Protein Shell Research Articles

Angiotensin-I-converting enzyme and renin inhibitions by antioxidant shrimp shell protein hydrolysate and ultrafiltration peptide fractions

Protein hydrolysates with 20% and 30% degrees of hydrolysis (DH) were produced from alcalase hydrolysis of Pacific white shrimp shells. The study aimed to investigate the antioxidant and antihypertensive activities of these protein hydrolysates, focusing on peptide fractions of various molecular weights (MW) obtained through ultrafiltration. The 30% DH protein hydrolysate (SSPH) showed the highest antioxidant activities and was subjected to ultrafiltration to produce peptides of various molecular weights (MW) (F1:10–50, F2:5–10, F3:3–5, F4:1-3, and F5:<1 kDa). SSPH showed higher hydrophilic and non-essential amino acid content, among which alanine and aspartic acid were at higher levels. The obtained peptide fractions were analyzed for various antioxidant activities and inhibitory activities against angiotensin-converting enzyme and renin. F4 and F2 samples showed the highest DPPH (2.00 mM TE/g sample) and ABTS (60.68 mM TE/g sample) radical scavenging activities, respectively. Superoxide and hydrogen peroxide radical scavenging activity augmented with decreasing MW, aside from for F1, which showed higher activity than F2–F4 (p < 0.05). The highest ACE-inhibitory activity was found for the F2 fraction (44%–55%), and renin inhibitory activity increased with decreasing MW, in which F5 (12%–22%) was the most effective (p < 0.05). F5 showed 6 major peptides, among which KLVRGSKS and LPKKCLSARPG were the dominant sequences. Thus, this study suggests that shrimp shell protein isolate could be an alternative protein source for peptides with various antioxidant and antihypertensive activities, with potential applications in functional foods and nutraceuticals aimed at mitigating oxidative stress and hypertension.

The Nature and Origin of Plant Viruses with an Incursion into Virus Nomenclature

Eversince, the chemical nature of not only the anisometric tobacco mosaic virus (TMV) but also the crystalline viruses like bushy stunt of tomato, tobacco necrosis virus, turnip yellow mosaic virus and others have been characterized, sap transmissible viruses have been shown to be good antigens and that their antisera had group specificity aiding identification. Whilst symptomatology alone was found unreliable and of insufficient means for diagnosis and classification of viruses, serology, chemical and physical structure of viruses and the modes of transmission have played an important role in virus nomenclature. However, it is premature to think of orthodox binomial and trinomial nomenclature as practised in fungal classification playing a role in virus terminology, Anisometric and crystalline viruses are comparatively simple chemical entities (as compared with animal viruses) and are essentially nucleoproteins where the RNA (ribonucleic acid) core has a shell of protein in a helical pattern serving as a protective coating. The infectivity of the nucleic acid alone (which is hardly 6% of the nucleoproteiri) has been proved beyond doubt whereas, the protein (which is the bulk of the virus) does not count for infectivity but plays an important role in serological reactions and consequently is of immense value in grouping viruses. Nevertheless, size, shapes and structure of viruses are of considerable significance as a tool in virus classification of rodshaped particles. Spherical virus particles, however, have not lent themselves to this approach. A somewhat similar approach to classification has been made by using specific vector-virus relationships.In the speculative field of origin of viruses, the free gene or plasmagene theory of Darlington seems to find little support at present. Nonetheless, a biochemical approach is still valid and as all the ribonucleic acid (RNA) in the TMV appears to be present in a single polynucleotide chain, a break in this chain has to be transmitted intact to the recipient cell to enable reduplication. That the RNA may be replicated in the cells is, therefore, not to be regarded as a shortlived messenger carrying genetic information from nuclear deoxyribonucleic acid (DNA) to protein. Stretching this argument one could conceive of a further step to the self-perpetuating RNA molecule capable of directing protein synthetic mechanisms in recipient cells to specific products.

Patterning of multicomponent elastic shells by gaussian curvature.

Recent findings suggest that shell protein distribution and the morphology of bacterial microcompartments regulate the chemical fluxes facilitating reactions which dictate their biological function. We explore how the morphology and component patterning are coupled through the competition of mean and gaussian bending energies in multicomponent elastic shells that form three-component irregular polyhedra. We observe two softer components with lower bending rigidities allocated on the edges and vertices while the harder component occupies the faces. When subjected to a nonzero interfacial line tension, the two softer components further separate and pattern into subdomains that are mediated by the gaussian curvature. We find that this degree of fractionation is maximized when there is a weaker line tension and when the ratio of bending rigidities between the two softer domains ≈2. Our results reveal a patterning mechanism in multicomponent shells that can capture the observed morphologies of bacterial microcompartments, and moreover, can be realized in synthetic vesicles.

Two peptides LLRLTDL and GYALPCDCL inhibit foam cell formation through activating PPAR-γ/LXR-α signaling pathway in oxLDL-treated RAW264.7 macrophages.

Foam cell formation plays a pivotal role in atherosclerosis-associated cardiovascular diseases. Bioactive peptides generated from marine sources have been found to provide multifunctional health advantages. In the present study, we investigated the anti-atherosclerotic effects of LLRLTDL (Bu1) and GYALPCDCL (Bu2) peptides, isolated from ark shell protein hydrolysates by assessing their inhibitory effect on oxidized LDL (oxLDL)-induced foam cell formation. The two peptides showed a promising anti-atherosclerotic effect by inhibiting foam cell formation, which was evidenced by inhibiting lipid accumulation in oxLDL-treated RAW264.7 macrophages and oxLDL-treated primary human aortic smooth muscle cells (HASMC). Two peptides effectively reduced total cholesterol, free cholesterol, cholesterol ester, and triglyceride levels by upregulating cholesterol efflux and downregulating cholesterol influx. Expression of cholesterol influx-related proteins such as SR-A1 and CD36 were reduced, whereas cholesterol efflux-related proteins such as ATP-binding cassette transporter ABCA-1 and ABCG-1 were highly expressed. In addition, Bu1 and Bu2 peptides increased PPAR-γ and LXR-α expression. However, PPAR-γ siRNA transfection reversed the foam cell formation inhibitory activity of Bu1 and Bu2 peptides. Furthermore, the synergistic effect of Bu1 and Bu2 peptides on foam cell formation inhibition was observed with PPAR-γ agonist thiazolidinediones, indicating that PPAR-γ signaling pathway plays a key role in foam cell formation of macrophages. Beyond their impact on foam cell formation, Bu1 and Bu2 peptides demonstrated anti-inflammatory potential by inhibiting the generation of pro-inflammatory cytokines and nitric oxide and NF-κB nuclear activation. Taken together, these results suggest that Bu1 and Bu2 peptides may be useful for atherosclerosis and associated anti-inflammatory therapies.

Myxococcus xanthus encapsulin cargo protein EncD is a flavin-binding protein with ferric reductase activity

Encapsulins are protein nanocompartments that regulate cellular metabolism in several bacteria and archaea. Myxococcus xanthus encapsulins protect the bacterial cells against oxidative stress by sequestering cytosolic iron. These encapsulins are formed by the shell protein EncA and three cargo proteins: EncB, EncC, and EncD. EncB and EncC form rotationally symmetric decamers with ferroxidase centers (FOCs) that oxidize Fe+2 to Fe+3 for iron storage in mineral form. However, the structure and function of the third cargo protein, EncD, have yet to be determined. Here, we report the x-ray crystal structure of EncD in complex with flavin mononucleotide. EncD forms an α-helical hairpin arranged as an antiparallel dimer, but unlike other flavin-binding proteins, it has no β-sheet, showing that EncD and its homologs represent a unique class of bacterial flavin-binding proteins. The cryo-EM structure of EncA-EncD encapsulins confirms that EncD binds to the interior of the EncA shell via its C-terminal targeting peptide. With only 100 amino acids, the EncD α-helical dimer forms the smallest flavin-binding domain observed to date. Unlike EncB and EncC, EncD lacks a FOC, and our biochemical results show that EncD instead is a NAD(P)H-dependent ferric reductase, indicating that the M. xanthus encapsulins act as an integrated system for iron homeostasis. Overall, this work contributes to our understanding of bacterial metabolism and could lead to the development of technologies for iron biomineralization and the production of iron-containing materials for the treatment of various diseases associated with oxidative stress.

Enzyme-cargo encapsulation peptides bind between tessellating tiles of the bacterial microcompartment shell

Bacterial microcompartments are prokaryotic organelles comprising encapsulated enzymes within a thin protein shell. They facilitate metabolic processing including propanediol, choline, glycerol, and ethanolamine utilization, and they accelerate carbon fixation in cyanobacteria. Enzymes targeted to the inside of the microcompartment frequently possess a cargo-encapsulation peptide, but the site to which the peptide binds is unclear. We provide evidence that the encapsulation peptides bind to the hydrophobic groove formed between tessellating subunits of the shell proteins. In silico docking studies provide a compelling model of peptide binding to this prominent hydrophobic groove. This result is consistent with the now widely accepted view that the convex side of the shell oligomers faces the lumen of the microcompartment. Binding of the encapsulation peptide to the groove between tessellating shell protein tiles explains why it has been difficult to define the peptide binding site using other methods, provides a mechanism by which encapsulation-peptide bearing enzymes can promote shell assembly, and explains how the presence of cargo affects the size and shape of the bacterial microcompartment. This knowledge may be exploited in engineering microcompartments or in disease prevention by hampering cargo-encapsulation.

Ultrasonication-assisted enzymatic hydrolysis of shrimp shell protein isolate: characterization, antioxidant, and functional properties

Ultrasonication-assisted enzymatic hydrolysis of shrimp shell protein isolate: characterization, antioxidant, and functional properties

Stimulus-responsive assembly of nonviral nucleocapsids

Controlled assembly of a protein shell around a viral genome is a key step in the life cycle of many viruses. Here we report a strategy for regulating the co-assembly of nonviral proteins and nucleic acids into highly ordered nucleocapsids in vitro. By fusing maltose binding protein to the subunits of NC-4, an engineered protein cage that encapsulates its own encoding mRNA, we successfully blocked spontaneous capsid assembly, allowing isolation of the individual monomers in soluble form. To initiate RNA-templated nucleocapsid formation, the steric block can be simply removed by selective proteolysis. Analyses by transmission and cryo-electron microscopy confirmed that the resulting assemblies are structurally identical to their RNA-containing counterparts produced in vivo. Enzymatically triggered cage formation broadens the range of RNA molecules that can be encapsulated by NC-4, provides unique opportunities to study the co-assembly of capsid and cargo, and could be useful for studying other nonviral and viral assemblies.

Development of CuO Nanoparticles from the Mucus of Garden Snail Cornu aspersum as New Antimicrobial Agents.

Several biologically active compounds involved in the green synthesis of silver and gold nanoparticles have been isolated from snail mucus and characterized. This paper presents a successful method for the application of snail mucus from Cornu aspersum as a bioreducing agent of copper sulfate and as a biostabilizer of the copper oxide nanoparticles (CuONPs-Muc) obtained. The synthesis at room temperature and neutral pH yielded nanoparticles with a spherical shape and an average diameter of 150 nm. The structure and properties of CuONPs-Muc were characterized using various methods and techniques, such as ultraviolet-visible spectroscopy (UV-vis), high-performance liquid chromatography (HPLC), one-dimensional polyacrylamide gel electrophoresis (1D-PAGE), up-conversion infrared spectroscopy Fourier transform (FTIR), scanning electron microscopy combined with energy dispersive spectroscopy (SEM/EDS), Raman spectroscopy and imaging, thermogravimetric analysis (TG-DSC), etc. Mucus proteins with molecular weights of 30.691 kDa and 26.549 kDa were identified, which are involved in the biogenic production of CuONPs-Muc. The macromolecular shell of proteins formed around the copper ions contributes to a higher efficiency of the synthesized CuONPs-Muc in inhibiting the bacterial growth of several Gram-positive (Bacillus subtilis NBIMCC2353, Bacillus spizizenii ATCC 6633, Staphylococcus aureus ATCC 6538, Listeria innocua NBIMCC8755) and Gram-negative (Escherichia coli ATCC8739, Salmonella enteitidis NBIMCC8691, Salmonella typhimurium ATCC 14028, Stenotrophomonas maltophilia ATCC 17666) bacteria compared to baseline mucus. The bioorganic synthesis of snail mucus presented here provides CuONPs-Muc with a highly pronounced antimicrobial effect. These results will expand knowledge in the field of natural nanomaterials and their role in emerging dosage forms.

Elucidating the role of ferric chloride on carbon capture from low-strength municipal wastewater in high-rate activated sludge process: Parameter optimization and crucial mechanism

To enhance organics capture efficiency from low-strength municipal wastewater of China, FeCl3 enhanced high-rate activated sludge (FC-HRAS) process was established in this work. Effects of sludge concentration and FeCl3 dosage on carbon capture in FC-HRAS were investigated. The optimum sludge concentration of 2.0 g/L and FeCl3 dosage of 30 mg Fe/L were obtained, with total COD removal efficiency of 76.8%. Carbon balance analysis showed that FC-HRAS increased organics capture proportion by 91.8% while reducing loss from oxidative metabolism compared to HRAS. The potential mechanism of enhanced carbon capture for FC-HRAS was further explored. Adding Fe(III) caused coagulation of organics by increasing the Zeta potential in wastewater. Impacted by charge neutralization “compression” and coagulation floc “encirclement”, sludge particle sizes decreased, leading to increases of internal surface area and adsorption site of sludge for binding with bacteria; it facilitated the biological flocculation of FC-HRAS. Meanwhile, Fe(III) binding with proteins in EPS induced formation of “protein shell – β polysaccharides kernel” sludge structure and reduction of sludge negative charge, which intensified sludge stability and agglomeration. These factors explained the increase in organics capture proportion. The decrease in metabolism loss of organics could be attributed to the increase in organics transfer resistance in sludge EPS and selective elimination of heteromorphic bacteria (e.g., denitrifiers) in sludge. This work provided guidance for energy-neutral and cost-saving wastewater treatment in China.

Single-cell analysis reveals microbial spore responses to sodium hypochlorite.

Pollution from toxic spores has caused us a lot of problems because spores are extremely resistant and can survive most disinfectants. Therefore, the detection of spore response to disinfectant is of great significance for the development of effective decontamination strategies. In this work, we investigated the effect of 0.5% sodium hypochlorite on the molecular and morphological properties of single spores of Bacillus subtilis using single-cell techniques. Laser tweezers Raman spectroscopy showed that sodium hypochlorite resulted in Ca2+-dipicolinic acid release and nucleic acid denaturation. Atomic force microscopy showed that the surface of treated spores changed from rough to smooth, protein shells were degraded at 10 min, and the permeability barrier was destroyed at 15 min. The spore volume decreased gradually over time. Live-cell imaging showed that the germination and growth rates decreased with increasing treatment time. These results provide new insight into the response of spores to sodium hypochlorite.

Diverting the Use of Hand-Operated Tablet Press Machines to Bioassays: A Novel Protocol to Test 'Waste' Insoluble Shell Matrices.

To mineralize their shells, molluscs secrete a complex cocktail of proteins-collectively defined as the calcifying shell matrix-that remains occluded in the exoskeleton. Nowadays, protein extracts from shells are recognized as a potential source of bioactive substances, among which signalling molecules, bactericides or protease inhibitors offer the most tangible perspectives in applied sciences, health, and aquaculture. However, one technical obstacle in testing the activity of shell extracts lies in their high insolubility. In this paper, we present a protocol that circumvents this impediment. After an adapted shell protein extraction and the production of two organic fractions-one soluble, one insoluble-we employ a hand-operated tablet press machine to generate well-calibrated tablets composed of 100% insoluble shell matrix. FT-IR monitoring of the quality of the tablets shows that the pressure used in the press machine does not impair the molecular properties of the insoluble extracts. The produced tablets can be directly tested in different biological assays, such as the bactericidal inhibition zone assay in Petri dish, as illustrated here. Diverting the use of the hand-operated tablet press opens new perspectives in the analysis of insoluble shell matrices, for discovering novel bioactive components.

RNA genome packaging and capsid assembly of bluetongue virus visualized in host cells

Unlike those of double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), and ssRNA viruses, the mechanism of genome packaging of dsRNA viruses is poorly understood. Here, we combined the techniques of high-resolution cryoelectron microscopy (cryo-EM), cellular cryoelectron tomography (cryo-ET), and structure-guided mutagenesis to investigate genome packaging and capsid assembly of bluetongue virus (BTV), a member of the Reoviridae family of dsRNA viruses. A total of eleven assembly states of BTV capsid were captured, with resolutions up to 2.8Å, with most visualized in the host cytoplasm. ATPase VP6 was found underneath the vertices of capsid shell protein VP3 as an RNA-harboring pentamer, facilitating RNA packaging. RNA packaging expands the VP3 shell, which then engages middle- and outer-layer proteins to generate infectious virions. These revealed "duality" characteristics of the BTV assembly mechanism reconcile previous contradictory co-assembly and core-filling models and provide insights into the mysterious RNA packaging and capsid assembly of Reoviridae members and beyond.

Interfacial Assembly of Bacterial Microcompartment Shell Proteins in Aqueous Multiphase Systems (Small 15/2024)

Interfacial Assembly of Bacterial Microcompartment Shell Proteins in Aqueous Multiphase Systems (Small 15/2024)

Carboxysomes: Green Solutions for Sustainable Agriculture and Renewable Energy

Carboxyomes are emerging as potential tools in the sustainable agriculture and biofuel production. They are proteinaceous organelles that are distributed in different species of photosynthetic bacteria and archaea and are significantly involved in carbon fixation. They enable the organisms to thrive in diverse environmental conditions and enhance the efficacy of photosynthesis. They have shown promising potential to address challenging regarding global food security, climate change and renewable energy. These nanocompartments encapsulate Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), an enzyme that catalyzes the first step of the Calvin-Benson-Bassham cycle that is a key pathway in carbon fixation. These specialized structures concentrate CO2 around RuBisCO ad shield it from the competing oxygen, thereby optimizing the efficiency of photosynthetic process and minimize wasteful photorespiration. The photosynthetic organisms having carboxysomes are therefore ideal candidates for sustainable agriculture as they are able to thrive in the harsh conditions such as low CO2 concentrations, water scarcity and high temperatures. They are recently being studied for enhancing the productivity and yield of crops. Efforts are being exerted to introduce carboxysome shell proteins and RuBisCO enzymes into crop genomes. Researchers are aiming to create plants with the ability to efficiently capture and utilize CO2 for photosynthesis. These genetically modified crops can potentially increase crop yields, improve water and nutrient efficiency significantly. Moreover, these carboxysomal transgenes are also able to enhance the resilience of GM plants to different environmental stressors such as drought and heat, and ultimately contribute to global food security and sustainable agriculture. In addition to their applications in agriculture, carboxysomes hold promise for biofuel production as well, as they are capable of carbon fixation. They have enabled researchers to engineer photosynthetic organisms to produce renewable fuels such as ethanol, biodiesel and hydrogen. Furthermore, nanobioreactors that are based on carboxysomes can contribute protectively against climate change as they have the potential to mitigate greenhouse gas emissions by capturing CO2 from industrial emissions and converting it into valuable bioproducts. This approach represents a promising avenue to address global challenges of food insecurity, climate crisis and rapidly declining non-renewable energy sources. If leveraged appropriately, these nanocompartments can significantly contribute in paving a way for more sustainable and resilient future.

A phage nucleus-associated RNA-binding protein is required for jumbo phage infection.

Large-genome bacteriophages (jumbo phages) of the proposed family Chimalliviridae assemble a nucleus-like compartment bounded by a protein shell that protects the replicating phage genome from host-encoded restriction enzymes and DNA-targeting CRISPR-Cas nucleases. While the nuclear shell provides broad protection against host nucleases, it necessitates transport of mRNA out of the nucleus-like compartment for translation by host ribosomes, and transport of specific proteins into the nucleus-like compartment to support DNA replication and mRNA transcription. Here, we identify a conserved phage nuclear shell-associated protein that we term Chimallin C (ChmC), which adopts a nucleic acid-binding fold, binds RNA with high affinity in vitro, and binds phage mRNAs in infected cells. ChmC also forms phase-separated condensates with RNA in vitro. Targeted knockdown of ChmC using mRNA-targeting dCas13d results in accumulation of phage-encoded mRNAs in the phage nucleus, reduces phage protein production, and compromises virion assembly. Taken together, our data show that the conserved ChmC protein plays crucial roles in the viral life cycle, potentially by facilitating phage mRNA translocation through the nuclear shell to promote protein production and virion development.

Phase transition of GvpU regulates gas vesicle clustering in bacteria.

Gas vesicles (GVs) are microbial protein organelles that support cellular buoyancy. GV engineering has multiple applications, including reporter gene imaging, acoustic control and payload delivery. GVs often cluster into a honeycomb pattern to minimize occupancy of the cytosol. The underlying molecular mechanism and the influence on cellular physiology remain unknown. Using genetic, biochemical and imaging approaches, here we identify GvpU from Priestia megaterium as a protein that regulates GV clustering in vitro and upon expression in Escherichia coli. GvpU binds to the C-terminal tail of the core GV shell protein and undergoes a phase transition to form clusters in subsaturated solution. These properties of GvpU tune GV clustering and directly modulate bacterial fitness. GV variants can be designed with controllable sensitivity to GvpU-mediated clustering, enabling design of genetically tunable biosensors. Our findings elucidate the molecular mechanisms and functional roles of GV clustering, enabling its programmability for biomedical applications.

Structural diversity of tick-borne encephalitis virus particles in the inactivated vaccine based on strain Sofjin

ABSTRACT The main approach to preventing tick-borne encephalitis (TBE) is vaccination. Formaldehyde-inactivated TBE vaccines have a proven record of safety and efficiency but have never been characterized structurally with atomic resolution. We report a cryoelectron microscopy (cryo-EM) structure of the formaldehyde-inactivated TBE virus (TBEV) of Sofjin-Chumakov strain representing the Far-Eastern subtype. A 3.8 Å resolution reconstruction reveals the structural integrity of the envelope E proteins, specifically the E protein ectodomains. The comparative study shows a high structural similarity to the previously published structures of the TBEV European subtype strains Hypr and Kuutsalo-14. A fraction of inactivated virions exhibits asymmetric features including the deformations of the membrane profile. We propose that the heterogeneity is caused by inactivation and perform a local variability analysis on the small parts of the envelope protein shell to reveal membrane curvature features possibly induced by the inactivation. The results of this study will have implications for the design of novel vaccines against diseases caused by flaviviruses.

The structure of inactivated mature tick-borne encephalitis virus at 3.0 Å resolution

ABSTRACT Tick-borne encephalitis virus (TBEV) causes a severe disease, tick-borne encephalitis (TBE), that has a substantial epidemiological importance for Northern Eurasia. Between 10,000 and 15,000 TBE cases are registered annually despite the availability of effective formaldehyde-inactivated full-virion vaccines due to insufficient vaccination coverage, as well as sporadic cases of vaccine breakthrough. The development of improved vaccines would benefit from the atomic resolution structure of the antigen. Here we report the refined single-particle cryo-electron microscopy (cryo-EM) structure of the inactivated mature TBEV vaccine strain Sofjin–Chumakov (Far-Eastern subtype) at a resolution of 3.0 Å. The increase of the resolution with respect to the previously published structures of TBEV strains Hypr and Kuutsalo-14 (European subtype) was reached due to improvement of the virus sample quality achieved by the optimized preparation methods. All the surface epitopes of TBEV were structurally conserved in the inactivated virions. ELISA studies with monoclonal antibodies supported the hypothesis of TBEV protein shell cross-linking upon inactivation with formaldehyde.

The Expanding Diversity of Viruses from Extreme Environments.

Viruses are nonliving biological entities whose host range encompasses all known forms of life. They are deceptively simple in description (a protein shell surrounding genetic material with an occasional lipid envelope) and yet can infect all known forms of life. Recently, due to technological advancements, viruses from more extreme environments can be studied through both culture-dependent and independent means. Viruses with thermophilic, halophilic, psychrophilic, and barophilic properties are highlighted in this paper with an emphasis on the properties that allow them to exist in said environments. Unfortunately, much of this field is extremely novel and thus, not much is yet known about these viruses or the microbes they infect when compared to non-extremophilic host-virus systems. With this review, we hope to shed some light on these relatively new studies and highlight their intrinsic value.