Reconstruction and validation of entire virus model with complete genome from mixed resolution cryo-EM density.

It is very difficult to reconstruct computationally a large biomolecular complex in its biological entirety from experimental data. The resulting atomistic model should not contain gaps structurally and it should yield stable dynamics. We, for the first time, reconstruct from the published incomplete cryo-EM density a complete MS2 virus at atomistic resolution, that is, the capsid with the genome, and validate the result by all-atom molecular dynamics with explicit water. The available experimental data includes a high resolution protein capsid and an inhomogeneously resolved genome map. For the genomic RNA, apart from 16 hairpins with atomistic resolution, the strands near the capsid's inner surface were resolved up to the nucleic backbone level, and the innermost density was completely unresolved. As a result, only 242 nucleotides (out of 3569) were positioned, while only a fragmented backbone was outlined for the rest of the genome, making a detailed model reconstruction necessary. For model reconstruction, in addition to the available atomistic structure information, we extensively used the predicted secondary structure of the genome (base pairing). The technique was based on semi-automatic building of relatively large strands of RNA with subsequent manual positioning over the traced backbone. The entire virus structure (capsid + genome) was validated by a molecular dynamics run in physiological solution with ions at standard conditions confirming the stability of the model.

Character of Localization and Microenvironment of Solvatochromic Reichardt's Betaine Dye in Sodium n-Dodecyl Sulfate and Cetyltrimethylammonium Bromide Micelles: Molecular Dynamics Simulation Study.

The problem of using surfactant micellar aqueous solutions as reaction media centers on estimating the polarity of the micellar pseudophase. The most popular approach is the utilization of solvatochromic dyes. Among the last, the strongest ones are the dipolar pyridinium N-phenolate dyes. The complication of such approach, however, consists in the nonuniform character of the environment of the indicator fixed in the micellar pseudophase. The aim of this study is to reveal the character of localization and orientation of the standard solvatochromic pyridinium N-phenolate dye, 4-(2,4,6-triphenylpyridinium-1-yl)-2,6-diphenylphenolate, the so-called Reichardt's dye, within the micellar pseudophase of an anionic (sodium n-dodecyl sulfate, SDS) and cationic (cetyltrimethylammonium bromide, CTAB) surfactants using MD simulations. The locus and hydration of the dye are found to be dependent on the surfactant nature. New approaches are proposed to quantitatively describe the state of the dye within the pseudophase. The results confirm the experimental data, which indicate the higher polarity of the interfacial region in the case of the SDS micelles. Because this dye is also used as an interfacial acid-base probe, the corresponding study is simultaneously performed for its protonated, i.e., cationic form. The neutral and protonated forms of the dye are found to be localized and hydrated in a different way in both SDS and CTAB micelles. This should be taken into account when using the Reichardt's dye as an acid-base indicator for estimating the electrical surface potential of micelles. The presented approach may be recommended to shed light upon the locus of other solvatochromic and acid-base indicators in micelles and micellar-like aggregates.

A hybrid molecular dynamics/fluctuating hydrodynamics method for modelling liquids at multiple scales in space and time.

A new 3D implementation of a hybrid model based on the analogy with two-phase hydrodynamics has been developed for the simulation of liquids at microscale. The idea of the method is to smoothly combine the atomistic description in the molecular dynamics zone with the Landau-Lifshitz fluctuating hydrodynamics representation in the rest of the system in the framework of macroscopic conservation laws through the use of a single "zoom-in" user-defined function s that has the meaning of a partial concentration in the two-phase analogy model. In comparison with our previous works, the implementation has been extended to full 3D simulations for a range of atomistic models in GROMACS from argon to water in equilibrium conditions with a constant or a spatially variable function s. Preliminary results of simulating the diffusion of a small peptide in water are also reported.

Impact of mutations in SARS-CoV-2 recombinant sub-variant XBB.1.16 on the binding affinity with human ACE2 receptor.

Despite the waning threat of the COVID-19 pandemic, its detrimental impact on global health persists. Regardless of natural immunity or immunity obtained through vaccination, emerging variants of the virus continue to undergo mutations and propagate globally. The persistent mutations in SARS-CoV-2, along with the subsequent formation of recombinant sub-variants has become a challenge for researchers and health professionals, raising concerns about the efficacy of current vaccines. Gaining a better understanding of the biochemical interactions between the Spike Protein (RBD) of SARS-CoV-2 variants and the human ACE2 receptor can prove to be beneficial in designing and developing antiviral therapeutics that are equally effective against all strains and emerging variants. Our objective in this study was to investigate the interfacial binding pattern of the SARS-CoV-2 RBD-ACE2 complex of the Wild Type (WT), Omicron, and the Omicron recombinant sub-variant XBB.1.16. We aimed to examine the atomic level factors and observe how mutations influence the interaction between the virus and its host using Molecular Dynamics simulation, MM/GBSA energy calculations, and Principal Component Analysis. Our findings reveal a higher degree of structural deviation and flexibility in XBB.1.16 compared to WT and Omicron. PCA indicated a wider cluster and significant flexibility in the movements of XBB.1.16 which can also be observed in free energy landscapes, while the normal mode analysis revealed converging motions within the RBD-ACE2 complexes which can facilitate the interaction between them. A pattern of decreased binding affinity was observed in case of XBB.1.16 when compared to the WT and Omicron. These observed deviations in XBB.1.16 when compared to its parent lineage Omicron, and WT can be attributed to the mutations specific to it. Collectively, these results enhance our understanding of the impact of mutations on the interaction between this strain and the host, taking us one step closer to designing effective antiviral therapeutics against the continually mutating strains.

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.

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.

Estimation of Nanoparticle's Surface Electrostatic Potential in Solution Using Acid-Base Molecular Probes. III. Experimental Hydrophobicity/Hydrophilicity and Charge Distribution of MS2 Virus Surface.

MS2 bacteriophage is often used as a model for evaluating pathogenic viruses' behavior in aqueous solution. However, the questions of the virus surface's hydrophilic/hydrophobic balance, the charge distribution, and the binding mechanism are open. Using the dynamic light scattering method and laser Doppler electrophoresis, the hydrodynamic diameter and the ζ-potential of the virus particles were measured at their concentration of 5 × 1011 particles per mL and ionic strength 0.03 M. The values were found to be 30 nm and -29 or -34 mV (by Smoluchowski or Ohshima approximations), respectively. The MS2 bacteriophage surface was also investigated using a series of acid-base indicator dyes of various charge type, size, and structure. Their spectral and acid-base properties (pKa) are very sensitive to the microenvironment in aqueous solution, including containing nanoparticles. The electrostatic potential of the surface Ψ was estimated using the common formula: Ψ = 59 × (pKai - pKa) in mV at 25 °C. The Ψ values were -50 and +10 mV, respectively, which indicate the "mosaic" way of the charge distribution on the surface. These data are in good agreement with the obtained ζ-potential values and provide even more information about the virus surface. It was found that the surface of the MS2 virus is hydrophilic in solution in contrast to the commonly accepted hypothesis of the hydrophobicity of virus particles. No hydrophobic interactions between various molecular probes and the capsid were observed.

Protein-Ligand Dissociation Rate Constant from All-Atom Simulation.

Dissociation of a ligand isoniazid from a protein catalase was investigated using all-atom molecular dynamics (MD) simulations. Random acceleration MD (τ-RAMD) was used, in which a random artificial force applied to the ligand facilitates its dissociation. We have suggested a novel approach to extrapolate such obtained dissociation times to the zero-force limit assuming never before attempted universal exponential dependence of the bond strength on the applied force, allowing direct comparison with experimentally measured values. We have found that our calculated dissociation time was equal to 36.1 s with statistically significant values distributed in the interval of 0.2-72.0 s, which quantitatively matches the experimental value of 50 ± 8 s despite the extrapolation over 9 orders of magnitude in time.

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.

Computing pKa Shifts Using Traditional Molecular Dynamics: Example of Acid-Base Indicator Dyes in Organized Solutions.

A compound's acidity constant (Ka) in a given medium determines its protonation state and, thus, its behavior and physicochemical properties. Therefore, it is among the key characteristics considered during the design of new compounds for the needs of advanced technology, medicine, and biological research, a notable example being pH sensors. The computational prediction of Ka for weak acids and bases in homogeneous solvents is presently rather well developed. However, it is not the case for more complex media, such as microheterogeneous solutions. The constant-pH molecular dynamics (MD) method is a notable contribution to the solution of the problem, but it is not commonly used. Here, we develop an approach for predicting Ka changes of weak small-molecule acids upon transfer from water to colloid solutions by means of traditional classical molecular dynamics. The approach is based on free energy (ΔG) computations and requires limited experiment data input during calibration. It was successfully tested on a series of pH-sensitive acid-base indicator dyes in micellar solutions of surfactants. The difficulty of finite-size effects affecting ΔG computation between states with different total charges is taken into account by evaluating relevant corrections; their impact on the results is discussed, and it is found non-negligible (0.1-0.4 pKa units). A marked bias is found in the ΔG values of acid deprotonation, as computed from MD, which is apparently caused by force-field issues. It is hypothesized to affect the constant-pH MD and reaction ensemble MD methods as well. Consequently, for these methods, a preliminary calibration is suggested.

Disordered protein-graphene oxide co-assembly and supramolecular biofabrication of functional fluidic devices.

Supramolecular chemistry offers an exciting opportunity to assemble materials with molecular precision. However, there remains an unmet need to turn molecular self-assembly into functional materials and devices. Harnessing the inherent properties of both disordered proteins and graphene oxide (GO), we report a disordered protein-GO co-assembling system that through a diffusion-reaction process and disorder-to-order transitions generates hierarchically organized materials that exhibit high stability and access to non-equilibrium on demand. We use experimental approaches and molecular dynamics simulations to describe the underlying molecular mechanism of formation and establish key rules for its design and regulation. Through rapid prototyping techniques, we demonstrate the system's capacity to be controlled with spatio-temporal precision into well-defined capillary-like fluidic microstructures with a high level of biocompatibility and, importantly, the capacity to withstand flow. Our study presents an innovative approach to transform rational supramolecular design into functional engineering with potential widespread use in microfluidic systems and organ-on-a-chip platforms.

MS2 bacteriophage capsid studied using all-atom molecular dynamics.

The all-atom model of an MS2 bacteriophage particle without its genome (the capsid) was built using high-resolution cryo-electron microscopy (EM) measurements for initial conformation. The structural characteristics of the capsid and the dynamics of the surrounding solution were examined using molecular dynamics simulation. The model demonstrates the overall preservation of the cryo-EM structure of the capsid at physiological conditions (room temperature and ions composition). The formation of a dense anion layer near the inner surface and a diffuse cation layer near the outer surface of the capsid was detected. The flow of water molecules and ions across the capsid through its pores were quantified, which was considerable for water and substantial for ions.

Developing and Validating a Set of All-Atom Potential Models for Sodium Dodecyl Sulfate.

We present a set of novel all-atom potential models for sodium dodecyl sulfate (SDS), developed within the framework of the widely used OPLS-AA and General AMBER force fields. The choice of the parameters for the models is made by rigorously following the methodology of the used force fields to ensure full compatibility with the models for other compounds. For the GAFF model, extensive quantum-chemical computations are performed to obtain reliable Boltzmann-averaged atomic point charges, and the latter are compared with the single-conformation charges. For representation of the hydrocarbon tail, we use recently published improved parameters that correctly reproduce the properties of lipids and long alkanes. The models are validated on the basis of correct reproduction of the main properties of micelles (size, degree of counterion binding) as well as diffusion coefficient of the SDS monomer. As an extended test, a simulation of a micelle with a high aggregation number (382) and unnatural initial shape is performed, and a restructuring to the correct shape is observed. This proves the suitability of the developed models for simulations of concentrated SDS solutions containing large micelles and also emphasizes importance of hydrocarbon tail parameters for the micelle properties. Finally, the developed DS- models are tested in combination with several common Na+ and water models. Their effect on the properties of SDS micelles is discussed, and suitable combinations are determined.

All-Atom Molecular Dynamics Simulations of Entire Virus Capsid Reveal the Role of Ion Distribution in Capsid's Stability.

Present experimental methods do not have sufficient resolution to investigate all processes in virus particles at atomistic details. We report the results of molecular dynamics simulations and analyze the connection between the number of ions inside an empty capsid of PCV2 virus and its stability. We compare the crystallographic structures of the capsids with unresolved N-termini and without them in realistic conditions (room temperature and aqueous solution) and show that the structure is preserved. We find that the chloride ions play a key role in the stability of the capsid. A low number of chloride ions results in loss of the native icosahedral symmetry, while an optimal number of chloride ions create a neutralizing layer next to the positively charged inner surface of the capsid. Understanding the dependence of the capsid stability on the distribution of the ions will help clarify the details of the viral life cycle that is ultimately connected to the role of packaged viral genome inside the capsid.