Thermodynamics of Hydrogen Bonding in Hydrophilic and Hydrophobic Media

Destabilization of the Alzheimer's amyloid-β protofibrils by THC: A molecular dynamics simulation study

Alzheimer's disease is a leading cause of dementia in the elderly population for which there is no cure at present. Deposits of neurotoxic plaques are found in the brains of patients which are composed of fibrils of the amyloid-β peptide. Molecules which can disrupt these fibrils have gained attention as potential therapeutic agents. Δ-tetrahydrocannabidiol (THC) is a cannabinoid, which can bind to the receptors in the brain, and has shown promise in reducing the fibril content in many experimental studies. In our present study, by employing all atom molecular dynamics simulations, we have investigated the mechanism of the interaction of the THC molecules with the amyloid-β protofibrils. Our results show that the THC molecules disrupt the protofibril structure by binding strongly to them. The driving force for the binding was the hydrophobic interactions with the hydrophobic residues in the fibrils. As a result of these interactions, the tight packing of the hydrophobic core of the protofibrils was made loose, and salt bridges, which were important for stability were disrupted. Hydrogen bonds between the chains of the protofibrils which are important for stability were disrupted, as a result of which the β-sheet content was reduced. The destabilization of the protofibrils by the THC molecules leads to the conclusion that THC molecules may be considered for the therapy in treating Alzheimer's disease.

Enhancing the binding of the β-sheet breaker peptide LPFFD to the amyloid-β fibrils by aromatic modifications: A molecular dynamics simulation study

Alzheimer's is a fatal neurodegenerative disease for which there is no cure at present. The disease is characterized by the presence of plaques in the brains of a patient, which are composed mainly of aggregates of the amyloid-β peptide in the form of β-sheet fibrils. Here, we investigated the possibility of exploiting the superior binding ability of aromatic amino acids to a particular model of the amyloid-β fibrils. which is a difficult target for drug design. The β-sheet breaker peptide LPFFD was modified with aromatic amino acids and its binding to these fibrils was studied. We found that the orientation and the electrostatic complementarity of the modified peptide with respect to the fibrils played a crucial role in determining whether its binding was improved by the aromatic amino acids. The modified LPFFD peptides were able to bind to those fibril residues. which are important in the aggregation of amyloid-β peptides and thus can potentially inhibit the further aggregation of the amyloid-beta peptides by blocking their interactions. We found that the tryptophan modified LPFFD peptides had the best binding affinities. In most cases, the aromatic amino acids in the N-terminus of the modified peptides made more contacts with the fibrils than those in the C-terminus. We also found that increasing the aromatic content did not significantly improve the binding of the LPFFD peptide to the fibrils. Our study can serve as a basis for the design of novel peptide-based drugs for Alzheimer's disease in which aromatic interactions play an important role.

Mechanistic Insights into the Co-Aggregation of Aβ and hIAPP: An All-Atom Molecular Dynamic Study

Patients with Alzheimer's disease (AD) have a high risk of developing Type II diabetes (T2D). The co-aggregation of the two disease-related proteins, Aβ and hIAPP, has been proposed as a potential molecular mechanism. However, the detailed Aβ-hIAPP interactions and structural characteristics of co-aggregates are mostly unknown at atomic level. Here, we explore the conformational ensembles of the Aβ-hIAPP heterodimer and Aβ or hIAPP homodimer by performing all-atom explicit-solvent replica exchange molecular dynamic simulations. Our simulations show that the interaction propensity of Aβ-hIAPP in the heterodimer is comparable with that of Aβ-Aβ/hIAPP-hIAPP in the homodimer. Similar hot spot residues of Aβ/hIAPP in the homodimer and heterodimer are identified, indicating that both Aβ and hIAPP have similar molecular recognition sites for self-aggregation and co-aggregation. Aβ in the heterodimer possesses three high β-sheet probability regions: the N-terminal region E3-H6, the central hydrophobic core region K16-E22, and the C-terminal hydrophobic region I31-A41, which is highly similar to Aβ in the homodimer. More importantly, in the heterodimer, the regions E3-H6, F19-E22, and I31-M35 of Aβ and the amyloid core region N20-T30 of hIAPP display higher β-sheet probability than they do in homodimer, implying their crucial roles in the formation of β-sheet-rich co-aggregates. Our study sheds light on the co-aggregation of Aβ and hIAPP at an atomic level, which will be helpful for an in-depth understanding of the molecular mechanism for epidemiological correlation of AD and T2D.

Quantitative and Anisotropic Mechanochromism of Polydiacetylene at Nanoscale

Quantitative and anisotropic mechanochromism of polydiacetylene over nanoscale distances remains unaddressed even after 50 years of extensive research. This is because its anisotropic structure on substrates necessitates the application of both vertical and lateral forces (shear forces) to characterize it, whereas atomic force microscopy, which is the usual technique used to investigate nanoscale forces, is only capable of quantifying vertical forces. In this study, we address this lacuna by utilizing quantitative friction force microscopy that measures lateral forces. Our data confirm that polydiacetylene reacts only to lateral forces, F_//, and disprove the previously claimed hypothesis that the edges of the polymer crystals exhibit higher force sensitivity than the rest of the crystal. In addition, we report a correlation between mechanochromism and thermochromism, which can be attributed to the fact that both work and heat are different means of providing the same transition energy.

Why the Orientational Mobility in Arginine and Lysine Spacers of Peptide Dendrimers Designed for Gene Delivery Is Different?

New peptide dendrimer with Lys-2Arg repeating units was recently studied experimentally by NMR (RSC Advances, 2019, 9, 18018) and tested as gene carrier successfully (Int. J. Mol. Sci., 2020, 21, 3138). The unusual slowing down of the orientational mobility of 2Arg spacers in this dendrimer was revealed. It has been suggested that this unexpected behavior is caused by the Arg-Arg pairing effect in water, which leads to entanglements between dendrimer branches. In this paper, we determine the reason for this slowing down using atomistic molecular dynamics simulation of this dendrimer. We present that the structural properties of Lys-2Arg dendrimer are close to those of the Lys-2Lys dendrimer at all temperatures (Polymers, 2020, 12, 1657). However, the orientational mobility of the H-H vector in CH2-N groups of 2Arg spacers in Lys-2Arg dendrimer is significantly slower than the mobility of the same vector in the Lys-2Lys dendrimer. This result is in agreement with the recent NMR experiments for the same systems. We revealed that this difference is not due to the arginine-arginine pairing, but is due to the semiflexibility effect associated with the different contour length from CH2-N group to the end of the side arginine or lysine segment in spacers.

Quantifications of Oleocolloid Matrices Made of Whey Protein and Oleogels

Consumer demand for high protein content and plant-based fat has necessitated novel approaches to healthy food products. In response to this need, oleogels (OG) (structured liquid oils) emerged as a possible means of not only replacing saturated and trans fats but also delivering food protein. Nevertheless, an in-depth view of the structure of networks made of OG and protein is deficient. Hence, the objective of this study is developing oleocolloid (OC) (whey protein and rice bran wax OG) and hydro-oleocolloid (HOC) (OC + water) matrices with varying protein content (2.5–7.5%) to characterize their structural properties. Thermal analysis of the matrices via differential scanning calorimetry (DSC) documented the effects of hydrophobic interactions on the protein structure and its stability. Whey protein denaturation temperature increased from 74.9 °C to 102.8 °C in the presence of high oleic soybean oil. The effects of vegetable oil on WPI structure was also verified by FTIR spectroscopy. Data analysis revealed slight structural changes of the WPI secondary structure in the hydrophobic oil medium and the α-helix and β-sheet proportion in the emulsion medium was significantly altered. Similar analysis was performed in OC and HOC networks to quantify possible interactions between protein and rice bran wax. Results indicated that the protein was denatured during the thermal and mechanical conditions required for the oleogelation process, while it did not affect the systems’ solid fat content (SFC) and polymorphic patterns of the oleogels. However, DSC analysis showed different onset of melting for OC and HOC samples due to colloidal interactions between the protein and the lipid phase. The role of these chemistry was confirmed by microscopy analyses where OC and HOC matrices displayed notably different microstructural properties. The observed differences in the structural properties between OC and HOC matrices indicate the different colloidal interactions mediated by oleogelation process and the liquid medium type (oil vs. emulsion).

The role of NMR in leveraging dynamics and entropy in drug design

Nuclear magnetic resonance (NMR) spectroscopy has contributed to structure-based drug development (SBDD) in a unique way compared to the other biophysical methods. The potency of a ligand binding to a protein is dictated by the binding free energy, which is an intricate interplay between entropy and enthalpy. In addition to providing the atomic resolution structural information, NMR can help to identify protein-ligand interactions that potentially contribute to the enthalpic component of the free energy. NMR can also illuminate dynamic aspects of the interaction, which correspond to the entropic term of the free energy. The ability of NMR to access both terms in the free energy equation stems from the suite of experiments developed to shed light on various aspects that contribute to both entropy and enthalpy, deepening our understanding of the biological function of macromolecules and assisting to target them in physiological conditions. Here we provide a brief account of the contribution of NMR to SBDD, highlighting hallmark examples and discussing the challenges that demand further method development. In the era of integrated biology, the unique ability of NMR to directly ascertain structural and dynamical aspects of macromolecule and monitor changes in these properties upon engaging a ligand can be combined with computational and other structural and biophysical methods to provide a more complete picture of the energetics of drug engagement with the target. Such efforts can be used to engineer better drugs.

Thermosensitive Hydration of Four Acrylamide-Based Polymers in Coil and Globule Conformations

To characterize the thermosensitive coil–globule transition in atomistic detail, the conformational dynamics of linear polymer chains of acrylamide-based polymers have been investigated at multiple temperatures. Therefore, molecular dynamic simulations of 30mers of polyacrylamide (AAm), poly-N-methylacrylamide (NMAAm), poly-N-ethylacrylamide (NEAAm), and poly-N-isopropylacrylamide (NIPAAm) have been performed at temperatures ranging from 250 to 360 K for 2 μs. While two of the polymers are known to exhibit thermosensitivity (NEAAm, NIPAAm), no thermosensitivity is observed for AAm and NMAAm in aqueous solution. Our computer simulations consistently reproduce these properties. To understand the thermosensitivity of the respective polymers, the conformational ensembles at different temperatures have been separated according to the coil–globule transition. The coil and globule conformational ensembles were exhaustively analyzed in terms of hydrogen bonding with the solvent, the change of the solvent accessible surface, and enthalpic contributions. Surprisingly, independent of different thermosensitive properties of the four polymers, the surface affinity to water of coil conformations is higher than for globule conformations. Therefore, polymer–solvent interactions stabilize coil conformations at all temperatures. Nevertheless, the enthalpic contributions alone cannot explain the differences in thermosensitivity. This clearly implies that entropy is the distinctive factor for thermosensitivity. With increasing side chain length, the lifetime of the hydrogen bonds between the polymer surface and water is extended. Thus, we surmise that a longer side chain induces a larger entropic penalty due to immobilization of water molecules.

Nitrogen-containing naringenin derivatives for reversing multidrug resistance in cancer

Naringenin (1), isolated from Euphorbia pedroi, was previously derivatized yielding compounds 2-13. In this study, aiming at expanding the pool of analogues of the flavanone core towards better multidrug resistance (MDR) reversal agents, alkylation reactions and chemical modification of the carbonyl moiety was performed (15-39). Compounds structures were assigned mainly by 1D and 2D NMR experiments. Compounds 1-39 were assessed as MDR reversers, in human ABCB1-transfected mouse T-lymphoma cells, overexpressing P-glycoprotein (P-gp). The results revealed that O-methylation at C-7, together with the introduction of nitrogen atoms and aromatic moieties at C-4 or C-4', significantly improved the activity, being compounds 27 and 37 the strongest P-gp modulators and much more active than verapamil. In combination assays, synergistic interactions of selected compounds with doxorubicin substantiated the results. While molecular docking suggested that flavanone derivatives act as competitive modulators, molecular dynamics showed that dimethylation promotes binding to a modulator-binding site. Moreover, flavanones may also interact with a vicinal ATP-binding site in both nucleotide-binding domains, hypothesizing an allosteric mode of action.

The effect of the degree of substitution on the solubility of cellulose acetoacetates in water: A molecular dynamics simulation and density functional theory study

The effect of the degree of substitution (DS) on the aqueous solubility of cellulose acetoacetates (CAA) was investigated by molecular dynamics simulations and density functional theory calculations. Using average non-covalent interaction and the electrostatic potential analyses done on cellobiose as the model, it was showed both polar and non-polar areas of the system increased as the more hydroxyls were replaced by acetoacetate groups. Analyses of the solvation free energies of a celludecose (glucan containing 10 monosaccharide sugar units) at constant pressure and temperature showed the polar solvation free energies and the number of decose-water hydrogen bonds increased as DS was varied from 0.3 to 0.8, which contributes to higher solubility in water. When the DS of CAA increased from 0.8 to 1.5, it became insoluble again because the plateaued increase in solvation free energy could no longer compensate for the decreasing CAA-water hydrogen bonding interactions. The growing van der Waals interactions among CAA molecules as the molecule grows bigger with each attached AA group also contributes to the decreasing water solubility.

Molecular dynamic simulation: Conformational properties of single-stranded curdlan in aqueous solution

Recently, molecular dynamic simulation technique has been proved to be a powerful tool providing structural insights for better understanding the functionality of carbohydrates. Here, by using molecular dynamic simulation method we investigated the detailed conformational properties of the single-stranded curdlan with 12 glucose units. The results showed that the right-handed 6/1 helix structure was thermodynamically the most stable conformation in solution. The formation of the helix conformation was determined by many factors such as the glycosidic linkage, explicit water solvation and hydrogen bonds. When temperature was increased, the representative helix conformation was found becoming unstable giving rise to metastable conformations because when water mobility was accelerated with temperature, the hydrogen bonding strength between the curdlan chain and water went down, breaking the continuity of the hydrogen bonding network of water and hydroxyl groups. When the number of repeating glucose units varied from 6 to 24, the major helix conformation remained, but the conformational properties of longer chains were more apparently aff ;ected by chain flexibility.

Theoretical insights on helix repacking as the origin of P-glycoprotein promiscuity

P-glycoprotein (P-gp, ABCB1) overexpression is, currently, one of the most important multidrug resistance (MDR) mechanisms in tumor cells. Thus, modulating drug efflux by P-gp has become one of the most promising approaches to overcome MDR in cancer. Yet, more insights on the molecular basis of drug specificity and efflux-related signal transmission mechanism between the transmembrane domains (TMDs) and the nucleotide binding domains (NBDs) are needed to develop molecules with higher selectivity and efficacy. Starting from a murine P-gp crystallographic structure at the inward-facing conformation (PDB ID: 4Q9H), we evaluated the structural quality of the herein generated human P-gp homology model. This initial human P-gp model, in the presence of the “linker” and inserted in a suitable lipid bilayer, was refined through molecular dynamics simulations and thoroughly validated. The best human P-gp model was further used to study the effect of four single-point mutations located at the TMDs, experimentally related with changes in substrate specificity and drug-stimulated ATPase activity. Remarkably, each P-gp mutation is able to induce transmembrane α-helices (TMHs) repacking, affecting the drug-binding pocket volume and the drug-binding sites properties (e.g. volume, shape and polarity) finally compromising drug binding at the substrate binding sites. Furthermore, intracellular coupling helices (ICH) also play an important role since changes in the TMHs rearrangement are shown to have an impact in residue interactions at the ICH-NBD interfaces, suggesting that identified TMHs repacking affect TMD-NBD contacts and interfere with signal transmission from the TMDs to the NBDs.

Deciphering the Self-Cleavage Reaction Mechanism of Hairpin Ribozyme

Hairpin ribozyme catalyzes the reversible self-cleavage of phosphodiester bonds which plays prominent roles in key biological processes involving RNAs. Despite impressive advances on ribozymatic self-cleavage, critical aspects of its molecular reaction mechanism remain controversially debated. Here, we generate and analyze the multidimensional free energy landscape that underlies the reaction using extensive QM/MM metadynamics simulations to investigate in detail the full self-cleavage mechanism. This allows us to answer several pertinent yet controversial questions concerning activation of the 2'-OH group, the mechanistic role of water molecules present in the active site, and the full reaction pathway including the structures of transition states and intermediates. Importantly, we find that a sufficiently unrestricted reaction subspace must be mapped using accelerated sampling methods in order to compute the underlying free energy landscape. It is shown that lower-dimensional sampling where the bond formation and cleavage steps are coupled does not allow the system to sufficiently explore the landscape. On the basis of a three-dimensional free energy surface spanned by flexible generalized coordinates, we find that 2'-OH is indirectly activated by adjacent G8 nucleobase in conjunction with stabilizing H-bonding involving water. This allows the proton of the 2'-OH group to directly migrate toward the 5'-leaving group via a nonbridging oxygen of the phosphodiester link. At variance with similar enzymatic processes where water wires connected to protonable side chains of the protein matrix act as transient proton shuttles, no such de/reprotonation events of water molecules are found to be involved in this ribozymatic transesterification. Overall, our results support an acid-catalyzed reaction mechanism where A38 nucleobase directly acts as an acid whereas G8, in stark contrast, participates only indirectly via stabilizing the nascent nucleophile for subsequent attack. Moreover, we conclude that self-cleavage of hairpin ribozyme follows an A_N + D_N two-step associative pathway where the rate-determining step is the cleavage of the phosphodiester bond. These results provide a major advancement in our understanding of the unique catalytic mechanism of hairpin ribozyme which will fruitfully impact on the design of synthetic ribozymes.

Insight into structural properties of polyethylene glycol monolaurate in water and alcohols from molecular dynamics studies

By means of molecular dynamics (MD) simulations, we explored the structural properties of polyethylene glycol monolaurate (PEGML) in water and in various aliphatic alcohols (methanol, ethanol, 2-propanol, 2-butanol, tert-butanol, and 1-pentanol). The PEGML and the alcohols were simulated using the optimized potentials for liquid simulations, all-atom (OPLS-AA) force field and water using the extended simple point charge (SPC/E) model. From the isothermal-isobaric (NPT, constant number of particles, constant pressure, and constant temperature) ensemble, we extracted the densities from the simulations and compared them with those from experimental results in order to confirm the validity of the selected force fields. The densities from MD simulations are in good agreement with the experimental values. To gain more insight into the nature of interactions between the PEGML and the solvent molecules, we analyzed the hydrogen-bonds, the electrostatic (Coulomb) interactions, and the van der Waals (Lennard-Jones) interaction energies extracted from MD simulations. The results were further strengthened by computing the solvation free energy by employing the free energy perturbation (FEP) approach. In this method, the free energy difference was computed by using the Bennet Acceptance Ratio (BAR) method. Moreover, the radial distribution functions were analyzed in order to gain more understanding of the solution behavior at the molecular level.

Hydrogen-Bond Free Energy of Local Biological Water

Here, we propose an experimental methodology based on femtosecond-resolved fluorescence spectroscopy to measure the hydrogen (H)-bond free energy of water at protein surfaces under isothermal conditions. A demonstration was conducted by installing a non-canonical isostere of tryptophan (7-azatryptophan) at the surface of a coiled-coil protein to exploit the photoinduced proton transfer of its chromophoric moiety, 7-azaindole. The H-bond free energy of this biological water was evaluated by comparing the rates of proton transfer, sensitive to the hydration environment, at the protein surface and in bulk water, and it was found to be higher than that of bulk water by 0.4 kcal mol^-1 . The free-energy difference is dominated by the entropic cost in the H-bond network among water molecules at the hydrophilic and charged protein surface. Our study opens a door to accessing the energetics and dynamics of local biological water to give insight into its roles in protein structure and function.

Calcium-Lipid Interactions Observed with Isotope-Edited Infrared Spectroscopy

Calcium ions bind to lipid membranes containing anionic lipids; however, characterizing the specific ion-lipid interactions in multicomponent membranes has remained challenging because it requires nonperturbative lipid-specific probes. Here, using a combination of isotope-edited infrared spectroscopy and molecular dynamics simulations, we characterize the effects of a physiologically relevant (2 mM) Ca²⁺ concentration on zwitterionic phosphatidylcholine and anionic phosphatidylserine lipids in mixed lipid membranes. We show that Ca²⁺ alters hydrogen bonding between water and lipid headgroups by forming a coordination complex involving the lipid headgroups and water. These interactions distort interfacial water orientations and prevent hydrogen bonding with lipid ester carbonyls. We demonstrate, experimentally, that these effects are more pronounced for the anionic phosphatidylserine lipids than for zwitterionic phosphatidylcholine lipids in the same membrane.

Capturing Deuteration Effects in a Molecular Mechanics Force Field: Deuterated THF and the THF-Water Miscibility Gap

Deuteration is a common chemical modification used in conjunction with experiments such as neutron scattering, NMR, and Fourier-transform infrared for the study of molecular systems. Under the Born-Oppenheimer (BO) approximation, while the underlying potential energy surface remains unchanged by isotopic substitutions, isotopic substitution still alters intramolecular vibrations, which in turn may alter intermolecular interactions. Molecular mechanics (MM) force fields used in classical molecular dynamics simulations are assumed to represent local approximations of the BO potential energy surfaces, and hence, MD simulations using simple isotopic mass substitutions should capture BO-compatible isotope effects. However, standard MM force-field parameterizations do not directly fit to the local harmonic quantum mechanical (QM) Hessian that describes the BO surface, but rather to QM normal-modes and/or mass-dependent internal-coordinate derived distortion energies. Here, using tetrahydrofuran (THF)-water mixtures as our model system, we show that not only does a simple mass-substitution approach fail to capture an experimentally characterized deuteration effect (the loss of the closed-loop miscibility gap associated with the complete deuteration of THF) but also it is necessary to generate new MM force-field parameters that correctly describe isotopic dependent vibrations to capture the experimental deuteration effect. We show that the origin of this failure is a result of using mass-dependent features to fit the THF MM force field, which unintentionally biases the bonded terms of the force field to represent only the isotopologue used during the original force-field parameterization. In addition, we make use of our isotopologue-corrected force field for D₈THF to examine the molecular origins of the isotope-dependent loss of the THF-water miscibility gap.

Adsorption of impurities in vegetable oil: A molecular modelling study

Here, the adsorption of impurity species from triglyceride solvent representing a model vegetable oil is studied using atomistic molecular dynamics simulations. We compare the adsorption of water, glycerol, oleic acid, monoolein, and two types of phospholipids on model silica adsorbents differing in their OH-group density, i.e. hydrogen bonding ability, quartz and cristobalite. We find that the species containing charged groups, phospholipids DOPC and DOPE, adsorb significantly stronger than the nonionic impurities. Secondary contribution to adsorption arises from hydrogen bonding capability of the impurity species, the silica surface, and also the triglyceride solvent: in general, more hydrogen bonding sites in impurity species leads to enhanced adsorption but hydrogen bonding with solvent competes for the available sites. Interestingly, adsorption is weaker on cristobalite even though it has a higher hydrogen bonding site density than quartz. This is because the hydrogen bonds can saturate each other on the adsorbent. The finding demonstrates that optimal adsorption response is obtained with intermediate adsorbent hydrogen bonding site densities. Additionally, we find that monoolein and oleic acid show a concentration driven adsorption response and reverse micelle like aggregate formation in bulk triglyceride solvent even in the absence of water. The findings offer insight into adsorption phenomena at inorganic adsorbent - apolar solvent interfaces and provide guidelines for enhanced design of adsorbent materials for example for vegetable oil purification.

Aggregation behaviors of thermo-responsive methylcellulose in water: A molecular dynamics simulation study

The aggregation behaviors of methylcellulose (MC) in aqueous solution were investigated using all-atom molecular dynamic simulations (MD). The interactions between MC chains and water molecules at different temperatures were investigated by a series of MD analyses, such as the solvent accessible surface area, number of hydrogen bonds, radial distribution functions and the interaction energies. Constant temperature simulations and heating simulations of MC aqueous solution were carried out in this work. In the simulations at three constant temperatures (25 °C, 50 °C and 75 °C), the aggregation behaviors of MC chains were affected by the temperature. In the heating simulation (25 °C ∼ 75 °C), temperature increases were accompanied by decreases in interactions between MC and water molecules, and by increases in interactions between MC chains, which led to the aggregation of MC chains. The degree of aggregation of MC chains increased with the rise of temperature.

Temperature-dependence of the dielectric relaxation of water using non-polarizable water models

Key physical and chemical properties of aqueous fluids are determined by the structure and dynamics of the hydrogen bond network of water but we lack adequate models for the linkages between hydrogen bonding and aqueous chemistry, particularly in non-ambient conditions or in confinement. Dielectric relaxation spectroscopy (DRS) provides a sensitive approach for probing water dynamics but sound interpretation of DRS data requires molecular simulation and associated computational methods capable of accurately representing aqueous fluids and their frequency dependent, complex permittivity. Here, we test the accuracy of dielectric spectra of bulk liquid water calculated from molecular dynamics simulations using 19 non-polarizable water models at 298 K. In contrast to prior studies, the simulation size, time-step and duration allow calculation of the dielectric function from 107-1012 Hz without assuming an analytical form. The accuracy of the prediction of the low-frequency (static) dielectric constant at room temperature is related to the water molecule dipole moment, specifically models with μ ≥ 2.4 D give ε(0) with a relative error lower than 5%. However, no water model tested can fully reproduce the complex dielectric spectra of water. For a subset of models, calculations of the dielectric response from -5 to 60 °C reproduces the experimental trend in water dynamics with temperature but the characteristic relaxation time is always underestimated. The calculated water dipole relaxation time and hydrogen-bond lifetime are both exponentially decaying functions of temperature, and exhibit a linear correlation very close to equality. The comparison provides new computational support for the concept that the Debye relaxation of liquid water is determined by the dynamics of the hydrogen-bond network, and that both are ensemble properties.

Empirical S=O stretch vibrational frequency map

Dimethyl sulfoxide (DMSO) water mixtures have been widely studied due to their unique concentration-dependent bulk properties. Here, we present an empirical spectroscopic map for the sulfinyl (S=O) stretching mode. The model can be used to interpret infrared (IR) absorption and ultrafast two-dimensional infrared (2D IR) spectra and quantify hydrogen bond populations and lifetimes by directly connecting spectroscopic measurements with structures and dynamics from molecular dynamics simulations. The electrostatic map is directly parameterized against experimental absorption spectra in the S=O stretching region (980-1100 cm^-1) of dilute DMSO in water. A comparison of center peak frequencies shows that the map performs well across the entire DMSO concentration range, accurately reproducing the ∼10 cm^-1 red-shift per hydrogen bond observed in the experiments. We further benchmark the map by comparing experimental and simulated 2D IR spectra generated by direct numerical integration of the Schrödinger equation. We expect that this empirical frequency map will provide a quantitative platform for investigating intermolecular interactions, microscopic heterogeneity, and ultrafast dynamics in complex liquid mixtures containing DMSO.

Rotational and Translational Diffusion of Proteins as a Function of Concentration

Atomistic simulations of three different proteins at different concentrations are performed to obtain insight into protein mobility as a function of protein concentration. We report on simulations of proteins from diluted to the physiological water concentration (about 70% of the mass). First, the viscosity was computed and found to increase by a factor of 7-9 going from pure water to the highest protein concentration, in excellent agreement with in vivo nuclear magnetic resonance results. At a physiological concentration of proteins, the translational diffusion is found to be slowed down to about 30% of the in vitro values. The slow-down of diffusion found here using atomistic models is slightly more than that of a hard sphere model that neglects the electrostatic interactions. Interestingly, rotational diffusion of proteins is slowed down somewhat more (by about 80-95% compared to in vitro values) than translational diffusion, in line with experimental findings and consistent with the increased viscosity. The finding that rotation is retarded more than translation is attributed to solvent-separated clustering. No direct interactions between the proteins are found, and the clustering can likely be attributed to dispersion interactions that are stronger between proteins than between protein and water. Based on these simulations, we can also conclude that the internal dynamics of the proteins in our study are affected only marginally under crowding conditions, and the proteins become somewhat more stable at higher concentrations. Simulations were performed using a force field that was tuned for dealing with crowding conditions by strengthening the protein-water interactions. This force field seems to lead to a reproducible partial unfolding of an α-helix in one of the proteins, an effect that was not observed in the unmodified force field.

Polarization Effects in Simulations of Kaolinite-Water Interfaces

Computational models of clay minerals and their interactions with the surrounding medium are highly valuable to study adsorption processes at an atomistic resolution, which may be relevant in different areas such as chromatography, environmental chemistry, and so forth. In this work, we analyzed the effect of the treatment of long-range interactions on the polarization of kaolinite-water interfacial systems in terms of structural, electric and dynamic properties, and hydrogen bonds. When using conventional three-dimensional (3D) Ewald summation, water molecules were more structured on the alumina interface of the kaolinite compared to simulations, in which the periodicity perpendicular to the plane was effectively removed. By applying an external electric field to the latter simulations, we were able to reproduce results obtained with the 3D Ewald summation. We proved that the induced polarization promotes adsorption processes of polar and charged species from aqueous solutions using a glyphosate molecule (widely used herbicide) as a particular example. The polarization phenomena raised from the simulation setup should be accounted for carefully in simulations of adsorption processes, which involve periodic images of polar interfaces. An inappropriate treatment of long-range electrostatic interactions can easily lead to artifacts and/or erroneous results.

Extending the Detection Limit in Fragment Screening of Proteins Using Reverse Micelle Encapsulation

Detection of very weak (K_d > 10 mM) interactions of proteins with small molecules has been elusive. This is particularly important for fragment-based drug discovery, where it is suspected that the majority of potentially useful fragments will be invisible to current screening methodologies. We describe an NMR approach that permits detection of protein-fragment interactions in the very low affinity range and extends the current detection limit of ∼10 mM up to ∼200 mM and beyond. Reverse micelle encapsulation is leveraged to effectively reach very high fragment and protein concentrations, a principle that is validated by binding model fragments to E. coli dihydrofolate reductase. The method is illustrated by target-detected screening of a small polar fragment library against interleukin-1β, which lacks a known ligand-binding pocket. Evaluation of binding by titration and structural context allows for validation of observed hits using rigorous structural and statistical criteria. The 21 curated hit molecules represent a remarkable hit rate of nearly 10% of the library. Analysis shows that fragment binding involves residues comprising two-thirds of the protein's surface. Current fragment screening methods rely on detection of relatively tight binding to ligand binding pockets. The method presented here illustrates a potential to faithfully discover starting points for development of small molecules that bind to a desired region of the protein, even if the targeted region is defined by a relatively flat surface.

Polyproline chains destabilize the Alzheimer's amyloid-β protofibrils: A molecular dynamics simulation study

Alzheimer's is a fatal neurodegenerative disease for which there is no cure at present. The disease is characterized by the presence of plaques, principally comprising the amyloid-β peptide (viz., β-sheet) in the brains of a patient. In our present work, we study the interaction of these β-sheets with a different number of repeating units of proline (β-sheet breaker) by docking and all atom molecular dynamics simulations. Our results indicate that proline can break the amyloid protofibrils apart, cause them to break their β-sheet structure, and in some cases even induce the formation of 3₁₀ helices, which may be intermediates in the unfolding of these β-sheets. We have also observed that some of the important hydrogen bonds and salt bridges between chains were disrupted by proline and the tight interatomic packing of atoms in the fibrils was made relatively loose. Proline chains had a tendency to make several contacts with charged residues. Proline chains binded well to the fibrils by strong electrostatic interactions while hydrophobic interactions played a less important role. This leads to the conclusion that proline can break the amyloid fibrils apart and can be considered in the design of novel peptide-based drugs to treat Alzheimer's disease and potentially other diseases caused by the misfolding of proteins into β-sheets.

Insight into the antimicrobial mechanism of action of β2,2-amino acid derivatives from molecular dynamics simulation: Dancing the can-can at the membrane surface

The development of antimicrobial agents that target and selectively disrupt biofilms is a pressing issue since, so far, no antibiotics have been developed that achieve this effectively. Previous experimental work has found a promising set of antibacterial peptides: β^2,2-amino acid derivatives, relatively small molecules with common structural elements composed of a polar head group and two non-polar hydrocarbon arms. In order to develop insight into possible mechanisms of action of these novel antibacterial agents, we have performed an in silico investigation of four leading β^2,2-amino acid derivatives, interacting with models of both bacterial (target) and eukaryotic (host) membranes, using molecular dynamics simulation with a model with all-atom resolution. We found an unexpected result that could shed light on the mechanism of action of these antimicrobial agents: the molecules assume a conformation where one of the hydrophobic arms is directed downward into the membrane core while the other is directed upwards, out of the membrane and exposed above the position of the membrane headgroups; we dubbed this conformation the "can-can pose". Intriguingly, the can-can pose was most closely linked to the choice of headgroup. Also, the compound previously found to be most effective against biofilms displayed the strongest extent of this behavior and, additionally, this behavior was more pronounced for this compound in the bacterial than in the eukaryotic membrane. We hypothesize that adopting the can-can pose could possibly disrupt the protective peptidoglycan macronet found on the exterior of the bacterial membrane.

Characterization of hydration water in supercooled water-trehalose solutions: The role of the hydrogen bonds network

The structural and dynamical properties of hydration water in aqueous solutions of trehalose are studied with molecular dynamics simulation. We simulate the systems in the supercooled region to investigate how the interaction with the trehalose molecules modifies the hydrogen bond network, the structural relaxation, and the diffusion properties of hydration water. The analysis is performed by considering the radial distribution functions, the residence time of water molecules in the hydration shell, the two body excess entropy, and the hydrogen bond water-water and water-trehalose correlations of the hydration water. The study of the two body excess entropy shows the presence of a fragile to strong crossover in supercooled hydration water also found in the relaxation time of the water-water hydrogen bond correlation function, and this is in agreement with predictions of the mode coupling theory and of previous studies of the oxygen-oxygen density correlators [A. Iorio et al., J. Mol. Liq. 282, 617 (2019); Sci. China: Phys., Mech. Astron. 62, 107011 (2019)]. The water-trehalose hydrogen bond correlation function instead evidences a strong to strong crossover in the relaxation time, and this crossover is related to a trehalose dynamical transition. This signals the role that the strong interplay between the soluted molecules and the surrounding solvent has in determining the dynamical transition common to both components of the system that happens upon cooling and that is similar to the well known protein dynamical transition. We connect our results with the cryoprotecting role of trehalose molecules.

In Silico Characterization of the Binding Modes of Surfactants with Bovine Serum Albumin

The binding interactions of the surfactants: anionic sodium dodecyl sulphate (SDS), cationic cetyltrimethylammonium bromide (CTAB), non-ionic octyl glucoside (OG), and zwitterionic 3-[Hexadecyl(dimethyl)ammonio]-1-propanesulfonate (HPS), with bovine serum albumin (BSA) were investigated by computer simulation. The results disclosed that the surfactants bound stably between hydrophobic subdomain IIA and IIIA where tryptophan-213 residue, an important intrinsic fluorophore in BSA is housed. The interactions of the surfactants with the BSA were electrostatic and hydrophobic interactions. The head-groups of SDS, HPS and OG formed hydrogen bonds with the BSA, while that of CTAB was shielded from intermolecular hydrogen-bonding due to intervening methyl groups. Subsequently, molecular dynamics (MD) simulation of the protein-surfactant complexes revealed that hydrogen bonds formed by OG were stronger than those of SDS and HPS. However, the decomposed force-field energies showed that OG had the least interaction energy with the BSA. In addition to MD simulation, it was found by density functional theory (DFT) that the differences in the coulomb interaction energies can be attributed to charge distribution in the surfactants. Overall, free energies calculated by linear interaction energy (LIE) proved that the binding of each surfactant was dominated by differences between van der Waals interactions in bound and free states.

Dynamical aspects of supercooled TIP3P-water in the grooves of DNA

We investigate by molecular dynamics simulations the mobility of the water located at the DNA minor and major grooves. We employ the TIP3P water model, and our system is analyzed for a range of temperatures 190-300 K. For high temperatures, the water at the grooves shows an Arrhenius behavior similar to that observed in the bulk water. At lower temperatures, a departure from the bulk behavior is observed. This slowing down in the dynamics is compared with the dynamics of the hydrogen of the DNA at the grooves and with the autocorrelation functions of the water hydrogen bonds. Our results indicate that the hydrogen bonds of the water at the minor grooves are highly correlated, which suggests that this is the mechanism for the slow dynamics at this high confinement.

Erodibility assessment of compacted biochar amended soil for geo-environmental applications

Biochar amended soil (BAS) has been explored as a cover material for geo-environmental applications such as landfill cover due to its vegetation potential. Soil erosion in these infrastructures can progressively lead to failure and hamper the workability of the system. BAS is compacted for geo-environmental applications, unlike agricultural soil, which are loose in nature. Furthermore, the love-hate relationship of biochar with water can potentially affect the functioning of compacted cover system. Thus, the performance of compacted BAS in the context of erosion potential is not well understood. The major objective of this technical note was to explore the erosion potential of compacted BAS sourced from four distinct biochars. Biochar were produced in-house and mixed with soil at 5% and 10% by weight. In total, 81 pinhole erosion tests were performed to gauge the erosion rate of bare soil and BAS at three different compaction states at same compaction energy. It was revealed that the erosion rate decreased with gradual increment in water content for BAS, which was mainly attributed to the change of particle orientation from flocculated to dispersed along the compaction curve. Addition of biochar to soil resulted in decrease of erosion along the dry state whereas the opposite was observed for wet state. This was attributed to the surface functional groups as well as particle gradation of biochar. Erodibility coefficient and critical shear stress plot of soil and BAS revealed that addition of biochar had minimal effect on erosion of compacted silty sand.

Aqueous Mixtures of Urea and Trimethylamine-N-oxide: Evidence for Kosmotropic or Chaotropic Behavior?

Trimethylamine-N-oxide (TMAO) and urea are commonly produced in many extremophilic microorganisms that live in harsh environments. In view of high temperature, high pressure, or high salt content, TMAO is known as a protein structure stabilizer, whereas urea destabilizes protein structures even under ambient conditions. Despite clear evidence, destabilizers are often regarded as chaotropes, meaning water-structure breakers, whereas kosmotropes as water-structure makers are classified as stabilizers. Using atomistic molecular dynamics simulations, we study aqueous mixtures of TMAO and urea in various biologically relevant concentrations to gain insight into the molecular details of their mutual cross-interactions and their influence on water dynamics and structure. Our results for binary and ternary solutions in combination with different mixing ratios show that both co-solutes strengthen the water network in terms of dynamic and structural aspects. Slight differences in the water binding behavior between both species result in only negligible compensation effects. The outcomes of our simulations thus question the validity and the ill-considered use of attributes like kosmotropic or chaotropic substances for stabilizers and destabilizers.