Electrostatic Complementarity Drives Amyloid/Nucleic Acid Co-Assembly

A Matter of Charge: Electrostatically Tuned Coassembly of Amphiphilic Peptides

Coassembly of peptide biomaterials offers a compelling avenue to broaden the spectrum of hierarchically ordered supramolecular nanoscale structures that may be relevant for biomedical and biotechnological applications. In this work coassemblies of amphiphilic and oppositely charged, anionic and cationic, β-sheet peptides are studied, which may give rise to a diverse range of coassembled forms. Mixtures of the peptides show significantly lower critical coassembly concentration (CCC) values compared to those of the individual pure peptides. Intriguingly, the highest formation of coassembled fibrils is found to require excess of the cationic peptide whereas equimolar mixtures of the peptides exhibited the maximum folding into β-sheet structures. Mixtures of the peptides coassembled sequentially from solutions at concentrations surpassing each peptide's intrinsic critical assembly concentration (CAC), are also found to require a higher portion of the cationic peptide to stabilize hydrogels. This study illuminates a systematic investigation of oppositely charged β-sheet peptides over a range of concentrations, in solutions and in hydrogels. The results may be relevant to the fundamental understanding of such intricate charge-driven assembly systems and to the formulation of peptide-based nanostructures with diverse functionalities.

Engineering Synthetic Electron Transfer Chains from Metallopeptide Membranes

The energetic and geometric features enabling redox chemistry across the copper cupredoxin fold contain key components of electron transfer chains (ETC), which have been extended here by templating the cross-β bilayer assembly of a synthetic nonapeptide, HHQALVFFA-NH2 (K16A), with copper ions. Similar to ETC cupredoxin plastocyanin, these assemblies contain copper sites with blue-shifted (λmax 573 nm) electronic transitions and strongly oxidizing reduction potentials. Electron spin echo envelope modulation and X-ray absorption spectroscopies define square planar Cu(II) sites containing a single His ligand. Restrained molecular dynamics of the cross-β peptide bilayer architecture support metal ion coordination stabilizing the leaflet interface and indicate that the relatively high reduction potential is not simply the result of distorted coordination geometry (entasis). Cyclic voltammetry (CV) supports a charge-hopping mechanism across multiple copper centers placed 10-12 Å apart within the assembled peptide leaflet interface. This metal-templated scaffold accordingly captures the electron shuttle and cupredoxin functionality in a peptide membrane-localized electron transport chain.

An Analysis of Nucleotide-Amyloid Interactions Reveals Selective Binding to Codon-Sized RNA

Interactions between RNA and proteins are the cornerstone of many important biological processes from transcription and translation to gene regulation, yet little is known about the ancient origin of said interactions. We hypothesized that peptide amyloids played a role in the origin of life and that their repetitive structure lends itself to building interfaces with other polymers through avidity. Here, we report that short RNA with a minimum length of three nucleotides binds in a sequence-dependent manner to peptide amyloids. The 3'-5' linked RNA backbone appears to be well-suited to support these interactions, with the phosphodiester backbone and nucleobases both contributing to the affinity. Sequence-specific RNA-peptide interactions of the kind identified here may provide a path to understanding one of the great mysteries rooted in the origin of life: the origin of the genetic code.

Intrinsic SERS Fingerprints of Aptamer-Peptide Conjugates for Direct High-Specific Profiling Abnormal Protein Levels in Cancer Patients

Surface-enhanced Raman spectroscopy (SERS) with ultrasensitive vibrational fingerprints enables quick identification and trace detection of various kinds of molecules. But proteins usually have low Raman cross sections and are difficult to generate recognizable signals in direct SERS detection. Recently, nucleic acid-peptide conjugates are emerging with great potential in structuring, assembling, catalyzing, sensing, etc., and the coupling of aptamers further enables superior biological recognition and programmability. Here, we develop the aptamer-peptide conjugates as a new kind of SERS probe for direct high-specific profiling abnormal protein levels in cancer patients. The aptamer conjugated with glutathione (GSH) functions as both the recognition element and the SERS reporters that can simultaneously generate SERS fingerprints of both peptides and nucleic acids. This kind of biocompatible probe appears to have excellent performance in high-salt environments and realizes rapid, simple, and multisignal detection of thrombin (TB). Data-driven soft independent modeling of class analogy (DD-SIMCA) is used to distinguish SERS profiles of actual blood samples and realize the identification and classification of cancer patients. Furthermore, the effect of low-temperature storage time on blood samples is analyzed by tracking the changes of SERS profiles; the results hint that plasma samples stored under 4 °C for more than 2 days could generate false negative results due to TB hydrolysis, which has important implications for clinical sample analysis. This kind of nucleic acid-peptide conjugate provides new ideas for SERS sensing strategy in the future.

DNA-templated self-assembly of bradykinin into bioactive nanofibrils

Bradykinin (BK) is a peptide hormone that plays a crucial role in blood pressure control, regulates inflammation in the human body, and has recently been implicated in the pathophysiology of COVID-19. In this study, we report a strategy for fabricating highly ordered 1D nanostructures of BK using DNA fragments as a template for self-assembly. We have combined synchrotron small-angle X-ray scattering and high-resolution microscopy to provide insights into the nanoscale structure of BK-DNA complexes, unveiling the formation of ordered nanofibrils. Fluorescence assays hint that BK is more efficient at displacing minor-groove binders in comparison with base-intercalant dyes, thus, suggesting that interaction with DNA strands is mediated by electrostatic attraction between cationic groups at BK and the high negative electron density of minor-grooves. Our data also revealed an intriguing finding that BK-DNA complexes can induce a limited uptake of nucleotides by HEK-293t cells, which is a feature that has not been previously reported for BK. Moreover, we observed that the complexes retained the native bioactivity of BK, including the ability to modulate Ca²⁺ response into endothelial HUVEC cells. Overall, the findings presented here demonstrate a promising strategy for the fabrication of fibrillar structures of BK using DNA as a template, which keep bioactivity features of the native peptide and may have implications in the development of nanotherapeutics for hypertension and related disorders.

Dynamic exchange controls the assembly structure of nucleic-acid-peptide chimeras

Recent attempts to develop the next generation of functional biomaterials focus on systems chemistry approaches exploiting dynamic networks of hybrid molecules. This task is often found challenging, but we herein present ways for profiting from the multiple interaction interfaces forming Nucleic-acid-Peptide assemblies and tuning their formation. We demonstrate that the formation of well-defined structures by double-stranded DNA-peptide conjugates (dsCon) is restricted to a specific range of environmental conditions and that precise DNA hybridization, satisfying the interaction interfaces, is a crucial factor in this process. We further reveal the impact of external stimuli, such as competing free DNA elements or salt additives, which initiate dynamic interconversions, resulting in hybrid structures exhibiting spherical and fibrillar domains or a mixture of spherical and fibrillar particles. This extensive analysis of the co-assembly systems chemistry offers new insights into prebiotic hybrid assemblies that may now facilitate the design of new functional materials. We discuss the implications of these findings for the emergence of function in synthetic materials and during early chemical evolution.

Peptidyl Virus-Like Nanovesicles as Reconfigurable "Trojan Horse" for Targeted siRNA Delivery and Synergistic Inhibition of Cancer Cells

The self-assembly of peptidyl virus-like nanovesicles (pVLNs) composed of highly ordered peptide bilayer membranes that encapsulate the small interfering RNA (siRNA) is reported. The targeting and enzyme-responsive sequences on the bilayer's surface allow the pVLNs to enter cancer cells with high efficiency and control the release of genetic drugs in response to the subcellular environment. By transforming its structure in response to the highly expressed enzyme matrix metalloproteinase 7 (MMP-7) in cancer cells, it helps the siRNA escape from the lysosomes, resulting in a final silencing efficiency of 92%. Moreover, the pVLNs can serve as reconfigurable "Trojan horse" by transforming into membranes triggered by the MMP-7 and disrupting the cytoplasmic structure, thereby achieving synergistic anticancer effects and 96% cancer cell mortality with little damage to normal cells. The pVLNs benefit from their biocompatibility, targeting, and enzyme responsiveness, making them a promising platform for gene therapy and anticancer therapy.

Tuning dynamic DNA- and peptide-driven self-assembly in DNA-peptide conjugates

DNA-peptide conjugates offer an opportunity to marry the benefits of both biomolecular classes, combining the high level of programmability found with DNA, with the chemical diversity of peptides. These hybrid systems offer potential in fields such as therapeutics, nanotechnology, and robotics. Using the first DNA-β-turn peptide conjugate, we present three studies investigating the self-assembly of DNA-peptide conjugates over a period of 28 days. Time-course studies, such as these have not been previously conducted for DNA-peptide conjugates, although they are common in pure peptide assembly, for example in amyloid research. By using aging studies to assess the structures produced, we gain insights into the dynamic nature of these systems. The first study explores the influence varying amounts of DNA-peptide conjugates have on the self-assembly of our parent peptide. Study 2 explores how DNA and peptide can work together to change the structures observed during aging. Study 3 investigates the presence of orthogonality within our system by switching the DNA and peptide control on and off independently. These results show that two orthogonal self-assemblies can be combined and operated independently or in tandem within a single macromolecule, with both spatial and temporal effects upon the resultant nanostructures.

Polyanion order controls liquid-to-solid phase transition in peptide/nucleic acid co-assembly

The Central Dogma highlights the mutualistic functions of protein and nucleic acid biopolymers, and this synergy appears prominently in the membraneless organelles widely distributed throughout prokaryotic and eukaryotic organisms alike. Ribonucleoprotein granules (RNPs), which are complex coacervates of RNA with proteins, are a prime example of these membranelles organelles and underly multiple essential cellular functions. Inspired by the highly dynamic character of these organelles and the recent studies that ATP both inhibits and templates phase separation of the fused in sarcoma (FUS) protein implicated in several neurodegenerative diseases, we explored the RNA templated ordering of a single motif of the Aβ peptide of Alzheimer's disease. We now know that this strong cross-β propensity motif alone assembles through a liquid-like coacervate phase that can be externally templated to form distinct supramolecular assemblies. Now we provide evidence that structured phosphates, ranging from complex structures like double stranded and quadraplex DNA to simple trimetaphosphate, differentially impact the liquid to solid phase transition necessary for paracrystalline assembly. The results from this simple model illustrate the potential of ordered environmental templates in the transition to potentially irreversible pathogenic assemblies and provides insight into the ordering dynamics necessary for creating functional synthetic polymer co-assemblies.

Amyloid protein-induced sequestration of the eukaryotic ribosome: effect of stoichiometry and polyphenolic inhibitors

Alzheimer's disease (AD) is characterized by the appearance of neurofibrillary tangles comprising of the Tau protein and aggregation of amyloid-β peptides (Aβ 1-40 and Aβ 1-42). A concomitant loss of the ribosomal population is also observed in AD-affected neurons. Our studies demonstrate that, similarly to Tau protein aggregation, in vitro aggregation of Aβ peptides in the vicinity of the yeast 80S ribosome can induce co-aggregation of ribosomal components. The RNA-stimulated aggregation of Aβ peptides and the Tau-K18 variant is dependent on the RNA:protein stoichiometric ratio. A similar effect of stoichiometry is also observed on the ribosome-protein co-aggregation process. Polyphenolic inhibitors of amyloid aggregation, such as rosmarinic acid and myricetin, inhibit RNA-stimulated Aβ and Tau-K18 aggregation and can mitigate the co-aggregation of ribosomal components.

Primitive selection of the fittest emerging through functional synergy in nucleopeptide networks

Many fundamental cellular and viral functions, including replication and translation, involve complex ensembles hosting synergistic activity between nucleic acids and proteins/peptides. There is ample evidence indicating that the chemical precursors of both nucleic acids and peptides could be efficiently formed in the prebiotic environment. Yet, studies on nonenzymatic replication, a central mechanism driving early chemical evolution, have focused largely on the activity of each class of these molecules separately. We show here that short nucleopeptide chimeras can replicate through autocatalytic and cross-catalytic processes, governed synergistically by the hybridization of the nucleobase motifs and the assembly propensity of the peptide segments. Unequal assembly-dependent replication induces clear selectivity toward the formation of a certain species within small networks of complementary nucleopeptides. The selectivity pattern may be influenced and indeed maximized to the point of almost extinction of the weakest replicator when the system is studied far from equilibrium and manipulated through changes in the physical (flow) and chemical (template and inhibition) conditions. We postulate that similar processes may have led to the emergence of the first functional nucleic-acid-peptide assemblies prior to the origin of life. Furthermore, spontaneous formation of related replicating complexes could potentially mark the initiation point for information transfer and rapid progression in complexity within primitive environments, which would have facilitated the development of a variety of functions found in extant biological assemblies.

Metal Complex Lipids for Fluid-Fluid Phase Separation in Coassembled Phospholipid Membranes

We demonstrate a fluid-fluid phase separation in 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) membranes using a metal complex lipid of type [Mn(L1)] (1; HL1=1-(2-hydroxybenzamide)-2-(2-hydroxy-3-formyl-5-hexadecyloxybenzylideneamino)ethane). Small amount of 1 produces two separated domains in DMPC, whose phase transition temperatures of lipids (T_c ) are both lower than that of the pristine DMPC. Variable temperature fluorescent microscopy for giant-unilamellar vesicles of DMPC/1 hybrids demonstrates that visible phase separations remain in fluid phases up to 37 °C, which is clearly over the T_c of DMPC. This provides a new dimension for the application of metal complex lipids toward controlling lipid distributions in fluid membranes.

Chemical control of peptide material phase transitions

Progressive solute-rich polymer phase transitions provide pathways for achieving ordered supramolecular assemblies. Intrinsically disordered protein domains specifically regulate information in biological networks via conformational ordering. Here we consider a molecular tagging strategy to control ordering transitions in polymeric materials and provide a proof-of-principle minimal peptide phase network captured with a dynamic chemical network.

Substrate initiated assembly of a dynamic chemical network.

Supramolecular Architectures of Nucleic Acid/Peptide Hybrids

Supramolecular architectures that are built artificially from biomolecules, such as nucleic acids or peptides, with structural hierarchical orders ranging from the molecular to nano-scales have attracted increased attention in molecular science research fields. The engineering of nanostructures with such biomolecule-based supramolecular architectures could offer an opportunity for the development of biocompatible supramolecular (nano)materials. In this review, we highlighted a variety of supramolecular architectures that were assembled from both nucleic acids and peptides through the non-covalent interactions between them or the covalently conjugated molecular hybrids between them.

Unraveling diverse action of triton X-100 and methimazole on lysozyme fibrillation/aggregation: Physicochemical insights

Identification of functionalities responsible for prevention of fibrillation in proteins is important to design effective drugs in addressing neurodegenerative diseases. We have used nonionic surfactant triton X-100 (TX-100) and antithyroid drug methimazole (MMI) to understand mechanistic aspects of action of these molecules having different functionalities on hen egg-white lysozyme at different stages of fibrillation. After establishing the nucleation, elongation and maturation stages of fibrillation of protein at 57 °C, energetics of interactions with these molecules have been determined by using isothermal titration calorimetry. Differential scanning calorimetry has permitted assessment of thermal stability of the protein at these stages, with or without these molecular entities. The enthalpies of interaction of TX-100 and MMI with protein fibrils suggest importance of hydrogen bonding and polar interactions in their effectiveness towards prevention of fibrils. TX-100, in spite of several polar centres, is unable to prevent fibrillation, rather it promotes. MMI is able to establish polar interactions with interacting strands of the protein and disintegrate fibrils. A rigorous comparison with inhibitors reported in literature highlights importance -OH and >CO functionalities in fibrillation prevention. Even though MMI has hydrogen bonding centres, its efficiency as inhibitor falls after the inhibited lysozyme fibrils further interact and form amorphous aggregates.

Peak Force Infrared-Kelvin Probe Force Microscopy

Correlative scanning probe microscopy of chemical identity, surface potential, and mechanical properties provide insight into the structure-function relationships of nanomaterials. However, simultaneous measurement with comparable and high resolution is a challenge. We seamlessly integrated nanoscale photothermal infrared imaging with Coulomb force detection to form peak force infrared-Kelvin probe force microscopy (PFIR-KPFM), which enables simultaneous nanomapping of infrared absorption, surface potential, and mechanical properties with approximately 10 nm spatial resolution in a single-pass scan. MAPbBr₃ perovskite crystals of different degradation pathways were studied in situ. Nanoscale charge accumulations were observed in MAPbBr₃ near the boundary to PbBr₂ . PFIR-KPFM also revealed correlations between residual charges and secondary conformation in amyloid fibrils. PFIR-KPFM is applicable to other heterogeneous materials at the nanoscale for correlative multimodal characterizations.