Supramolecular assembly of protein building blocks: from folding to function

Fluoride-Ion-Responsive Sol-Gel Transition in an L-Cysteine/AgNO3 System: Self-Assembly Peculiarities and Anticancer Activity

Supramolecular hydrogels based on low-molecular-weight compounds are a unique class of so-called "soft" materials, formed by weak non-covalent interactions between precursors at their millimolar concentrations. Due to the variety of structures that can be formed using different low-molecular-weight gelators, they are widely used in various fields of technology and medicine. In this study, we report for the first time an unusual self-assembly process of mixing a hydrosol obtained from L-cysteine and silver nitrate (cysteine-silver sol-CSS) with sodium halides. Modern instrumental techniques such as viscosimetry, UV spectroscopy, dynamic light scattering, zeta potential measurements, SEM and EDS identified that adding fluoride anions to CSS is able to form stable hydrogels of a thixotropic nature, while Cl-, Br- and I- lead to precipitation. The self-assembly process proceeds using a narrow concentration range of F-. An increase in the fluoride anion content in the system leads to a change in the gel network morphology from elongated structures to spherical ones. This fact is reflected in a decrease in the gel viscosity and a number of gel-sol-gel transition cycles. The mechanism of F-'s interaction with hydrosol includes the condensation of anions on the positive surface of the CSS nanoparticles, their binding via electrostatic forces and the formation of a resulting gel carcass. In vitro analysis showed that the hydrogels suppressed human squamous carcinoma cells at a micromolar sample concentration. The obtained soft gels could have potential applications against cutaneous malignancy and as carriers for fluoride anion and other bioactive substance delivery.

Active Dual-Protein Coating Assisted by Stepwise Protein-Protein Interactions Assembly Reduces Thrombosis and Infection

Universal protein coatings have recently gained wide interest in medical applications due to their biocompatibility and ease of fabrication. However, the challenge persists in protein activity preservation, significantly complicating the functional design of these coatings. Herein, an active dual-protein surface engineering strategy assisted by a facile stepwise protein-protein interactions assembly (SPPIA) method for catheters to reduce clot formation and infection is proposed. This strategy is realized first by the partial oxidation of bovine serum albumin (BSA) and lysozyme (LZM) for creating stable nucleation platforms via hydrophobic interaction, followed by the assembly of nonoxidized BSA (pI, the isoelectric point, ≈4.7) and LZM (pI ≈11) through electrostatic interaction owing to their opposite charge under neutral conditions. The SPPIA method effectively preserves the conformation and functionality of both BSA and LZM, thus endowing the resultant coating with potent antithrombotic and bactericidal properties. Furthermore, the stable nucleation platform ensures the adhesion and durability of the coating, resisting thrombosis and bacterial proliferation even after 15 days of PBS immersion. Overall, the SPPIA approach not only provides a new strategy for the fabrication of active protein coatings but also shows promise for the surface engineering technology of catheters.

Designing Multifunctional Biomaterials via Protein Self-Assembly

Protein self-assembly is a fundamental biological process where proteins spontaneously organize into complex and functional structures without external direction. This process is crucial for the formation of various biological functionalities. However, when protein self-assembly fails, it can trigger the development of multiple disorders, thus making understanding this phenomenon extremely important. Up until recently, protein self-assembly has been solely linked either to biological function or malfunction; however, in the past decade or two it has also been found to hold promising potential as an alternative route for fabricating materials for biomedical applications. It is therefore necessary and timely to summarize the key aspects of protein self-assembly: how the protein structure and self-assembly conditions (chemical environments, kinetics, and the physicochemical characteristics of protein complexes) can be utilized to design biomaterials. This minireview focuses on the basic concepts of forming supramolecular structures, and the existing routes for modifications. We then compare the applicability of different approaches, including compartmentalization and self-assembly monitoring. Finally, based on the cutting-edge progress made during the last years, we summarize the current knowledge about tailoring a final function by introducing changes in self-assembly and link it to biomaterials' performance.

Formation of Supplementary Metal-Binding Centers in Proteins under Stress Conditions

In many proteins, supplementary metal-binding centers appear under stress conditions. They are known as aberrant or atypical sites. Physico-chemical properties of proteins are significantly changed after such metal binding, and very stable protein aggregates are formed, in which metals act as "cross-linking" agents. Supplementary metal-binding centers in proteins often arise as a result of posttranslational modifications caused by reactive oxygen and nitrogen species and reactive carbonyl compounds. New chemical groups formed as a result of these modifications can act as ligands for binding metal ions. Special attention is paid to the role of cysteine SH-groups in the formation of supplementary metal-binding centers, since these groups are the main target for the action of reactive species. Supplementary metal binding centers may also appear due to unmasking of amino acid residues when protein conformation changing. Appearance of such centers is usually considered as a pathological process. Such unilateral approach does not allow to obtain an integral view of the phenomenon, ignoring cases when formation of metal complexes with altered proteins is a way to adjust protein properties, activity, and stability under the changed redox conditions. The role of metals in protein aggregation is being studied actively, since it leads to formation of non-membranous organelles, liquid condensates, and solid conglomerates. Some proteins found in such aggregates are typical for various diseases, such as Alzheimer's and Huntington's diseases, amyotrophic lateral sclerosis, and some types of cancer.

Controllably Self-Assembled Antibacterial Nanofibrils Based on Insect Cuticle Protein for Infectious Wound Healing

Developing self-assembled biomedical materials based on insect proteins is highly desirable due to their advantages of green, rich, and sustainable characters as well as excellent biocompatibility, which has been rarely explored. Herein, salt-induced controllable self-assembly, antibacterial performance, and infectious wound healing performance of an insect cuticle protein (OfCPH-2) originating from the Ostrinia furnacalis larva head capsule are investigated. Interestingly, the addition of salts could trigger the formation of beaded nanofibrils with uniform diameter, whose length highly depends on the salt concentration. Surprisingly, the OfCPH-2 nanofibrils not only could form functional films with broad-spectrum antibacterial abilities but also could promote infectious wound healing. More importantly, a possible wound healing mechanism was proposed, and it is the strong abilities of OfCPH-2 nanofibrils in promoting vascular formation and antibacterial activity that facilitate the process of infectious wound healing. Our exciting findings put forward instructive thoughts for developing innovative bioinspired materials based on insect proteins for wound healing and related biomedical fields.

Multivalent protein-drug conjugates - An emerging strategy for the upgraded precision and efficiency of drug delivery to cancer cells

With almost 20 million new cases per year, cancer constitutes one of the most important challenges for public health systems. Unlike traditional chemotherapy, targeted anti-cancer strategies employ sophisticated therapeutics to precisely identify and attack cancer cells, limiting the impact of drugs on healthy cells and thereby minimizing the unwanted side effects of therapy. Protein drug conjugates (PDCs) are a rapidly growing group of targeted therapeutics, composed of a cancer-recognition factor covalently coupled to a cytotoxic drug. Several PDCs, mainly in the form of antibody-drug conjugates (ADCs) that employ monoclonal antibodies as cancer-recognition molecules, are used in the clinic and many PDCs are currently in clinical trials. Highly selective, strong and stable interaction of the PDC with the tumor marker, combined with efficient, rapid endocytosis of the receptor/PDC complex and its subsequent effective delivery to lysosomes, is critical for the efficacy of targeted cancer therapy with PDCs. However, the bivalent architecture of contemporary clinical PDCs is not optimal for tumor receptor recognition or PDCs internalization. In this review, we focus on multivalent PDCs, which represent a rapidly evolving and highly promising therapeutics that overcome most of the limitations of current bivalent PDCs, enhancing the precision and efficiency of drug delivery to cancer cells. We present an expanding set of protein scaffolds used to generate multivalent PDCs that, in addition to folding into well-defined multivalent molecular structures, enable site-specific conjugation of the cytotoxic drug to ensure PDC homogeneity. We provide an overview of the architectures of multivalent PDCs developed to date, emphasizing their efficacy in the targeted treatment of various cancers.

Peptide-Assembled Single-Chain Atomic Crystal Enhances Pluripotent Stem Cell Differentiation to Neurons

Nanomaterials hybridized with biological components have widespread applications. among many candidates, peptides are attractive in that their peptide sequences can self-assemble with the surface of target materials with high specificity without perturbing the intrinsic properties of nanomaterials. Here, a 1D hybrid nanomaterial was developed through self-assembly of a designed peptide. A hexagonal coiled-coil motif geometrically matched to the diameter of the inorganic nanomaterial was fabricated, whose hydrophobic surface was wrapped along the axis of the hydrophobic core of the coiled coil. Our morphological and spectroscopic analyses revealed rod-shaped, homogeneous peptide-inorganic nanomaterial complexes. Culturing embryonic stem cells on surfaces coated with this peptide-assembled single-chain atomic crystal increased the growth and adhesion of the embryonic stem cells. The hybridized nanomaterial also served as an ECM for brain organoids, accelerating the maturation of neurons. New methods to fabricate hybrid materials through peptide assembly can be applied.

Design, synthesis, and characterization of protein origami based on self-assembly of a brick and staple artificial protein pair

A versatile strategy to create an inducible protein assembly with predefined geometry is demonstrated. The assembly is triggered by a binding protein that staples two identical protein bricks together in a predictable spatial conformation. The brick and staple proteins are designed for mutual directional affinity and engineered by directed evolution from a synthetic modular repeat protein library. As a proof of concept, this article reports on the spontaneous, extremely fast and quantitative self-assembly of two designed alpha-repeat (αRep) brick and staple proteins into macroscopic tubular superhelices at room temperature. Small-angle X-ray scattering (SAXS) and transmission electron microscopy (TEM with staining agent and cryoTEM) elucidate the resulting superhelical arrangement that precisely matches the a priori intended 3D assembly. The highly ordered, macroscopic biomolecular construction sustains temperatures as high as 75 °C thanks to the robust αRep building blocks. Since the α-helices of the brick and staple proteins are highly programmable, their design allows encoding the geometry and chemical surfaces of the final supramolecular protein architecture. This work opens routes toward the design and fabrication of multiscale protein origami with arbitrarily programmed shapes and chemical functions.

Supermolecular Nanoentities of Vitamin B12 Derivative as a Link in the Evolution of the Parent Molecules During Self-Assembly at the Air-Water Interface

Nanoarchitectures with promising properties have now been formed from many important biomolecules. However, the preparation of nanoparticles of vitamin B₁₂ and its derivatives remains an ongoing research challenge. This paper describes the formation of supermolecular nanoentities (SMEs) of vitamin B₁₂ derivatives, unique nanoparticles with strong noncovalent intermolecular interactions, emerging properties, and activity. These were created by a nanoarchitectonic approach using directed assembly of layers at the air-water interface as a link in the chain of evolution of the parent molecules under specially created conditions. Such layers can be represented as a nanocosm, where, at a critical density, the assemblies act as nanoreactors in which the transformation of the original material occurs. The discovered SMEs not only replicate the functioning of vitamin B₁₂ assemblies with proteins in living organisms and act as vitamin B₁₂-depended enzymes but also demonstrate important advantages over vitamin B₁₂. They are more efficient in oxygen reduction/evolution reactions and in transformation into other forms. These SMEs, in performing advanced tasks, are an alternative to widely used materials based on noble metals for catalysis, medicine, and environment protection. Our findings open new perspectives both for the fabrication of novel SMEs of biomolecules and for a better understanding of the evolution of biomolecules in nature.

Self-Assembly, Self-Folding, and Origami: Comparative Design Principles

Self-assembly is usually considered a parallel process while self-folding and origami are usually considered to be serial processes. We believe that these distinctions do not hold in actual experiments. Based upon our experience with 4D printing, we have developed three additional hybrid classes: (1) templated-assisted (tethered) self-assembly: e.g., when RNA is bound to viral capsomeres, the subunits are constricted in their interactions to have aspects of self-folding as well; (2) self-folding can depend upon interactions with the environment; for example, a protein synthesized on a ribosome will fold as soon as peptides enter the intracellular environment in a serial process whereas if denatured complete proteins are put into solution, parallel folding can occur simultaneously; and, (3) in turbulent environments, chaotic conditions continuously alternate processes. We have examined the 43,380 Dürer nets of dodecahedra and 43,380 Dürer nets of icosahedra and their corresponding duals: Schlegel diagrams. In order to better understand models of self-assembly of viral capsids, we have used both geometric (radius of gyration, convex hulls, angles) and topological (vertex connections, leaves, spanning trees, cutting trees, and degree distributions) perspectives to develop design principles for 4D printing experiments. Which configurations fold most rapidly? Which configurations lead to complete polyhedra most of the time? By using Hamiltonian circuits of the vertices of Dürer nets and Eulerian paths of cutting trees of polyhedra unto Schlegel diagrams, we have been able to develop a systematic sampling procedure to explore the 86,760 configurations, models of a T1 viral capsid with 60 subunits and to test alternatives with 4D printing experiments, use of Magforms^TM, and origami models to demonstrate via movies the five processes described above.

Conformational switch and multiple supramolecular structures of a newly identified self-assembling protein-mimetic peptide from Pseudomonas aeruginosa YeaZ protein

Protein-mimetic peptides (PMPs) are shorter sequences of self-assembling proteins, that represent remarkable building blocks for the generation of bioinspired functional supramolecular structures with multiple applications. The identification of novel aminoacidic sequences that permit the access to valuable biocompatible materials is an attractive area of research. In this work, in silico analysis of the Pseudomonas aeruginosa YeaZ protein (PaYeaZ) led to the identification of a tetradecapeptide that represents the shortest sequence responsible for the YeaZ-YeaZ dimer formation. Based on its sequence, an innovative 20-meric peptide, called PMP-2, was designed, synthesized, and characterized in terms of secondary structure and self-assembly properties. PMP-2 conserves a helical character and self-assembles into helical nanofibers in non-polar solvents (DMSO and trifluoroethanol), as well as in dilute (0.5 mM) aqueous solutions. In contrast, at higher concentrations (>2 mM) in water, a conformational transition from α-helix to β-sheet occurs, which is accompanied by the Protein-mimetic peptide aggregation into 2D-sheets and formation supramolecular gel in aqueous environment. Our findings reveal a newly identified Protein-mimetic peptide that could turn as a promising candidate for future material applications.

Effect of Secondary Structures on the Adsorption of Peptides onto Hydrophobic Solid Surfaces Revealed by SALDI-TOF and MD Simulations

The adsorption of peptides and proteins on hydrophobic solid surfaces has received considerable research attention owing to their wide applications to biocompatible nanomaterials and nanodevices, such as biosensors and cell adhesion materials with reduced nanomaterial toxicity. However, fundamental understandings about physicochemical hydrophobic interactions between peptides and hydrophobic solid surfaces are still unknown. In this study, we investigate the effect of secondary structures on adsorption energies between peptides and hydrophobic solid surfaces via experimental and theoretical analyses using surface-assisted laser desorption/ionization-time-of-flight (SALDI-TOF) and molecular dynamics (MD) simulations. The hydrophobic interactions between peptides and hydrophobic solid surfaces measured via SALDI-TOF and MD simulations indicate that the hydrophobic interaction of peptides with random coil structures increased more than that of peptides with an α-helix structure when polar amino acids are replaced with hydrophobic amino acids. Additionally, our study sheds new light on the fundamental understanding of the hydrophobic interaction between hydrophobic solid surfaces and peptides that have diverse secondary structures.

Dimers of D76N-β2-microglobulin display potent antiamyloid aggregation activity

Self-association of WT β_2-microglobulin (WT-β₂m) into amyloid fibrils is associated with the disorder dialysis related amyloidosis. In the familial variant D76N-β₂m, the single amino acid substitution enhances the aggregation propensity of the protein dramatically and gives rise to a disorder that is independent of renal dysfunction. Numerous biophysical and structural studies on WT- and D76N-β₂m have been performed in order to better understand the structure and dynamics of the native proteins and their different potentials to aggregate into amyloid. However, the structural properties of transient D76N-β₂m oligomers and their role(s) in assembly remained uncharted. Here, we have utilized NMR methods, combined with photo-induced crosslinking, to detect, trap, and structurally characterize transient dimers of D76N-β₂m. We show that the crosslinked D76N-β₂m dimers have different structures from those previously characterized for the on-pathway dimers of ΔN6-β₂m and are unable to assemble into amyloid. Instead, the crosslinked D76N-β₂m dimers are potent inhibitors of amyloid formation, preventing primary nucleation and elongation/secondary nucleation when added in substoichiometric amounts with D76N-β₂m monomers. The results highlight the specificity of early protein-protein interactions in amyloid formation and show how mapping these interfaces can inform new strategies to inhibit amyloid assembly.

Microfabrication of peptide self-assemblies: inspired by nature towards applications

Peptide self-assemblies show intriguing and tunable physicochemical properties, and thus have been attracting increasing interest over the last two decades. However, the micro/nano-scale dimensions of the self-assemblies severely restrict their extensive applications. Inspired by nature, to genuinely realize the practical utilization of the bio-organic super-architectures, it is beneficial to further organize the peptide self-assemblies to integrate the properties of the individual supermolecules and fabricate higher-level organizations for smart functional devices. Therefore, cumulative studies have been reported on peptide microfabrication giving rise to diverse properties. This review summarizes the recent development of the microfabrication of peptide self-assemblies, discussing each methodology along with the diverse properties and practical applications of the engineered peptide large-scale, highly-ordered organizations. Finally, the current limitations of the state-of-the-art microfabrication strategies are critically assessed and alternative solutions are suggested.

Precise and Prompt Analyte Detection via Ordered Orientation of Receptor in WSe2-Based Field Effect Transistor

Field-effect transistors (FET) composed of transition metal dichalcogenide (TMDC) materials have gained huge importance as biosensors due to their added advantage of high sensitivity and moderate bandgap. However, the true potential of these biosensors highly depends upon the quality of TMDC material, as well as the orientation of receptors on their surfaces. The uncontrolled orientation of receptors and screening issues due to crossing the Debye screening length while functionalizing TMDC materials is a big challenge in this field. To address these issues, we introduce a combination of high-quality monolayer WSe₂ with our designed Pyrene-based receptor moiety for its ordered orientation onto the WSe₂ FET biosensor. A monolayer WSe₂ sheet is utilized to fabricate an ideal FET for biosensing applications, which is characterized via Raman spectroscopy, atomic force microscopy, and electrical prob station. Our construct can sensitively detect our target protein (streptavidin) with 1 pM limit of detection within a short span of 2 min, through a one-step functionalizing process. In addition to having this ultra-fast response and high sensitivity, our biosensor can be a reliable platform for point-of-care-based diagnosis.