Self-assembly Of Proteins Research Articles

Effect of protein charge manipulation on αs1-casein-enriched protein self-assembly

Enzymatic dephosphorylation of casein removes phosphate groups from serine residues and reduces the negative charge. In contrast, succinylation caps the ε-amino group of lysine residues and increases the negative charge on the caseins. The effect of these modifications on the self-association of αs1-casein was studied using analytical ultracentrifugation. Dephosphorylation and succinylation have contrasting effects on αs1-casein self-assembly. Native αs1-casein was a mixture of dimers, trimers and higher order oligomers under these experimental conditions. Increasing the level of succinylation dissociated oligomeric αs1-casein resulting in an increase in the monomeric protein. In contrast, dephosphorylated samples formed larger assemblies compared to the native αs1-casein. Experiments performed at protein concentrations of 1, 2 or 3 mg mL−1 provided consistent results indicating that across this concentration range there is no major difference in the assembly formation. This study demonstrated the utility of analytical ultracentrifugation to understand casein assembly, which will underpin the understanding of proteins structures in dairy foods.

Robust and resilient piezoresistive sensor made of MWCNT-embedded aerogel prepared with elongated amyloid fibrils of α-synuclein

Pressure sensors are widely employed in various fields from biomedical to aerospace engineering. Each field requires pressure sensors with specific sensitivity, response time, recovery time, durability, and detection limit. However, developing pressure sensors that meet the increasing demands of high mechanical strength and sensitive electrical responsiveness influencing reliability and accuracy still remains challenging. Herein, a highly robust and resilient piezoresistive sensor was developed by combining elongated amyloid fibrils (eAFs) aerogel made of a self-assembly protein of α-synuclein, which provided stable porous 3D interconnected network and thus increased surface area, and multi-walled carbon nanotube (MWCNT) as a reinforcement material for improved mechanical and electrical properties. Owing to the integration between eAFs aerogel and MWCNT, the MWCNT-embedded eAFs aerogel exhibited augmentation in mechanical strength and resiliency depending on the amount of MWCNT introduced. Additionally, the MWCNT-embedded eAFs aerogel showed piezoresistive properties with stable pressure sensing capability toward human motions, airflow, and underwater pressure. It is, therefore, suggested that the pressure sensor fabricated with the eAFs aerogel containing MWCNT could be utilized in diverse areas including wearable device and artificial skin development.

Robust self-assembly of nonconvex shapes in two dimensions.

We present fast simulation methods for the self-assembly of complex shapes in two dimensions. The shapes are modeled via a general boundary curve and interact via a standard volume term promoting overlap and an interpenetration penalty. To efficiently realize the Gibbs measure on the space of possible configurations we employ the hybrid Monte Carlo algorithm together with a careful use of signed distance functions for energy evaluation. Motivated by the self-assembly of identical coat proteins of the tobacco mosaic virus which assemble into a helical shell, we design a nonconvex two-dimensional model shape and demonstrate its robust self-assembly into a unique final state. Our numerical experiments reveal certain essential prerequisites for this self-assembly process: blocking and matching (i.e., local repulsion and attraction) of different parts of the boundary, and nonconvexity and handedness of the shape.

Investigation of numerical transport models in protein-based molecular junctions with cofactors of diverse chemical natures

The cofactors of proteins dictate the charge transport mechanism across molecular junctions when self-assembled protein monolayers are sandwiched between two metal electrodes. Here, we summarized how the chemical coordination nature of cofactors in various proteins modulates electrical conductance by investigating electronic transport studies across different protein-based molecular junctions under various forces applied under the AFM tip. We have utilized several numerical techniques of electronic transport to analyse the experimentally obtained current–voltage measurements across various protein-based molecular junctions and depicted the origin of electronic modulation in the electrical conductance under different external stimuli. We could also find the origin of electronic conductance modulation under external stimuli at various applied forces by obtaining several analytical transport parameters such as energy barrier, coupling strength, and electrical conductance values. Utilizing density-functional-theory calculations, we further validate that the electronic density of states present in the cofactors within the proteins dominates the electronic transport behaviours across protein-based molecular junctions. Our findings reveal the limiting factor for applying various external stimuli on different proteins, which could be further valuable in bioelectronic applications. We have also found that the organic cofactor containing protein follows all the tunneling mechanism-related numerical transport models and the electronic transport across proteins with pure inorganic cofactors follows Landauer transport formalism.

Dynamic interfacial adsorption and emulsifying performance of self-assembled coconut protein and fucoidan mixtures

The functional properties of protein are affected by their aggregation behavior and morphology. In this study, the self-assembled coconut protein aggregates with specific morphology, including small amorphous aggregates (WLA), spherical-like aggregates (SLA) and rod-like aggregates (RLA), were regulated to form. The self-assembled process resulted in a decrease in fluorescence intensity and an increase in the surface hydrophobicity of coconut protein. Fucoidan was added to improve the stability of protein solutions, and the interfacial adsorption behavior was evaluated by dilatational rheology analysis. The results showed that the aggregation state of coconut protein affected its ability to reduce surface tension, and the interfacial layers mainly exhibited elastic property at oil-water interface (tanφ < 0.5). For macroscale analysis, the emulsions based on self-assembled coconut protein exhibited smaller droplet size, better rheological properties and centrifugal stability, especially WLA and RLA. This study may provide a reference to inspire the utilization of self-assembled coconut protein in the food industry.

Engineering a Self-Assembled Protein Cage for Targeted Dual Functionalization.

Self-assembled protein cages are attractive scaffolds for organizing various proteins of interest (POIs) toward applications in synthetic biology and medical science. However, specifically attaching multiple POIs to a single protein cage remains challenging, resulting in diversity among the functionalized particles. Here, we present the engineering of a self-assembled protein cage, DTMi3ST, capable of independently recruiting two different POIs using SpyCatcher (SC)/SpyTag (ST) and DogCatcher (DC)/DogTag (DT) chemistries, thereby reducing variability between assemblies. Using fluorescent proteins as models, we demonstrate controlled targeting of two different POIs onto DTMi3ST protein cages both in vitro and inside living cells. Furthermore, dual functionalization of the DTMi3ST protein cage with a membrane-targeting peptide and β-galactosidase resulted in the construction of membrane-bound enzyme assemblies in Escherichia coli, leading to a 69.6% enhancement in substrate utilization across the membrane. This versatile protein cage platform provides dual functional nanotools for biological and biomedical applications.

Development and Characterization of 50 nanometer diameter Genetically Encoded Multimeric Nanoparticles.

The mechanisms that regulate the physical properties of the cell interior remain poorly understood, especially at the mesoscale (10nm-100nm). Changes in these properties have been suggested to be crucial for both normal physiology and disease. Many crucial macromolecules and molecular assemblies such as ribosomes, RNA polymerase, and biomolecular condensates span the mesoscale size range. Therefore, we need better tools to study the cellular environment at this scale. A recent approach has been to use genetically encoded multimeric nanoparticles (GEMs), which consist of self-assembling scaffold proteins fused to fluorescent tags. After translation of the fusion protein, the monomers self-assemble into bright and stable nanoparticles of defined geometry that can be visualized by fluorescence microscopy. Physical properties of the cell can then be inferred through analysis of the motion of these particles, an approach called nanorheology. Previously, 40nm-GEMs elucidated TORC1 kinase as a regulator of cytoplasmic crowding. However, extremely sensitive microscopes were required. Here, we describe the development and characterization of a 50 nm diameter GEM that is brighter and probes a larger length scale. 50nm-GEMs will make high-throughput nanorheology accessible to a broader range of researchers and reveal new insights into the biophysical properties of cells.

Genetically Programmed Temperature-Responsive Barnacle-Derived Protein with an Enhanced Adhesion Ability.

There is an emerging strong demand for smart environmentally responsive protein-based biomaterials with improved adhesion properties, especially underwater adhesion for potential environmental and medical applications. Based on the fusion of elastin-like polypeptides (ELPs), SpyCatcher and SpyTag modules, biosynthetic barnacle-derived protein was genetically engineered and self-assembled with an enhanced adhesion ability and temperature response. The water resistance ability of the synthetic protein biopolymer with a network structure increased to 98.8 from 58.5% of the original Cp19k, and the nonaqueous adhesion strength enhanced to 1.26 from 0.68 MPa of Cp19k. The biopolymer showed an improved adhesion ability toward hydrophilic and hydrophobic surfaces as well as diatomite powders. The combination of functional module ELPs and SpyTag/SpyCatcher could endow the biosynthetic protein with temperature response, an insoluble form above 42 °C and a soluble form at 4 °C. The combinational advantages including temperature response and adhesion performance make the self-assembled protein an excellent candidate in surgical adhesion, underwater repair, and surface modification of various coatings. Distinct from the traditional approach of utilizing solely ELPs, the integration of short ELPs with Spy partners exhibited a synergistic enhancement in the temperature response. The synergistic effects of two functional modules provide a technical method and insight for designing smart self-assembled protein-based biopolymers.

Heteromeric amyloid filaments of ANXA11 and TDP-43 in FTLD-TDP Type C.

Neurodegenerative diseases are characterised by the abnormal filamentous assembly of specific proteins in the central nervous system 1 . Human genetic studies established a causal role for protein assembly in neurodegeneration 2 . However, the underlying molecular mechanisms remain largely unknown, which is limiting progress in developing clinical tools for these diseases. Recent advances in electron cryo-microscopy (cryo-EM) have enabled the structures of the protein filaments to be determined from patient brains 1 . All diseases studied to date have been characterised by the self-assembly of a single intracellular protein in homomeric amyloid filaments, including that of TAR DNA-binding protein 43 (TDP-43) in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration with TDP-43 inclusions (FTLD-TDP) Types A and B 3,4 . Here, we used cryo-EM to determine filament structures from the brains of individuals with FTLD-TDP Type C, one of the most common forms of sporadic FTLD-TDP. Unexpectedly, the structures revealed that a second protein, annexin A11 (ANXA11), co-assembles with TDP-43 in heteromeric amyloid filaments. The ordered filament fold is formed by TDP-43 residues G282/284-N345 and ANXA11 residues L39-L74 from their respective low-complexity domains (LCDs). Regions of TDP-43 and ANXA11 previously implicated in protein-protein interactions form an extensive hydrophobic interface at the centre of the filament fold. Immunoblots of the filaments revealed that the majority of ANXA11 exists as a ∼22 kDa N-terminal fragment (NTF) lacking the annexin core domain. Immunohistochemistry of brain sections confirmed the co-localisation of ANXA11 and TDP-43 in inclusions, redefining the histopathology of FTLD-TDP Type C. This work establishes a central role for ANXA11 in FTLD-TDP Type C. The unprecedented formation of heteromeric amyloid filaments in human brain revises our understanding of amyloid assembly and may be of significance for the pathogenesis of neurodegenerative diseases.

Disulfide bond cleavage combined with critical pH induced unfolding and assembly of soy protein and its encapsulation effect on curcumin

The limited water solubility and bioactivity of hydrophobic phytochemicals can be improved and preserved by encapsulation technologies. In this research, a low-cost and low-energy encapsulation method was explored based on the self-assembly characteristics of soy protein (SP). The disulfide bond of SP was broken by Na2S2O5, and then the pH of SP was adjusted to the critical pH 10.5 with NaOH, which was the critical point of protein unfolding. The treated protein was added to curcumin (Cur), which was encapsulated in self-assembled protein nanoparticles during the subsequent neutralization process to obtain the soy protein-curcumin complex (SP-Cur). This process was known as the disulfide bond breaking combined with critical pH-driven technology. The cleavage of SP disulfide bonds was studied by the methods of 4, 4′-dithiopyridine (DPS) and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). When the SP:Cur mass ratio was 1:1, the encapsulation efficiency (EE%) of Cur in SP-Cur obtained by disulfide bond breaking combined with the critical pH-driven method increased to 85.36 ± 1.03%. It was notably greater than the EE% of Cur in SP-Cur prepared by the pH-driven method (61.82 ± 1.54%) and the EE% of Cur in SP-Cur prepared by disulfide bond breaking treatment (66.38 ± 1.2%). The encapsulation of Cur in SP particles exhibited significant resistance to light and temperature, leading to enhanced stability. Soy protein treated with disulfide bond cleavage combined with critical pH-driven method can serve as a potential functional carrier to further incorporate hydrophobic compounds into food systems.

Bioengineered self-assembled nanofibrils for high-affinity SARS-CoV-2 capture and neutralization

The recent coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spurred intense research efforts to develop new materials with antiviral activity. In this study, we genetically engineered amyloid-based nanofibrils for capturing and neutralizing SARS-CoV-2. Building upon the amyloid properties of a short Sup35 yeast prion sequence, we fused it to SARS-CoV-2 receptor-binding domain (RBD) capturing proteins, LCB1 and LCB3. By tuning the reaction conditions, we achieved the spontaneous self-assembly of the Sup35-LCB1 fusion protein into a highly homogeneous and well-dispersed amyloid-like fibrillar material. These nanofibrils exhibited high affinity for the SARS-CoV-2 RBD, effectively inhibiting its interaction with the angiotensin-converting enzyme 2 (ACE2) receptor, the primary entry point for the virus into host cells. We further demonstrate that this functional nanomaterial entraps and neutralizes SARS-CoV-2 virus-like particles (VLPs), with a potency comparable to that of therapeutic antibodies. As a proof of concept, we successfully fabricated patterned surfaces that selectively capture SARS-CoV-2 RBD protein on wet environments. Collectively, these findings suggest that these protein-only nanofibrils hold promise as disinfecting coatings endowed with selective SARS-CoV-2 neutralizing properties to combat viral spread or in the development of sensitive viral sampling and diagnostic tools.

Comparative Simulative Analysis and Design of Single-Chain Self-Assembled Protein Cages.

Coiled-coil protein origami (CCPO) is a modular strategy for the de novo design of polypeptide nanostructures. It represents a type of modular design based on pairwise-interacting coiled-coil (CC) units with a single-chain protein programmed to fold into a polyhedral cage. However, the mechanisms underlying the self-assembly of the protein tetrahedron are still not fully understood. In the present study, 18 CCPO cages with three different topologies were modeled in silico. Then, molecular dynamics simulations and CC parameters were calculated to characterize the dynamic properties of protein tetrahedral cages at both the local and global levels. Furthermore, a deformed CC unit was redesigned, and the stability of the new cage was significantly improved.

Ultrasensitive dynamic light scattering immunodetection of alpha-fetoprotein using heptamer-amplified nanoparticle crosslinking aggregation.

Anovel construction strategy is introducedfor an ultrasensitive dynamic light scattering (DLS) immunosensor targeting alpha fetoprotein (AFP). This approach relies on a self-assembled heptamer fusion protein (A1-C4bpα), incorporating the dual functions of multivalent recognition and crosslinking aggregation amplification due to the presence of seven AFP-specific A1 nanobodies on the A1-C4bpα heptamer. Leveraging antibody-functionalized magnetic nanoparticles for target AFP capture and DLS signal output, the proposed heptamer-assisted DLS immunosensor offers high sensitivity, strong specificity, and ease of operation. Under the optimized conditions, the designed DLS immunosensor demonstrates excellent linear detection of AFP in the concentration range 0.06 ng mL-1 to 512 ng mL-1, with a detection limit of 15 pg mL-1. The selectivity, accuracy, precision, practicability, and reliability of this newly developed method were further validated through an assay of AFP levels in spiked and actual human serum samples. Thiswork introduces a novel approach for constructing ultrasensitive DLS immunosensors, easily extendable to the sensitive determination of other targets via simply replacing the nanobody sequence, holding great promise in various applications, particularly in disease diagnosis.

Self-assembled protein vesicles as vaccine delivery platform to enhance antigen-specific immune responses

Self-assembling protein nanoparticles are beneficial platforms for enhancing the often weak and short-lived immune responses elicited by subunit vaccines. Their benefits include multivalency, similar sizes as pathogens and control of antigen orientation. Previously, the design, preparation, and characterization of self-assembling protein vesicles presenting fluorescent proteins and enzymes on the outer vesicle surface have been reported. Here, a full-size model antigen protein, ovalbumin (OVA), was genetically fused to the recombinant vesicle building blocks and incorporated into protein vesicles via self-assembly. Characterization of OVA protein vesicles showed room temperature stability and tunable size. Immunization of mice with OVA protein vesicles induced strong antigen-specific humoral and cellular immune responses. This work demonstrates the potential of protein vesicles as a modular platform for delivering full-size antigen proteins that can be extended to pathogen antigens to induce antigen specific immune responses.

A new modality of anti-cancer drug: Ferritin-drug conjugates.

e14590 Background: Success criteria of ADCs is the target overexpression in tumor, i.e. in general ~ 14-fold in tumor vs. normal cells, which is the reason why it is hardly possible to develop clinically potent ADCs against several cancers with low target expression, which remains a major challenge yet, although fam-trastuzumab deruxtecan-nxki (Enhertu; AZN) and sacituzumab govitecan-hziy (Trodelvy; Gilead) recently exhibit an exceptionally enhanced efficacy for TNBC. Methods: Payloads were conjugated to a human apoferritin-derived, cancer-targeting scaffold (a self-assembled 24-mer protein with a diameter of ~ 12 nm, showing a high avidity for cancer cells) via a particular payload-releasing linker based on thiol-maleimide/imidazole-metal ion/EDC-NHS chemistry. Results: A new modality of anti-cancer drug - ferritin-drug conjugates (FDCs) - was developed, demonstrating a notably enhanced performance in cancer treatment as compared to current, clinically available anti-cancer drugs such as fam-trastuzumab deruxtecan-nxki, which is due to the important advantages such as far lowered EC50, high cancer-targeting efficiency, excellent structural stability (even in DMSO (up to 30%)), high loading capacity (high drug to ferritin ratio (DFR &gt; 20)) and consistent homogeneity in drug conjugation, no immune side effects, reduced drug resistance, and/or reduced off-target toxicity. Conclusions: FDCs are believed to open up a novel, attractive clinical route for both potent and safe therapy of a broad range of cancers.

Interfacial multilayer self-assembly of protein and polysaccharides: Ultrasonic regulation, stability and application in delivery lutein

In this study, the layer-by-layer adsorption behavior of sodium caseinate, pectin, and chitosan on the oil-water interface was illustrated using multi-frequency ultrasound. We investigated the impact of ultrasound on various factors, such as particle size, zeta potential, and interfacial protein/polysaccharide concentration. It was observed that ultrasound has significantly decreased droplet size and increased the surface area at the interface, hence promoting the adsorption of protein/polysaccharide. In the sonicated multilayer emulsion, the concentrations of interface proteins, pectin, and chitosan increased to 84.82 %, 90.49 %, and 83.31 %, respectively. The findings of the study indicated that the application of ultrasonic treatment had a significant impact on the emulsion's surface charge and the prevention of droplet aggregation. As a result, the stability of the emulsion system, including its resistance to salt, temperature, and storage conditions, has been significantly improved. Moreover, the emulsion showed an increase in the retention rate of lutein by 21.88 % after a high-temperature water bath and by 19.35 % after UV irradiation. Certainly, the multilayer emulsion treated with ultrasound demonstrated a superior and prolonged releasing behavior. These findings demonstrated the suitability of the ultrasound treatment for the preparation of emulsions to deliver bioactive compounds.

Purification of Self-Assembling Protein Nanoparticles using Affinity Chromatography

Purification of Self-Assembling Protein Nanoparticles using Affinity Chromatography

Purification of Self-Assembling Protein Nanoparticles using Affinity Chromatography

Purification of Self-Assembling Protein Nanoparticles using Affinity Chromatography

Nanoparticle display of neuraminidase elicits enhanced antibody responses and protection against influenza A virus challenge

Current Influenza virus vaccines primarily induce antibody responses against variable epitopes in hemagglutinin (HA), necessitating frequent updates. However, antibodies against neuraminidase (NA) can also confer protection against influenza, making NA an attractive target for the development of novel vaccines. In this study, we aimed to enhance the immunogenicity of recombinant NA antigens by presenting them multivalently on a nanoparticle carrier. Soluble tetrameric NA antigens of the N1 and N2 subtypes, confirmed to be correctly folded by cryo-electron microscopy structural analysis, were conjugated to Mi3 self-assembling protein nanoparticles using the SpyTag-SpyCatcher system. Immunization of mice with NA-Mi3 nanoparticles induced higher titers of NA-binding and -inhibiting antibodies and improved protection against a lethal challenge compared to unconjugated NA. Additionally, we explored the co-presentation of N1 and N2 antigens on the same Mi3 particles to create a mosaic vaccine candidate. These mosaic nanoparticles elicited antibody titers that were similar or superior to the homotypic nanoparticles and effectively protected against H1N1 and H3N2 challenge viruses. The NA-Mi3 nanoparticles represent a promising vaccine candidate that could complement HA-directed approaches for enhanced potency and broadened protection against influenza A virus.

Transformation of a Viral Capsid from Nanocages to Nanotubes and Then to Hydrogels: Redirected Self-Assembly and Effects on Immunogenicity.

The ability to manipulate the self-assembly of proteins is essential to understanding the mechanisms of life and beneficial to fabricating advanced nanomaterials. Here, we report the transformation of the MS2 phage capsid from nanocages to nanotubes and then to nanotube hydrogels through simple point mutations guided by interfacial interaction redesign. We demonstrate that site 70, which lies in the flexible FG loop of the capsid protein (CP), is a "magic" site that can largely dictate the final morphology of assemblies. By varying the amino acid at site 70, with the aid of a cysteine-to-alanine mutation at site 46, we achieved the assembly of double-helical or single-helical nanotubes in addition to nanocages. Furthermore, an additional cysteine substitution on the surface of nanotubes mediated their cross-linking to form hydrogels with reducing agent responsiveness. The hierarchical self-assembly system allowed for the investigation of morphology-related immunogenicity of MS2 CPs, which revealed dramatic differences among nanocages, nanotubes, and nanotube hydrogels in terms of immune response types, antibody levels and T cell functions. This study provides insights into the assembly manipulation of protein nanomaterials and the customized design of nanovaccines and drug delivery systems.