Peptide Self-assembly: From Ordered to Disordered.

Biomolecular self-assembly is a ubiquitous occurrence in nature that gives rise to sophisticated superstructures that enable the implementation of complex biological functions. It encompasses both ordered structures, such as the DNA double helix, and disordered structures, such as the nucleolus and other nonmembranous organelles. In contrast to these highly organized ordered structures, which exhibit specific patterns or symmetry, disordered structures are characterized by their flexible and randomized molecular organization, which provides versatility, dynamicity, and adaptability to biological systems and contributes to the complexity and functionality of living organisms. However, these disordered structures usually exist in a thermodynamically metastable state. This means that these disordered structures are unstable and difficult to observe due to their short existence time. Achieving disordered structures through precise control of the assembly process and ensuring their stability and integrity pose significant challenges. Currently, ongoing research efforts are focused on the self-assembly of proteins with intrinsically disordered regions (IDRs). However, the structural complexity and instability of proteins present prohibitive difficulties in elucidating the multiscale self-assembly process. Therefore, simple peptides, as a segment of proteins, hold great promise in constructing self-assembly systems for related research. Since our finding on droplet-like disordered structures that occur transiently during the peptide self-assembly (PSA), our research is centered around the dynamic evolution of peptide supramolecular systems, particularly the modulation of a variety of assembled structures ranging from ordered to disordered.In this Account, we narrate our recent research endeavors on supramolecular structures formed by PSA, spanning from ordered structures to disordered structures. We delve into the mechanisms of structural regulation, shedding light on how these peptide-based structures can be controlled more precisely. Moreover, we emphasize the functional applications that arise from these structures. To begin, we conduct a comprehensive overview of various types of ordered structures that emerge from PSA, showcasing their diverse applications. Following, we elaborate on the discovery and development of droplet-like disordered structures that arise during PSA. A mechanistic study on multistep self-assembly processes mediated by liquid-liquid phase separation (LLPS) is critically emphasized. Ordered structures with different morphologies and functions can be obtained by subtly controlling and adjusting the metastable liquid droplets. In particular, we have recently developed solid glasses with long-range disorder, including noncovalent biomolecular glass based on amino acid and peptide derivatives, as well as high-entropy glass based on cyclic peptides. This demonstrates the great potential of using biologically derived molecules to create green and sustainable glassy materials.

Effective Treatment of Helicobacter pylori Infection Using Supramolecular Antimicrobial Peptide Hydrogels.

Helicobacter pylori can cause various gastric conditions including stomach cancer in an acidic environment. Although early H. pylori infections can be treated by antibiotics, prolonged antibiotic administrations may lead to the development of antimicrobial resistance, compromising the effectiveness of the treatments. Antimicrobial peptides (AMPs) have been reported to possess unique advantages against antimicrobial-resistant bacteria due to their rapid physical membrane disruptions and anti-inflammation/immunoregulation properties. Herein, we have developed an AMP hydrogel, which can be orally administered for the treatment of H. pylori infection. The hydrogel has potent antimicrobial activity against H. pylori, achieving bacterial eradication within minutes of action. Compared with the AMP solution, the hydrogel formulation significantly reduced the cytotoxicity and enhanced proteolytic stability. In vivo experiments suggested that the hydrogel formed at pH 4 had superior therapeutic effects to those at pH 7 and 10 hydrogels, attributed to its rapid release and bactericidal action within the acidic stomach environment. Compared to conventional antibiotic treatments, the AMP hydrogel had the advantages of fast bacterial killing in the gastric juice and obviated proton pump inhibitors during the treatment. Although both the AMP hydrogel and antibiotics suppressed the expression of pro-inflammatory cytokines, the former uniquely promoted inflammation resolution. These results indicate that the AMP hydrogels with effectiveness and biosafety may be potential candidates for the clinical treatment of H. pylori infections.

Molecular Engineering of Ordered Piezoelectric Sulfonic Acid-Containing Assemblies.

Sulfonic acid-containing bioorganic monomers with wide molecular designability and abundant hydrogen bonding sites hold great potential to design diverse functional biocrystals but have so far not been explored for piezoelectric energy harvesting applications due to the lack of strategies to break the centrosymmetry of their assemblies. Here, a significant molecular packing transformation from centrosymmetric into non-centrosymmetric conformation by the addition of an amide terminus in the sulfonic acid-containing bioorganic molecule is demonstrated, allowing a high electromechanical response. The amide-functionalized molecule self-assembles into a polar supramolecular parallel ß-sheet-like structure with a high longitudinal piezoelectric coefficient d11 = 15.9 pm V-1 that produces the maximal open-circuit voltage of >1 V and the maximal power of 18 nW in nanogenerator devices pioneered. By contrast, molecules containing an amino or a cyclohexyl terminus assemble into highly symmetric 3D hydrogen bonding diamondoid-like networks or 2D double layer structures that show tunable morphologies, thermostability, and mechanical properties but non-piezoelectricity. This work not only presents a facile approach to achieving symmetry transformation of bioorganic assemblies but also demonstrates the terminal group and the property correlation for tailor-made design of high-performance piezoelectric biomaterials.

Multifunctional Antimicrobial Biometallohydrogels Based on Amino Acid Coordinated Self-Assembly.

There is a real need for new antibiotics against self-evolving bacteria. One option is to use biofriendly broad-spectrum and mechanically tunable antimicrobial hydrogels that can combat multidrug-resistant microbes. Whilst appealing, there are currently limited options. Herein, broad-spectrum antimicrobial biometallohydrogels based on the self-assembly and local mineralization of Ag+ -coordinated Fmoc-amino acids are reported. Such biometallohydrogels have the advantages of localized delivery and sustained release, reduced drug dosage and toxicity yet improved bioavailability, prolonged drug effect, and tunable mechanical strength. Furthermore, they can directly interact with the cell walls and membrane, resulting in the detachment of the plasma membrane and leakage of the cytoplasm. This leads to cell death, triggering a significant antibacterial effect against both Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus aureus) bacteria in cells and mice. This study paves the way for developing a multifunctional integration platform based on simple biomolecules coordinated self-assembly toward a broad range of biomedical applications.

Porphyrin/Ionic-Liquid Co-assembly Polymorphism Controlled by Liquid-Liquid Phase Separation.

Understanding and controlling multicomponent co-assembly is of primary importance in different fields, such as materials fabrication, pharmaceutical polymorphism, and supramolecular polymerization, but these aspects have been a long-standing challenge. Herein, we discover that liquid-liquid phase separation (LLPS) into ion-cluster-rich and ion-cluster-poor liquid phases is the first step prior to co-assembly nucleation based on a model system of water-soluble porphyrin and ionic liquids. The LLPS-formed droplets serve as the nucleation precursors, which determine the resulting structures and properties of co-assemblies. Co-assembly polymorphism and tunable supramolecular phase transition behaviors can be achieved by regulating the intermolecular interactions at the LLPS stage. These findings elucidate the key role of LLPS in multicomponent co-assembly evolution and enable it to be an effective strategy to control co-assembly polymorphism as well as supramolecular phase transitions.

Acid-Activatable Transmorphic Peptide-Based Nanomaterials for Photodynamic Therapy.

Inspired by the dynamic morphology control of molecular assemblies in biological systems, we have developed pH-responsive transformable peptide-based nanoparticles for photodynamic therapy (PDT) with prolonged tumor retention times. The self-assembled peptide-porphyrin nanoparticles transformed into nanofibers when exposed to the acidic tumor microenvironment, which was mainly driven by enhanced intermolecular hydrogen bond formation between the protonated molecules. The nanoparticle transformation into fibrils improved their singlet oxygen generation ability and enabled high accumulation and long-term retention at tumor sites. Strong fluorescent signals of these nanomaterials were detected in tumor tissue up to 7 days after administration. Moreover, the peptide assemblies exhibited excellent anti-tumor efficacy via PDT in vivo. This in situ fibrillar transformation strategy could be utilized to design effective stimuli-responsive biomaterials for long-term imaging and therapy.

The Dominant Role of Oxygen in Modulating the Chemical Evolution Pathways of Tyrosine in Peptides: Dityrosine or Melanin.

In diverse biological systems, the oxidation of tyrosine to melanin or dityrosine is crucial for the formation of crosslinked proteins and thus for the realization of their structural, biological, and photoactive functionalities; however, the predominant factor in determining the pathways of this chemical evolution has not been revealed. Herein, we demonstrate for tyrosine-containing amino acid derivatives, peptides, and proteins that the selective oxidation of tyrosine to produce melanin or dityrosine can be readily realized by manipulating the oxygen concentration in the reaction system. This oxygen-dependent pathway selection reflects the selective chemical evolution of tyrosine to dityrosine and melanin in anaerobic and aerobic microorganisms, respectively. The resulting melanin- and dityrosine-containing nanomaterials reproduce key functions of their natural counterparts with respect to their photothermal and photoluminescent characteristics, respectively. This work reveals the plausible role of oxygen in the chemical evolution of tyrosine derivatives and provides a versatile strategy for the rational design of tyrosine-based multifunctional biomaterials.

Nucleation and Growth of Amino Acid and Peptide Supramolecular Polymers through Liquid-Liquid Phase Separation.

The transition of peptides and proteins from the solution phase into fibrillar structures is a general phenomenon encountered in functional and aberrant biology and is increasingly exploited in soft materials science. However, the fundamental molecular events underpinning the early stages of their assembly and subsequent growth have remained challenging to elucidate. Here, we show that liquid-liquid phase separation into solute-rich and solute-poor phases is a fundamental step leading to the nucleation of supramolecular nanofibrils from molecular building blocks, including peptides and even amphiphilic amino acids. The solute-rich liquid droplets act as nucleation sites, allowing the formation of thermodynamically favorable nanofibrils following Ostwald's step rule. The transition from solution to liquid droplets is entropy driven while the transition from liquid droplets to nanofibrils is mediated by enthalpic interactions and characterized by structural reorganization. These findings shed light on how the nucleation barrier toward the formation of solid phases can be lowered through a kinetic mechanism which proceeds through a metastable liquid phase.

Smart Peptide-Based Supramolecular Photodynamic Metallo-Nanodrugs Designed by Multicomponent Coordination Self-Assembly.

Supramolecular photosensitizer nanodrugs that combine the flexibility of supramolecular self-assembly and the advantage of spatiotemporal, controlled drug delivery are promising for dedicated, precise, noninvasive tumor therapy. However, integrating robust blood circulation and targeted burst release in a single photosensitizer nanodrug platform that can simultaneously improve the therapeutic performance and reduce side effects is challenging. Herein, we demonstrate a multicomponent coordination self-assembly strategy that is versatile and potent for the development of photodynamic nanodrugs. Inspired by the multicomponent self-organization of polypeptides, pigments, and metal ions in metalloproteins, smart metallo-nanodrugs are constructed based on the combination and cooperation of multiple coordination, hydrophobic, and electrostatic noncovalent interactions among short peptides, photosensitizers, and metal ions. The resulting metallo-nanodrugs have uniform sizes, well-defined nanosphere structures, and high loading capacities. Most importantly, multicomponent assembled nanodrugs have robust colloidal stability and ultrasensitive responses to pH and redox stimuli. These properties prolong blood circulation, increase tumor accumulation, and enhance the photodynamic tumor therapeutic efficacy. This study offers a new strategy to harness robust, smart metallo-nanodrugs with integrated flexibility and multifunction to enhance tumor-specific delivery and therapeutic effects, highlighting opportunities to develop next-generation, smart photosensitizing nanomedicines.

Ultrafast Deep-Ultraviolet Laser Ionization Mass Spectrometry Applicable To Identify Phenylenediamine Isomers.

The application of low-fragmentation mass spectrometry to identify chemicals has been recognized to be of particular importance in chemistry, biomedicine, and materials science. Utilizing a customized all-solid-state picosecond-pulsed deep-ultraviolet (DUV) laser, here we present new advances into photoionization mass spectrometry. The DUV laser ionization mass spectrometry (DUV-LIMS) results in very clean spectra pertaining to minimized structure relaxation and fragmentation under the ultrafast ionization process. Typical DUV-LIMS applications are illustrated not only for small organic molecules but also for long-chain unsaturated hydrocarbons and clusters of benzene. The unique advantages of DUV-LIMS enable us to detect and analyze confusing organic compound mixtures, indicating promising applications. DUV-LIMS is also found to be applicable in the identification of phenylenediamine isomers. An in-depth analysis of reaction dynamics is provided showing how hydrogen-atom-transfer (HAT) initiates the distinguishable photodissociation of phenylenediamines under near-resonant excitation. In particular, ortho-phenylenediamine (OPD) finds a remarkable dehydrogenation product with comparable intensity to the molecular ion peak, which is associated with the quantum tunnelling tautomers, providing new subjects for studying intramolecular noncovalent interactions.

Charge-Induced Secondary Structure Transformation of Amyloid-Derived Dipeptide Assemblies from ß-Sheet to α-Helix.

Secondary structures such as α-helix and ß-sheet are the major structural motifs within the three-dimensional geometry of proteins. Therefore, structure transitions from ß-sheet to α-helix not only can serve as an effective strategy for the therapy of neurological diseases through the inhibition of ß-sheet aggregation but also extend the application of α-helix fibrils in biomedicine. Herein, we present a charge-induced secondary structure transition of amyloid-derived dipeptide assemblies from ß-sheet to α-helix. We unravel that the electrostatic (charge) repulsion between the C-terminal charges of the dipeptide molecules are responsible for the conversion of the secondary structure. This finding provides a new perspective to understanding the secondary structure formation and transformation in the supramolecular organization and life activity.

Amino Acid Coordination Driven Self-Assembly for Enhancing both the Biological Stability and Tumor Accumulation of Curcumin.

Clinical translation of curcumin has been highly obstructed by the rapid degradation and poor tissue absorption of this agent. Herein, we report on the generation of supramolecular curcumin nanoagents through amino acid coordination driven self-assembly to simultaneously increase the biological stability and tumor accumulation of curcumin. The biological stability of curcumin was significantly improved both through coordination and through molecular stacking. The sizes of these nanoagents can be readily manipulated to facilitate tumor accumulation. These favorable therapeutic features, together with high drug-loading capacities and responses to pH and redox stimuli, substantially enhanced the antitumor activity of curcumin without discernible side effects. Hence, supramolecular curcumin nanoagents may hold promise in moving forward the clinical application of curcumin as an effective anticancer drug.

Trace Water as Prominent Factor to Induce Peptide Self-Assembly: Dynamic Evolution and Governing Interactions in Ionic Liquids.

The interaction between water and biomolecules including peptides is of critical importance for forming high-level architectures and triggering life's functions. However, the bulk aqueous environment has limitations in detecting the kinetics and mechanisms of peptide self-assembly, especially relating to interactions of trace water. With ionic liquids (ILs) as a nonconventional medium, herein, it is discovered that trace amounts of water play a decisive role in triggering self-assembly of a biologically derived dipeptide. ILs provide a suitable nonaqueous environment, enabling us to mediate water content and follow the dynamic evolution of peptide self-assembly. The trace water is found to be involved in the assembly process of dipeptide, especially leading to the formation of stable noncovalent dipeptide oligomers in the early stage of nucleation, as evident by both experimental studies and theoretical simulations. The thermodynamics of the growth process is mainly governed by a synergistic effect of hydrophobic interaction and hydrogen bonds. Each step of assembly presents a different trend in thermodynamic energy. The dynamic evolution of assembly process can be efficiently mediated by changing trace water content. The decisive role of trace water in triggering and mediating self-assembly of biomolecules provides a new perspective in understanding supramolecular chemistry and molecular self-organization in biology.

Multiscale simulations for understanding the evolution and mechanism of hierarchical peptide self-assembly.

Hierarchical self-assembly, abundant in biological systems, has been explored as an effective bottom-up method to fabricate highly ordered functional superstructures from elemental building units. Biomolecules, especially short peptides consisting of several amino acids, are a type of elegant building blocks due to their advantages of structural, mechanical, and functional diversity as well as high biocompatibility and biodegradability. The hierarchical self-assembly of peptides is a spontaneous process spanning multiple time and length scales under certain thermodynamics and kinetics conditions. Therefore, understanding the mechanisms of dynamic processes is crucial to directing the construction of complicated biomimetic systems with multiple functionalities. Multiscale molecular simulations that combine and systematically link several hierarchies can provide insights into the evolution and dynamics of hierarchical self-assembly from the molecular level to the mesoscale. Herein, we provided an overview of the simulation hierarchies in the general field of peptide self-assembly modeling. In particular, we highlighted multiscale simulations for unraveling the mechanisms underlying the dynamic self-assembly process with an emphasis on weak intermolecular interactions in the process stages and the energies of different molecular alignments as well as the role of thermodynamic and kinetic factors at the microscopic level.

Self-Assembled Zinc/Cystine-Based Chloroplast Mimics Capable of Photoenzymatic Reactions for Sustainable Fuel Synthesis.

Prototypes of biosystems provide good blueprints for the design and creation of biomimetic systems. However, mimicking both the sophisticated natural structures and their complex biological functions still remains a great challenge. Herein, chloroplast mimics have been fabricated by one-step bioinspired amino acid mineralization and simultaneous integration of catalytically active units. Hierarchically structured crystals were obtained by the metal-ion-directed self-assembly of cystine (the oxidized dimer of the amino acid cysteine), with a porous structure and stacks of nanorods, which show similar architectural principles to chloroplasts. Porphyrins and enzymes can both be encapsulated inside the crystal during mineralization, rendering the crystal photocatalytically and enzymatically active for an efficient and sustainable synthesis of hydrogen and acetaldehyde in a coupled photoenzymatic reaction.

A theoretical study of weak interactions in phenylenediamine homodimer clusters.

Weak intermolecular interactions in phenylenediamine dimer (pdd) clusters are studied by dispersion-corrected density functional theory (DFT) calculations. Along with the optimization of geometric structures and the calculation of interaction energies, we employ molecular electrostatic potential (MEP) mapping, natural bond orbital (NBO) analysis and quantum theory of atoms in molecule (AIM) to analyze the origin and relative energetic contributions of the weak interactions in these pdd systems. It is revealed that the most stable o-phenylenediamine dimer (opdd) cluster is dominated by N-HN hydrogen bonds, the p-phenylenediamine dimer (ppdd) cluster is largely stabilized by N-Hπ and ππ stacking interactions, while the m-phenylenediamine dimer (mpdd) cluster is mainly held by a combination of n → π*, C-Hπ and C-HN interactions. Energy decomposition analysis (EDA) of the total interaction energies of these clusters further demonstrates that the weak intermolecular interactions are associated with electrostatic and dispersion contributions. Structural spectroscopic analysis is also addressed depicting the coexistence of multiple intermolecular interactions which give rise to the spectral variation in wavenumbers of the infrared and Raman activities. Insights into the weak interactions of pdds help us to understand the molecular mechanisms involved in biochemistry and self-assembly materials.

Charge-transfer interactions between TCNQ and silver clusters Ag20 and Ag13.

Interactions between tetracyanoquinodimethane (TCNQ) and two typical silver clusters Ag13 and Ag20 are studied by first-principles DFT calculations. Charge transfer (CT) from silver clusters to TCNQ molecules initiates the Ag-N bond formation at selective sites resulting in the formation of different isomers of Ag13-TCNQ and Ag20-TCNQ complexes. We show here a comprehensive spectroscopic analysis for the two CT complexes on the basis of Raman and infrared activities. Furthermore, frontier molecular orbital (FMO) and natural bond orbital (NBO) analysis of the complexes provides a vivid illustration of electron cloud overlap and interactions. The behavior of TCNQ adsorbed on the tetrahedral Ag20 cluster was even found in good agreement with the experimental measurement of TCNQ molecules on a single-crystal Ag(111) surface. This study not only endeavors to clarify the charge-transfer interactions of TCNQ with silver, but also presents a finding of enhanced charge transfer between Ag13 and TCNQ indicating potential for candidate building blocks of granular materials.

High-entropy non-covalent cyclic peptide glass.

Biomolecule-based non-covalent glasses are biocompatible and biodegradable, and offer a sustainable alternative to conventional glass. Cyclic peptides (CPs) can serve as promising glass formers owing to their structural rigidity and resistance to enzymatic degradation. However, their potent crystallization tendency hinders their potential in glass construction. Here we engineered a series of CP glasses with tunable glass transition behaviours by modulating the conformational complexity of CP clusters. By incorporating multicomponent CPs, the formation of high-entropy CP glass is facilitated, which-in turn-inhibits the crystallization of individual CPs. The high-entropy CP glass demonstrates enhanced mechanical properties and enzyme tolerance compared with individual CP glass and a unique biorecycling capability that is unattainable by traditional glasses. These findings provide a promising paradigm for the design and development of stable non-covalent glasses based on naturally derived biomolecules, and advance their application in pharmaceutical formulations and smart functional materials.

The Dimensionality of Hydrogen Bond Networks Induces Diverse Physical Properties of Peptide Crystals.

Short peptides are attractive building blocks for the fabrication of self-assembled materials with significant biological, chemical, and physical properties. The microscopic and macroscopic properties of assemblies are usually closely related to the dimensionality of formed hydrogen bond networks. Here, two completely different supramolecular architectures connected by distinct hydrogen bond networks were obtained by simply adding a hydroxyl group to switch from cyclo-tryptophan-alanine (cyclo-WA) to cyclo-tryptophan-serine (cyclo-WS). While hydroxyl-bearing cyclo-WS molecules provided an additional hydrogen bond donor that links to adjacent molecules, forming a rigid three-dimensional network, cyclo-WA arranged into a water-mediated zipper-like structure with a softer two-dimensional layer template. This subtle alteration resulted in a 14-fold enhancement of Young's modulus values in cyclo-WS compared to cyclo-WA. Both cyclo-dipeptides exhibit biocompatibility, high fluorescence, and piezoelectricity. The demonstrated role of dimensionality of hydrogen bond networks opens new avenues for rational design of materials with precise morphologies and customizable properties for bioelectronic applications.

Biomolecular glass with amino acid and peptide nanoarchitectonics.

Glass is ubiquitous in life and widely used in various fields. However, there is an urgent need to develop biodegradable and biorecyclable glasses that have a minimal environmental footprint toward a sustainable society and a circular materials economy. Here, we report a family of eco-friendly glasses of biological origin fabricated using biologically derived amino acids or peptides through the classic heating-quenching procedure. Amino acids and peptides with chemical modification at their ends are found able to form a supercooled liquid before decomposition and eventually glass upon quenching. These developed glasses exhibit excellent glass-forming ability and optical characteristics and are amenable to three-dimensional-printed additive manufacturing and mold casting. Crucially, the glasses show biocompatibility, biodegradability, and biorecyclability beyond the currently used commercial glasses and plastic materials.