Use of simplified models for theoretical prediction of the interactions between available antibodies and the receptor-binding domain of SARS-CoV-2 spike protein.

The negative impact of infectious diseases like COVID-19 on public health and the global economy is evident. This pandemic represents a significant challenge for the scientific community to develop new practical analytical methods for accurately diagnosing emerging cases. Due to their selectivity and sensitivity, new methodologies based on antigen/antibody interactions to detect COVID-19 biomarkers are necessary. In this context, the theoretical, computational modeling reduces experimental efforts and saves resources for rational biosensor design. This study proposes using molecular dynamics to predict the interactions between the Receptor Binding Domain (RBD) of the SARS-CoV-2 spike protein simplified model and a set of highly characterized antibodies. The binding free energy of the antigen/antibody complexes was calculated for the simplified models and compared against the complete SARS-CoV-2 ectodomain to validate the methodology. The structural data derived from our molecular dynamics and end-point free energy calculations showed a positive correlation between both approximations, with a 0.82 Pearson correlation coefficient; t = 3.661, df = 3, p-value = 0.03522, with a 95% confident interval. Furthermore, we identified the interfacial residues that could generate covalent bonds with a specific chemical surface without perturbing the binding dynamics to develop highly sensitive and specific diagnostic devices. Communicated by Ramaswamy H. Sarma.

Rotavirus VP6 protein as a bio-electrochemical scaffold: Molecular dynamics and experimental electrochemistry.

This paper reports a theoretical and experimental investigation on the recombinant protein rotavirus VP6 as a bioelectrochemical interface. Our motivation arises from the highly active zones of VP6 which can interact with biological structures and metals, as well as its useful features such as self-assembly, polymorphism, and active surface charge. A molecular simulation study was performed to analyze the charge transfer properties of theVP6 trimer under an applied electric field. The electrostatic properties were evaluated via the nonlinear second-order Poisson-Boltzmann equation, using finite element methods based on parameter discretization and calculation of solute/solvent interaction forces, which account for mean-field screening effects. The electrochemical study validated the theoretical predictions for VP6 in their different assemblies (trimers and nanotubes) when they are used as electrodes in 10 mM K3[Fe(CN)6], 1 M KCl. Applying a potential sweep promotes charge transfer, facilitates redox activity of the ferricyanide ion. Furthermore, protein assemblies decreased electrode electrical resistance and enabled gold particle electrodeposition on the protein VP6. These results suggest that VP6 is a promising conductive biomaterial that promotes charge transfer of redox probes and could be used as a new scaffold to create bio-electrochemical interfaces.

Influence of the major pilA transcriptional regulator in electrochemical responses of Geobacter sulfureducens PilR-deficient mutant biofilm formed on FTO electrodes.

Geobacter sulfurreducens is a model organism for understanding the role of bacterial structures in extracellular electron transfer mechanism (EET). This kind of bacteria relies on different structures such as type IV pili and over 100 c-type cytochromes to perform EET towards soluble and insoluble electron acceptors, including electrodes. To our knowledge, this work is the first electrochemical study comparing a G. sulfurreducens PilR-deficient mutant and wild type biofilms developed on fluorine-doped tin oxide (FTO) electrodes. Open circuit potential (OCP), electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV), were used to evaluate the electroactive properties of biofilms grown without externally imposed potential. Parallel studies of Confocal Laser Scanning Microscopy (CLSM) correlated with the electrochemical results. PilR is a transcriptional regulator involved in the expression of a wide variety of genes, including pilA (pilus structural protein) relevant c-type cytochromes and some other genes involved in biofilm formation and EET processes. Our findings suggest that PilR-deficient mutant forms a thinner (CLSM analysis) and less conductive biofilm (EIS analysis) than wild type, exhibiting different and irreversible redox processes at the interface (CV analysis). Additionally, this work reinforces some of the remarkable features described in previous reports about this G. sulfurreducens mutant.

Gold nanoparticles/4-aminothiophenol interfaces for direct electron transfer of horseradish peroxidase: Enzymatic orientation and modulation of sensitivity towards hydrogen peroxide detection.

Hydrogen peroxide electrochemical detection by horseradish peroxidase has been widely studied. The use of gold nanoparticles to prepare electrode/enzyme bioconjugates has attracted attention due to their catalytic properties. In this work, it is reported the use of gold nanoparticles and 4-aminothiophenol as a scaffold to obtain a suitable matrix for enzyme bioconjugation with horseradish peroxidase. A critical factor in biosensors design and development is the enzymatic electrochemical activity understanding. Comparison of voltammetric studies of the heme prosthetic group showed a reversible electrochemical behavior when the enzymes were immobilized in a well-dispersed gold deposit; on the other hand, a discrete redox response was observed on a randomly deposited gold electrode. These results show that the distance between enzymes is essential. Hydrogen peroxide catalysis and the enzymatic behavior were analyzed considering two types of nanoparticles dispositions. The catalytic behavior observed in the well-dispersed nanoparticles configuration suggests a preserved enzyme folding, a decrease of steric impediments, and appears to be a better immobilization strategy. In contrast, the randomly electrodeposited gold electrode decreased the enzyme orientation and the electrochemical activity. The advantages of this methodology are the electrode fabrication affordable cost and the enzymatic direct electron transfer response improvement.

Raman and electrochemical impedance studies of sol-gel titanium oxide and single walled carbon nanotubes composite films.

Titanium oxide grown by a sol-gel route on single-walled carbon nanotubes was studied by Raman and Electrochemical Impedance techniques and compared with mixtures obtained by mechanical grinding. In spite of the superior dispersion of single-walled carbon nanotubes bundles in sol-gel composites, the lost of the small-diameter carbon nanotubes in the oxidizing sol-gel bath was inferred from their Raman spectra and the lower capacitive current of the voltammograms in 0.1 M H2SO4. We proposed proton electrosorption as the main charge storage mechanism for sol-gel composites, favoured by the hydroxylation and n-type conductivity of the oxide, while electrodes based on mixtures were dominated by double-layer charging, developing some pseudocapacitance with potential cycling due to the reversible oxidation of carbon nanotubes. Comparsion with TiO2/Carbon Blacks composites shows the effective role of single-walled carbon nanotubes as templates to control the mesoporous nature of sol-gel composite electrodes.

Electrochemical treatments for selective growth of different calcium carbonate allotropic forms on carbon steel.

Different allogropic forms of calcium carbonate scales (calcite and aragonite) were electrochemically deposited on carbon steel surfaces, using different electrochemical techniques: cyclic voltammetry or potentiostatic pulses. To simulate conditions of Mexican refinery cooling systems, this study was performed in the presence of known concentrations of other salts at pH 7.8 and 40 degrees C with low and high calcium carbonate concentrations. Reduction reactions for dissolved oxygen and water occurring in such systems modified the pH at the substrate-solution interface to promote scaling of the calcium carbonate present. A systematic scanning electron microscopy and X-ray diffraction analysis of the carbon steel surface showed that the formation of calcite and aragonite depended on the initial state of substrate surface (clean or damaged) and on the concentration of calcium carbonate present in the system.