Three-Dimensional Structural Stability and Local Electrostatic Potential at Point Mutations in Spike Protein of SARS-CoV-2 Coronavirus

The contagiousness of SARS-CoV-2 β-coronavirus is determined by the virus-receptor electrostatic association of its positively charged spike (S) protein with the negatively charged angiotensin converting enzyme-2 (ACE2 receptor) of the epithelial cells. If some mutations occur, the electrostatic potential on the surface of the receptor-binding domain (RBD) could be altered, and the S-ACE2 association could become stronger or weaker. The aim of the current research is to investigate whether point mutations can noticeably alter the electrostatic potential on the RBD and the 3D stability of the S1-subunit of the S-protein. For this purpose, 15 mutants with different hydrophilicity and electric charge (positive, negative, or uncharged) of the substituted and substituting amino acid residues, located on the RBD at the S1-ACE2 interface, are selected, and the 3D structure of the S1-subunit is reconstructed on the base of the crystallographic structure of the S-protein of the wild-type strain and the amino acid sequence of the unfolded polypeptide chain of the mutants. Then, the Gibbs free energy of folding, isoelectric point, and pH-dependent surface electrostatic potential of the S1-subunit are computed using programs for protein electrostatics. The results show alterations in the local electrostatic potential in the vicinity of the mutant amino acid residue, which can influence the S-ACE2 association. This approach allows prediction of the relative infectivity, transmissibility, and contagiousness (at equal social immune status) of new SARS-CoV-2 mutants by reconstruction of the 3D structure of the S1-subunit and calculation of the surface electrostatic potential.

Omicron Coronavirus: pH-Dependent Electrostatic Potential and Energy of Association of Spike Protein to ACE2 Receptor

The association of the S-protein of the SARS-CoV-2 beta coronavirus to ACE2 receptors of the human epithelial cells determines its contagiousness and pathogenicity. We computed the pH-dependent electric potential on the surface of the interacting globular proteins and pH-dependent Gibbs free energy at the association of the wild-type strain and the omicron variant. The calculated isoelectric points of the ACE2 receptor (pI 5.4) and the S-protein in trimeric form (pI 7.3, wild type), (pI 7.8, omicron variant), experimentally verified by isoelectric focusing, show that at pH 6-7, the S1-ACE2 association is conditioned by electrostatic attraction of the oppositely charged receptor and viral protein. The comparison of the local electrostatic potentials of the omicron variant and the wild-type strain shows that the point mutations alter the electrostatic potential in a relatively small area on the surface of the receptor-binding domain (RBD) of the S1 subunit. The appearance of seven charge-changing point mutations in RBD (equivalent to three additional positive charges) leads to a stronger S1-ACE2 association at pH 5.5 (typical for the respiratory tract) and a weaker one at pH 7.4 (characteristic of the blood plasma); this reveals the reason for the higher contagiousness but lower pathogenicity of the omicron variant in comparison to the wild-type strain.

Composite Hydrogels with Included Solid-State Nanoparticles Bearing Anticancer Chemotherapeutics

Hydrogels have many useful physicochemical properties which, in combination with their biocompatibility, suggest their application as a drug delivery system for the local and prorogated release of drugs. However, their drug-absorption capacity is limited because of the gel net's poor adsorption of hydrophilic molecules and in particular, hydrophobic molecules. The absorption capacity of hydrogels can be increased with the incorporation of nanoparticles due to their huge surface area. In this review, composite hydrogels (physical, covalent and injectable) with included hydrophobic and hydrophilic nanoparticles are considered as suitable for use as carriers of anticancer chemotherapeutics. The main focus is given to the surface properties of the nanoparticles (hydrophilicity/hydrophobicity and surface electric charge) formed from metal and dielectric substances: metals (gold, silver), metal-oxides (iron, aluminum, titanium, zirconium), silicates (quartz) and carbon (graphene). The physicochemical properties of the nanoparticles are emphasized in order to assist researchers in choosing appropriate nanoparticles for the adsorption of drugs with hydrophilic and hydrophobic organic molecules.

Montmorillonite colloid plates with adsorbed cytochrome c: in vitro cytotoxic effect on colon cancer cell culture

Background

The apoptosis (a cascade of biochemical reactions leading to suicide of damaged biological cells) is blocked in the cancer cells because of impossibility of cytochrome c (cytC) go out from the mitochondria. However, the apoptosis can be started by introducing of exogenous cytC into cytoplasm using colloid particles as a protein carrier due to ability of the cancer cells to phagocytize extracellular particles with submicron size.

Results

The clay mineral montmorillonite (MM) were used to prepare aqueous suspension of protein/mineral composite particles by electrostatic adsorption of the positively charged cytC globules on the negatively charged MM colloid plates, and then added to colon cancel culture. The results shows out that separately cytC and MM have no effect but the composite cytC-MM particles kill 95% of the cancer cells after 96 h treatment using equine cytC which is 97% structurally identical with the human cytC. To reach this high cytotoxicity we have formulated requirements to: (a) bare colloid particles (electric charge, form and size), (b) conditions for protein adsorption (concentrations, pH, ionic strength), and (c) suspension with the composite particles (positive total charge and optimal concentration). Due to satisfying these requirements we have reached cytotoxicity which is 1/3 higher than the reached by other authors using different artificial particles. The cytotoxicity rapidly increases with concentration of the cytC-MM particles but further it shows tendency to saturation.

Methods

The optimal pH 6.5 and the 10:3 mg/mg cytC/MM concentration ratio at adsorption were found out by employing computer (protein electrostatics) and physicochemical methods (microelectrophoresis and colloid electrooptics) to prepare cytC-MM suspension. The anticancer capability of cytC-MM nanoplates were investigated using cell culture of metastasizing colon cancer.

Conclusion

The in vitro experiments with colon cancer cell culture disclose that cytC-MM composite particles have potential for application in anticancer therapy of superficial neoplasms of the skin and the alimentary system (mouth cavity, esophagus, stomach, jejunum and colon).

Graphic abstract

Adsorption of carboxymethyl cellulose on alumina particles

The polyelectrolyte adsorption on colloid particles is often used for stabilization or flocculation of water suspensions. The aim of this work is to study the adsorption of carboxymethyl cellulose (CMC) on alumina (γ-Al2O3) colloid particles. The particles and polymer are chosen because of the capability of the metal-oxide ampholyte surface and the weak polyelectrolytes to alter their charge by pH. The measurements are done at pH 6.0 where the CMC carboxylic gropes are almost fully dissociated and the alumina surface is positively charged. The high linear charge density of the polyelectrolyte chain provides Na(+) counterions condensation on the COO(-) groups. The main employed method is the electric light scattering based on particle orientation in sinusoidal electric field. The electric polarizability and the relaxation time after field switching off (both depending on the particle charge and size) are used as criteria for polymer adsorption and particle aggregation. Micro-electrophoresis is applied as additional techniques indicating the sign and density of the surface charge. The results obtained give the conditions (time dependence, particle and polymer concentrations) where the CMC adsorption is complete and the suspension is stable.

Polymer concentration dependence of kilohertz electric polarizability of alumina colloid particles with adsorbed carboxymethyl cellulose

Polyelectrolytes are soluble polymers composed of units having charged groups. Because of the high charge density, some of the counterions are adsorbed electrostatically (ion condensation) on the polyelectrolyte chain. It was shown that in direct electric field the condensed counterions and the chain move together as one whole but it is assumed that they are mobile in alternating field and participate in the polarization. Experimental evidence is obtained by electro-optical investigations of polyelectrolytes adsorbed on colloid particles-the observed low-frequency shift of the polarizability relaxation has been interpreted as condensed counterions' mobility. The present investigation aims to verify the reports for the condensed counterions' mobility in sinusoidal electric field. By means of electric light scattering we investigated a water suspension of γ-alumina particles with adsorbed carboxymethyl cellulose. Instead of the previously used frequency approach (dispersion dependence at saturated adsorption of the polyelectrolyte) we applied an amplitude approach-determination of the polarizability at frequency 1 kHz and increasing polyelectrolyte concentration (from zero to full adsorption saturation). The results indicate the absence of polarization owing to the condensed counterions. The main evidence was obtained by comparison of the concentration dependences of the polarizability (depending on all mobile counterions) and the electrophoretic mobility (determined only by the diffuse counterions). We concluded that the condensed counterions are immobile in sinusoidal field with intensity up to 0.5  kV cm (- 1) and frequency of 1 kHz and higher.

Influence of cytoplasm electrolyte concentration on Maxwell-Wagner polarizability of bacteria E. coli

The electric polarizability of bacteria is considered in the literature to have a surface charge dependent (ChD) and a Maxwell-Wagner (MW) mechanism. We distinguish experimentally both the types of interface polarizability by the frequency of the electric field and the medium electrolyte concentration. It was shown in a previous work ( Zhivkov , A. M. ; Gyurova , A. Y. Colloids Surf., B 2008 , 66 , 201. ) that the ChD component is shown up on the outer bacteria surface even at megahertz frequencies. The MW polarizability is studied in the present work in the range from 20 kHz to 20 MHz by change in the inner (cytoplasm) electrolyte concentration. The ion transport through the cytoplasmic membrane of alive and fixed by formaldehyde E. coli K12 is accelerated by adding of ethanol in low concentration. The frequency dependence and the kinetics of the electric polarizability and the size of the bacteria are investigated by conservative electric dichroism, based on the alteration of the optical density at orientation of the cells in electric field. The conclusion is that the internal MW component has the main contribution to the change in the total bacteria polarizability, as well as the external MW and the internal ChD components are not shown up.

Electric polarizability changes during E. coli culture growth

The electric polarizability of bacteria has two main components: surface-charge dependent (SChD) and Maxwell-Wagner (MW). It has been reported that the low frequency SChD component of Escherichia coli K12 still arise in the frequency range 20kHz - 2MHz, together with the high-frequency MW one. All the previous experiments were carried out with bacterial cultures of E. coli K12 in the stationary phase. In the present work we study electric polarizability during culture growth with the aim of finding out how it is influenced by the physiological state of the cells. The electro-optical method of electric turbidimetry is used, which is based on the change in the optical density as a result of orientation of bacterial cells under the action of an applied electric field. Our results show that until the cell concentration increases exponentially, the polarizability and the cell size change synchronously, so that the polarizability is approximately a quadratic function of the average bacterial length. We explain this with dominance of the SChD component. However, that after the polarizability deceases twofold at insignificant length oscillations and the power of the function decreases to 1.5. The last result is interpreted as an increase in the MW component.

Influence of the medium electrolyte concentration on the electric polarizability of bacteria Escherichia coli in presence of ethanol

The electric polarizability is an important parameter of bacteria, giving information about the electric properties of the cells. In our previous works [A.M. Zhivkov, A.Y. Gyurova, Colloids Surf. B: Biointerfaces 66 (2008) 201; A.Y. Gyurova, A.M. Zhivkov, Biophys. Chem., 139 (2009) 8; A.M. Zhivkov, A.Y. Gyurova, J. Phys. Chem. B, 113 (2009) 8375] we have applied an experimental approach to distinguish the contribution of the components of the two types of interface electric polarizability-surface charge dependent (ChD) and Maxwell-Wagner (MW) polarizability. It is based on electro-optical study of the separate influence of the outer and inner medium electrolyte concentration, which changes the external ChD and internal MW components of polarizability; the last effect is reached by the membrane permeability increase in low ethanol concentration. In the present work we investigate the behavior of electric polarizability of Escherichia coli K12 at increasing the outer KCl concentration in presence of 10 vol.% ethanol in order to check if the polarizability components change independently from one another. The conclusion is that the outer electrolyte concentration influence indirectly the internal MW component by the trans-membrane concentration gradient, but the polarizability components themselves change independently.

Influence of ethanol on the high frequency electric polarizability of E. coli

The interface electric polarizability of bacteria (charge dependent (ChD) and Maxwell-Wagner (MW) polarizabilities) gives information about their electric charge, determined by the structure and functional state. It is well known that the polarizability could be changed significantly by adding some substances to the suspension, and can be measured using an electro-optical (EO) method. There are some literature data, according to which the adding of ethanol decreases the electric polarizability of the cells. However the reason for the change in this parameter is not clear, as well as which component (ChD and/or MW) of polarizability has the main contribution. Generally the present work shows that the effect of ethanol is connected to the change of the internal (cytoplasm) MW polarizability and is mainly caused by increasing the cell membrane permeability. This results in an ionic flow through the membrane, which velocity and direction depends on the relative values of the inner (cytoplasm) and the outer medium ionic strength.

Change of purple membranes geometry induced by protein adsorption

Earlier it was an orthodoxy that purple membranes (PMs) in aqueous medium are shaped as flat hard disks. In a few newer articles it has been shown that PMs are bent and their curvature varies with surface charge density. The purpose of this work is to answer which is the dominant factor for PM bending--structural or electrostatic forces. Two positively charged proteins are used: phytohemagglutinin (PhHA) and protamine. The electrophoretic mobility and electric polarizability of PMs are measured by microelectrophoresis and electric dichroism. The results show that both proteins reduce the mobility because they are adsorbed on PM surface. However, their influence on the electric polarizability is in the opposite direction--protamine reduces it (trivial effect) while PhHA increases the polarizability (non-trivial effect). The last result is explained by a straightening the initially bent PM because of specific bonding of PhHA to asymmetrically disposed glycolipids of PM in contrast to the electrostatic adsorption of protamine. It has been concluded that PMs in water medium are bent in the same manner as in in vivo--the intracellular surface with a higher negative charge is concave. The results indicate that electrostatic forces play a significant role in PM curvature but the shape of structural elements is the main factor determining the geometry of PM.