Thermodynamics of Hydrogen Bonding in Hydrophilic and Hydrophobic Media

Assessing gastric toxicity of xanthone derivatives of anti-inflammatory activity using simulation and experimental approaches

Xanthones are tricyclic compounds of natural or synthetic origin exhibiting a broad spectrum of therapeutic activities. Three synthetic xanthone derivatives (KS1, KS2, and KS3) with properties typical for nonsteroidal anti-inflammatory drugs (NSAID) were objects of the presented model study. NSAIDs are in common use however; several of them exhibit gastric toxicity predominantly resulting from their direct interactions with the outermost lipid layer of the gastric mucosa that impair its hydrophobic barrier property. Among the studied xanthones, gastric toxicity of only KS2 has been determined in previous pharmacological studies, and it is low. In this study, carried out using X-ray diffraction and computer simulation, a palmitoyloleoylphosphatidylcholine-cholesterol bilayer (POPC-Chol) was used as a model of a hydrophobic layer of lipids protecting gastric mucosa as POPC and Chol are the main lipids in human mucus. X-ray diffraction data were used to validate the computer model. The aim of the study was to assess potential gastric toxicity of the xanthones by analysing their atomic level interactions with lipids, ions, and water in the lipid bilayer and their effect on the bilayer physicochemical properties. The results show that xanthones have small effect on the bilayer properties except for its rigidity whereas their interactions with water, ions, and lipids depend on their protonation state and for a given state, are similar for all the xanthones. As gastric toxicity of KS2 is low, based on MD simulations one can predict that toxicity of KS1 and KS3 is also low.

Effect of salt valency and concentration on structure and thermodynamic behavior of anionic polyelectrolyte Na+-polyethacrylate aqueous solution

The intermolecular structure and solvation enthalpy of anionic polyelectrolyte atactic Na⁺-polyethacrylate (PEA) in aqueous solution, as a function of added salt concentration C _s (dilute to concentrated) and valency (NaCl versus CaCl₂), were investigated via molecular dynamics simulations with explicit-ion-solvent and atomistic polymer description. An increase in C _s leads to a decrease in α, which stabilizes to a constant value beyond critical C _s. A significant reduction in R _g in the presence of CaCl₂ salt was observed, due to ion bridging of PEA by Ca²⁺ ions, in agreement with results available in literature on other similar polycarboxylates. An increase in salt valency reduces the value of critical C _s for the onset of stabilization of the overall size and shape of the polymer chain. The critical C _s ratio for the divalent to monovalent salt case is in excellent agreement with results of Langevin dynamics studies on model systems available in the literature. PEA-water H-bond half-life increases with C _s for CaCl₂, but no appreciable effect is seen for NaCl. The hydration of PEA becomes stronger in the presence of divalent salt. The strength of H-bond interaction energy is greater for cations as compared to anions of the salt. The salt cation effect in displacing water molecules from the vicinity of PEA, with increase in C _s, is greater for NaCl solution. The decrease in water coordination to PEA carboxylate groups, due to increased C _s, is more pronounced in NaCl solution. The nature of the behavior of the solvation enthalpy of PEA and the type of intermolecular interactions contributing to it, is in agreement with experimental observations from the literature. The hydration enthalpy of PEA in divalent CaCl₂ aqueous salt solution is more exothermic compared to monovalent NaCl salt solution, in agreement with experimental data. The solvation of PEA is thermodynamically more favorable in the case of CaCl₂ solution. The exothermic solvation enthalpy, H-bond lifetime, number of H-bonds and H-bond interaction energy are greater in magnitude in CaCl₂ aqueous solution.

Stoichiometric and Non-Stoichiometric Hydrates of Brucine

The complex interplay of temperature and water activity (a_w) / relative humidity (RH) on the solid form stability and transformation pathways of three hydrates (HyA, HyB and HyC), an isostructural dehydrate (HyA_dehy ), an anhydrate (AH) and amorphous brucine has been elucidated and the transformation enthalpies quantified. The dihydrate (HyA) shows a non-stoichimetric (de)hydration behavior at RH < 40% at 25 °C and the removal of the water molecules results in an isomorphic dehydrate structure. The metastable dehydration product converts to AH upon storage at driest conditions or to HyA if exposed to moisture. HyB is a stoichiometric tetrahydrate. The loss of the water molecules causes HyB to collapse to an amorphous phase. Amorphous brucine transforms to AH at RH < 40% RH and a mixture of hydrated phases at higher RH values. The third hyrdate (HyC) is only stable at RH ≥ 55% at 25 °C and contains 3.65 to 3.85 mole equivalent of water. Dehydration of HyC occurs in one step at RH < 55% at 25 °C or upon heating and AH is obtained. The AH is the thermodynamically most stable phase of brucine at RH < 40% at 25 °C. Depending on the conditions, temperature and a_w, each of the three hydrates becomes the thermodynamically most stable form. This study demonstrates the importance of applying complimentary analytical techniques and appropriate approaches for understanding the stability ranges and transition behavior between the solid forms of compounds with multiple hydrates.

Computational investigation of cold denaturation in the Trp-cage miniprotein

The functional native states of globular proteins become unstable at low temperatures, resulting in cold unfolding and impairment of normal biological function. Fundamental understanding of this phenomenon is essential to rationalizing the evolution of freeze-tolerant organisms and developing improved strategies for long-term preservation of biological materials. We present fully atomistic simulations of cold denaturation of an α-helical protein, the widely studied Trp-cage miniprotein. In contrast to the significant destabilization of the folded structure at high temperatures, Trp-cage cold denatures at 210 K into a compact, partially folded state; major elements of the secondary structure, including the α-helix, are conserved, but the salt bridge between aspartic acid and arginine is lost. The stability of Trp-cage's α-helix at low temperatures suggests a possible evolutionary explanation for the prevalence of such structures in antifreeze peptides produced by cold-weather species, such as Arctic char. Although the 310-helix is observed at cold conditions, its position is shifted toward Trp-cage's C-terminus. This shift is accompanied by intrusion of water into Trp-cage's interior and the hydration of buried hydrophobic residues. However, our calculations also show that the dominant contribution to the favorable energetics of low-temperature unfolding of Trp-cage comes from the hydration of hydrophilic residues.

Spontaneous Insertion, Helix Formation, and Hydration of Polyethylene Oxide in Carbon Nanotubes

Hydration strongly affects macromolecular conformation in solution and under nanoconfinement as encountered in nature and nanomaterials. Using atomistic molecular dynamics simulations we demonstrate that polyethylene oxide spontaneously enters single wall carbon nanotubes (CNTs) from aqueous solutions and forms rodlike, helix, and wrapped chain conformations depending on the CNT diameter. We show that water organization and the stability of the polyethylene oxide hydration shell under confinement is responsible for the helix formation, which can have significant implications for nanomaterial design.

How van der Waals interactions determine the unique properties of water

Whereas the interactions between water molecules are dominated by strongly directional hydrogen bonds (HBs), it was recently proposed that relatively weak, isotropic van der Waals (vdW) forces are essential for understanding the properties of liquid water and ice. This insight was derived from ab initio computer simulations, which provide an unbiased description of water at the atomic level and yield information on the underlying molecular forces. However, the high computational cost of such simulations prevents the systematic investigation of the influence of vdW forces on the thermodynamic anomalies of water. Here, we develop efficient ab initio-quality neural network potentials and use them to demonstrate that vdW interactions are crucial for the formation of water's density maximum and its negative volume of melting. Both phenomena can be explained by the flexibility of the HB network, which is the result of a delicate balance of weak vdW forces, causing, e.g., a pronounced expansion of the second solvation shell upon cooling that induces the density maximum.

Water Determines the Structure and Dynamics of Proteins

Water is an essential participant in the stability, structure, dynamics, and function of proteins and other biomolecules. Thermodynamically, changes in the aqueous environment affect the stability of biomolecules. Structurally, water participates chemically in the catalytic function of proteins and nucleic acids and physically in the collapse of the protein chain during folding through hydrophobic collapse and mediates binding through the hydrogen bond in complex formation. Water is a partner that slaves the dynamics of proteins, and water interaction with proteins affect their dynamics. Here we provide a review of the experimental and computational advances over the past decade in understanding the role of water in the dynamics, structure, and function of proteins. We focus on the combination of X-ray and neutron crystallography, NMR, terahertz spectroscopy, mass spectroscopy, thermodynamics, and computer simulations to reveal how water assist proteins in their function. The recent advances in computer simulations and the enhanced sensitivity of experimental tools promise major advances in the understanding of protein dynamics, and water surely will be a protagonist.

Insights into Medium-chain Acyl-CoA Dehydrogenase Structure by Molecular Dynamics Simulations

The medium-chain acyl-CoA dehydrogenase (MCAD) is a mitochondrial enzyme that catalyzes the first step of mitochondrial fatty acid β-oxidation (mFAO) pathway. Its deficiency is the most common genetic disorder of mFAO. Many of the MCAD disease-causing variants, including the most common p.K304E variant, show loss of function due to protein misfolding. Herein, we used molecular dynamics simulations to provide insights into the structural stability and dynamic behavior of MCAD wild-type (MCADwt) and validate a structure that would allow reliable new studies on its variants. Our results revealed that in both proteins the flavin adenine dinucleotide (FAD) has an important structural role on the tetramer stability and also in maintaining the volume of the enzyme catalytic pockets. We confirmed that the presence of substrate changes the dynamics of the catalytic pockets and increases FAD affinity. A comparison between the porcine MCADwt (pMCADwt) and human MCADwt (hMCADwt) structures revealed that both proteins are essentially similar and that the reversion of the double mutant E376G/T255E of hMCAD enzyme does not affect the structure of the protein neither its behavior in simulation. Our validated hMCADwt structure is crucial for complementing and accelerating the experimental studies aiming for the discovery and development of potential stabilizers of MCAD variants as candidates for the treatment of MCAD deficiency (MCADD).

Influence of the R823W mutation on the interaction of the ANKS6-ANKS3: insights from molecular dynamics simulation and free energy analysis

The sterile alpha motif (SAM) domain of the protein ANKS6, a protein-protein interaction domain, is responsible for autosomal dominant polycystic kidney disease. Although the disease is the result of the R823W point mutation in the SAM domain of the protein ANKS6, the molecular details are still unclear. We applied molecular dynamics simulations, the principal component analysis, and the molecular mechanics Poisson-Boltzmann surface area binding free energy calculation to explore the structural and dynamic effects of the R823W point mutation on the complex ANKS6-ANKS3 (PDB ID: 4NL9) in comparison to the wild proteins. The energetic analysis presents that the wild type has a more stable structure than the mutant. The R823W point mutation not only disrupts the structure of the ANKS6 SAM domain but also negatively affects the interaction of the ANKS6-ANKS3. These results further clarify the previous experiments to understand the ANKS6-ANKS3 interaction comprehensively. In summary, this study would provide useful suggestions to understand the interaction of these proteins and their fatal action on mediating kidney function.

Concentration dependent effects of urea binding to poly(N-isopropylacrylamide) brushes: a combined experimental and numerical study

The concentration-dependent binding of urea to PNIPAM influences the chain conformation as a result of the subtle interplay between hydration properties and urea repartition around the polymer surface.

Confinement and surface effects of aqueous solutions within charged carbon nanotubes

Size-charge effects of brines in charged nanotubes from a molecular dynamics investigation of ion hydration, water coordination, and hydrogen bonding.

Polyelectrolyte conformational transition in aqueous solvent mixture influenced by hydrophobic interactions and hydrogen bonding effects: PAA-water-ethanol

Molecular dynamics simulations of poly(acrylic acid) PAA chain in water-ethanol mixture were performed for un-ionized and ionized cases at different degree-of-ionization 0%, 80% and 100% of PAA chain by Na(+) counter-ions and co-solvent (ethanol) concentration in the range 0-90vol% ethanol. Aspects of structure and dynamics were investigated via atom pair correlation functions, number and relaxation of hydrogen bonds, nearest-neighbor coordination numbers, and dihedral angle distribution function for back-bone and side-groups of the chain. With increase in ethanol concentration, chain swelling is observed for un-ionized chain (f=0) and on the contrary chain shrinkage is observed for partially and fully ionized cases (i.e., f=0.8 and 1). For un-ionized PAA, with increase in ethanol fraction ϕeth the number of PAA-ethanol hydrogen bonds increases while PAA-water decreases. Increase in ϕeth leads to PAA chain expansion for un-ionized case and chain shrinkage for ionized case, in agreement with experimental observations on this system. For ionized-PAA case, chain shrinkage is found to be influenced by intermolecular hydrogen bonding with water as well as ethanol. The localization of ethanol molecules near the un-ionized PAA backbone at higher levels of ethanol is facilitated by a displacement of water molecules indicating presence of specific ethanol hydration shell, as confirmed by results of the RDF curves and coordination number calculations. This behavior, controlled by hydrogen bonding provides a significant contribution to such a conformational transition behavior of the polyelectrolyte chain. The interactions between counter-ions and charges on the PAA chain also influence chain collapse. The underlying origins of polyelectrolyte chain collapse in water-alcohol mixtures are brought out for the first time via explicit MD simulations by this study.

Influence of the Compatible Solute Ectoine on the Local Water Structure: Implications for the Binding of the Protein G5P to DNA

Microorganisms accumulate molar concentrations of compatible solutes like ectoine to prevent proteins from denaturation. Direct structural or spectroscopic information on the mechanism and about the hydration shell around ectoine are scarce. We combined surface plasmon resonance (SPR), confocal Raman spectroscopy, molecular dynamics simulations, and density functional theory (DFT) calculations to study the local hydration shell around ectoine and its influence on the binding of a gene-5-protein (G5P) to a single-stranded DNA (dT25). Due to the very high hygroscopicity of ectoine, it was possible to analyze the highly stable hydration shell by confocal Raman spectroscopy. Corresponding molecular dynamics simulation results revealed a significant change of the water dielectric constant in the presence of a high molar ectoine concentration as compared to pure water. The SPR data showed that the amount of protein bound to DNA decreases in the presence of ectoine, and hence, the protein-DNA dissociation constant increases in a concentration-dependent manner. Concomitantly, the Raman spectra in terms of the amide I region revealed large changes in the protein secondary structure. Our results indicate that ectoine strongly affects the molecular recognition between the protein and the oligonucleotide, which has important consequences for osmotic regulation mechanisms.

Segmented molecular design of self-healing proteinaceous materials

Hierarchical assembly of self-healing adhesive proteins creates strong and robust structural and interfacial materials, but understanding of the molecular design and structure–property relationships of structural proteins remains unclear. Elucidating this relationship would allow rational design of next generation genetically engineered self-healing structural proteins. Here we report a general self-healing and -assembly strategy based on a multiphase recombinant protein based material. Segmented structure of the protein shows soft glycine- and tyrosine-rich segments with self-healing capability and hard beta-sheet segments. The soft segments are strongly plasticized by water, lowering the self-healing temperature close to body temperature. The hard segments self-assemble into nanoconfined domains to reinforce the material. The healing strength scales sublinearly with contact time, which associates with diffusion and wetting of autohesion. The finding suggests that recombinant structural proteins from heterologous expression have potential as strong and repairable engineering materials.

Anomalous surface diffusion of protons on lipid membranes

The cellular energy machinery depends on the presence and properties of protons at or in the vicinity of lipid membranes. To asses the energetics and mobility of a proton near a membrane, we simulated an excess proton near a solvated DMPC bilayer at 323 K, using a recently developed method to include the Grotthuss proton shuttling mechanism in classical molecular dynamics simulations. We obtained a proton surface affinity of -13.0 ± 0.5 kJ mol(-1). The proton interacted strongly with both lipid headgroup and linker carbonyl oxygens. Furthermore, the surface diffusion of the proton was anomalous, with a subdiffusive regime over the first few nanoseconds, followed by a superdiffusive regime. The time- and distance dependence of the proton surface diffusion coefficient within these regimes may also resolve discrepancies between previously reported diffusion coefficients. Our simulations show that the proton anomalous surface diffusion originates from restricted diffusion in two different surface-bound states, interrupted by the occasional bulk-mediated long-range surface diffusion. Although only a DMPC membrane was considered in this work, we speculate that the restrictive character of the on-surface diffusion is highly sensitive to the specific membrane conditions, which can alter the relative contributions of the surface and bulk pathways to the overall diffusion process. Finally, we discuss the implications of our findings for the energy machinery.

Do adsorbed drugs onto P-glycoprotein influence its efflux capability?

The membrane biophysical aspects by which multidrug resistance (MDR) relate to the ABC transporter function still remain largely unknown. Notwithstanding the central role that efflux pumps like P-glycoprotein have in MDR onset, experimental studies classified additionally the lipid micro-environment where P-gp is inserted as a determinant for the increased efflux capability demonstrated in MDR cell lines. Recently, a nonlinear model for drug-membrane interactions showed that, upon drug adsorption, long-range mechanical alterations are predicted to affect the P-gp ATPase function at external drug concentrations of ∼10-100 μM. However, our results also show that drug adsorption may also occur at P-gp nucleotide-binding domains where conformational changes drive the efflux cycle. Thus, we assessed the effect of drug adsorption to both protein-water and lipid-water interfaces by means of molecular dynamics simulations. The results show that free energies of adsorption are lower for modulators in both lipid/water and protein/water interfaces. Important differences in drug-protein interactions, protein dynamics and membrane biophysical characteristics were observed between the different classes. Therefore, we hypothesize that drug adsorption to the protein and lipid-water interface accounts for a complex network of events that affect the ability of transporters to efflux drugs.

The love-hate relationship of pyrolysis biochar and water: a perspective

Biochar is being considered for environmental sustainability by the scientific community and as a result is extensively investigated for various applications in agriculture, remediation and construction. Hence, a sound knowledge of biochar's physical and chemical properties is critical. However, the dynamics of biochar-water interaction remain ambiguous. We hypothesize that the hydrophobicity of a biochar made at low pyrolysis temperature is not permanent under water-rich conditions. Our results suggest that the aliphatic functional groups responsible for biochar's hydrophobicity are displaced when subjected to water which eventually increases the affinity of the biochar towards water. We envisage that commentary would stimulate researchers to investigate the biochar-water interaction in a new light and eventually help design a biochar which would be apt for their intended end use.

Surface behavior of amphiphiles in aqueous solution: a comparison between different pentanol isomers

Molecular-level understanding of concentration-dependent changes in the surface structure of different amphiphilic isomers at the water–vapor interface was gained by molecular dynamics (MD) simulation and X-ray photoelectron spectroscopy (XPS).

Simultaneous solvent screening and reaction optimization in microliter slugs

An automated microfluidic system rapidly discovers optimal and scalable reaction conditions for alkylation while teasing-out integrated discrete and continuous variable relationships.

Solvent effects of 1-ethyl-3-methylimidazolium acetate: solvation and dynamic behavior of polar and apolar solutes

We study the solvation properties of the ionic liquid 1-ethyl-3-methylimidazolium acetate ([eMIM]⁺[ACE]⁻) and the resulting dynamic behavior for differently charged model solutes at room temperature via atomistic molecular dynamics (MD) simulations of 500 ns length.

Why genetic modification of lignin leads to low-recalcitrance biomass

Molecular dynamics simulations show genetically modified lignin to associate less with hemicellulose than does wild type.

Temperature dependence of internal motions of protein side-chain NH3(+) groups: insight into energy barriers for transient breakage of hydrogen bonds

Although charged side chains play important roles in protein function, their dynamic properties are not well understood. Nuclear magnetic resonance methods for investigating the dynamics of lysine side-chain NH3(+) groups were established recently. Using this methodology, we have studied the temperature dependence of the internal motions of the lysine side-chain NH3(+) groups that form ion pairs with DNA phosphate groups in the HoxD9 homeodomain-DNA complex. For these NH3(+) groups, we determined order parameters and correlation times for bond rotations and reorientations at 15, 22, 28, and 35 °C. The order parameters were found to be virtually constant in this temperature range. In contrast, the bond-rotation correlation times of the NH3(+) groups were found to depend strongly on temperature. On the basis of transition state theory, the energy barriers for NH3(+) rotations were analyzed and compared to those for CH3 rotations. Enthalpies of activation for NH3(+) rotations were found to be significantly higher than those for CH3 rotations, which can be attributed to the requirement of hydrogen bond breakage. However, entropies of activation substantially reduce the overall free energies of activation for NH3(+) rotations to a level comparable to those for CH3 rotations. This entropic reduction in energy barriers may accelerate molecular processes requiring hydrogen bond breakage and play a kinetically important role in protein function.