Structure Of Water Molecules Research Articles

A Protein Data Bank survey of multimodal binding of thiocyanate to proteins: Evidence for thiocyanate promiscuity

Over the last one and half century, a myriad of studies has demonstrated that Hofmeister ions have a major impact on protein stability and solubility. Nevertheless, the definition of the physico-chemical basis of their activity has proved to be highly challenging and controversial. Here, by exploiting the enormous information content of the Protein Data Bank, we explored the binding to proteins of thiocyanate, the anion of the series exerting the highest solubilization/destabilization effects. The survey, which led to the identification and characterization of 712 thiocyanate binding sites, provides a comprehensive and atomic-level view of the varied interactions that the ion forms with proteins. The inspection of these sites highlights a limited tendency of thiocyanate to interact with structured water molecules, in line with the reported poor hydration of the ion. On the other hand, the thiocyanate makes interactions with protein nonpolar moieties, especially with the backbone Cα atom. In as many as 104 cases, the ion exclusively makes nonpolar contacts. In conclusion, these findings suggest that the ability of thiocyanate to bind all types of protein exposed patches may lead to the formation of a negatively charged electrostatic barrier that could prevent protein-protein aggregation and promote protein solubility. Moreover, the denaturing action of thiocyanate may be ascribed to its ability to establish multiple attractive interactions with protein surfaces.

High-resolution structure of phosphoketolase from Bifidobacterium longum determined by cryo-EM single-particle analysis

In bifidobacteria, phosphoketolase (PKT) plays a key role in the central hexose fermentation pathway called “bifid shunt.” The three-dimensional structure of PKT from Bifidobacterium longum with co-enzyme thiamine diphosphate (ThDpp) was determined at 2.1 Å resolution by cryo-EM single-particle analysis using 196,147 particles to build up the structural model of a PKT octamer related by D4 symmetry. Although the cryo-EM structure of PKT was almost identical to the X-ray crystal structure previously determined at 2.2 Å resolution, several interesting structural features were observed in the cryo-EM structure. Because this structure was solved at relatively high resolution, it was observed that several amino acid residues adopt multiple conformations. Among them, Q546–D547–H548–N549 (the QN-loop) demonstrate the largest structural change, which seems to be related to the enzymatic function of PKT. The QN-loop is at the entrance to the substrate binding pocket. The minor conformer of the QN-loop is similar to the conformation of the QN-loop in the crystal structure. The major conformer is located further from ThDpp than the minor conformer. Interestingly, the major conformer in the cryo-EM structure of PKT resembles the corresponding loop structure of substrate-bound Escherichia coli transketolase. That is, the minor and major conformers may correspond to “closed” and “open” states for substrate access, respectively. Moreover, because of the high-resolution analysis, many water molecules were observed in the cryo-EM structure of PKT. Structural features of the water molecules in the cryo-EM structure are discussed and compared with water molecules observed in the crystal structure.

How osmotic stress and crowding affect G-protein-coupled receptor activation

G-protein-coupled receptors (GPCRs) are integral membrane proteins responsible for signal transduction across cellular membranes and constitute the largest class of medicinal targets. Although three-dimensional structures show the presence of structural water molecules within GPCRs, functional role of these water molecules has remained unknown. Our previous work has further shown a bulk influx of water stabilizing the active rhodopsin conformation [1]. Here we broadened the experimental approach to investigate how the conformational energetics of GPCR activation are modulated by water using a series of hydrophilic polymers including polyethylene glycols (PEGs), dextrans, polyvinylpyrrolidones, and their monomers.

Insights on the proton translocation pathways in FоF1-ATP synthase using molecular dynamics simulations

Proton translocation through the Fo fraction of FoF1-ATP synthase is one of the crucial processes in the catalytic cycle of the enzyme. However, the exact trace of protons movement has not been finally established yet because the location and structure of the half-channels are still the subject of investigation. We described the possible network of polar amino acids residues and water molecules that can favor the preferential proton pathway using molecular dynamics simulation of the membrane part of the E. coli ATP synthase embedded in the lipid bilayer and water environment. The inlet half-channel was a complex structure with two entrances in the form of aqueous lacunae and a highly conservative proton transfer chain near Asp61 of c-subunit including amino acids residues and three structural water molecules (W1–W3), while the outlet half-channel was just a water cavity through which a proton can easily move into the cytoplasm. Moreover, the side chains of Asn214 and Gln252 of a-subunit had the stable spatial positions (SP1-SP3). аAsn214 in position SP3 and аGln252 in SP1, SP2 were oriented towards cAsp61 and could presumably protonate it via W1. Herewith aAsn214 in SP1, SP2 was oriented to aHis245. Thus, the proton transfer chain is always unclosed, and switching between positions SP1/SP2 and SP3 of aAsn214 determines the time of proton transport and the movement in this region is the rate-limiting step. In addition, we found another rare position SP3, in which aGln252 is oriented to aAsn116 and aSer144, located outside of the "main H+ route" and being a dead end. The new findings would help to evaluate the whole process of the proton translocation through FoF1-ATP synthase.

Unconventional assemblies of bisacylhydrazones: The role of water for circularly polarized luminescence

AbstractUnderstanding the precise molecular arrangement of chiral supramolecular polymers is essential not only to comprehend complex superstructures like proteins and DNA but also for the development of next‐generation optoelectronic materials, including materials displaying high‐performance circularly polarized luminescence (CPL). Herein, we report the first chiral supramolecular polymer systems based on hydrazone–pyridinium conjugates comprising alkyl chains of different lengths, which afforded control of the apparent supramolecular chirality. Although supramolecular chirality is governed basically by the remote chiral centers of alkyl chains, helicity inversion was achieved by controlling the conditions under which the hydrazone building blocks underwent aggregation (i.e., solvent compositions or temperature). More importantly, the addition of water to the system led to aggregation‐induced hydrazone deprotonation, which resulted in a completely different self‐assembly behavior. Structural water molecules played an essential role, forming the assembly's channel‐like backbone, around which hydrazone molecules gathered as a result of hydrogen bonding interactions. Further co‐assembly of an achiral hydrazone luminophore with the given supramolecular polymer system allowed the fabrication of a novel CPL‐active hydrazone‐based material exhibiting a high maximum value for the photoluminescence dissymmetry factor of −2.6 × 10−2.

Evaluation of the experimental and computed properties of choline chloride-water formulated deep eutectic solvents

In this study, experimental and computed IR and Raman spectroscopic techniques helped to prove how water as a sole hydrogen bond donor (HBD) participates to form a deep eutectic solvent. Interactions among the components and contributions of the water and chloride have been successfully illustrated by quantum chemical (QC) and radial distribution function (RDF) calculations. These studies suggested that the spontaneous intercalation of water molecules with choline chloride (ChCl) helps to attain the stable cluster structure, where Cl- works as a bridge among the Ch+ and water molecules. Hydrogen bonds played major roles to form the water-based DESs. Solubilities of the studied drug molecules were found to be 1.3 to 6.7 times higher in the solvents than their solubilities in water. Cell viability assay of the WDES1 (1:3 ChCl:H2O) compared to dimethyl sulfoxide (DMSO) against HEK293 cell line proved that the solvent is applicable to the biological system. The RDF analysis from MD simulation suggest the spontaneous intercalation of water molecule in Choline Chloride structure disrupted the ordered structure as well as the Cl-, working as bridge in between Ch+ and water.

Enhanced electrochromism from non-stoichiometric electrodeposited tungsten oxide thin films

Nanocrystalline structure tungsten oxide (nc-WO3; WO3·2H2O) thin films were deposited on fluorine-doped tin oxide (FTO) substrates via a facile electrochemical deposition (ECD) method. The X-ray diffraction (XRD), Fourier Transform Infrared (FT-IR) spectrum, and scanning electron microscope (SEM) results confirmed the gradual temperature dependent structural transitions from nanocrystalline tungsten oxide (nc-WO3) to amorphous tungsten oxide (a-WO3) at 200 °C. Electrochromic (EC) performances of the films were examined in an aqueous solution of 0.5 M H2SO4 by cyclic voltammetry tests integrated in-situ transmittance measurements. The results showed that the EC properties of WO3 films were closely correlated to its structural arrangements of –OH groups and the structural water molecules present in the WO3 matrix. A fast-switching speed (5 s for coloration and 3 s for bleaching), a significant optical modulation (above 89 % at 632 nm), a high coloration efficiency of 51.1 cm2/C and cycling stability of more than 1000 cycles were achieved for nc-WO3 film. Additionally, an EC device was successfully assembled using NiO film prepared by chemical bath deposition as a complementary electrode and exhibited fascinating performance.

A dual conducting network corbelled hydrated vanadium pentoxide cathode for high-rate aqueous zinc-ion batteries.

Aqueous zinc-ion batteries (ZIBs) are widely recognized for their excellent safety and high theoretical capacity but are hindered by the scarcity of cathode materials with high-rate performance and stability. Herein, a dual conducting network corbelled hydrated vanadium pentoxide that involves structural water as a pillar to enlarge the layer spacing of vanadium pentoxide and ensure cycling stability was reported. Along with the proton co-insertion, the hydrated vanadium pentoxide delivers nearly theoretical specific capacities of 524.6 mA h g-1 at 0.3 A g-1 and 258.7 mA h g-1 at 10 A g-1, which was largely due to non-faradaic contribution, and retains 196.8 mA h g-1 at 4.8 A g-1 after 1100 cycles. Notably, a high energy density of 409.3 W h kg-1 at 0.3 A g-1 and a power density of 6666.4 W kg-1 at 10 A g-1 have also been achieved. The design strategy offers a potential path to develop high-rate ZIBs.

Dynamic Pt-OH-·H2O-Ag species mediate coupled electron and proton transfer for catalytic hydride reduction of 4-nitrophenol at the confined nanoscale interface.

Generally, the catalytic transformation of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP) at heterogeneous metal surfaces follows a Langmuir-Hinshelwood (L-H) mechanism when sodium borohydride (NaBH4) is used as the sacrificial reductant. Herein, with Pt-Ag bimetallic nanoparticles confined in dendritic mesoporous silica nanospheres (DMSNs) as a model catalyst, we demonstrated that the conversion of 4-NP did not pass through the direct hydrogen transfer route with the hydride equivalents being supplied by borohydride via the bimolecular L-H mechanism, since Fourier transform infrared (FTIR) spectroscopy with the use of isotopically labeled reactants (NaBD4 and D2O) showed that the final product of 4-AP was composed of protons (or deuterons) that originated from the solvent water (or heavy water). Combined characterization by X-ray photoelectron spectroscopy (XPS), 1H nuclear magnetic resonance (NMR) and the optical excitation and photoluminescence spectrum evidenced that the surface hydrous hydroxide complex bound to the metal surface (also called structural water molecules, SWs), due to the space overlap of p orbitals of two O atoms in SWs, could form an ensemble of dynamic interface transient states, which provided the alternative electron and proton transfer channels for selective transformation of 4-NP. The cationic Pt species in the Ag-Pt bimetallic catalyst mainly acts as a dynamic adsorption center to temporally anchor SWs and related reactants, and not as the active site for hydrogen activation.

Influences of micropores and water molecules in the palygorskite structure on the color and stability of Maya blue pigment

Maya blue is an ancient hybrid pigment composed of indigo and microporous palygorskite, with a fantastic hue and outstanding stability. Its color-causing and stabilization mechanism are unsolved problems. In this work, different palygorskite materials were obtained by heating at 180, 300 and 570 °C, with raw palygorskite as a reference. Maya blue-like pigments were prepared from these palygorskite materials and solid indigo. The microporous structure of palygorskite and the status of inside water molecules were investigated by thermal analysis, X-ray diffraction, Fourier transform infrared and microporous analysis. The color properties, chemical resistance and photostability of pigments were characterized by reflectance spectra, CIE color parameters and color differences after the attack of concentrated nitric acid, dimethyl sulfoxide, and visible light exposure equaling to about 100 years. It was confirmed that the greenish-blue and stable hybrid pigment could only be prepared when indigo molecules were inserted into the micropores of palygorskite. Zeolitic water molecules inside the micropores should be removed because they hindered the insertion of indigo molecules. The key to immobilizing indigo molecules inside micropores was hydrogen bonds between indigo and coordinated water (CO … …H–OH). This study emphasized the important role of micropores and hydrogen bonds in the synthesis of organic-inorganic hybrid pigments.

Diffusion characteristics of water molecules in a lamellar structure formed by triblock copolymers

The distribution and diffusion of water molecules are playing important roles in determining self-assembly and transport properties of polymeric systems.

Engineering enhanced thermostability into the Geobacillus pallidus nitrile hydratase.

Nitrile hydratases (NHases) are important biocatalysts for the enzymatic conversion of nitriles to industrially-important amides such as acrylamide and nicotinamide. Although thermostability in this enzyme class is generally low, there is not sufficient understanding of its basis for rational enzyme design. The gene expressing the Co-type NHase from the moderate thermophile, Geobacillus pallidus RAPc8 (NRRL B-59396), was subjected to random mutagenesis. Four mutants were selected that were 3 to 15-fold more thermostable than the wild-type NHase, resulting in a 3.4–7.6 ​kJ/mol increase in the activation energy of thermal inactivation at 63 ​°C. High resolution X-ray crystal structures (1.15–1.80 ​Å) were obtained of the wild-type and four mutant enzymes. Mutant 9E, with a resolution of 1.15 ​Å, is the highest resolution crystal structure obtained for a nitrile hydratase to date. Structural comparisons between the wild-type and mutant enzymes illustrated the importance of salt bridges and hydrogen bonds in enhancing NHase thermostability. These additional interactions variously improved thermostability by increased intra- and inter-subunit interactions, preventing cooperative unfolding of α-helices and stabilising loop regions. Some hydrogen bonds were mediated via a water molecule, specifically highlighting the significance of structured water molecules in protein thermostability. Although knowledge of the mutant structures makes it possible to rationalize their behaviour, it would have been challenging to predict in advance that these mutants would be stabilising.

Sensitive Micro-Breathing Sensing and Highly-Effective Photothermal Antibacterial Cinnamomum camphora Bark Micro-Structural Cotton Fabric via Electrostatic Self-Assembly of MXene/HACC.

Natural fabrics are gradually becoming the ideal substrate for flexible smart wearable devices due to their excellent moisture absorption, softness, and skin-friendliness. However, the bonding fastness of the conductive layer and the corresponding durability during service have not yet been well satisfied. In this report, we successfully prepared a smart wearable multifunctional protective cotton fabric with microbreathing monitoring and rapid-photothermal antibacterial abilities of Cinnamomum camphora bark microstructure, by combining chitosan quaternary ammonium salt (HACC) with MXene nanosheets through electrostatic self-assembly. Impressively, MXene nanosheets and HACC established a strong interaction using the electrostatic attraction, endowing the fiber surface with ordered nanosheets. Meanwhile, the fabric decorated with MXene/HACC retains its original characteristics of outstanding breathability and softness, and its conductivity exhibits noticeable stability in terms of resistances to oxidation, washing, various solvents, and long-term bending cycles. On the basis of the principle of adsorption and release of water molecules in the MXene multilayer structures, the MXene/HACC fabric could accurately monitor the physiological health activities of users according to their breathing frequency and depth. Benefiting from the local surface plasmon resonance (LSPR) effect, the MXene/HACC shows encouraging photothermal conversion ability, photothermal stability under long time irradiation, washing resistance, and cycle stability. In addition, the fabric achieved an antibacterial efficiency of nearly 100% against Gram-negative Escherichia coli and Gram-positive Staphylococcus aureus within 5 min under an irradiation intensity of 400 mW/cm2. More importantly, after 10 washes, the antibacterial efficiency against the two bacteria could still reach 99.975% and 99.98%, respectively. This multifunctional protective MXene/HACC cotton fabric is expected to play a unique role in the new generation of smart wearable microbreathing sensing and against to bacterial attack, and shows a broad application prospect.

Structured Waters Mediate Small Molecule Binding to G-Quadruplex Nucleic Acids.

The role of G-quadruplexes in human cancers is increasingly well-defined. Accordingly, G-quadruplexes can be suitable drug targets and many small molecules have been identified to date as G-quadruplex binders, some using computer-based design methods and co-crystal structures. The role of bound water molecules in the crystal structures of G-quadruplex-small molecule complexes has been analyzed in this study, focusing on the water arrangements in several G-quadruplex ligand complexes. One is the complex between the tetrasubstituted naphthalene diimide compound MM41 and a human intramolecular telomeric DNA G-quadruplex, and the others are in substituted acridine bimolecular G-quadruplex complexes. Bridging water molecules form most of the hydrogen-bond contacts between ligands and DNA in the parallel G-quadruplex structures examined here. Clusters of structured water molecules play essential roles in mediating between ligand side chain groups/chromophore core and G-quadruplex. These clusters tend to be conserved between complex and native G-quadruplex structures, suggesting that they more generally serve as platforms for ligand binding, and should be taken into account in docking and in silico studies.

Role of Water in the Lyotropic Liquid Crystalline Mesophase of Lithium Salts and Non-ionic Surfactants.

The lyotropic liquid crystalline (LLC) mesophase forms upon evaporation of water from aqueous solutions of LiX salts (X is Cl-, Br-, NO3-, or SCN-) and a surfactant [C12H25(OCH2CH2)10OH, abbreviated as C12E10]. The LiX/C12E10/H2O aqueous solutions have been monitored (during evaporation of their excess water to obtain stable LLC mesophases) by gravimetric, spectroscopic, and conductivity measurements to elucidate the role of water in these mesophases. The water/salt molar ratio in stable mesophases changes from 1.5 to 8.0, depending on the counteranion of the salt and the ambient humidity of the laboratory. The LiX/C12E10/H2O LLC mesophases lose water at lower humidity levels and absorb water at higher humidity levels. The LiCl-containing mesophase holds as few as four structural water molecules per LiCl, whereas the LiNO3 mesophase holds 1.5 waters per salt (least among those assessed). This ratio strongly depends on the atmospheric humidity level; the water/LiX mole ratio increases by 0.08 ± 0.01 H2O in the LLC mesophases per percent humidity unit. Surprisingly, the LLC mesophases are stable (no salt leaching) in broad humidity (10-85%) and salt/surfactant mole ratio (2-10 LiX/C12E10) ranges. Attenuated total reflectance Fourier transform infrared spectroscopic data show that the water molecules in the mesophase interact with salt species more strongly in the LiCl mesophase and more weakly in the case of the nitrate ion, which is evident by the shift of the O-H stretching band of water. The O-H stretching peak position in the mesophases decreases in the order νLiCl > νLiBr > νLiSCN > νLiNO3 and accords well with the H2O/LiX mole ratio. The conductivity of the LLC mesophase also responds to the amount of water as well as the nature of the counteranion (X-). The conductivity decreases in the order σLiCl > σLiBr > σLiNO3 > σLiSCN at low salt mole ratios and in the order σLiBr > σLiCl > σLiNO3 > σLiSCN at higher ratios due to structural changes in the mesophase.

Graphene wettability control: Texturing of the substrate and removal of airborne contaminants in the atmosphere of various gases

Experimental and theoretical studies on the wettability of graphene coating are carried out. Molecular dynamic modeling is used to structure water molecules on the surface of copper and graphene-copper, as well as to assess wettability. The instability of the properties of graphene coatings over time is one of the reasons that inhibit their widespread use as highly sensitive sensors. The adsorption of water vapor and airborne contaminations on the graphene surface leads to a change in the electrical properties of the coating. The influence of key parameters (copper recrystallization, copper oxidation due to graphene surface defects, wall textures and airborne contaminations) on the wettability of the graphene coating is investigated for the first time. It is shown that the predominant effect on the change in wettability is exerted by hydrocarbon impurities. Molecular dynamic modeling demonstrates that an insignificant local separation of copper, as well as an inhomogeneous graphene coating, increases the angle on the graphene coating from 25 to 30° to 60-65°. To remove the hydrocarbon layer, annealing is carried out in a wide temperature range, as well as in the atmosphere of argon and hydrogen. A comparison of various methods of removing impurities is carried out. After prolonged annealing, the contact angle of the drop decreases from 80 to 90° to 55°.

Pore-Mouth Structure of Highly Agglomerated Detonation Nanodiamonds.

Detonation nanodiamond aggregates contain water that is removed by thermal treatments in vacuo, leaving available pores for the adsorption of target molecules. A hard hydrogel of detonation nanodiamonds was thermally treated at 423 K for 2 h, 10 h, and 52 h in vacuo to determine the intensive water adsorption sites and clarify the hygroscopic nature of nanodiamonds. Nanodiamond aggregates heated for long periods in vacuo agglomerate due to the removal of structural water molecules through the shrinkage and/or collapse of the pores. The agglomerated nanodiamond structure that results from long heating periods decreases the nitrogen adsorption but increases the water adsorption by 40%. Nanodiamonds heated for long times possess ultramicropores <0.4 nm in diameter in which only water molecules can be adsorbed, and the characteristic mouth-shaped mesopores adsorb 60% more water than nitrogen. The pore mouth controls the adsorption in the mesopores. Long-term dehydration partially distorts the pore mouth, decreasing the nitrogen adsorption. Furthermore, the nitrogen adsorbed at the pore mouth suppresses additional nitrogen adsorption. Consequently, the mesopores are not fully accessible to nitrogen molecules because the pore entrances are blocked by polar groups. Thus, mildly oxidized detonation nanodiamond particles can show a unique molecular sieving behavior.

Structural Water Molecules Confined in Soft and Hard Nanocavities as Bright Color Emitters.

Molecules confined in the nanocavity and nanointerface exhibit rich, unique physicochemical properties, e.g., the chromophore in the β-barrel can of green fluorescent protein (GFP) exhibits tunable bright colors. However, the physical origin of their photoluminescence (PL) emission remains elusive. To mimic the microenvironment of the GFP protein scaffold at the molecule level, two groups of nanocavities were created by molecule self-assembly using organic chromophores and by organic functionalization of mesoporous silica, respectively. We provide strong evidence that structural water molecules confined in these nanocavities are color emitters with a universal formula of {X+·(OH-·H2O)·(H2O) n-1}, in which X is hydrated protons (H3O+) or protonated amino (NH3 +) groups as an anchoring point, and that the efficiency of PL is strongly dependent on the stability of the main emitter centers of the structural hydrated hydroxide complex (OH-·H2O), which is a key intermediate to mediate electron transfer dominated by proton transfer at confined nanospace. Further controlled experiments and combined characterizations by time-resolved steady-state and ultrafast transient optical spectroscopy unveil an unusual multichannel radiative and/or nonradiative mechanism dominated by quantum transient states with a distinctive character of topological excitation. The finding of this work underscores the pivotal role of structurally bound H2O in regulating the PL efficiency of aggregation-induced emission luminogens and GFP.

Pore-Bound Water at the Key Residue Histidine 37 in Influenza A M2.

Atomic details of structured water molecules are indispensable to understand the thermodynamics of important biological processes including the proton conduction mechanism of the M2 protein. Despite the expectation of structured water molecules based on crystal structures of Influenza A M2, only two water populations have been observed by NMR in reconstituted lipid bilayer samples. These are the bulk‐ and lipid‐associated water populations typically seen in membrane samples. Here, we detect a bound water molecule at a chemical shift of 11 ppm, located near the functional histidine 37 residue in the M2 conductance domain, which comprises residues 18 to 60. Combining 100 kHz magic‐angle spinning NMR, dynamic nuclear polarization and density functional theory calculations, we show that the bound water forms a hydrogen bond to the δ1 nitrogen of histidine 37.

Just Add Water: Modulating the Structure-Derived Acidity of Catalytic Hexameric Resorcinarene Capsules.

The hexameric undecyl-resorcin[4]arene capsule (C11R6) features eight discrete structural water molecules located at the vertices of its cubic suprastructure. Combining NMR spectroscopy with classical molecular dynamics (MD), we identified and characterized two distinct species of this capsule, C11R6-A and C11R6-B, respectively featuring 8 and 15 water molecules incorporated into their respective hydrogen-bonded networks. Furthermore, we found that the ratio of the C11R6-A and C11R6-B found in solution can be modulated by controlling the water content of the sample. The importance of this supramolecular modulation in C11R6 capsules is highlighted by its ability to perform acid-catalyzed transformations, which is an emergent property arising from the hydrogen bonding within the suprastructure. We show that the conversion of C11R6-A to C11R6-B enhances the catalytic rate of a model Diels–Alder cyclization by 10-fold, demonstrating the cofactor-derived control of a supramolecular catalytic process that emulates natural enzymatic systems.