The sedimentation properties of ferritins. New insights and analysis of methods of nanoparticle preparation

Determination of mRNA copy number in degradable lipid nanoparticles via density contrast analytical ultracentrifugation

Lipid nanoparticles as delivery system for mRNA have recently attracted attention to a broader audience as COVID-19 mRNA vaccines. Their low immunogenicity and capability to deliver a variety of nucleic acids renders them an interesting and complementary alternative to gene therapy vectors like AAVs. An important quality attribute of LNPs is the copy number of the encapsulated cargo molecule. This work describes how density and molecular weight distributions obtained by density contrast sedimentation velocity can be used to calculate the mRNA copy number of a degradable lipid nanoparticle formulation. The determined average copy number of 5 mRNA molecules per LNP is consistent with the previous studies using other biophysical techniques, such as single particle imaging microscopy and multi-laser cylindrical illumination confocal spectroscopy (CICS).

Nonmonotonic Superparamagnetic Behavior of the Ferritin Iron Core Revealed via Quantum Spin Relaxometry

Ferritin is the primary storage protein in our body and is of significant interest in biochemistry, nanotechnology, and condensed matter physics. More specifically within this sphere of interest are the magnetic properties of the iron core of ferritin, which have been utilized as a contrast agent in applications such as magnetic resonance imaging. This magnetism depends on both the number of iron atoms present, L, and the nature of the magnetic ordering of their electron spins. In this work, we create a series of ferritin samples containing homogeneous iron loads and apply diamond-based quantum spin relaxometry to systematically study their room temperature magnetic properties. We observe anomalous magnetic behavior that can be explained using a theoretical model detailing a morphological change to the iron core occurring at relatively low iron loads. This model provides an L^0.35±0.06 scaling of the uncompensated Fe spins, in agreement with previous theoretical predictions. The necessary inclusion of this morphological change within the model is also supported by electron microscopy studies of ferritin with low iron content. This provides evidence for a magnetic consequence of this morphological change and positions diamond-based quantum spin relaxometry as an effective, noninvasive tool for probing the magnetic properties of metalloproteins. The low detection limit (ferritin 2% loaded at a concentration of 7.5 ± 0.4 μg/mL) also makes this a promising method for precision applications where low analyte concentrations are unavoidable, such as in biological research or even clinical analysis.

Maximum iron loading of ferritin: half a century of sustained citation distortion

Analysis of citation networks in biomedical research has indicated that belief in a specific scientific claim can gain unfounded authority through citation bias (systematic ignoring of papers that contain content conflicting with a claim), amplification (citation to papers that don't contain primary data), and invention (citing content but claiming it has a different meaning). There is no a priori reason to expect that citation distortion is limited to particular fields of science. This Pespective presents a case study of the literature on maximum iron loading of the ferritin protein to illustrate that the field of metallomics is no exception to the rule that citation distortion is a widespread phenomenon.

HullRad: Fast Calculations of Folded and Disordered Protein and Nucleic Acid Hydrodynamic Properties

Hydrodynamic properties are useful parameters for estimating the size and shape of proteins and nucleic acids in solution. The calculation of such properties from structural models informs on the solution properties of these molecules and complements corresponding structural studies. Here we report, to our knowledge, a new method to accurately predict the hydrodynamic properties of molecular structures. This method uses a convex hull model to estimate the hydrodynamic volume of the molecule and is orders of magnitude faster than common methods. It works well for both folded proteins and ensembles of conformationally heterogeneous proteins and for nucleic acids. Because of its simplicity and speed, the method should be useful for the modification of computer-generated, intrinsically disordered protein ensembles and ensembles of flexible, but folded, molecules in which rapid calculation of experimental parameters is needed. The convex hull method is implemented in a Python script called HullRad. The use of the method is facilitated by a web server and the code is freely available for batch applications.

Effects of surface functionalization of hydrophilic NaYF4 nanocrystals doped with Eu3+ on glutamate and GABA transport in brain synaptosomes

Specific rare earth doped nanocrystals (NCs), a recent class of nanoparticles with fluorescent features, have great bioanalytical potential. Neuroactive properties of NaYF4 nanocrystals doped with Eu3+ were assessed based on the analysis of their effects on glutamate- and γ-aminobutyric acid (GABA) transport process in nerve terminals isolated from rat brain (synaptosomes). Two types of hydrophilic NCs were examined in this work: (i) coated by polyethylene glycol (PEG) and (ii) with OH groups at the surface. It was found that NaYF4:Eu3+-PEG and NaYF4:Eu3+-OH within the concentration range of 0.5-3.5 and 0.5-1.5 mg/ml, respectively, did not influence Na+-dependent transporter-dependent l-[14C]glutamate and [3H]GABA uptake and the ambient level of the neurotransmitters in the synaptosomes. An increase in NaYF4:Eu3+-PEG and NaYF4:Eu3+-OH concentrations up to 7.5 and 3.5 mg/ml, respectively, led to the (1) attenuation of the initial velocity of uptake of l-[14C]glutamate and [3H]GABA and (2) elevation of ambient neurotransmitters in the suspension of nerve terminals. In the mentioned concentrations, nanocrystals did not influence acidification of synaptic vesicles that was shown with pH-sensitive fluorescent dye acridine orange, however, decreased the potential of the plasma membrane of synaptosomes. In comparison with other nanoparticles studied with similar methodological approach, NCs start to exhibit their effects on neurotransmitter transport at concentrations several times higher than those shown for carbon dots, detonation nanodiamonds and an iron storage protein ferritin, whose activity can be registered at 0.08, 0.5 and 0.08 mg/ml, respectively. Therefore, NCs can be considered lesser neurotoxic as compared to above nanoparticles.

Unsaturated Long-Chain Fatty Acids Are Preferred Ferritin Ligands That Enhance Iron Biomineralization

Ferritin is a ubiquitous nanocage protein, which can accommodate up to thousands of iron atoms inside its cavity. Aside from its iron storage function, a new role as a fatty acid binder has been proposed for this protein. The interaction of apo horse spleen ferritin (HoSF) with a variety of lipids has been here investigated through NMR spectroscopic ligand-based experiments, to provide new insights into the mechanism of ferritin-lipid interactions, and the link with iron mineralization. 1D ¹ H, diffusion (DOSY) and saturation-transfer difference (STD) NMR experiments provided evidence for a stronger interaction of ferritin with unsaturated fatty acids compared to saturated fatty acids, detergents, and bile acids. Mineralization assays showed that oleate c aused the most efficient increase in the initial rate of iron oxidation, and the highest formation of ferric species in HoSF. The comprehension of the factors inducing a faster biomineralization is an issue of the utmost importance, given the association of ferritin levels with metabolic syndromes, such as insulin resistance and diabetes, characterized by fatty acid concentration dysregulation. The human ferritin H-chain homopolymer (HuHF), featuring ferroxidase activity, was also tested for its fatty acid binding capabilities. Assays show that oleate can bind with high affinity to HuHF, without altering the reaction rates at the ferroxidase site.

Enrichment and characterization of ferritin for nanomaterial applications

Ferritin is a ubiquitous iron storage protein utilized as a nanomaterial for labeling biomolecules and nanoparticle construction. Commercially available preparations of horse spleen ferritin, widely used as a starting material, contain a distribution of ferritins with different iron loads. We describe a detailed approach to the enrichment of differentially loaded ferritin molecules by common biophysical techniques such as size exclusion chromatography and preparative ultracentrifugation, and characterize these preparations by dynamic light scattering, and analytical ultracentrifugation. We demonstrate a combination of methods to standardize an approach for determining the chemical load of nearly any particle, including nanoparticles and metal colloids. Purification and characterization of iron content in monodisperse ferritin species is particularly critical for several applications in nanomaterial science.

A comparative study of neurotoxic potential of synthesized polysaccharide-coated and native ferritin-based magnetic nanoparticles

AIM

To analyze the neurotoxic potential of synthesized magnetite nanoparticles coated by dextran, hydroxyethyl starch, oxidized hydroxyethyl starch, and chitosan, and magnetic nanoparticles combined with ferritin as a native protein.

METHODS

The size of nanoparticles was analyzed using photon correlation spectroscopy, their effects on the conductance of planar lipid membrane by planar lipid bilayer technique, membrane potential and acidification of synaptic vesicles by spectrofluorimetry, and glutamate uptake and ambient level of glutamate in isolated rat brain nerve terminals (synaptosomes) by radiolabeled assay.

RESULTS

Uncoated synthesized magnetite nanoparticles and nanoparticles coated by different polysaccharides had no significant effect on synaptic vesicle acidification, the initial velocity of L-[(14)C]glutamate uptake, ambient level of L-[(14)C]glutamate and the potential of the plasma membrane of synaptosomes, and conductance of planar lipid membrane. Native ferritin-based magnetic nanoparticles had no effect on the membrane potential but significantly reduced L-[(14)C]glutamate transport in synaptosomes and acidification of synaptic vesicles.

CONCLUSIONS

Our study indicates that synthesized magnetite nanoparticles in contrast to ferritin have no effects on the functional state and glutamate transport of nerve terminals, and so ferritin cannot be used as a prototype, analogue, or model of polysaccharide-coated magnetic nanoparticle in toxicity risk assessment and manipulation of nerve terminals by external magnetic fields. Still, the ability of ferritin to change the functional state of nerve terminals in combination with its magnetic properties suggests its biotechnological potential.

Self-assembly of ferritin nanocages into linear chains induced by poly(α, L-lysine)

The widespread occurrence of protein channels offers a good opportunity to fabricate protein architectures. Herein, we have developed a novel strategy for linear self-assembly of ferritin cages induced by poly(α, L-lysine) through channel-directed electrostatic interactions at pH 7.0. The length of the formed filaments can be controlled.

Mobilization of stored iron in mammals: a review

From the nutritional standpoint, several aspects of the biochemistry and physiology of iron are unique. In stark contrast to most other elements, most of the iron in mammals is in the blood attached to red blood cell hemoglobin and transporting oxygen to cells for oxidative phosphorylation and other purposes. Controlled and uncontrolled blood loss thus has a major impact on iron availability. Also, in contrast to most other nutrients, iron is poorly absorbed and poorly excreted. Moreover, amounts absorbed (~1 mg/day in adults) are much less than the total iron (~20 mg/day) cycling into and out of hemoglobin, involving bone marrow erythropoiesis and reticuloendothelial cell degradation of aged red cells. In the face of uncertainties in iron bioavailability, the mammalian organism has evolved a complex system to retain and store iron not immediately in use, and to make that iron available when and where it is needed. Iron is stored innocuously in the large hollow protein, ferritin, particularly in cells of the liver, spleen and bone marrow. Our current understanding of the molecular, cellular and physiological mechanisms by which this stored iron in ferritin is mobilized and distributed-within the cell or to other organs-is the subject of this review.

Ferritins for Chemistry and for Life

Ferritins, highly symmetrical protein nanocages, are reactors for Fe2+ and dioxygen or hydrogen peroxide that are found in all kingdoms of life and in many different cells of multicellular organisms. They synthesize iron concentrates required for cells to make cofactors of iron proteins (heme, FeS, mono and diiron). The caged ferritin biominerals, Fe2O3•H2O are also antioxidants, acting as sinks for iron and oxidants scavenged from damaged proteins; genetic regulation of ferritin biosynthesis is sensitive to both iron and oxidants. Here, the emphasis here is ferritin oxidoreductase chemistry, ferritin ion channels for Fe 2+ transit into and out of the protein cage and Fe 3+ O mineral nucleation, and uses of ferritin cages in nanocatalysis and nanomaterial synthesis. The Fe2+ and O ferritin protein reactors, likely critical in the transition from anaerobic to aerobic life on earth, play central, contemporary roles that balance iron and oxygen chemistry in biology and have emerging roles in nanotechnology.

Titanium mineralization in ferritin: a room temperature nonphotochemical preparation and biophysical characterization

The incremental addition of titanium(III) citrate to H-chain homopolymers of human ferritin results in the formation of 1.5-6.5-nm particles of amorphous TiO(2) within the nanocage of the protein. The mineralization conditions are mild, featuring ambient temperature and no need for photochemical activation. Low ratios of titanium to protein favor intraprotein mineralization, and the products are characterized by stained and unstained transmission electron microscopy, UV-vis spectroscopy, dynamic light scattering, analytical ultracentrifugation, and metal analysis. With up to 1,000 equiv of metal, there is no change to the protein hydrodynamic radius or diffusion constant. There is, however, a systematic shift in the sedimentation coefficient, which confirms mineralization within the protein core.

Determination of nanoparticle size distribution together with density or molecular weight by 2D analytical ultracentrifugation

Nanoparticles are finding many research and industrial applications, yet their characterization remains a challenge. Their cores are often polydisperse and coated by a stabilizing shell that varies in size and composition. No single technique can characterize both the size distribution and the nature of the shell. Advances in analytical ultracentrifugation allow for the extraction of the sedimentation (s) and diffusion coefficients (D). Here we report an approach to transform the s and D distributions of nanoparticles in solution into precise molecular weight (M), density (ρ(P)) and particle diameter (d(p)) distributions. M for mixtures of discrete nanocrystals is found within 4% of the known quantities. The accuracy and the density information we achieve on nanoparticles are unparalleled. A single experimental run is sufficient for full nanoparticle characterization, without the need for standards or other auxiliary measurements. We believe that our method is of general applicability and we discuss its limitations.

Ferritin protein nanocages use ion channels, catalytic sites, and nucleation channels to manage iron/oxygen chemistry

The ferritin superfamily is composed of ancient, nanocage proteins with an internal cavity, 60% of total volume, that reversibly synthesize solid minerals of hydrated ferric oxide; the minerals are iron concentrates for cell nutrition as well as antioxidants due to ferrous and oxygen consumption during mineralization. The cages have multiple iron entry/exit channels, oxidoreductase enzyme sites, and, in eukaryotes, Fe(III)O nucleation channels with clustered exits that extend protein activity to include facilitated mineral growth. Ferritin protein cage differences include size, amino acid sequence, and location of the active sites, oxidant substrate and crystallinity of the iron mineral. Genetic regulation depends on iron and oxygen signals, which in animals includes direct ferrous signaling to RNA to release and to ubiquitin-ligases to degrade the protein repressors. Ferritin biosynthesis forms, with DNA, mRNA and the protein product, a feedback loop where the genetic signals are also protein substrates. The ferritin protein nanocages, which are required for normal iron homeostasis and are finding current use in the delivery of nanodrugs, novel nanomaterials, and nanocatalysts, are likely contributors to survival and success during the transition from anaerobic to aerobic life.

Mathematical modeling of the dynamic storage of iron in ferritin

BACKGROUND

Iron is essential for the maintenance of basic cellular processes. In the regulation of its cellular levels, ferritin acts as the main intracellular iron storage protein. In this work we present a mathematical model for the dynamics of iron storage in ferritin during the process of intestinal iron absorption. A set of differential equations were established considering kinetic expressions for the main reactions and mass balances for ferritin, iron and a discrete population of ferritin species defined by their respective iron content.

RESULTS

Simulation results showing the evolution of ferritin iron content following a pulse of iron were compared with experimental data for ferritin iron distribution obtained with purified ferritin incubated in vitro with different iron levels. Distinctive features observed experimentally were successfully captured by the model, namely the distribution pattern of iron into ferritin protein nanocages with different iron content and the role of ferritin as a controller of the cytosolic labile iron pool (cLIP). Ferritin stabilizes the cLIP for a wide range of total intracellular iron concentrations, but the model predicts an exponential increment of the cLIP at an iron content > 2,500 Fe/ferritin protein cage, when the storage capacity of ferritin is exceeded.

CONCLUSIONS

The results presented support the role of ferritin as an iron buffer in a cellular system. Moreover, the model predicts desirable characteristics for a buffer protein such as effective removal of excess iron, which keeps intracellular cLIP levels approximately constant even when large perturbations are introduced, and a freely available source of iron under iron starvation. In addition, the simulated dynamics of the iron removal process are extremely fast, with ferritin acting as a first defense against dangerous iron fluctuations and providing the time required by the cell to activate slower transcriptional regulation mechanisms and adapt to iron stress conditions. In summary, the model captures the complexity of the iron-ferritin equilibrium, and can be used for further theoretical exploration of the role of ferritin in the regulation of intracellular labile iron levels and, in particular, as a relevant regulator of transepithelial iron transport during the process of intestinal iron absorption.