Complete Virion Simulated: All-Atom Model of an MS2 Bacteriophage with Native Genome.

For the first time, a complete all-atom molecular dynamics (MD) model of a virus, bacteriophage MS2, in its entirety, including a protein outer shell, native genomic RNA with necessary divalent ions, and surrounding explicit aqueous solution with ions at physiological concentration, was built. The model is based on an experimentally measured cryo-EM structure, which was substantially augmented by reconstructing missing or low-resolution parts of the measured density (where the atomistic structure cannot be fit unambiguously). The model was tested by a quarter of a microsecond MD run, and various biophysical characteristics are obtained and analyzed. The developed methodology of building the model can be used for reconstructing other large biomolecular structures when experimental data are fragmented and/or of varying resolution, while the model itself can be used for studying the biology of MS2, including the dynamics of its interaction with the host bacteria.

The nut-and-bolt motion of a bacteriophage sliding along a bacterial flagellum: a complete hydrodynamics model.

The 'nut-and-bolt' mechanism of a bacteriophage-bacteria flagellum translocation motion is modelled by numerically integrating the 3D Stokes equations using a Finite-Element Method (FEM). Following the works by Katsamba and Lauga (Phys Rev Fluids 4(1): 013101, 2019), two mechanical models of the flagellum-phage complex are considered. In the first model, the phage fiber wraps around the smooth flagellum surface separated by some distance. In the second model, the phage fiber is partly immersed in the flagellum volume via a helical groove imprinted in the flagellum and replicating the fiber shape. In both cases, the results of the Stokes solution for the translocation speed are compared with the Resistive Force Theory (RFT) solutions (obtained in Katsamba and Lauga Phys Rev Fluids 4(1): 013101, 2019) and the asymptotic theory in a limiting case. The previous RFT solutions of the same mechanical models of the flagellum-phage complex showed opposite trends for how the phage translocation speed depends on the phage tail length. The current work uses complete hydrodynamics solutions, which are free from the RFT assumptions to understand the divergence of the two mechanical models of the same biological system. A parametric investigation is performed by changing pertinent geometrical parameters of the flagellum-phage complex and computing the resulting phage translocation speed. The FEM solutions are compared with the RFT results using insights provided from the velocity field visualisation in the fluid domain.

Covalent conjugates based on nanodiamonds with doxorubicin and a cytostatic drug from the group of 1,3,5-triazines: Synthesis, biocompatibility and biological activity.

We report the synthesis of covalent conjugates of nanodiamonds with doxorubicin and a cytostatic drug from the class of 1,3,5-triazines. The obtained conjugates were identified using a number of physicochemical methods (IR-spectroscopy, NMR-spectroscopy, XRD, XPS, TEM). As a result of our study, it was found that ND-СONH-Dox and ND-COO-Diox showed good hemocompatibility, since they did not affect plasma coagulation hemostasis, platelet functional activity, and erythrocyte membrane. The ND-COO-Diox conjugates are also capable of binding to human serum albumin due to the presence of ND in their composition. In the study of the cytotoxic properties of ND-СONH-Dox and ND-COO-Diox in the T98G glioblastoma cell line, indicating that ND-СONH-Dox and ND-COO-Diox demonstrate greater cytotoxicity at lower concentrations of Dox and Diox in the composition of the conjugates compared to individual drugs; the cytotoxic effect of ND-COO-Diox was statistically significantly higher than that of ND-СONH-Dox at all concentrations studied. Greater cytotoxicity at lower concentrations of Dox and Diox in the composition of conjugates compared to individual cytostatics makes it promising to further study the specific antitumor activity and acute toxicity of these conjugates in models of glioblastoma in vivo. Our results demonstrated that ND-СONH-Dox and ND-COO-Diox enter HeLa cells predominantly via a nonspecific actin-dependent mechanism, while for ND-СONH-Dox a clathrin-dependent endocytosis pathway. All data obtained provide that the synthesized nanomaterials show a potential application as the agents for intertumoral administration.

Estimation of Nanoparticle's Surface Electrostatic Potential in Solution Using Acid-Base Molecular Probes I: In Silico Implementation for Surfactant Micelles.

Surface electrostatic potential Ψ is a key characteristic of colloid particles. Since the surface of the particles adsorbs various compounds and facilitates chemical reactions between them, Ψ largely affects the properties of adsorbed reactants and governs the flow of chemical reactions occurring between them. One of the most popular methods for estimating Ψ in hydrophilic colloids, such as micellar surfactant solutions and related systems, is the application of molecular probes, predominantly acid-base indicator dyes. The Ψ value is calculated from the difference of the probe's indices of the apparent acidity constant between the examined colloid solution and, usually, some other colloid solution with noncharged particles. Here, we show how to implement this method in silico using alchemical free energy calculations within the framework of molecular dynamics simulations. The proposed implementation is tested on surfactant micelles and is shown to predict experimental Ψ values with quantitative accuracy depending on the kind of surfactant. The sources of errors in the method are discussed, and recommendations for its application are given.

Estimation of Nanoparticle's Surface Electrostatic Potential in Solution Using Acid-Base Molecular Probes II: Insight from Atomistic Simulations of Micelles.

Exploiting acid-base indicators as molecular probes is one of the most popular methods for determining the surface electrostatic potential Ψ in hydrophilic colloids like micellar surfactant solutions and related systems. Specifically, the indicator's apparent acidity constant index is measured in the colloid solution of interest and, as a rule, in a nonionic surfactant solution; the difference between the two is proportional to Ψ. Despite the widespread use of this approach, a major problem remains unresolved, namely, the dissimilarity of Ψ values obtained with different indicators for the same system. The common point of view recognizes the effect of several factors (the choice of the nonionic surfactant, the probe's localization, and the degree of hydration of micellar pseudophase) but does not allow to quantitatively assess their impact and decide which indicator reports the most correct Ψ value. Here, based on the ability to predict the reported Ψ values in silico, we examined the role of these factors using molecular dynamics simulations for five probes and two surfactants. The probe's hydration in the Stern layer was found responsible for approximately half of the dissimilarity range. The probe's localization is found important but hard to quantify because of the irregular structure of the Stern layer. The most accurate indicators among the examined set were identified. Supplementing experiments on measuring Ψ with molecular dynamics simulation is proposed as a way of improving the efficacy of the indicator method: the simulations can guide the choice of the most suitable probe and nonionic surfactant for the given nanoparticles.

Graphene Oxide of Extra High Oxidation: A Wafer for Loading Guest Molecules.

We present a new modification of graphene oxide with very high content (85 wt %) of oxygen-containing functional groups (hydroxy, epoxy, lactol, carboxyl, and carbonyl groups) that forms stable aqueous dispersion in up to 9 g·L-1 concentration solutions. A novel faster method of the synthesis is described that produces up to 1 kg of the material and allows controlling the particle size in solution. The synthesized compound was characterized by various physicochemical methods and molecular dynamics modeling, revealing a unique structure in the form of a multilayered wafer of several sheets thick, where each sheet is highly corrugated. The ragged structure of the sheets forms pockets with hindered mobility of water that leads to the possibility of trapping guest molecules.

In Vitro and In Silico Investigation of Water-Soluble Fullerenol C60(OH)24: Bioactivity and Biocompatibility.

Light fullerenes, C60 and C70, have significant potential in biomedical applications due to their ability to absorb reactive oxygen species, inhibit the development of tumors, inactivate viruses and bacteria, and as the basis for developing systems for targeted drug delivery. However, the hydrophobicity of individual fullerenes complicates their practical use; therefore, creating water-soluble derivatives of fullerenes is increasingly important. Currently, the most studied soluble adducts of fullerenes are polyhydroxy fullerenes or fullerenols. Unfortunately, investigations of fullerenol biocompatibility are fragmental. They often lack reproducibility both in the synthesis of the compounds and their biological action. We here investigate the biocompatibility of a well-defined fullerenol C60(OH)24 obtained using methods that minimize the content of impurities and quantitatively characterize the product's composition. We carry out comprehensive biochemical and biophysical investigations of C60(OH)24 that include photodynamic properties, cyto- and genotoxicity, hemocompatibility (spontaneous and photo-induced hemolysis, platelet aggregation), and the thermodynamic characteristics of C60(OH)24 binding to human serum albumin and DNA. The performed studies show good biocompatibility of fullerenol C60(OH)24, which makes it a promising object for potential use in biomedicine.

Time-spatial drift of decelerating electromagnetic pulses.

A time dependent electromagnetic pulse generated by a current running laterally to the direction of the pulse propagation is considered in paraxial approximation. It is shown that the pulse envelope moves in the time-spatial coordinates on the surface of a parabolic cylinder for the Airy pulse and a hyperbolic cylinder for the Gaussian. These pulses propagate in time with deceleration along the dominant propagation direction and drift uniformly in the lateral direction. The Airy pulse stops at infinity while the asymptotic velocity of the Gaussian is nonzero.