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.