a hallmark of almost all amyloid species, yet the mechanisms underlying the formation of amyloid polymorphs and their complex architectures remain elusive. Commonly, two main mesoscopic topologies are found in amyloid polymorphs characterized by non-zero Gaussian and mean curvatures: twisted ribbons and helical fibrils, respectively. Here, a rich heterogeneity of configurations is demonstrated on insulin amyloid fibrils, where protofilament packing can occur, besides the common polymorphs, also in a combined mode forming mixed-curvature polymorphs. Through AFM statistical analysis, an extended array of heterogeneous architectures that are rationalized by mesoscopic theoretical arguments are identified. Notably, an unusual fibrillization pathway is also unraveled toward mixed-curvature polymorphs via the widespread recruitment and intertwining of protofilaments and protofibrils. The results present an original view of amyloid polymorphism and advance the fundamental understanding of the fibrillization mechanism from single protofilaments into mature amyloid fibrils.

Probing the Stability of a β-Hairpin Scaffold after Desolvation

Probing the structural characteristics of biomolecular ions in the gas phase following native mass spectrometry (nMS) is of great interest, because noncovalent interactions, and thus native fold features, are believed to be largely retained upon desolvation. However, the conformation usually depends heavily on the charge state of the species investigated. In this study, we combine transition metal ion Förster resonance energy transfer (tmFRET) and ion mobility-mass spectrometry (IM-MS) with molecular dynamics (MD) simulations to interrogate the β-hairpin structure of GB1p in vacuo. Fluorescence lifetime values and collisional cross sections suggest an unfolding of the β-hairpin motif for higher charge states. MD simulations are consistent with experimental constraints, yet intriguingly provide an alternative structural interpretation: preservation of the β-hairpin is not only predicted for 2+ but also for 4+ charged species, which is unexpected given the substantial Coulomb repulsion for small secondary structure scaffolds.

Probing Backbone Coupling within Hydrated Proteins with Two-Color 2D Infrared Spectroscopy

The vibrational coupling between protein backbone modes and the role of water interactions are important topics in biomolecular spectroscopy. Our work reports the first study of the coupling between amide I and amide A modes within peptides and proteins with secondary structure and water contacts. We use two-color two-dimensional infrared (2D IR) spectroscopy and observe cross peaks between amide I and amide A modes. In experiments with peptides with different secondary structures and side chains, we observe that the spectra are sensitive to secondary structure. Water interactions affect the cross peaks, which may be useful as probes for the accessibility of protein sites to hydration water. Moving to two-color 2D IR spectra of proteins, the data demonstrate that the cross peaks integrate the sensitivities of both amide I and amide A spectra and that a two-color detection scheme may be a promising tool for probing secondary structures in proteins.

Structural characterization of amyloid aggregates with spatially resolved infrared spectroscopy

The self-assembly of proteins and peptides into ordered structures called amyloid fibrils is a hallmark of numerous diseases, impacting the brain, heart, and other organs. The structure of amyloid aggregates is central to their function and thus has been extensively studied. However, the structural heterogeneities between aggregates as they evolve throughout the aggregation pathway are still not well understood. Conventional biophysical spectroscopic methods are bulk techniques and only report on the average structural parameters. Understanding the structure of individual aggregate species in a heterogeneous ensemble necessitates spatial resolution on the length scale of the aggregates. Recent technological advances have led to augmentation of infrared (IR) spectroscopy with imaging modalities, wherein the photothermal response of the sample upon vibrational excitation is leveraged to provide spatial resolution beyond the diffraction limit. These combined approaches are ideally suited to map out the structural heterogeneity of amyloid ensembles. AFM-IR, which integrates IR spectroscopy with atomic force microscopy enables identification of the structural facets the oligomers and fibrils at individual aggregate level with nanoscale resolution. These capabilities can be extended to chemical mapping in diseased tissue specimens with submicron resolution using optical photothermal microscopy, which combines IR spectroscopy with optical imaging. This book chapter provides the basic premise of these novel techniques and provides the typical methodology for using these approaches for amyloid structure determination. Detailed procedures pertaining to sample preparation and data acquisition and analysis are discussed and the aggregation of the amyloid β peptide is provided as a case study to provide the reader the experimental parameters necessary to use these techniques to complement their research efforts.

Mechanism of Protein Aggregation Inhibition by Arginine: Blockage of Anionic Side Chains Favors Unproductive Encounter Complexes

Aggregation refers to the assembly of proteins into nonphysiological higher order structures. While amyloid has been studied extensively, much less is known about amorphous aggregation, a process that interferes with protein expression and storage. Free arginine (Arg+) is a widely used aggregation inhibitor, but its mechanism remains elusive. Focusing on myoglobin (Mb), we recently applied atomistic molecular dynamics (MD) simulations for gaining detailed insights into amorphous aggregation (Ng J. Phys. Chem. B 2021, 125, 13099). Building on that approach, the current work for the first time demonstrates that MD simulations can directly elucidate aggregation inhibition mechanisms. Comparative simulations with and without Arg+ reproduced the experimental finding that Arg+ significantly decreased the Mb aggregation propensity. Our data reveal that, without Arg+, protein-protein encounter complexes readily form salt bridges and hydrophobic contacts, culminating in firmly linked dimeric aggregation nuclei. Arg+ promotes the dissociation of encounter complexes. These "unproductive" encounter complexes are favored because Arg+ binding to D- and E- lowers the tendency of these anionic residues to form interprotein salt bridges. Side chain blockage is mediated largely by the guanidinium group of Arg+, which binds carboxylates through H-bond-reinforced ionic contacts. Our MD data revealed Arg+ self-association into a dynamic quasi-infinite network, but we found no evidence that this self-association is important for protein aggregation inhibition. Instead, aggregation inhibition by Arg+ is similar to that mediated by free guanidinium ions. The computational strategy used here should be suitable for the rational design of aggregation inhibitors with enhanced potency.

Characterizing amyloid protein conformation with a multi-resonant metasurface based biosensor in the infrared window

Misfolding of amyloid protein will cause neurodegeneration and trigger conformational disease. The lack of an effective detection approach is a brake on unveiling the mechanism of protein misfolding. We theoretically proposed a novel metasurface-based biosensor for characterizing the protein's conformation. The coupling complementary split ring resonator (cSRR) was engineered to manipulate incident waves in the near-infrared (NIR) and mid-infrared (MIR) windows at the same sensing surface. The cSRRs had the advantages of intensifying the electric field and sharpening the resonance profile, resulting in a highly qualified biosensing performance. In the NIR window, the biolayer's refractive index and thickness change were detected by the dual-wavelength, which resolved into an optogeometrical parameter of the amyloid biolayer. In the MIR window, the resonant wave specifically triggered the rotation-vibration transition of amyloid protein molecules with different conformations, which was shown as the unique Amide I and II bands in the fingerprint spectrum. Thus, our proposed biosensor presented sensitive detection of biolayer and specific identification of constituent molecules. It is helpful to interpret the protein's misfolding behavior on the molecular level by associating the biolayer's structure and the constituent molecule's conformational change.

Noncovalent interaction network of chalcogen, halogen and hydrogen bonds for supramolecular β-sheet organization

An alanine-based bilateral building block, linked by 2,5-thiophenediamide motifs and equipped with C-terminal 4-iodoaniline groups, was designed, allowing a noncovalent interaction network consisting of intramolecular chalcogen bonds and intermolecular halogen/hydrogen bonds, which cooperatively maintain a supramolecular β-sheet organization in the solid state, as well as in dilute CH3CN solution with a high g factor of -0.017.

Collagen Mimicry with a Short Collagen Model Peptide

Mimicking triple helix and fibrillar network of collagen through collagen model peptide(CMP) with short GPO tripeptide repeats is a great challenge. Herein, a minimalistic CMP comprising only five GPO repeats [(GPO)5 ] is presented. This novel approach involves the fusion of ultrashort peptide with the synergetic power of π-system and β-sheet formation to short CMP (GPO)5 . Accordingly, a hydrogel-forming, fluorenylmethoxycarbonyl (Fmoc)-functionalized ultrashort peptide (NFGAIL) is fused at the N-terminus and phenylalanine at the C-terminus of (GPO)5 (Fmoc-NFGAIL-(GPO)5 -F-COOH, FmP-5GPO). At room temperature, it forms a robust triple helix in aqueous buffer solution and has a relatively high melting point of 35 °C. The fluorenyl motif stabilizes the triple helix by aromatic π-π interactions as in its absence, triple helix is not formed. NFGAIL, which forms a β-sheet, also aids in triple helix stabilization via intermolecular hydrogen bonding and hydrophobic interactions. FmP-5GPO forms highly entangled nanofibrils with a micrometer length, which have excellent cell viability. The achievement of stable triple helix and fibrils in such a short CMP(FmP-5GPO) sequence is a challenging feat, and its significance in CMP-based biomaterials is undeniable. The present strategy highlights the potential for developing new CMP sequences through intelligent tuning of fusion peptides and GPO repeats.

Transition Metal Ion FRET-Based Probe to Study Cu(II)-Mediated Amyloid- Ligand Binding

Recent therapeutic strategies suggest that small peptides can act as aggregation inhibitors of monomeric amyloid-β (Αβ) by inducing structural rearrangements upon complexation. However, characterizing the binding events in such dynamic and transient noncovalent complexes, especially in the presence of natively occurring metal ions, remains a challenge. Here, we deploy a combined transition metal ion Förster resonance energy transfer (tmFRET) and native ion mobility-mass spectrometry (IM-MS) approach to characterize the structure of mass- and charge-selected Aβ complexes with Cu(II) ions (a quencher) and a potential aggregation inhibitor, a small neuropeptide named leucine enkephalin (LE). We show conformational changes of monomeric Αβ species upon Cu(II)-binding, indicating an uncoiled N-terminus and a close interaction between the C-terminus and the central hydrophobic region. Furthermore, we introduce LE labeled at the N-terminus with a metal-chelating agent, nitrilotriacetic acid (NTA). This allows us to employ tmFRET to probe the binding even in low-abundance and transient Aβ-inhibitor-metal ion complexes. Complementary intramolecular distance and global shape information from tmFRET and native IM-MS, respectively, confirmed Cu(II) displacement toward the N-terminus of Αβ, which discloses the binding region and the inhibitor's orientation.

Self-Assembly of a Novel Pentapeptide into Hydrogelated Dendritic Architecture: Synthesis, Properties, Molecular Docking and Prospective Applications

Currently, ultrashort oligopeptides consisting of fewer than eight amino acids represent a cutting-edge frontier in materials science, particularly in the realm of hydrogel formation. By employing solid-phase synthesis with the Fmoc/tBu approach, a novel pentapeptide, FEYNF-NH2, was designed, inspired by a previously studied sequence chosen from hen egg-white lysozyme (FESNF-NH2). Qualitative peptide analysis was based on reverse-phase high performance liquid chromatography (RP-HPLC), while further purification was accomplished using solid-phase extraction (SPE). Exact molecular ion confirmation was achieved by matrix-assisted laser desorption-ionization mass spectrometry (MALDI-ToF MS) using two different matrices (HCCA and DHB). Additionally, the molecular ion of interest was subjected to tandem mass spectrometry (MS/MS) employing collision-induced dissociation (CID) to confirm the synthesized peptide structure. A combination of research techniques, including Fourier-transform infrared spectroscopy (FTIR), fluorescence analysis, transmission electron microscopy, polarized light microscopy, and Congo red staining assay, were carefully employed to glean valuable insights into the self-assembly phenomena and gelation process of the modified FEYNF-NH2 peptide. Furthermore, molecular docking simulations were conducted to deepen our understanding of the mechanisms underlying the pentapeptide's supramolecular assembly formation and intermolecular interactions. Our study provides potential insights into amyloid research and proposes a novel peptide for advancements in materials science. In this regard, in silico studies were performed to explore the FEYNF peptide's ability to form polyplexes.

Self-Assembled Materials Based on Fully Aromatic Peptides: The Impact of Tryptophan, Tyrosine, and Dopa Residues

Peptides are able to self-organize in structural elements including cross-β structures. Taking advantage of this tendency, in the last decades, peptides have been scrutinized as molecular elements for the development of multivalent supramolecular architectures. In this context, different classes of peptides, also with completely aromatic sequences, were proposed. Our previous studies highlighted that the (FY)3 peptide, which alternates hydrophobic phenylalanine and more hydrophilic tyrosine residues, is able to self-assemble, thanks to the formation of both polar and apolar interfaces. It was observed that the replacement of Phe and Tyr residues with other noncoded aromatic amino acids like 2-naphthylalanine (Nal) and Dopa affects the interactions among peptides with consequences on the supramolecular organization. Herein, we have investigated the self-assembling behavior of two novel (FY)3 analogues with Trp and Dopa residues in place of the Phe and Tyr ones, respectively. Additionally, PEGylation of the N-terminus was analyzed too. The supramolecular organization, morphology, and capability to gel were evaluated using complementary techniques, including fluorescence, Fourier transform infrared spectroscopy, and scanning electron microscopy. Structural periodicities along and perpendicular to the fiber axis were detected by grazing incidence wide-angle X-ray scattering. Finally, molecular dynamics studies provided interesting insights into the atomic structure of the cross-β that constitutes the basic motif of the assemblies formed by these novel peptide systems.

Glucose-Responsive Self-Regulated Injectable Silk Fibroin Hydrogel for Controlled Insulin Delivery

Stimuli-responsive drug delivery systems are gaining importance in personalized medicine to deliver therapeutic doses in response to disease-specific stimulation. Pancreas-mimicking glucose-responsive insulin delivery systems offer improved therapeutic outcomes in the treatment of type 1 and advanced stage of type 2 diabetic conditions. Herein, we present a glucose-responsive smart hydrogel platform based on phenylboronic acid-functionalized natural silk fibroin protein for regulated insulin delivery. The modified protein was synergistically self-assembled and cross-linked through β-sheet and phenylboronate ester formation. The dynamic nature of the bonding confers smooth injectability through the needle. The cross-linked hydrogel structures firmly hold the glucose-sensing element and insulin in its pores and contribute to long-term sensing and drug storage. Under hyperglycemic conditions, the hydrogen peroxide generated from the sensing element induces hydrogel matrix degradation by oxidative cleavage, enabling insulin release. In vivo studies in a type 1 diabetic Wistar rat model revealed that the controlled insulin release from the hydrogel restored diabetic glucose level to physiological conditions for 36 h. This work establishes the functional modification of silk fibroin into a glucose-responsive hydrogel platform for regulated and functional insulin delivery application.

Transformable nano-antibiotics for mechanotherapy and immune activation against drug-resistant Gram-negative bacteria

The dearth of antibiotic candidates against Gram-negative bacteria and the rise of antibiotic resistance create a global health concern. The challenge lies in the unique Gram-negative bacterial outer membrane that provides the impermeable barrier for antibiotics and sequesters antigen presentation. We designed a transformable nano-antibiotics (TNA) that can transform from nontoxic nanoparticles to bactericidal nanofibrils with reasonable rigidity (Young's modulus, 21.6 ± 5.9 MPa) after targeting β-barrel assembly machine A (BamA) and lipid polysaccharides (LPSs) of Gram-negative bacteria. After morphological transformation, the TNA can penetrate and damage the bacterial envelope, disrupt electron transport and multiple conserved biosynthetic and metabolic pathways, burst bacterial antigen release from the outer membrane, and subsequently activate the innate and adaptive immunity. TNA kills Gram-negative bacteria in vitro and in vivo with undetectable resistance through multiple bactericidal modes of action. TNA treatment-induced vaccination results in rapid and long-lasting immune responses, protecting against lethal reinfections.

A Hairpin Motif in the Amyloid-β Peptide Is Important for Formation of Disease-Related Oligomers

The amyloid-β (Aβ) peptide is associated with the development of Alzheimer's disease and is known to form highly neurotoxic prefibrillar oligomeric aggregates, which are difficult to study due to their transient, low-abundance, and heterogeneous nature. To obtain high-resolution information about oligomer structure and dynamics as well as relative populations of assembly states, we here employ a combination of native ion mobility mass spectrometry and molecular dynamics simulations. We find that the formation of Aβ oligomers is dependent on the presence of a specific β-hairpin motif in the peptide sequence. Oligomers initially grow spherically but start to form extended linear aggregates at oligomeric states larger than those of the tetramer. The population of the extended oligomers could be notably increased by introducing an intramolecular disulfide bond, which prearranges the peptide in the hairpin conformation, thereby promoting oligomeric structures but preventing conversion into mature fibrils. Conversely, truncating one of the β-strand-forming segments of Aβ decreased the hairpin propensity of the peptide and thus decreased the oligomer population, removed the formation of extended oligomers entirely, and decreased the aggregation propensity of the peptide. We thus propose that the observed extended oligomer state is related to the formation of an antiparallel sheet state, which then nucleates into the amyloid state. These studies provide increased mechanistic understanding of the earliest steps in Aβ aggregation and suggest that inhibition of Aβ folding into the hairpin conformation could be a viable strategy for reducing the amount of toxic oligomers.

Computation meets experiment: identification of highly efficient fibrillating peptides

Self-assembling peptides are of huge interest for biological, medical and nanotechnological applications. The enormous chemical variety that is available from the 20 amino acids offers potentially unlimited peptide sequences, but it is currently an issue to predict their supramolecular behavior in a reliable and cheap way. Herein we report a computational method to screen and forecast the aqueous self-assembly propensity of amyloidogenic pentapeptides. This method was found also as an interesting tool to predict peptide crystallinity, which may be of interest for the development of peptide based drugs.

Amyloid peptide hydrogels via formation of coordination polymers with Ag+ by its core peptide equipped with a C-cysteine

We report that the core sequence of amyloid β (Aβ) peptide, KLVFF, when equipped with a C-terminal cysteine residue, exhibited an extremely low minimum hydrogelation concentration of 0.05 wt% in the presence of Ag+ in pH 5 buffer, with this concentration 2 orders of magnitude lower than that of the pentapeptide itself. The CD signal of the Ag+-L-KLVFFC hydrogel was observed to be sensitive to the early-stage aggregation of amyloid β peptide.

Glycopeptide-Based Supramolecular Hydrogels Induce Differentiation of Adipose Stem Cells into Neural Lineages

We applied a bottom-up approach to develop biofunctional supramolecular hydrogels from an aromatic glycodipeptide. The self-assembly of the glycopeptide was induced by either temperature manipulation (heating-cooling cycle) or solvent (DMSO to water) switch. The sol-gel transition was salt-triggered in cell culture media and resulted in gels with the same chemical compositions but different mechanical properties. Human adipose derived stem cells (hASCs) cultured on these gels under basal conditions (i.e., without differentiation factors) overexpressed neural markers, such as GFAP, Nestin, MAP2, and βIII-tubulin, confirming the differentiation into neural lineages. The mechanical properties of the gels influenced the number and distribution of the adhered cells. A comparison with gels obtained from the nonglycosylated peptide showed that glycosylation is crucial for the biofunctionality of the hydrogels by capturing and preserving essential growth factors, e.g., FGF-2.

A class of peptides designed to replicate and enhance the Receptor for Hyaluronic Acid Mediated Motility binding domain

The extra-cellular matrix (ECM) is a complex and rich microenvironment that is exposed and over-expressed across several injury or disease pathologies. Biomaterial therapeutics are often enriched with peptide binders to target the ECM with greater specificity. Hyaluronic acid (HA) is a major component of the ECM, yet to date, few HA adherent peptides have been discovered. A class of HA binding peptides was designed using B(X₇)B hyaluronic acid binding domains inspired from the helical face of the Receptor for Hyaluronic Acid Mediated Motility (RHAMM). These peptides were bioengineered using a custom alpha helical net method, allowing for the enrichment of multiple B(X₇)B domains and the optimisation of contiguous and non-contiguous domain orientations. Unexpectedly, the molecules also exhibited the behaviour of nanofiber forming self-assembling peptides and were investigated for this characteristic. Ten 23-27 amino acid residue peptides were assessed. Simple molecular modelling was used to depict helical secondary structures. Binding assays were performed with varying concentrations (1-10 mg/mL) and extra-cellular matrices (HA, collagens I-IV, elastin, and Geltrex). Concentration mediated secondary structures were assessed using circular dichroism (CD), and higher order nanostructures were visualized using transmission electron microscopy (TEM). All peptides formed the initial apparent 3₁₀/alpha-helices, yet peptides 17x-3, 4, BHP3 and BHP4 were HA specific and potent (i.e., a significant effect) binders at increasing concentrations. These peptides shifted from apparent 3₁₀/alpha-helical structures at low concentration to beta-sheets at increasing concentration and also formed nanofibers which are noted as self-assembling structures. Several of the HA binding peptides outperformed our positive control (mPEP35) at 3-4 times higher concentrations, and were enhanced by self-assembly as each of these groups had observable nanofibers. STATEMENT OF SIGNIFICANCE: Specific biomolecules or peptides have played a crucial role in developing materials or systems to deliver key drugs and therapeutics to a broad spectrum of diseases and disorders. In these diseased tissues, cells build protein/sugar networks, which are uniquely exposed and great targets to deliver drugs to. Hyaluronic acid (HA) is involved in every stage of injury and is abundant in cancer. To date, only two HA specific peptides have been discovered. In our work, we have designed a way to model and trace binding regions as they appear on the face of a helical peptide. Using this method we have created a family of peptides enriched with HA binding domains that stick with 3-4 higher affinity than those previously discovered.

Probing the binding and activation of small molecules by gas-phase transition metal clusters via IR spectroscopy

Isolated transition metal clusters have been established as useful models for extended metal surfaces or deposited metal particles, to improve the understanding of their surface chemistry and of catalytic reactions. For this objective, an important milestone has been the development of experimental methods for the size-specific structural characterization of clusters and cluster complexes in the gas phase. This review focusses on the characterization of molecular ligands, their binding and activation by small transition metal clusters, using cluster-size specific infrared action spectroscopy. A comprehensive overview and a critical discussion of the experimental data available to date is provided, reaching from the initial results obtained using line-tuneable CO₂ lasers to present-day studies applying infrared free electron lasers as well as other intense and broadly tuneable IR laser sources.

Effect of the spacer on the structure and self-assembly of FF peptide mimetics

We have designed and synthesized a series of FF peptide mimetics with conformationally rigid and flexible spacers to study the effect of spacers on their structure and self-assembly. The results help in understanding biomolecular aggregation and provide a strategy to obtain fractal pattern materials. From X-ray single crystal analysis, the m-diaminobenzene appended FF peptide mimetic adopts a duplex structure stabilized by multiple intermolecular hydrogen bonds. There is also a water molecule bridging between two strands of the duplex. Moreover, the duplex is stabilized by three face-to-face, face-to-edge and edge-to-edge π-π interactions. The duplex formation is also supported by mass spectrometry. In higher order packing, the dimeric subunits further self-assembled to form a complex sheet-like structure stabilized by multiple intermolecular hydrogen bonding and π-π stacking interactions. Moreover, the 1,4-butadiene and m-xylylenediamine appended FF peptide mimetics form stimuli-responsive organogels in a wide range of solvents including methanol. The rheology data of FF peptide mimetic gels as a function of angular frequency and oscillatory strain also supported the formation of strong physically crosslinked gels. The FE-SEM images of the xerogels obtained from different organic solvents show that the network morphology of FF peptide mimetics varies depending on the nature of the solvents.

Quantitative Ratiometric Biosensors Based on Fluorescent Ferrocene-Modified Histidine Dipeptide Nanoassemblies

Fluorescent proteins (FPs) provide a ratiometric readout for quantitative assessment of the destination of internalized biomolecules. FP-inspired peptide nanostructures that can compete with FPs in their capacity are the most preferred building blocks for the synthesis of fluorescent soft matter. However, realizing a ratiometric emission from a single peptide fluorophore remains exclusive since multicolor emission is a rare property in peptide nanostructures. Here, we describe a bioinspired peptidyl platform for ratiometric intracellular quantitation by employing a single ferrocene-modified histidine dipeptide. The intensiometric ratio of green to blue fluorescence correlates linearly with the concentration of the peptide by three orders of magnitude. The ratiometric fluorescence of the peptide is an assembly-induced emission originating from hydrogen bonds and aromatic interactions. Additionally, modular design enables ferrocene-modified histidine dipeptides to use as a general platform for the construction of intricate peptides that retain the ratiometric fluorescent properties. The ratiometric peptide technique promises flexibility in the design of a wide spectrum of stoichiometric biosensors for quantitatively understanding the trafficking and subcellular fate of biomolecules.

Silver-Nanoparticle-Embedded Short Amphiphilic Peptide Nanostructures and Their Plausible Application to Reduce Bacterial Infections

The microbiota-gut-brain axis (GBA) plays a critical role in the development of neurodegenerative diseases. Dysbiosis of the intestinal microbiome causes a significant alteration in the gut microbiota of Alzheimer's disease (AD) patients, followed by neuroinflammatory processes. Thus, AD beginning in the gut is closely related to an imbalance in gut microbiota, and hence a multidomain approach to reduce this imbalance by exerting positive effects on the gut microbiota is needed. In one example, a tyrosine-based short peptide amphiphile (sPA) was used to synthesize antibacterial AgNPs-sPA nanostructures. Such nanostructures showed high biocompatibility and low cytotoxicity, and therefore work as model drug delivery agents for addressing local bacterial infections. These may have therapeutic value for the treatment of microbiota-triggered progression of neurodegenerative diseases.

Developments in Trapped Ion Mobility Mass Spectrometry to Probe the Early Stages of Peptide Aggregation

Ion mobility mass spectrometry (IM-MS) has proven to be an excellent method to characterize the structure of amyloidogenic protein and peptide aggregates, which are formed in coincidence with the development of neurodegenerative diseases. However, it remains a challenge to obtain detailed structural information on all conformational intermediates, originating from the early onset of those pathologies, due to their complex and heterogeneous environment. One way to enhance the insights and the identification of these early stage oligomers is by employing high resolution ion mobility mass spectrometry experiments. This would allow us to enhance the mobility separation and MS characterization. Trapped ion mobility spectrometry (TIMS) is an ion mobility technique known for its inherently high resolution and has successfully been applied to the analysis of protein conformations among others. To obtain conformational information on fragile peptide aggregates, the instrumental parameters of the TIMS-Quadrupole-Time-of-Flight mass spectrometer (TIMS-qToF-MS) have to be optimized to allow the study of intact aggregates and ensure their transmission toward the detector. Here, we investigate the suitability and application of TIMS to probe the aggregation process, targeting the well-characterized M307-N319 peptide segment of the TDP-43 protein, which is involved in the development of amyotrophic lateral sclerosis. By studying the influence of key parameters over the full mass spectrometer, such as source temperature, applied voltages or RFs among others, we demonstrate that by using an optimized instrumental method TIMS can be used to probe peptide aggregation.

Toward Reagent-Free Discrimination of Alzheimer's Disease Using Blood Plasma Spectral Digital Biomarkers and Machine Learning

BACKGROUND

Alzheimer's disease (AD) is the most prevalent neurodegenerative disease. The detection of early-stage AD is particularly desirable because it would allow early intervention. However, a minimally invasive, low-cost, and accurate discrimination or diagnostic method for AD is especially difficult in the earliest stage of AD.

OBJECTIVE

The aim of this research is to discover blood plasma spectral digital biomarkers of AD, develop a novel intelligent method for the discrimination of AD and accelerate the translation of Fourier transform infrared (FTIR) spectral-based disease discrimination methods from the laboratory to clinical practice.

METHODS

Since vibration spectroscopy can provide the structure and chemical composition information of biological samples at the molecular level, we investigated the potential of FTIR spectral biomarkers of blood plasma to differentiate between AD patients and healthy controls. Combined with machine learning technology, we designed a hierarchical discrimination system that provides reagent-free and accurate AD discrimination based on blood plasma spectral digital biomarkers of AD.

RESULTS

Accurate segregation between AD patients and healthy controls was achieved with 89.3% sensitivity and 85.7% specificity for early-stage AD patients, 92.8% sensitivity and 87.5% specificity for middle-stage AD patients, and 100% sensitivity and 100% specificity for late-stage AD patients.

CONCLUSIONS

Our results show that blood plasma spectral digital biomarkers hold great promise as discrimination markers of AD, indicating the potential for the development of an inexpensive, reagent-free, and less laborious clinical test. As a result, our research outcome will accelerate the clinical application of spectral digital biomarkers and machine learning.

Long-range ordered amino acid assemblies exhibit effective optical-to-electrical transduction and stable photoluminescence

Bio-endogenous peptide molecules are ideal components for fabrication of biocompatible and environmentally friendly semiconductors materials. However, to date, their applications have been limited due to the difficulty in obtaining stable, high-performance devices. Herein, simple amino acid derivatives fluorenylmethoxycarbonyl-leucine (Fmoc-L) and fluorenylmethoxycarbonyl-tryptophan (Fmoc-W) are utilized to form long-range ordered supramolecular nanostructures by tight aromatic stacking and extensive hydrogen bonding with mechanical, electrical and optical properties. For the first time, without addition of any photosensitizers, pure Fmoc-L microbelts and Fmoc-W microwires exhibit Young's modulus up to 28.79 and 26.96 GPa, and unprecedently high values of photocurrent responses up to 2.2 and 2.3 μA/cm², respectively. Meanwhile, Fmoc-W microwires with stable blue fluorescent emission under continuous excitation are successfully used as LED phosphors. Mechanism analysis shows that these two amino acids derivatives firstly formed dimers to reduce the bandgap, then further assemble into bioinspired semiconductor materials using the dimers as the building blocks. In this process, aromatic residues of amino acids are more conducive to the formation of semiconducting characteristics than fluorenyl groups. STATEMENT OF SIGNIFICANCE: Long-range ordered amino acid derivative assemblies with mechanical, electrical and optical properties were fabricated by a green and facile biomimetic strategy. These amino acid assemblies have Young's modulus comparable to that of concrete and exhibit typical semiconducting characteristics. Even without the addition of any photosensitizer, pure amino acid assemblies can still produce a strong photocurrent response and an unusually stable photoluminescence. The results suggest that amino acid structures with hydrophilic C-terminal and aromatic residues are more conducive to the formation of semiconducting characteristics. This work unlocks the potential for amino acid molecules to self-assemble into high-performance bioinspired semiconductors, providing a reference for customized development of biocompatible and environmentally friendly semiconductor materials through rational molecular design.

Converting lysozyme to hydrogel: A multifunctional wound dressing that is more than antibacterial

Wounds are usually irregular in shapes, and accompanied with a series of disorders such as hemorrhage and bacteria contamination. Here, we report a multifunctional hydrogel prepared by phase-transited lysozyme (PTL), which presents antimicrobial, injectable, self-healing, tissue adhesive, hemostatic and biodegradable properties that fit the requirements of wound treatment. The lysozyme was unfolded under the action of tris(2-carboxyethyl)phosphine (TCEP), and then self-assembled into a hydrogel (PTLG). The phase transition expanded the antibacterial spectrum of lysozyme, PTLG effectively killed both Gram-positive bacteria (Staphylococcus aureus, Staphylococcus epidermidis) and Gram-negative bacteria (Escherichia coli, Acinetobacter baumannii) on contact. This dynamically cross-linked hydrogel exhibited injectable and self-healing abilities, and was capable of adapting to various wound morphologies. The tissue-adhesive nature derived from phase-transition, endowed PTLG with hemostatic effect. Meanwhile, PTLG exhibited biocompatibility towards mammalian cells. Furthermore, its anti-infective ability in vivo was verified in a mouse subcutaneous infection model, more than 98 % of S. epidermidis was reduced under PTLG injection. And PTLG could be biodegraded within four weeks in mice body. Overall, the proposed PTLG is a promising multifunctional dressing material that could accommodate the various demands of complex and deep wounds.

Designer D-peptides targeting the N-terminal region of α-synuclein to prevent parkinsonian-associated fibrilization and cytotoxicity

The deposition of α-synuclein (αS) aggregates in the gut and the brain is ever present in cases of Parkinson's disease. While the central non-amyloidogenic-component (NAC) region of αS plays a critical role in fibrilization, recent studies have identified a specific sequence from within the N-terminal region (NTR, residues 36-42) as a key modulator of αS fibrilization. Due to the lack of effective therapeutics which specifically target αS aggregates, we have developed a strategy to prevent the aggregation and subsequent toxicity attributed to αS fibrilization utilizing NTR targeting peptides. In this study, L- and D-isoforms of a hexa- (VAQKTV-Aib, 77-82 NAC) and heptapeptide (GVLYVGS-Aib, 36-42 NTR) containing a self-recognition component unique to αS, as well as a C-terminal disruption element, were synthesized to target primary sequence regions of αS that modulate fibrilization. The D-peptide that targets the NTR (NTR-TP-D) was shown by ThT fluorescence assays and TEM to be the most effective at preventing fibril formation and elongation, as well as increasing the abundance of soluble monomeric αS. In addition, NTR-TP-D alters the conformation of destabilised monomers into a less aggregation-prone state and reduces the hydrophobicity of αS fibrils via fibril remodelling. Furthermore, both NTR-TP isoforms alleviate the cytotoxic effects of αS aggregates in both Neuro-2a and Caco-2 cells. Together, this study highlights how targeting the NTR of αS using D-isoform peptide inhibitors may effectively combat the deleterious effects of αS fibrilization and paves the way for future drug design to utilise such an approach to treat Parkinson's disease.

How change in chirality prevents β-amyloid type interaction in a protonated cyclic dipeptide dimer

The protonated dimers of the diketopiperazine dipeptide cyclo (LPhe-LHis) and cyclo (LPhe-DHis) are studied by laser spectroscopy combined with mass spectrometry to shed light on the influence of stereochemistry on the clustering propensity of cyclic dipeptides. The marked spectroscopic differences experimentally observed in the hydride stretch region are well accounted for by the results of DFT calculations. Both diastereomeric protonated dimers involve a strong ionic hydrogen bond from the protonated imidazole ring of one monomer to the neutral imidazole nitrogen of the other. While this strong interaction is accompanied by a single NH⋯O hydrogen bond between the amide functions of the two moieties for the protonated dimer of cyclo (LPhe-DHis), that of cyclo (LPhe-LHis) involves two NH⋯O interactions, forming the motif of an antiparallel β sheet. Therefore, a change in chirality of the residue prevents the formation of the β sheet pattern observed in the amyloid type aggregation. These results emphasize the peculiar role of the histidine residue in peptide structure and interaction.

Color-Tunable Fluorescent Hierarchical Nanoassemblies with Concentration-Encoded Emission

Cephalopods possess a dynamic coloration behavior to change their iridescence due to the concentration-induced optical properties of chromatophores and hierarchical assembly of reflectin. However, cephalopods rarely have iridescence in the darkfield. It would be interesting to develop color-tunable fluorescent hierarchical nanoassemblies with concentration-encoded emission. Herein, to construct the bioavailable fluorophore with dynamic coloration properties, a histidine-rich peptide is designed, which can self-assemble into hierarchical nanoassemblies stabilized by hydrogen bonds and π-π stacking interactions. The peptidyl nanoassemblies emit fluorescent iridescence, encompassing the blue to orange region due to the assembly-induced emission. The fluorescence of histidine-rich peptides is color-tunable and reversible, which can be dynamically controlled in a concentration-encoded mode. Due to the coloration ability of histidine-rich peptides, fluorescent polychromatic human cells are developed, highlighting its potential role as a fluorescent candidate for future applications such as bioimaging, implantable light-emitting diodes, and photochromic camouflage.

Amyloid-β Inspired Short Peptide Amphiphile Facilitates Synthesis of Silver Nanoparticles as Potential Antibacterial Agents

An amyloid-β inspired biocompatible short peptide amphiphile (sPA) molecule was used for controlled and targeted delivery of bioactive silver nanoparticles via transforming sPA nanostructures. Such sPA-AgNPs hybrid structures can be further used to develop antibacterial materials to combat emerging bacterial resistance. Due to the excellent antibacterial activity of silver, the growth of clinically relevant bacteria was inhibited in the presence of AgNPs-sPA hybrids. Bacterial tests demonstrated that the high biocompatibility and low cytotoxicity of the designed sPA allow it to work as a model drug delivery agent. It therefore shows great potential in locally addressing bacterial infections. The results of our study suggest that these nanodevices have the potential to trap and then engage in the facile delivery of their chemical payload at the target site, thereby working as potential delivery materials. This system has potential therapeutic value for the treatment of microbiota triggered progression of neurodegenerative diseases.

Multiscale Exploration of Concentration-Dependent Amyloid-β(16-21) Amyloid Nucleation

Atomic descriptions of peptide aggregation nucleation remain lacking due to the difficulty of exploring complex configurational spaces on long time scales. To elucidate this process, we develop a multiscale approach combining a metadynamics-based method with cluster statistical mechanics to derive concentration-dependent free energy surfaces of nucleation at near-atomic resolution. A kinetic transition network of nucleation is then constructed and employed to systematically explore nucleation pathways and kinetics through stochastic simulations. This approach is applied to describe Aβ_16-21 amyloid nucleation, revealing a two-step mechanism involving disordered aggregates at millimolar concentration, and an unexpected mechanism at submillimolar concentrations that exhibits kinetics reminiscent of classical nucleation but atypical pathways involving growing clusters with structured cores wrapped by disordered surface. When this atypical mechanism is operative, critical nucleus size can be reflected by the nucleation reaction order. Collectively, our approach paves the way for a more quantitative and detailed understanding of peptide aggregation nucleation.

Supramolecular Hybrids from Cyanometallate Complexes and Diblock Copolypeptide Amphiphiles in Water

The self-assembly of discrete cyanometallates has attracted significant interest due to the potential of these materials to undergo soft metallophilic interactions as well as their optical properties. Diblock copolypeptide amphiphiles have also been investigated concerning their capacity for self-assembly into morphologies such as nanostructures. The present work combined these two concepts by examining supramolecular hybrids comprising cyanometallates with diblock copolypeptide amphiphiles in aqueous solutions. Discrete cyanometallates such as [Au(CN)2]-, [Ag(CN)2]-, and [Pt(CN)4]2- dispersed at the molecular level in water cannot interact with each other at low concentrations. However, the results of this work demonstrate that the addition of diblock copolypeptide amphiphiles such as poly-(L-lysine)-block-(L-cysteine) (Lysm-b-Cysn) to solutions of these complexes induces the supramolecular assembly of the discrete cyanometallates, resulting in photoluminescence originating from multinuclear complexes with metal-metal interactions. Electron microscopy images confirmed the formation of nanostructures of several hundred nanometers in size that grew to form advanced nanoarchitectures, including those resembling the original nanostructures. This concept of combining diblock copolypeptide amphiphiles with discrete cyanometallates allows the design of flexible and functional supramolecular hybrid systems in water.

Mass Spectrometry-Based Techniques to Elucidate the Sugar Code

Cells encode information in the sequence of biopolymers, such as nucleic acids, proteins, and glycans. Although glycans are essential to all living organisms, surprisingly little is known about the "sugar code" and the biological roles of these molecules. The reason glycobiology lags behind its counterparts dealing with nucleic acids and proteins lies in the complexity of carbohydrate structures, which renders their analysis extremely challenging. Building blocks that may differ only in the configuration of a single stereocenter, combined with the vast possibilities to connect monosaccharide units, lead to an immense variety of isomers, which poses a formidable challenge to conventional mass spectrometry. In recent years, however, a combination of innovative ion activation methods, commercialization of ion mobility-mass spectrometry, progress in gas-phase ion spectroscopy, and advances in computational chemistry have led to a revolution in mass spectrometry-based glycan analysis. The present review focuses on the above techniques that expanded the traditional glycomics toolkit and provided spectacular insight into the structure of these fascinating biomolecules. To emphasize the specific challenges associated with them, major classes of mammalian glycans are discussed in separate sections. By doing so, we aim to put the spotlight on the most important element of glycobiology: the glycans themselves.

Biomaterials via peptide assembly: Design, characterization, and application in tissue engineering

A core challenge in biomaterials, with both fundamental significance and technological relevance, concerns the rational design of bioactive microenvironments. Designed properly, peptides can undergo supramolecular assembly into dynamic, physical hydrogels that mimic the mechanical, topological, and biochemical features of native tissue microenvironments. The relatively facile, inexpensive, and automatable preparation of peptides, coupled with low batch-to-batch variability, motivates the expanded use of assembling peptide hydrogels for biomedical applications. Integral to realizing dynamic peptide assemblies as functional biomaterials for tissue engineering is an understanding of the molecular and macroscopic features that govern assembly, morphology, and biological interactions. In this review, we first discuss the design of assembling peptides, including primary structure (sequence), secondary structure (e.g., α-helix and β-sheets), and molecular interactions that facilitate assembly into multiscale materials with desired properties. Next, we describe characterization tools for elucidating molecular structure and interactions, morphology, bulk properties, and biological functionality. Understanding of these characterization methods enables researchers to access a variety of approaches in this ever-expanding field. Finally, we discuss the biological properties and applications of peptide-based biomaterials for engineering several important tissues. By connecting molecular features and mechanisms of assembling peptides to the material and biological properties, we aim to guide the design and characterization of peptide-based biomaterials for tissue engineering and regenerative medicine. STATEMENT OF SIGNIFICANCE: Engineering peptide-based biomaterials that mimic the topological and mechanical properties of natural extracellular matrices provide excellent opportunities to direct cell behavior for regenerative medicine and tissue engineering. Here we review the molecular-scale features of assembling peptides that result in biomaterials that exhibit a variety of relevant extracellular matrix-mimetic properties and promote beneficial cell-biomaterial interactions. Aiming to inspire and guide researchers approaching this challenge from both the peptide biomaterial design and tissue engineering perspectives, we also present characterization tools for understanding the connection between peptide structure and properties and highlight the use of peptide-based biomaterials in neural, orthopedic, cardiac, muscular, and immune engineering applications.

Laser Photodissocation, Action Spectroscopy and Mass Spectrometry Unite to Detect and Separate Isomers

The separation and detection of isomers remains a challenge for many areas of mass spectrometry. This article highlights laser photodissociation and ion mobility strategies that have been deployed to tackle...

Porphyrinoids, a unique platform for exploring excited-state aromaticity

Recently, Baird (anti)aromaticity has been referred to as a description of excited-state (anti)aromaticity. With the term of Baird's rule, recent studies have intensively verified that the Hückel aromatic [4n + 2]π (or antiaromatic [4n]π) molecules in the ground state are reversed to give Baird aromatic [4n]π (or Baird antiaromatic [4n + 2]π) molecules in the excited states. Since the Hückel (anti)aromaticity has great influence on the molecular properties and reaction mechanisms, the Baird (anti)aromaticity has been expected to act as a dominant factor in governing excited-state properties and processes, which has attracted intensive scientific investigations for the verification of the concept of reversed aromaticity in the excited states. In this scientific endeavor, porphyrinoids have recently played leading roles in the demonstration of the aromaticity reversal in the excited states and its conceptual development. The distinct structural and electronic nature of porphyhrinoids depending on their (anti)aromaticity allow the direct observation of excited-state aromaticity reversal, Baird's rule. The explicit experimental demonstration with porphyrinoids has contributed greatly to its conceptual development and application in novel functional organic materials. Based on the significant role of porphyrinoids in the field of excited-state aromaticity, this review provides an overview of the experimental verification of the reversal concept of excited-state aromaticity by porphyrinoids and the recent progress on its conceptual application in novel functional molecules.

Singular value decomposition analysis of the secondary structure features contributing to the circular dichroism spectra of model proteins

Amyloid fibril formation occurs in restricted environment, such as the interface between intercellular fluids and bio-membranes. Conformational interconversion from α-helix to β-structure does not progress in fluids; however, it can occur after sedimentary aggregation during amyloid fibril formation induced by heat treatment of hen egg white lysozyme (HEWL). Secondary structures of various proteins and denatured proteins titrated with 2,2,2-trifluoroethanol (TFE) were examined using their CD spectra. Gaussian peak/trough and singular value decompositions (SVD) showed that the spectral pattern of the α-helix comprised a sharp trough at wavelength 207 nm and a broad trough at 220 nm. Conversely, we distinguished two patterns for β-sheet-a spread barrel type, corresponding to ConA, and a tightly weaved type, corresponding to the soybean trypsin inhibitor. Herein, we confirmed that the spectral/conformational interconversion of the heat-treated HEWL was not observed in the dissolved fluid.

Amyloidogenicity of peptides targeting diabetes and obesity

Since the discovery of insulin, a century ago, the repertoire of therapeutic polypeptides targeting diabetes - and now also obesity - have increased substantially. The focus on quality has shifted from impure and unstable preparations of animal insulin to highly pure, homologous recombinant insulin, along with other peptide-based hormones and analogs such as amylin analogs (pramlintide, davalintide, cagrilintide), glucagon and glucagon-like peptide-1 receptor agonists (GLP-1, liraglutide, exenatide, semaglutide). Proper formulation, storage, manipulation and usage by professionals and patients are required in order to avoid agglomeration into high molecular weight products (HMWP), either amorphous or amyloid, which could result in potential loss of biological activity and short- or long-term immune reaction and silent inactivation. In this narrative review, we present perspective of the aggregation of therapeutic polypeptides used in diabetes and other metabolic diseases, covering the nature and mechanisms, analytical techniques, physical and chemical stability, strategies aimed to hamper the formation of HMWP, and perspectives on future biopharmaceutical developments.

Cross-Seeded Fibrillation Induced by Pyroglutamate-3 and Truncated Aβ40 Variants Leads to Aβ40 Structural Polymorphism Modulation and Elevated Toxicity

The pathological amyloid plaques in Alzheimer's disease (AD) patients contain not only the wild-type β-amyloid (wt-Aβ) peptide sequences but also a variety of post-translationally modified variants. The pyroglutamate-3 Aβ (pyroE3-Aβ), which is generated from its truncated precursors ΔE3-Aβ, shows the highest abundance among all modified Aβ variants. Previous works have shown that pyroE3-Aβ and/or ΔE3-Aβ, compared with the wild-type sequences, led to a more rapid fibrillation process and final fibrils with higher neuronal cytotoxicity levels. However, much less is known about how the formation of pyroE3/ΔE3-Aβ fibrils would affect the amyloid deposition of wt-Aβ peptides, which are the main pathological events in AD. We show in the present work that the pyroE3/ΔE3-Aβ₄₀ fibrils differ significantly from the wt-Aβ₄₀ fibrils in terms of their molecular structures. When added into monomeric wt-Aβ₄₀ peptides, these variant fibrils can cross-seed the formation of wt-Aβ₄₀ fibrils with fibrillation kinetics that are greater than the self-seeded fibrillation of wt-Aβ₄₀. Furthermore, the cross-seeding process modulates the molecular structures of the yielded wt-Aβ₄₀ fibrils, which show similar features as their variant seeds. The cross-seeded fibrillation process also induces higher cytotoxicity levels compared with the self-seeded fibrillation of wt-Aβ₄₀. Overall, our results support the hypothesis that pyroE3 and ΔE3-Aβ₄₀ variants may serve as triggering factors of the pathological amyloid aggregation of wt-Aβ₄₀ and may underlie the pathological significance of pyroE3/ΔE3-Aβ₄₀ variants on the structural polymorphism of Aβ deposits.

Weight average approaches for predicting dynamical properties of biomolecules

Recent advances in atomistic molecular dynamics (MD) simulations of biomolecules allow us to explore their conformational spaces widely, observing large-scale conformational fluctuations or transitions between distinct structures. To reproduce or refine experimental data using MD simulations, structure ensembles, which are characterized by multiple structures and their statistical weights on the rugged free-energy landscapes, are often used. Here, we summarize weight average approaches for various experimental measurements. Weight average approaches are now applied to hybrid quantum mechanics/molecular mechanics MD simulations to predict fast vibrational motions in a protein with a high accuracy for better understanding of molecular functions from atomic structures.

AI-based spectroscopic monitoring of real-time interactions between SARS-CoV-2 and human ACE2

The COVID-19 caused by SARS-CoV-2 virus has posed a tremendous threat to human health. The interactions between human angiotensin-converting enzyme 2 and the spike glycoprotein of SARS-CoV-2 hold the key to understanding the molecular mechanism to develop treatment and vaccines. However, the simulation of these interactions in fluctuating surroundings is challenging because it requires many electronic structure calculations at the quantum mechanics level for a large number of representative configurations. We report a machine learning protocol that can efficiently predict the IR spectra of SARS-CoV-2 with high efficiency and characterize fine changes in IR spectra associated with variations of protein secondary structures. Machine learning provides a cost-effective tool for monitoring of real-time interactions between the SARS-CoV-2 and human ACE2.

The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), invades a human cell via human angiotensin-converting enzyme 2 (hACE2) as the entry, causing the severe coronavirus disease (COVID-19). The interactions between hACE2 and the spike glycoprotein (S protein) of SARS-CoV-2 hold the key to understanding the molecular mechanism to develop treatment and vaccines, yet the dynamic nature of these interactions in fluctuating surroundings is very challenging to probe by those structure determination techniques requiring the structures of samples to be fixed. Here we demonstrate, by a proof-of-concept simulation of infrared (IR) spectra of S protein and hACE2, that time-resolved spectroscopy may monitor the real-time structural information of the protein−protein complexes of interest, with the help of machine learning. Our machine learning protocol is able to identify fine changes in IR spectra associated with variation of the secondary structures of S protein of the coronavirus. Further, it is three to four orders of magnitude faster than conventional quantum chemistry calculations. We expect our machine learning protocol would accelerate the development of real-time spectroscopy study of protein dynamics.