Ferritin self-assembly, structure, function, and biotechnological applications.

Ferritin is a vital protein complex responsible for storing iron in almost all living organisms. It plays a crucial role in various metabolic pathways, inflammation processes, stress response, and pathogenesis of cancer and neurodegenerative diseases. In this review we discuss the role of ferritin in diseases, cellular iron regulation, its structural features, and its role in biotechnology. We also show that molecular mechanisms of ferritin self-assembly are key for a number of biotechnological and pharmaceutical applications. The assembly pathways strongly depend on the interface context of ferritin monomers and the stability of its different intermediate oligomers. To date, several schemes of self-assembly kinetics have been proposed. Here, we compare different self-assembly mechanisms and discuss the possibility of self-assembly control by switching between deadlock intermediate states.

A feasible approach to tune the interaction of chitosan with sodium dodecyl sulfate.

Interaction of binary chitosan/nonionic surfactant (NIS) system with sodium dodecyl sulfate (SDS) in aqueous solution is described using turbodimetry, light scattering, electophoretic mobility and cryogenic electron microscopy. The formation of insoluble CHI/SDS complexes is weakened with a decrease in molecular weight of chitosan and critical micelle concentration of NIS as well as with an increase in NIS concentration. Soluble chitosan/NIS complexes absorb SDS molecules until the charge of mixed chitosan/NIS/SDS complexes reaches a critical value that depends on chitosan molecular weight followed by aggregation of primary electrostatic complexes via hydrogen bonding to complex nanoparticles. In contrast to formation of asymmetric swarm-like structures in the binary chitosan/SDS system, the aggregation of complex nanoparticles in the ternary chitosan/NIS/SDS system occurs by a head-to-tail binding mechanism with formation of elongated filamentous microstructures. The finding can be promising for preparation of microbiologically stable pharmaceutical and cosmetic compositions and drug delivery systems containing mixed surfactants.

Mechanisms of membrane protein crystallization in 'bicelles'.

Despite remarkable progress, mainly due to the development of LCP and 'bicelle' crystallization, lack of structural information remains a bottleneck in membrane protein (MP) research. A major reason is the absence of complete understanding of the mechanism of crystallization. Here we present small-angle scattering studies of the evolution of the "bicelle" crystallization matrix in the course of MP crystal growth. Initially, the matrix corresponds to liquid-like bicelle state. However, after adding the precipitant, the crystallization matrix transforms to jelly-like state. The data suggest that this final phase is composed of interconnected ribbon-like bilayers, where crystals grow. A small amount of multilamellar phase appears, and its volume increases concomitantly with the volume of growing crystals. We suggest that the lamellar phase surrounds the crystals and is critical for crystal growth, which is also common for LCP crystallization. The study discloses mechanisms of "bicelle" MP crystallization and will support rational design of crystallization.

ATP synthase FOF1 structure, function, and structure-based drug design.

ATP synthases are unique rotatory molecular machines that supply biochemical reactions with adenosine triphosphate (ATP)-the universal "currency", which cells use for synthesis of vital molecules and sustaining life. ATP synthases of F-type (FOF1) are found embedded in bacterial cellular membrane, in thylakoid membranes of chloroplasts, and in mitochondrial inner membranes in eukaryotes. The main functions of ATP synthases are control of the ATP synthesis and transmembrane potential. Although the key subunits of the enzyme remain highly conserved, subunit composition and structural organization of ATP synthases and their assemblies are significantly different. In addition, there are hypotheses that the enzyme might be involved in the formation of the mitochondrial permeability transition pore and play a role in regulation of the cell death processes. Dysfunctions of this enzyme lead to numerous severe disorders with high fatality levels. In our review, we focus on FOF1-structure-based approach towards development of new therapies by using FOF1 structural features inherited by the representatives of this enzyme family from different taxonomy groups. We analyzed and systematized the most relevant information about the structural organization of FOF1 to discuss how this approach might help in the development of new therapies targeting ATP synthases and design tools for cellular bioenergetics control.

Biogenic Ferrihydrite Nanoparticles Produced by Klebsiella oxytoca: Characterization, Physicochemical Properties and Bovine Serum Albumin Interactions.

The synthesis of nanoparticles inside microorganisms is an economical alternative to chemical and physical methods of nanoparticle synthesis. In this study, ferrihydrite nanoparticles synthesized by Klebsiella oxytoca bacterium in special conditions were characterized by scanning electron microscopy (SEM), energy-dispersive X-ray analysis (EDS), small-angle X-ray (SAXS), UV-Vis spectroscopy, fluorescence, fluorescence resonance energy transfer (FRET), and molecular docking. The morphology and the structure of the particles were characterized by means of SEM and SAXS. The elemental content was determined by means of the EDS method. The absorption properties of the ferrihydrite nanoparticles were investigated by UV-Vis spectroscopy. The binding mechanism of the biogenic ferrihydrite nanoparticles to Bovine Serum Albumin (BSA) protein, studied by fluorescence, showed a static and weak process, combined with FRET. Protein denaturation by temperature and urea in the presence of the ferrihydrite nanoparticles demonstrated their influence on the unfolding process. The AutoDock Vina and UCSF Chimera programs were used to predict the optimal binding site of the ferrihydrite to BSA and to find the location of the hydrophobic cavities in the sub-domain IIA of the BSA structure.

Ambiguities in and completeness of SAS data analysis of membrane proteins: the case of the sensory rhodopsin II-transducer complex.

Membrane proteins (MPs) play vital roles in the function of cells and are also major drug targets. Structural information on proteins is vital for understanding their mechanism of function and is critical for the development of drugs. However, obtaining high-resolution structures of membrane proteins, in particular, under native conditions is still a great challenge. In such cases, the low-resolution methods small-angle X-ray and neutron scattering (SAXS and SANS) might provide valuable structural information. However, in some cases small-angle scattering (SAS) provides ambiguous ab initio structural information if complementary measurements are not performed and/or a priori information on the protein is not taken into account. Understanding the nature of the limitations may help to overcome these problems. One of the main problems of SAS data analysis of solubilized membrane proteins is the contribution of the detergent belt surrounding the MP. Here, a comprehensive analysis of how the detergent belt contributes to the SAS data of a membrane-protein complex of sensory rhodopsin II with its cognate transducer from Natronomonas pharaonis (NpSRII-NpHtrII) was performed. The influence of the polydispersity of NpSRII-NpHtrII oligomerization is the second problem that is addressed here. It is shown that inhomogeneity in the scattering length density of the detergent belt surrounding a membrane part of the complex and oligomerization polydispersity significantly impacts on SAXS and SANS profiles, and therefore on 3D ab initio structures. It is described how both problems can be taken into account to improve the quality of SAS data treatment. Since SAS data for MPs are usually obtained from solubilized proteins, and their detergent belt and, to a certain extent, oligomerization polydispersity are sufficiently common phenomena, the approaches proposed in this work might be used in SAS studies of different MPs.

Molecular model of a sensor of two-component signaling system.

Two-component systems (TCS) are widespread signaling systems present in all domains of life. TCS typically consist of a signal receptor/transducer and a response regulator. The receptors (histidine kinases, chemoreceptors and photoreceptors) are often embedded in the membrane and have a similar modular structure. Chemoreceptors were shown to function in highly ordered arrays, with trimers of dimers being the smallest functional unit. However, much less is known about photoreceptors. Here, we use small-angle scattering (SAS) to show that detergent-solubilized sensory rhodopsin II in complex with its cognate transducer forms dimers at low salt concentration, which associate into trimers of dimers at higher buffer molarities. We then fit an atomistic model of the whole complex into the SAS data. The obtained results suggest that the trimer of dimers is "tripod"-shaped and that the contacts between the dimers occur only through their cytoplasmic regions, whereas the transmembrane regions remain unconnected.

Ferrihydrite nanoparticles insights: Structural characterization, lactate dehydrogenase binding and virtual screening assay.

The binding between the enzyme lactate dehydrogenase (LDH) and ferrihydrite nanoparticles (Fh-NPs) was investigated by means of small-angle neutron scattering (SANS), Fourier-transform infrared (FTIR) spectroscopy, fluorescence and Förster resonance energy transfer (FRET) and molecular docking. Fh-NPs - LDH compounds of dimensions under 100 nm are formed. The conformational changes and the mechanism of interaction between LDH and Fh-NPs simple and doped with Cu and Co, and the effect of these NPs on the thermal denaturation of LDH were monitored. The quenching mechanism is static, the binding occurring with moderate affinity, being mainly driven by hydrogen bonding and van der Waals forces. FRET occurs at a minimal distance of 2.55 nm. Thermal denaturation of LDH in the presence of simple and doped Fh-NPs shows that the thermodynamic parameters of protein unfolding are significantly changed with temperature. The denaturation temperature of LDH shifts to higher values in the presence of all Fh-NPs, than in the case of simple LDH. The docking approach estimates the energy corresponding to the best fit of the ferrihydrite in the LDH binding site near Trp. These results have direct implications on the uses of the complex of LDH with Fh-NPs in various biochemical, biological, or clinical applications.

A thermostable flavin-based fluorescent protein from Chloroflexus aggregans: a framework for ultra-high resolution structural studies.

Light-Oxygen-Voltage (LOV) domains are conserved parts of photoreceptors in plants, bacteria and fungi that bind flavins as chromophores and detect blue light. In the past, LOV domain variants have been developed as fluorescent reporter proteins (called flavin-based fluorescent proteins; FbFPs), which due to their ability to fluoresce under anaerobic conditions, fast folding kinetics and a small size of ∼12-16 kDa are a promising reporter system for quantitative real-time analysis of biological processes. Here, we present a small thermostable flavin-based fluorescent protein CagFbFP derived from a soluble LOV domain-containing histidine kinase from the thermophilic bacterium Chloroflexus aggregans. CagFbFP is composed of 107 amino acids with a molecular weight of 11.6 kDa and consists only of the conserved LOV core domain. The protein is thermostable with a melting point of about 68 °C. It crystallizes easily and its crystals diffract to 1.07 Å. Both the crystal structure and small angle scattering data show that the protein is a dimer. Unexpectedly, glutamine 148, which in LOV photoreceptor proteins is the key residue responsible for signal transduction, occupies two conformations. Molecular dynamics simulations show that the two conformations interconvert rapidly. The crystal structure of the wild-type Chloroflexus aggregans LOV domain determined at 1.22 Å resolution confirmed the presence of two alternative conformations of the glutamine 148 side chain. Overall, this protein, due to its stability and ease of crystallization, appears to be a promising model for ultra-high resolution structural studies of LOV domains and for application as a fluorescent reporter.

How a viscoelastic solution of wormlike micelles transforms into a microemulsion upon absorption of hydrocarbon: new insight.

In this article, we investigate the effect of hydrocarbon addition on the rheological properties and structure of wormlike micellar solutions of potassium oleate. We show that a viscoelastic solution of entangled micellar chains is extremely responsive to hydrocarbons-the addition of only 0.5 wt % n-dodecane results in a drastic drop in viscosity by up to 5 orders of magnitude, which is due to the complete disruption of micelles and the formation of microemulsion droplets. We study the whole range of the transition of wormlike micelles into microemulsion droplets and discover that it can be divided into three regions: (i) in the first region, the solutions retain a high viscosity (∼10-350 Pa·s), the micelles are entangled but their length is reduced by the solubilization of hydrocarbons; (ii) in the second region, the system transitions to the unentangled regime and the viscosity sharply decreases as a result of further micelle shortening and the appearance of microemulsion droplets; (iii) in the third region, the viscosity is low (∼0.001 Pa·s) and only microemulsion droplets remain in the solution. The experimental studies were accompanied by theoretical considerations, which allowed us to reveal for the first time that (i) one of the leading mechanisms of micelle shortening is the preferential accumulation of the solubilized hydrocarbon in the spherical end caps of wormlike micelles, which makes the end caps thermodynamically more favorable; (ii) the onset of the sharp drop in viscosity is correlated with the crossover from the entangled to unentangled regime of the wormlike micellar solution taking place upon the shortening of micellar chains; and (iii) in the unentangled regime short cylindrical micelles coexist with microemulsion droplets.