Showing papers in "Journal of Physical Chemistry B in 2022"
TL;DR: AI in structural biology is briefly overviewed, including in molecular dynamics simulations and prediction of microbiota–human protein–protein interactions, and their powerful impact on the life sciences.
Abstract: AlphaFold has burst into our lives. A powerful algorithm that underscores the strength of biological sequence data and artificial intelligence (AI). AlphaFold has appended projects and research directions. The database it has been creating promises an untold number of applications with vast potential impacts that are still difficult to surmise. AI approaches can revolutionize personalized treatments and usher in better-informed clinical trials. They promise to make giant leaps toward reshaping and revamping drug discovery strategies, selecting and prioritizing combinations of drug targets. Here, we briefly overview AI in structural biology, including in molecular dynamics simulations and prediction of microbiota–human protein–protein interactions. We highlight the advancements accomplished by the deep-learning-powered AlphaFold in protein structure prediction and their powerful impact on the life sciences. At the same time, AlphaFold does not resolve the decades-long protein folding challenge, nor does it identify the folding pathways. The models that AlphaFold provides do not capture conformational mechanisms like frustration and allostery, which are rooted in ensembles, and controlled by their dynamic distributions. Allostery and signaling are properties of populations. AlphaFold also does not generate ensembles of intrinsically disordered proteins and regions, instead describing them by their low structural probabilities. Since AlphaFold generates single ranked structures, rather than conformational ensembles, it cannot elucidate the mechanisms of allosteric activating driver hotspot mutations nor of allosteric drug resistance. However, by capturing key features, deep learning techniques can use the single predicted conformation as the basis for generating a diverse ensemble.
TL;DR: This work presents a thorough study of a typical hydrophobic DES formed by a 1:2 mole ratio of tetrabutyl ammonium chloride and decanoic acid, focusing on the effects of a low water content caused by absorbed water vapor, using multinuclear NMR techniques, molecular modeling, and several other physicochemical techniques.
Abstract: Deep eutectic solvents (DESs) formed by hydrogen bond donors and acceptors are a promising new class of solvents. Both hydrophilic and hydrophobic binary DESs readily absorb water, making them ternary mixtures, and a small water content is always inevitable under ambient conditions. We present a thorough study of a typical hydrophobic DES formed by a 1:2 mole ratio of tetrabutyl ammonium chloride and decanoic acid, focusing on the effects of a low water content caused by absorbed water vapor, using multinuclear NMR techniques, molecular modeling, and several other physicochemical techniques. Already very low water contents cause dynamic nanoscale phase segregation, reduce solvent viscosity and fragility, increase self-diffusion coefficients and conductivity, and enhance local dynamics. Water interferes with the hydrogen-bonding network between the chloride ions and carboxylic acid groups by solvating them, which enhances carboxylic acid self-correlation and ion pair formation between tetrabutyl ammonium and chloride. Simulations show that the component molar ratio can be varied, with an effect on the internal structure. The water-induced changes in the physical properties are beneficial for most prospective applications but water creates an acidic aqueous nanophase with a high halide ion concentration, which may have chemically adverse effects.
TL;DR: In this paper , the adsorption, reactivity, topological analysis, and sensing behavior of metal-doped (K, Na, and Mg) aluminum nitride (Al12N12) nanoclusters using the first-principle density functional theory (DFT) were investigated using the ωB97XD functional with the 6-311++G(d,p) basis set.
Abstract: This theoretical study focuses on the adsorption, reactivity, topological analysis, and sensing behavior of metal-doped (K, Na, and Mg) aluminum nitride (Al12N12) nanoclusters using the first-principle density functional theory (DFT). All quantum chemical reactivity, natural bond orbital (NBO), free energies (ΔG, ΔH), and sensor parameters were investigated using the ωB97XD functional with the 6-311++G(d,p) basis set. The trapping of carboplatin (cbp) onto the surfaces of doped Al12N12 was studied using four functionals PBE0-D3, M062X-D3, ωB97XD, and B3LYP-D3 at the 6-311++G(d,p) basis set. Overall, the substantial change in the energy gap of the surfaces after the adsorption process affects the work function, field emission, and the electrical conductivity of the doped clusters, hence making the studied surfaces a better sensor material for detecting carboplatin. Higher free energies of solvation were obtained in polar solvents compared to nonpolar solvents. Moreover, negative solvation energies and adsorption energies were obtained, which therefore shows that the engineered surfaces are highly efficient in trapping carboplatin. The relatively strong adsorption energies show that the mechanism of adsorption is by chemisorption, and K- and Na-doped metal clusters acted as better sensors for carboplatin. Also, the topological analysis in comparison to previous studies shows that the nanoclusters exhibited very high stability with regard to their relevant binding energies and hydrogen bond interactions.
TL;DR: In this paper , the authors analyzed the screening behavior and the resulting structural forces of a representative ion liquid confined between two charge-varied plates using both molecular dynamics simulations and a continuum theory, and compared the screening features of a more realistic asymmetric system and a less realistic symmetric one.
Abstract: Ionic liquids (ILs) are charged fluids composed of anions and cations of different size and shape. The ordering of charge and density in ILs confined between charged interfaces underlies numerous applications of IL electrolytes. Here, we analyze the screening behavior and the resulting structural forces of a representative IL confined between two charge-varied plates. Using both molecular dynamics simulations and a continuum theory, we contrast the screening features of a more-realistic asymmetric system and a less-realistic symmetric one. The ionic size asymmetry plays a nontrivial role in charge screening, affecting both the ionic density profiles and the disjoining pressure distance dependence. Ionic systems with size asymmetry are stronger coupled systems, and this manifests itself both in their response to the electrode polarization and spontaneous structure formation at the interface. Analytical expressions for decay lengths of the disjoining pressure are obtained in agreement with the pressure profiles computed from molecular dynamics simulations.
TL;DR: Extensive testing of DES-Amber indicates that it can describe the thermal stability and conformational flexibility of single- and double-stranded DNA systems with a level of accuracy comparable to or, especially for disordered systems, exceeding that of state-of-the-art nucleic acid force fields.
Abstract: Although molecular dynamics (MD) simulations have been used extensively to study the structural dynamics of proteins, the role of MD simulation in studies of nucleic acid based systems has been more limited. One contributing factor to this disparity is the historically lower level of accuracy of the physical models used in such simulations to describe interactions involving nucleic acids. By modifying nonbonded and torsion parameters of a force field from the Amber family of models, we recently developed force field parameters for RNA that achieve a level of accuracy comparable to that of state-of-the-art protein force fields. Here we report force field parameters for DNA, which we developed by transferring nonbonded parameters from our recently reported RNA force field and making subsequent adjustments to torsion parameters. We have also modified the backbone charges in both the RNA and DNA parameter sets to make the treatment of electrostatics compatible with our recently developed variant of the Amber protein and ion force field. We name the force field resulting from the union of these three parameter sets (the new DNA parameters, the revised RNA parameters, and the existing protein and ion parameters) DES-Amber. Extensive testing of DES-Amber indicates that it can describe the thermal stability and conformational flexibility of single- and double-stranded DNA systems with a level of accuracy comparable to or, especially for disordered systems, exceeding that of state-of-the-art nucleic acid force fields. Finally, we show that, in certain favorable cases, DES-Amber can be used for long-timescale simulations of protein–nucleic acid complexes.
TL;DR: It is shown that Omicron binds to human cells more strongly than the WT due to increased RBD charge, which enhances electrostatic interaction with negatively charged hACE2.
Abstract: The emergence of the variant of concern Omicron (B.1.1.529) of the severe acute respiratory syndrome coronavirus 2 has aggravated the Covid-19 pandemic due to its very contagious ability. The high infection rate may be due to the high binding affinity of Omicron to human cells, but both experimental and computational studies have yielded conflicting results on this issue. Some studies have shown that the Omicron variant binds to human angiotensin-converting enzyme 2 (hACE2) more strongly than the wild type (WT), but other studies have reported comparable binding affinities. To shed light on this open problem, in this work, we calculated the binding free energy of the receptor binding domain (RBD) of the WT and Omicron spike protein to hACE2 using all-atom molecular dynamics simulation and the molecular mechanics Poisson–Boltzmann surface area method. We showed that Omicron binds to human cells more strongly than the WT due to increased RBD charge, which enhances electrostatic interaction with negatively charged hACE2. N440K, T478K, E484A, Q493R, and Q498R mutations in the RBD have been found to play a critical role in the stability of the RBD-hACE2 complex. The effect of homogeneous and heterogeneous models of glycans coating the viral RBD and the peptidyl domain of hACE2 was examined. Although the total binding free energy is not sensitive to the glycan model, the distribution of per-residue interaction energies depends on it. In addition, glycans have a little effect on the binding affinity of the WT RBD to hACE2.
TL;DR: In this paper , the authors highlight the importance of functional aggregation of INPs for the exceptionally high ice nucleation activity of bacterial ice nucleators and emphasize that the bacterial cell membrane, as well as environmental conditions, is crucial for a precise functional INP aggregation.
Abstract: Bacterial ice nucleators (INs) are among the most effective ice nucleators known and are relevant for freezing processes in agriculture, the atmosphere, and the biosphere. Their ability to facilitate ice formation is due to specialized ice-nucleating proteins (INPs) anchored to the outer bacterial cell membrane, enabling the crystallization of water at temperatures up to -2 °C. In this Perspective, we highlight the importance of functional aggregation of INPs for the exceptionally high ice nucleation activity of bacterial ice nucleators. We emphasize that the bacterial cell membrane, as well as environmental conditions, is crucial for a precise functional INP aggregation. Interdisciplinary approaches combining high-throughput droplet freezing assays with advanced physicochemical tools and protein biochemistry are needed to link changes in protein structure or protein-water interactions with changes on the functional level.
TL;DR: This perspective explores the connection between the engineering of improved FPs and basic ideas from physical chemistry that explain their properties and drive the molecular design of brighter and more photostable variants.
Abstract: Fluorescent proteins (FPs) have become ubiquitous tools for biological research and concomitantly they are intriguing molecules that are amenable to study with a wide range of experimental and theoretical tools. This perspective explores the connection between the engineering of improved FPs and basic ideas from physical chemistry that explain their properties and drive the molecular design of brighter and more photostable variants. We highlight some of the progress and the many knowledge gaps in understanding the relationship between FP brightness and photostability. We also explore some of the pertinent remaining questions and suggest ways in which physical chemists might further examine the physical basis of brightness and photostability in these systems.
TL;DR: In this paper , a 1D/2D heterojunction was developed in the composite of CdS nanorod and g-C3N4 (CN) nanosheets.
Abstract: Effective separation of electron-hole and utilization of hot charge carriers are known to be the most important factors influencing the activity of a good photocatalyst. Herein, we developed a 1D/2D heterojunction in the composite of CdS nanorod and g-C3N4 (CN) nanosheets. These two form a quasi-type-II junction at the heterointerface. The photoexcited electrons are supposed to be transferred from CN to CdS, as observed from the enhanced photoluminescence of CdS. Transient studies revealed an absolute dominance of CdS exciton formation even in the composite system, although the dynamics were substantially modified in the presence of CN. The rise time of CdS band edge excitons were increased in the composite material, owing to the migration of hot electrons from CN to CdS. The hot electron transfer time was found to be ∼0.5 ps (rate constant ∼1.98 ps-1). The excitons decay in a much slower manner than that of the pristine CdS, confirming enhanced electron population in CdS. This migration of charge carriers was found to be immensely dependent on the applied excitation photon energy. Efficient migration of charge carriers leads to enhanced photocatalytic activity in the composite and an increased evolution of H2 evolution rate was witnessed. This detailed spectroscopic study toward the mechanistic pathway of the catalytic activity of an 1D/2D heterocomposite would be immensely helpful in fabricating many other effective heterojunctions which will advance the catalysis research.
TL;DR: A review of the recent work in CAZyme mechanism engineering can be found in this article , showing that computational simulations are instrumental to rationalize experimental data, providing mechanistic insight into how native and engineered CAZymes catalyze chemical reactions.
Abstract: Glycoside hydrolases and glycosyltransferases are the main classes of enzymes that synthesize and degrade carbohydrates, molecules essential to life that are a challenge for classical chemistry. As such, considerable efforts have been made to engineer these enzymes and make them pliable to human needs, ranging from directed evolution to rational design, including mechanism engineering. Such endeavors fall short and are unreported in numerous cases, while even success is a necessary but not sufficient proof that the chemical rationale behind the design is correct. Here we review some of the recent work in CAZyme mechanism engineering, showing that computational simulations are instrumental to rationalize experimental data, providing mechanistic insight into how native and engineered CAZymes catalyze chemical reactions. We illustrate this with two recent studies in which (i) a glycoside hydrolase is converted into a glycoside phosphorylase and (ii) substrate specificity of a glycosyltransferase is engineered toward forming O-, N-, or S-glycosidic bonds.
TL;DR: In this paper , a series of alkyl-substituted dual-state luminogens (DSEgens) were shown to have extremely high solid-state FLQY in even-numbered analogues and a dramatically pronounced odd-even effect in FLQy.
Abstract: Alkyl chain-resulted odd-even effects in fluorescence quantum yield (FLQY) have also been reported in organic luminescent materials (OLMs). However, the odd-even effects in FLQY caused by the alkyl substitutes in OLMs are generally very weak, with only single-digit differences. Here, we report a series of alkyl-substituted dual-state luminogens (DSEgens) showing extremely high solid-state FLQY in even-numbered analogues (>90% FLQY) and a dramatically pronounced odd-even effect in FLQY. The odd-even effect in FLQY is over 26% alternation, and a maximum of 48% difference in FLQY was observed between the compounds C1 and C2 with a methyl and ethyl substitution, respectively. C1 and C2 also displayed a crystallochromy with a 22 nm difference in emission wavelength. In addition, odd-even effects in the melting point and decomposition temperature were also observed. With these bright DSEgens, applications such as specific recognition of picric acid and ultrasensitive trace water detection have been demonstrated.
TL;DR: In this article , the authors describe the synthesis, spectroscopic studies, and theoretical calculations of nine original fluorophores based on the 2-(2'-hydroxyphenyl)benzazole (HBX) scaffold, functionalized at the 4-position of the phenol ring by ethynyl-extended aniline moieties.
Abstract: This article describes the synthesis, spectroscopic studies, and theoretical calculations of nine original fluorophores based on the 2-(2'-hydroxyphenyl)benzazole (HBX) scaffold, functionalized at the 4-position of the phenol ring by ethynyl-extended aniline moieties. HBX dyes are well-known to display an excited-state intramolecular proton transfer (ESIPT) process, owing to a strong six-membered hydrogen bond in their structure that allows for an enol/keto tautomerism after photoexcitation. Appropriate electronic substitution can perturb the ESIPT process, leading to dual fluorescence, both excited tautomers emitting at specific wavelengths. In the examples described herein, it is demonstrated that the proton transfer can be finely frustrated by a modification of the constitutive heteroring, leading to a single emission band from the excited enol or keto tautomer or a dual emission with relative intensities highly dependent on the environment. Moreover, the nature of the functionalization of the N-alkylated aniline moiety also has a significant importance on the relative excited-state stabilities of the two tautomers in solution. To shed more light on these features, quantum chemical calculations by the density functional theory are used to determine the excited-state energies and rationalize the experimental spectroscopic data.
TL;DR: In this article , the authors found that change in collective rotational dynamics of water in osmolyte solutions likely has a dominant effect on protein denaturation, which can be regarded as a pseudo-temperature change.
Abstract: There is a long, ongoing debate on how small molecules (osmolytes) affect the stability of proteins. The present study found that change in collective rotational dynamics of water in osmolyte solutions likely has a dominant effect on protein denaturation. According to THz spectroscopy analysis, osmolytes that stabilize proteins are accompanied by bound hydration water with slow dynamics, while the collective rotational dynamics of water is accelerated in the case of denaturant osmolytes. Among 15 osmolytes studied here, there is a good correlation between the change in mobility in terms of water rotational dynamics and the denaturation temperature of ribonuclease A. The changes in water dynamics due to osmolytes can be regarded as a pseudo-temperature-change, which agrees well with the change in protein denaturation temperature. These results indicate that the molecular dynamics of water around the protein is a key factor for protein denaturation.
TL;DR: In this article , a simulation of paraffin wax is presented, where the authors evaluate the contributions of every carbon atom to crystallization based on the occupied volume, structure entropy, and order parameter.
Abstract: Paraffin wax deposition has long been a vexing problem in industry. Especially, in offshore oil production, paraffin wax deposits and clogs pipes and containers because of low temperature, causing severe economic loss. It has been known that the crystallization of n-alkanes mainly causes the deposition of paraffin wax, which is necessary to understand the mechanism of the crystallization behavior of paraffin wax. We solve the challenge of describing the crystallization behavior of the alkane mixture system and evaluate the contributions of every carbon atom to crystallization based on the occupied volume, structure entropy, and order parameter. These results demonstrate that the middle atoms are the main contributor to crystallization, and the end atoms of n-alkanes are unfavorable for the crystallization of n-alkanes, showing that increasing the number of end atoms, for example, adding branched alkanes, will hinder the crystallization of paraffin wax. Furthermore, perhydrosqualene is chosen to study the inhibition of crystallization by adding branched alkanes. As there are different properties between the end and the middle atoms, based on the principle of dissolution with similar properties, a small number of branched alkanes will promote crystallization. Also, an inhibitory effect of the end atoms is observed when the proportion of branched alkanes increases to a certain percentage. Our simulation work describes the crystallization behavior of paraffin wax in detail, providing theoretical assistance for preventing and controlling paraffin deposition.
TL;DR: In this article , a lifetime-based directed evolution of a red-FP (RFP) called mCherry-XL was examined and the authors found a near-linear scaling of lifetime with quantum yield and consistent blue-shifts of the absorption and emission spectra.
Abstract: The approximately linear scaling of fluorescence quantum yield (ϕ) with fluorescence lifetime (τ) in fluorescent proteins (FPs) has inspired engineering of brighter fluorophores based on screening for increased lifetimes. Several recently developed FPs such as mTurquoise2, mScarlet, and FusionRed-MQV which have become useful for live cell imaging are products of lifetime selection strategies. However, the underlying photophysical basis of the improved brightness has not been scrutinized. In this study, we focused on understanding the outcome of lifetime-based directed evolution of mCherry, which is a popular red-FP (RFP). We identified four positions (W143, I161, Q163, and I197) near the FP chromophore that can be mutated to create mCherry-XL (eXtended Lifetime: ϕ = 0.70; τ = 3.9 ns). The 3-fold higher quantum yield of mCherry-XL is on par with that of the brightest RFP to date, mScarlet. We examined selected variants within the evolution trajectory and found a near-linear scaling of lifetime with quantum yield and consistent blue-shifts of the absorption and emission spectra. We find that the improvement in brightness is primarily due to a decrease in the nonradiative decay of the excited state. In addition, our analysis revealed the decrease in nonradiative rate is not limited to the blue-shift of the energy gap and changes in the excited state reorganization energy. Our findings suggest that nonradiative mechanisms beyond the scope of energy-gap models such the Englman-Jortner model are suppressed in this lifetime evolution trajectory.
TL;DR: In this paper , the mixtures of tetrabutylammonium bromide (TBAB) and nonanoic acid (NA) in different molar ratios are theoretically and experimentally investigated by applying a phase diagram constructed on the basis of differential scanning calorimetry measurements and COSMO-RS model.
Abstract: Deep eutectic solvents have quickly attracted the attention of researchers because they better meet the requirements of green chemistry and thus have the potential to replace conventional hazardous organic solvents in some areas. To better understand the nature of these mixtures, as well as expand the possibilities of their use in different industries, a detailed examination of their physical properties, such as density, viscosity, the nature of the interactions between their constituents, the phase diagrams, depression of their melting point, and interpretation of these results is necessary. In this work, the mixtures of tetrabutylammonium bromide (TBAB) and nonanoic acid (NA) in different molar ratios are theoretically and experimentally investigated by applying a phase diagram constructed on the basis of differential scanning calorimetry measurements and COSMO-RS model. Spectral properties are investigated based on Fourier transform infrared spectroscopy and density functional theory. The observed eutectic point indicates the formation of a DES in the TBAB−NA system in a 1:2 molar ratio. This is due to the presence of hydrogen bonds between the carboxyl group from the NA molecule and the bromine atom from the TBAB molecule. Other eutectic mixtures are most likely the solutions of TBAB in NA, in which hydrogen bonds predominate between acid molecules.
TL;DR: In this article , a machine learning-based approach was used to predict melting temperature (Tm) of polyhydroxyalkanoates (PHAs) based copolymers.
Abstract: Diminishing fossil fuel-based resources and ever-growing environmental concerns related to plastic pollution demand for the development of sustainable and biodegradable polymeric material alternatives. Polyhydroxyalkanoates (PHAs) represent an eco-friendly and economically viable class of polymers with a wide range of applications. However, the chemical diversity combined with tunable physical properties available within PHAs poses discovery and optimization challenges with respect to identifying optimal application-specific chemical compositions. Here we use an example of melting temperature (Tm) prediction to demonstrate the promise of machine learning (ML)-based techniques for establishing efficient structure-property mappings in PHA-based chemical space. We employ a manually curated data set of experimentally measured Tm values for a wide range of PHA homo- and copolymer chemistries along with their reported polymer molecular weights and polydispersity indices. Descriptors based on topology, shape, and charge/polarity of specific motifs forming the polymer backbone were then used to numerically represent the polymers. The ML models developed by using available data were used to rapidly predict the property of multicomponent PHA-based copolymers, while estimating uncertainties underlying the predictions. Combined with a previously developed glass transition temperature (Tg) prediction model and an evolutionary algorithm-based search strategy, the approach is demonstrated to address polymer design with multiobjective optimization challenges.
TL;DR: In this paper , the authors investigated the molecular nature of interprotein interaction and the associated free energy diagrams for the unbinding of the two proteins for SARS-CoV-2 and some of its known variants through all-atom simulations.
Abstract: The spike protein of SARS-CoV-2 is known to interact with the human ACE2 protein via its receptor binding domain (RBD). We have investigated the molecular nature of this interprotein interaction and the associated free energy diagrams for the unbinding of the two proteins for SARS-CoV-2 and some of its known variants through all-atom simulations. The present work involves generation and analysis of 2.5 μs of unbiased and 4.2 μs of biased molecular dynamics trajectories in total for five explicitly solvated RBD-ACE2 systems at full atomic level. First, we have made a comparative analysis of the details of residue-wise specific interactions of the spike protein with ACE2 for SARS-CoV-1 and SARS-CoV-2. It is found that the average numbers of both direct interprotein and water-bridged hydrogen bonds between the RBD and ACE2 are higher for SARS-CoV-2 than SARS-CoV-1. These higher hydrogen bonded interactions are further aided by enhanced nonspecific electrostatic attractions between the two protein surfaces for SARS-CoV-2. The free energy calculations reveal that there is an increase in the free energy barrier by ∼1.5 kcal/mol for the unbinding of RBD from ACE2 for SARS-CoV-2 compared to that for SARS-CoV-1. Subsequently, we considered the RBDs of three variants of SARS-CoV-2, namely N501Y, E484Q/L452R, and N440K. The free energy barrier of protein unbinding for the N501Y variant is found to be ∼4 kcal/mol higher than the wild type SARS-CoV-2 which can be attributed to additional specific interactions involving Tyr501 of RBD and Lys353 and Tyr42 of ACE2 and also enhanced nonspecific electrostatic interaction between the protein surfaces. For the other two mutant variants of E484Q/L452R and N440K, the free energy barrier for protein unbinding increases by ∼2 and ∼1 kcal/mol, respectively, compared with the wild type SARS-CoV-2, which can be attributed to an increase in the number of interprotein hydrogen bonds for the former and also to enhanced positive electrostatic potential on the RBD surfaces for both of the variants. The successive breaking of interprotein hydrogen bonds along the free energy pathway of the unbinding process is also found out for all five systems studied here.
TL;DR: In this paper , a paramagnetic NMR-based method for de novo determination of effective near-surface electrostatic potentials was proposed, which allows for straightforward examination of electrostatic models for biomolecules.
Abstract: Experimental validation of theoretical models for protein electrostatics remains rare. Recently, we have developed a paramagnetic NMR-based method for de novo determination of effective near-surface electrostatic potentials, which allows for straightforward examination of electrostatic models for biomolecules. In the current work, we expand this method and demonstrate that effective near-surface electrostatic potentials can readily be determined from 1H paramagnetic relaxation enhancement (PRE) data for protein CαH and CH3 groups. The experimental data were compared with those predicted from the Poisson-Boltzmann theory. The impact of structural dynamics on the effective near-surface electrostatic potentials was also assessed. The agreement between the experimental and theoretical data was particularly good for methyl 1H nuclei. Compared to the conventional pKa-based validation, our paramagnetic NMR-based approach can provide a far larger number of experimental data that can directly be used to examine the validity of theoretical electrostatic models for proteins.
TL;DR: In this article , a comparison between a numerical solution of the Poisson-Boltzmann equation and the analytical solution of its linearized version through the Debye-Hückel equations considering both size-dissimilar and common ion diameters approaches is presented.
Abstract: This work presents a comparison between a numerical solution of the Poisson-Boltzmann equation and the analytical solution of its linearized version through the Debye-Hückel equations considering both size-dissimilar and common ion diameters approaches. In order to verify the limits in which the linearized Poisson-Boltzmann equation is capable to satisfactorily reproduce the nonlinear version of Poisson-Boltzmann, we calculate mean ionic activity coefficients for different types of electrolytes as various temperatures. The divergence between the linearized and full Poisson-Boltzmann equations is higher for lower molalities, and both solutions tend to converge toward higher molalities. For electrolytes of lower valencies (1:1, 1:2, 2:1, and 1:3) and higher distances of closest approach, the full version of the Debye-Hückel equation is capable of representing the activity coefficients with a low divergence from the nonlinear Poisson-Boltzmann. The size-dissimilar full version of Debye-Hückel represents a clear improvement over the extended version that uses only common ion diameters when compared to the numerical solution of the Poisson-Boltzmann equation. We have derived a salt-specific index (Θ) to gradually classify electrolytes in order of increasing influence of nonlinear ion-ion interactions, which differentiate the Debye-Hückel equations from the nonlinear Poisson-Boltzmann equation.
TL;DR: Cryo-TEM is able to directly visualize the microstructure of the aggregates formed by lecithin–Tween 80 mixtures, thereby enhancing the understanding of morphological changes in the le cithin-tween 80 system.
Abstract: The phospholipid lecithin (L) and the nonionic surfactant Tween 80 (T) are used together in various contexts, including in drug delivery and oil spill remediation. There is hence a need to elucidate the nanostructures in LT mixtures, which is the focus of this paper. We study these mixtures using cryogenic transmission electron microscopy (cryo-TEM), coupled with dynamic light scattering and small-angle neutron scattering. As the concentration of Tween 80 is increased, the vesicles formed by lecithin are transformed into spherical micelles. We identify bicelles (i.e., disc-like micelles) as well as cylindrical micelles as the key stable nanostructures formed at intermediate L/T ratios. The bicelles have diameters ∼13–26 nm, and the bicelle size decreases as the Tween 80 content increases. We propose that the lecithin lipids form the body of the discs, while the Tween 80 surfactants occupy the rims. This hypothesis is consistent with geometric arguments because lecithin is double-tailed and favors minimal curvature, whereas the single-tailed Tween 80 molecules prefer curved interfaces. In the case of cylindrical micelles, cryo-TEM reveals that the micelles are short (length < 22 nm) and flexible. We are able to directly visualize the microstructure of the aggregates formed by lecithin–Tween 80 mixtures, thereby enhancing the understanding of morphological changes in the lecithin–Tween 80 system.
TL;DR: In this article , the influence of ultrasonic cavitation, surface modification of droplets, and solutes in the bulk liquid on H2O2 production was investigated and it was concluded that the air-water interface of water microdroplets itself does not generate H 2O2.
Abstract: Studying chemical processes at the air-water interface is always challenging. A recent report claimed that H2O2 was formed spontaneously on the surface of condensed water microdroplets. However, a newer report concluded that the detected H2O2 in the previous report could originate in part from the water vapor source that involved ultrasonic atomization of liquid water. Here, this phenomenon is reinvestigated regarding the influence of ultrasonic cavitation, surface modification of droplets, and solutes in the bulk liquid on H2O2 production. When the droplet surfaces were modified by surfactants, H2O2 production did not change, whereas adding gases or inorganic compounds to the bulk solution caused significant changes in H2O2 production. These results confirm that H2O2 formation originates from cavitation in bulk solutions. It is concluded that the air-water interface of water microdroplets itself does not generate H2O2.
TL;DR: In this paper , the spectral dielectric properties of liquid water in charged nanopores over a wide range of frequencies and pore widths were examined using classical molecular dynamics simulations of hydrated Na-smectite.
Abstract: In this study, we examine the spectral dielectric properties of liquid water in charged nanopores over a wide range of frequencies (0.3 GHz to 30 THz) and pore widths (0.3 to 5 nm). This has been achieved using classical molecular dynamics simulations of hydrated Na-smectite, the prototypical swelling clay mineral. We observe a drastic (20-fold) and anisotropic decrease in the static relative permittivity of the system as the pore width decreases. This large decrement in static permittivity reflects a strong attenuation of the main Debye relaxation mode of liquid water. Remarkably, this strong attenuation entails very little change in the time scale of the collective relaxation. Our results indicate that water confined in charged nanopores is a distinct solvent with a much weaker collective nature than bulk liquid water, in agreement with recent observations of water in uncharged nanopores. Finally, we observe remarkable agreement between the dielectric properties of the simulated clay system against a compiled set of soil samples at various volumetric water contents. This implies that saturation may not be the sole property dictating the dielectric properties of soil samples, rather that the pore-size distribution of fully saturated nanopores may also play a critically important role.
TL;DR: In this paper , the authors used molecular simulations to provide a quantitative assessment of the affinity and mass transport of CO2 and oxalic and formic acids in the mixed solvents, the solubilities and self-diffusivities of these solutes were also computed.
Abstract: Recently, deep eutectic solvents (DES) have been considered as possible electrolytes for the electrochemical reduction of CO2 to value-added products such as formic and oxalic acids. The applicability of pure DES as electrolytes is hindered by high viscosities. Mixtures of DES with organic solvents can be a promising way of designing superior electrolytes by exploiting the advantages of each solvent type. In this study, densities, viscosities, diffusivities, and ionic conductivities of mixed solvents comprising DES (i.e., reline and ethaline), methanol, and propylene carbonate were computed using molecular simulations. To provide a quantitative assessment of the affinity and mass transport of CO2 and oxalic and formic acids in the mixed solvents, the solubilities and self-diffusivities of these solutes were also computed. Our results show that the addition of DES to the organic solvents enhances the solubilities of oxalic and formic acids, while the solubility of CO2 in the ethaline-containing mixtures are in the same order of magnitude with the respective pure organic components. A monotonic increase in the densities and viscosities of the mixed solvents is observed as the mole fraction of DES in the mixture increases, with the exception of the density of ethaline-propylene carbonate which shows the opposite behavior due to the high viscosity of the pure organic component. The self-diffusivities of all species in the mixtures significantly decrease as the mole fraction of DES approaches unity. Similarly, the self-diffusivities of the dissolved CO2 and the oxalic and formic acids also decrease by at least 1 order of magnitude as the composition of the mixture shifts from the pure organic component to pure DES. The computed ionic conductivities of all mixed solvents show a maximum value for mole fractions of DES in the range from 0.2 to 0.6 and decrease as more DES is added to the mixtures. Since for most mixtures studied here no prior experimental measurements exist, our findings can serve as a first data set based on which further investigation of DES-containing electrolyte solutions can be performed for the electrochemical reduction of CO2 to useful chemicals.
TL;DR: The simulations reveal the dynamical properties of the membrane-bound state of the tau R3-R4 monomer, enabling insertion of the residues 306-318 and 376-378 and reveal a very heterogeneous ensemble of conformations with low β and helical contents.
Abstract: The aggregation of the tau protein plays a significant role in Alzheimer's disease, and the tau R3-R4 domain spanning residues 306-378 was shown to form the amyloid fibril core of a full-length tau. The conformations of the tau R3-R4 monomer in the bulk solution and at the surface of membranes are unknown. In this study, we address these questions by means of atomistic molecular dynamics. The simulations in the bulk solution show a very heterogeneous ensemble of conformations with low β and helical contents. The tau R3-R4 monomer has the propensity to form transient β-hairpins within the R3 repeat and between the R3 and R4 repeats and parallel β-sheets spanning the R3 and R4 repeats. The simulations also show that the surface of the membrane does not induce β-sheet insertion and leads to an ensemble of structures very different from those in the bulk solution. They also reveal the dynamical properties of the membrane-bound state of the tau R3-R4 monomer, enabling insertion of the residues 306-318 and 376-378.
TL;DR: It is shown that the repeated conformational transitions of adenylate kinase are essential for the relaxation of incorrectly bound substrates into the catalytically competent conformation by combining all-atom and coarse-grained molecular simulations.
Abstract: The catalytic cycle of the enzyme adenylate kinase involves large conformational motions between open and closed states. A previous single-molecule experiment showed that substrate binding tends to accelerate both the opening and the closing rates and that a single turnover event often involves multiple rounds of conformational switching. In this work, we showed that the repeated conformational transitions of adenylate kinase are essential for the relaxation of incorrectly bound substrates into the catalytically competent conformation by combining all-atom and coarse-grained molecular simulations. In addition, free energy calculations based on all-atom and coarse-grained models demonstrated that the enzyme with incorrectly bound substrates has much a lower free energy barrier for domain opening compared to that with the correct substrate conformation, which may explain the the acceleration of the domain opening rate by substrate binding. The results of this work provide mechanistic understanding to previous experimental observations and shed light onto the interplay between conformational dynamics and enzyme catalysis.
TL;DR: The aim of the current work is to provide a comprehensive set of molecular dynamics simulations using more than 180 μs of simulation time to reveal the ion-specific distributions and binding patterns for DNA and RNA duplexes.
Abstract: The distribution of cations around nucleic acids is essential for a broad variety of processes ranging from DNA condensation and RNA folding to the detection of biomolecules in biosensors. Predicting the exact distribution of ions remains challenging since the distribution and, hence, a broad variety of nucleic acid properties depend on the salt concentration, the valency of the ions, and the ion type. Despite the importance, a general theory to quantify ion-specific effects for highly charged biomolecules is still lacking. Moreover, recent experiments reveal that despite their similar building blocks, DNA and RNA duplexes can react differently to the same ionic conditions. The aim of our current work is to provide a comprehensive set of molecular dynamics simulations using more than 180 μs of simulation time. For the mono- and divalent cations Li+, Na+, K+, Cs+, Ca2+, Sr2+, and Ba2+, the simulations allow us to reveal the ion-specific distributions and binding patterns for DNA and RNA duplexes. The microscopic insights from the simulations display the origin of ion-specificity and shed light on the question of why DNA and RNA show opposing behavior in the same ionic conditions. Finally, the detailed binding patterns from the simulations reveal why RNA can capture more cations than DNA.
TL;DR: It is found that the viral protein fragment SK9 may alter α-synuclein amyloid formation by shifting the ensemble toward aggregation-prone and preferentially rod-like fibril seeding conformations, however, SK9 has only a small effect on the stability of pre-existing or newly formed fibrils.
Abstract: Aggregates of α-synuclein are thought to be the disease-causing agent in Parkinson's disease. Various case studies have hinted at a correlation between COVID-19 and the onset of Parkinson's disease. For this reason, we use molecular dynamics simulations to study whether amyloidogenic regions in SARS-COV-2 proteins can initiate and modulate aggregation of α-synuclein. As an example, we choose the nine-residue fragment SFYVYSRVK (SK9), located on the C-terminal of the envelope protein of SARS-COV-2. We probe how the presence of SK9 affects the conformational ensemble of α-synuclein monomers and the stability of two resolved fibril polymorphs. We find that the viral protein fragment SK9 may alter α-synuclein amyloid formation by shifting the ensemble toward aggregation-prone and preferentially rod-like fibril seeding conformations. However, SK9 has only a small effect on the stability of pre-existing or newly formed fibrils. A potential mechanism and key residues for potential virus-induced amyloid formation are described.
TL;DR: How molecular dynamics simulations have provided valuable molecular-level insight into LD targeting and LD biogenesis is highlighted and the physical properties of TG from different force fields compared with experimental data are reviewed.
Abstract: Lipid droplets (LDs) are intracellular organelles whose primary function is energy storage. Known to emerge from the endoplasmic reticulum (ER) bilayer, LDs have a unique structure with a core consisting of neutral lipids, triacylglycerol (TG) or sterol esters (SE), surrounded by a phospholipid (PL) monolayer and decorated by proteins that come and go throughout their complex lifecycle. In this Feature Article, we review recent developments in computational studies of LDs, a rapidly growing area of research. We highlight how molecular dynamics (MD) simulations have provided valuable molecular-level insight into LD targeting and LD biogenesis. Additionally, we review the physical properties of TG from different force fields compared with experimental data. Possible future directions and challenges are discussed.
TL;DR: The pigeon Cry4 (ClCry4) crystal structure was used to reconstruct the missing avian Cry4 protein structures via homology modeling for carefully selected bird species and shows flexibility in analogous regions pointing to similar activation mechanisms and/or signaling interaction partners.
Abstract: A recent study by Xu et al. (Nature, 2021, 594, 535-540) provided strong evidence that cryptochrome 4 (Cry4) is a key protein to endow migratory birds with the magnetic compass sense. The investigation compared the magnetic field response of Cry4 from migratory and nonmigratory bird species and suggested that a difference in magnetic sensitivity could exist. This finding prompted an in-depth investigation into Cry4 protein differences on the structural and dynamic levels. In the present study, the pigeon Cry4 (ClCry4) crystal structure was used to reconstruct the missing avian Cry4 protein structures via homology modeling for carefully selected bird species. The reconstructed Cry4 structure from European robin, Eurasian blackcap, zebra finch, chicken, and pigeon were subsequently simulated dynamically and analyzed. The studied avian Cry4 structures show flexibility in analogous regions pointing to similar activation mechanisms and/or signaling interaction partners. It can be concluded that the experimentally recorded difference in the magnetic field sensitivity of Cry4 from different birds is unlikely to be due to solely intrinsic dynamics of the proteins but requires additional factors that have not yet been identified.