Structural Flexibility and Disassembly Kinetics of Single Ferritin Molecules Using Optical Nanotweezers

Ferritin, a spherical protein shell assembled from 24 subunits, functions as an efficient iron storage and release system through its channels. Understanding how various chemicals affect the structural behavior of ferritin is crucial for unravelling the origins of iron-related diseases in living organisms including humans. In particular, the influence of chemicals on ferritin's dynamics and iron release is barely explored at the single-protein level. Here, by employing optical nanotweezers using double-nanohole (DNH) structures, we examined the effect of ascorbic acid (reducing reagent) and pH on individual ferritin's conformational dynamics. The dynamics of ferritin increased as the concentration of ascorbic acid approached saturation. At pH 2.0, ferritin exhibited significant structural fluctuations and eventually underwent a stepwise disassembly into fragments. This work demonstrated the disassembly pathway and kinetics of a single ferritin molecule in solution. We identified four critical fragments during its disassembly pathway, which are 22-mer, 12-mer, tetramer, and dimer subunits. Moreover, we present single-molecule evidence of the cooperative disassembly of ferritin. Interrogating ferritin's structural change in response to different chemicals holds importance for understanding their roles in iron metabolism, hence facilitating further development of medical treatments for its associated diseases.

Fusion of amyloid beta with ferritin yields an isolated oligomeric beta-sheet-rich aggregate inside the ferritin cage

Alzheimer's disease is a severe brain condition caused by the formation of amyloid plaques composed of amyloid beta (Aβ) peptides. These peptides form oligomers, protofibrils, and fibrils before deposition into amyloid plaques. Among these intermediates, Aβ oligomers (AβOs) were found to be the most toxic and therefore an appealing target for drug development and understanding their role in the disease. However, precise isolation and characterization of AβOs have proven challenging because AβOs tend to aggregate and form heterogeneous mixtures in solution. As a solution, we genetically fused the Aβ peptide with a ferritin monomer. Such fusion allowed the encapsulation of precisely 24 Aβ peptides inside the 24-mer ferritin cage. Using high-speed atomic force microscopy (HS-AFM), we disassembled ferritin and directly visualized the Aβ core enclosed within the cage. The thioflavin-T assay (ThT) and attenuated total reflection infrared spectroscopy (ATR-IR) revealed the presence of a β-sheet structure in the encapsulated oligomeric aggregate. Gallic acid, an amyloid inhibitor, can inhibit the fluorescence of ThT bound AβOs. Our approach represents a significant advancement in the isolation and characterization of β-sheet rich AβOs and is expected to be useful for future studies of other disordered peptides such as α-synuclein and tau.

Encapsulins: Nanotechnology's future in a shell

Encapsulins, virus capsid-like bacterial nanocompartments have emerged as promising tools in medicine, imaging, and material sciences. Recent work has shown that these protein-bound icosahedral 'organelles' possess distinct properties that make them exceptionally usable for nanotechnology applications. A key factor contributing to their appeal is their ability to self-assemble, coupled with their capacity to encapsulate a wide range of cargos. Their genetic manipulability, stability, biocompatibility, and nano-size further enhance their utility, offering outstanding possibilities for practical biotechnology applications. In particular, their amenability to engineering has led to their extensive modification, including the packaging of non-native cargos and the utilization of the shell surface for displaying immunogenic or targeting proteins and peptides. This inherent versatility, combined with the ease of expressing encapsulins in heterologous hosts, promises to provide broad usability. Although mostly not yet commercialized, encapsulins have started to demonstrate their vast potential for biotechnology, from drug delivery to biofuel production and the synthesis of valuable inorganic materials. In this review, we will initially discuss the structure, function and diversity of encapsulins, which form the basis for these emerging applications, before reviewing ongoing practical uses and highlighting promising applications in medicine, engineering and environmental sciences.

Modifications of Thermal-Induced Northern Pike (Esox lucius) Liver Ferritin on Structural and Self-Assembly Properties

Ferritin, as an iron storage protein, regulates iron metabolism and delivers bioactive substances. It has been regarded as a safe, new type of natural iron supplement, with high bioavailability. In this paper, we extracted and purified ferritin from northern pike liver (NPLF). The aggregation stabilities, assemble properties, and structural changes in NPLF were investigated using electrophoresis, dynamic light scattering (DLS), circular dichroism (CD), UV–Visible absorption spectroscopy, fluorescence spectroscopy, and transmission electron microscopy (TEM) under various thermal treatments. The solubility, iron concentration, and monodispersity of NPLF all decreased as the temperature increased, and macromolecular aggregates developed. At 60 °C and 70 °C, the α-helix content of ferritin was greater. The content of α-helix were reduced to 8.10% and 1.90% at 90 °C and 100 °C, respectively, indicating the protein structure became loose and lost its self-assembly ability. Furthermore, when treated below 80 °C, NPLF maintained a complete cage-like shape, according to the microstructure. Partially unfolded structures reassembled into tiny aggregates at 80 °C. These findings suggest that mild thermal treatment (80 °C) might inhibit ferritin aggregation while leaving its self-assembly capacity unaffected. Thus, this study provides a theoretical basis for the processing and use of NPLF.

Electrochemical atomic force microscopy of two-dimensional trinuclear ruthenium clusters molecular assembly and dynamics under redox state control

Mixed-valence ruthenium trinuclear clusters containing dichloroacetates were synthesized, and the self-assembly of a single molecular adlayer composed of these clusters on a graphite surface was investigated by atomic force microscopy (AFM). AFM clearly revealed the dynamics of two-dimensional (2D) structure formation as well as the molecular characteristics of the adlayers at different electrochemical interfaces. The results verified that the design of metal complexes is important not only for redox chemistry but also for molecular assembly and nanoarchitecture construction.

Importance of the Subunit-Subunit Interface in Ferritin Disassembly: A Molecular Dynamics Study

Ferritin is a spherical cage-like protein that is useful for loading large functional particles for various applications. To our knowledge, how pH affects the interfaces inside ferritin and the mechanism of ferritin disassembly is far from complete. For this article, we conducted a series of molecular dynamics simulations (MD) at different pH values to study how interfaces affect ferritins' stability. It is shown that dimers are stable even at extremely low pH (pH 2.0), indicating that the dimer is the essential subunit for disassembly, and the slight swelling of the dimer resulting from monomer rotation inside a dimer is what triggers disassembly. During ferritin disassembly, there are two types of interfaces involved, and the interface between dimers is crucial. We also found that the driving forces for maintaining dimer stability are different when a dimer is inside ferritin and in an acidic solution. At low pH, the protonation of residues can lead to the loss of the salt bridge and the hydrogen bond between dimers, resulting in the disassembly of ferritin in an acidic environment. The above simulations reveal the possible mechanism of ferritin disassembly in an acidic solution, which can help us to design innovative and functional ferritin cages for different applications.

Smart delivery of epirubicin to cancer cells using aptamer-modified ferritin nanoparticles

Epirubicin is a chemotherapy agent which is commonly used in treatment of cancers. However, despite being efficient, the tendency to use this drug is declining mostly due to its myocardiopathy and drug-resistance of tumor cells. Such side effects could be prevented using targeted nanocarriers. This study aims to evaluate targeted delivery of epirubicin (Epi) to colon cancer cells using ferritin nanoparticles (Ft NPs) and MUC1 aptamer (Apt) and formation of Apt-Epi Ft NPs. In the current study, Apt-Epi Ft NPs were prepared. Then, physicochemical properties of nanoparticles, including size and zeta potential, morphology, drug loading, drug release from nanoparticles, drug uptake of cancer cells, cytotoxicity and in vivo results were collected. The results showed that the nanoparticles were synthesized with a mean size of 37.9 nm and encapsulation efficiency of 67%. The drug release from these nanoparticles was about 90% within 4 h in acidic medium. Also, targeted delivery of Epi enhanced its anticancer effects in both in vitro and in vivo. In this study, targeted delivery of Epi using aptamer-modified ferritin nanoparticles improved in vitro and in vivo results which indicates that it could be useful as a successful drug delivery system against cancer cells.

New insight into the structural changes of apoferritin pores in the process of doxorubicin loading at an acidic pH: Molecular dynamics simulations

Apoferritin (APO-Fr) is one of the most investigated proteins proposed as an advanced structure for drug delivery systems. Herein, molecular dynamics simulation was employed to compare the opening of 3-fold and 4-fold pores in APO-Fr during the partial disassembly process at an acidic pH. We showed that more hydrophilic residues in the surface of 3-fold pores compared to 4-fold pores facilitate increased flexibility and a higher tendency to open. In particular, dissociation is induced by the presence of Doxorubicin (DOX) close to 3-fold pores. Our simulations showed loaded DOXs on the APO-Fr surface were mainly involved in the hydrogen bond interactions with the hydrophilic residues, suggesting the difficulty of hydrophobic drugs loading in APO-Fr with the partial disassembly process. However, π-π interactions as well as hydrogen bonds between protein and DOXs were mediated by the basic and acidic amino acids such as HIP128, GLU17, and LYS143 at the open pores, providing penetration of DOXs into the H-Apo-Fr. We conclude that increased drug encapsulations and loading capacity of hydrophobic drugs into the cavity of APO-Fr are feasible by further disassembly of openings to access the internal hydrophobic portions of the protein.

Kinetics of Ferritin Self-Assembly by Laser Light Scattering: Impact of Subunit Concentration, pH, and Ionic Strength

Ferritins, the cellular iron repositories, are self-assembled, hollow spherical nanocage proteins composed of 24 subunits. The self-assembly process in ferritin generates the electrostatic gradient to rapidly sequester Fe(II) ions, thereby minimizing its toxicity (Fenton reaction). Although the factors that drive self-assembly and control its kinetics are little investigated, its inherent reversibility has been utilized for cellular imaging and targeted drug delivery. The current work tracks the kinetics of ferritin self-assembly by laser light scattering and investigates the factors that influence the process. The formation of partially structured subunit-monomers/dimers, at pH ≤ 1.5, serves as the starting material for the self-assembly, which upon increasing the pH exhibits biphasic behavior (a rapid assembly process coupled with subunit folding followed by a slower reassembly/reorganization process) and completes within 10 min. The ferritin self-assembly accelerated with subunit concentration and ionic strength (t_1/2 decreases in both the cases) but slowed down with the pH of the medium from 5.5 to 7.5 (t_1/2 increases). These findings would help to regulate the ferritin self-assembly to enhance the loading/unloading of drugs/nanomaterials for exploiting it as a nanocarrier and nanoreactor.

Spatial organization of Dps and DNA-Dps complexes

DNA co-crystallization with Dps family proteins is a fundamental mechanism, which preserves DNA in bacteria from harsh conditions. Though many aspects of this phenomenon are well characterized, the spatial organization of DNA in DNA-Dps co-crystals is not completely understood, and existing models need further clarification. To advance in this problem we have utilized atomic force microscopy (AFM) as the main structural tool, and small-angle X-scattering (SAXS) to characterize Dps as a key component of the DNA-protein complex. SAXS analysis in the presence of EDTA indicates a significantly larger radius of gyration for Dps than would be expected for the core of the dodecamer, consistent with the N-terminal regions extending out into solution and being accessible for interaction with DNA. In AFM experiments, both Dps protein molecules and DNA-Dps complexes adsorbed on mica or highly oriented pyrolytic graphite (HOPG) surfaces form densely packed hexagonal structures with a characteristic size of about 9 nm. To shed light on the peculiarities of DNA interaction with Dps molecules, we have characterized individual DNA-Dps complexes. Contour length evaluation has confirmed the non-specific character of Dps binding with DNA and revealed that DNA does not wrap Dps molecules in DNA-Dps complexes. Angle analysis has demonstrated that in DNA-Dps complexes a Dps molecule contacts with a DNA segment of ~6 nm in length. Consideration of DNA condensation upon complex formation with small Dps quasi-crystals indicates that DNA may be arranged along the rows of ordered protein molecules on a Dps sheet.