Conformational flexibility of a protein-carbohydrate complex and the structure and ordering of surrounding water

Protein-carbohydrate non-covalent interactions are important to understand various biological processes in living organisms. One of the important issues in protein-carbohydrate binding is how the protein identifies the target carbohydrate and recognizes its conformational features. Surrounding water molecules are expected to play a critical role not only in mediating the recognition process but also in maintaining the structure of the complex. We carried out atomistic molecular dynamics (MD) simulations of an aqueous solution of the protein-carbohydrate complex formed between the hyaluronan binding domain (HABD) of the murine Cd44 protein and the octasaccharide hyaluronan (HA(8)). The conformational flexibilities of the protein and the carbohydrate, and the microscopic structure and ordering of water molecules around them in the complexed form have been explored. It is revealed that the formation of the complex is associated with significant immobilization of the monosaccharide units of the carbohydrate moiety that are involved in binding. Further, reduction in water densities around the binding residues of the two molecules in the complex with respect to their free forms clearly demonstrated that the recognition between the protein and the carbohydrate is facilitated by removal of a fraction of water molecules from regions around the binding domains.     

Conformational fluctuations of a protein-DNA complex and the structure and ordering of water around it

Protein-DNA binding is an important process responsible for the regulation of genetic activities in living organisms. The most crucial issue in this problem is how the protein recognizes the DNA and identifies its target base sequences. Water molecules present around the protein and DNA are also expected to play an important role in mediating the recognition process and controlling the structure of the complex. We have performed atomistic molecular dynamics simulations of an aqueous solution of the protein-DNA complex formed between the DNA binding domain of human TRF1 protein and a telomeric DNA. The conformational fluctuations of the protein and DNA and the microscopic structure and ordering of water around them in the complex have been explored. In agreement with experimental studies, the calculations reveal conformational immobilization of the terminal segments of the protein on complexation. Importantly, it is discovered that both structural adaptations of the protein and DNA, and the subsequent correlation between them to bind, contribute to the net entropy loss associated with the complex formation. Further, it is found that water molecules around the DNA are more structured with significantly higher density and ordering than that around the protein in the complex.     

Differential flexibility of the secondary structures of lysozyme and the structure and ordering of surrounding water molecules

We have performed an atomistic molecular dynamics simulation of an aqueous solution of hen egg-white lysozyme at room temperature with explicit water molecules. Several analyses have been carried out to explore the differential flexibility of the secondary structural segments of the protein and the structure and ordering of water around them. It is found that the overall flexibility of the protein molecule is primarily controlled by few large-amplitude bistable motions exhibited by two coils; one connecting two α-helical segments in domain-1 and the other connecting a 3(10) helix and a β-sheet in domain-2 of the protein. The heterogeneous structuring of water around the segments of the protein has been found to depend on the degree of exposure of the segments to water. The ordering of water molecules around the protein segments and their tagged potential energies have been found to be anticorrelated with each other. Some of these findings can be verified by suitable experimental studies.     

ExTTF-based dyes absorbing over the whole visible spectrum

New push-pull dyes featuring π-extended tetrathiafulvalene (exTTF) as the donor group and tricyanofuran (TCF) as the acceptor group were synthesized and characterized. Their broad absorption covers the entire visible spectral range and enters the near-infrared region. Electrochemistry and theoretical calculations provided an understanding of these singular electronic properties. The new dyes are appealing candidates as light harvesters in photovoltaic devices.     

Defect ordering in early transition-metal sulfides with the NaCl-type structure

The defect rock-salt type materials Zr_1?xS, Sc_1?xS, and Lu_1?xS have been shown to exhibit a complex variety of ordered superstructures. These superstructures are reviewed within the context of Landau's theory of symmetry and phase transitions, and it is concluded that there is a significant similarity in the transitions when they are considered from the point of view of reciprocal space.     

Supramolecular ordering of tripod dyes at the air/water interface

Monolayers of 2-(3,4,5-(trisdodecyloxyl)phenyl)[1,3,4]oxadiazole based "tripod" dye, P2G, has been studied at the air/water interface with in situ X-ray reflectivity. Compression of the disordered Langmuir-Blodgett monolayer film induces a transition to a unique ordered phase, representing a supramolecular assembly with a unique spatial distribution and orientation of the molecules. At low pressure, the molecules having face-on orientation are interdigitated by the three arms. After first transition in the pi-A isotherm, the molecular conformation is turned into an edge-on orientation, where the molecules are self-assembled into supramolecular structures.     

Comparative study of particle structure evolution during water sorption: skim and whole milk powders

Surface composition of dairy powders influences significantly a quantity of functional properties such as rehydration, caking, agglomeration. Nevertheless, the kinetic of water uptake by the powders was never directly related to the structure and the composition of the surface. In this work, the effect of relative humidity on the structural reorganization of two types of dairy powder was studied. The water-powder interaction for industrial whole milk powder, and skim milk powder was studied using dynamic vapor sorption. The water sorption isotherms were fitted with a Brunner-Emmet-Teller model and each stage of the sorption curve was analyzed with a Fickian diffusion. The water content in the monolayer predicted for each powder and the moisture diffusivity calculated were discussed and compared. Concurrently, powders microstructure and powders surface under variable relative humidity were assessed by X-ray photoelectron spectroscopy, scanning electron microscopy coupled with energy dispersive X-ray and atomic force microscopy. A correlation between the data obtained from the sorption isotherms and the modifications of structure allowed us to conclude that powder microstructure and chemical state of the components could play an important role in determining the water diffusivity.     

Roughness and ordering at the interface of oxidized polystyrene and water

For the first time, atomistically detailed molecular dynamics calculations revealed molecular ordering of the water-oxidized atactic polystyrene (aPS) interface. Both ordering of the water molecules and the phenyl rings occur. In addition, the natural roughness of the surface has been simulated and compared to experimental values. The composition of the simulated aPS films is based on spin-coated aPS films that have been oxidized and characterized experimentally. The aPS surfaces are oxidized with ultraviolet-ozone radiation and have been characterized by XPS, AFM, and water contact angle measurements. XPS measurements show that the oxygen content in the sample increases rapidly with exposure and reaches saturation near 24 at. % of oxygen. The molecular dynamics simulations show smoothening of an hydrophobic aPS surface upon transition from vacuum to water. The smoothening decreases with increasing hydrophilicity. The calculations reveal ordering of oxidized phenyl rings for aPS surfaces in water. The order increases with increasing hydrophilicity. Additionally, we investigated the water structure near the aPS-water interface as a function of the surface hydrophilicity. With increasing hydrophilicity, the density of water at the aPS-water interface increases. The water density profile is steeper in the presence of hydrophobic aPS. The water shows an ordered layer near both the hydrophobic and hydrophilic surfaces; the position of this layer shifts toward the interface with increasing hydrophilicity.     

Theoretical insights into the effect of surface structure and anion ordering on the properties of SrTaO2N for photocatalytic water splitting

As one of the representative perovskite-type oxynitride photocatalysts, SrTaO₂N has the ability to split water in the visible-light region. It was found that the surface modification and interfacial design of SrTaO₂N-based materials are closely related to the photocatalytic activity, but the microscopic mechanisms of these experimental phenomena are not well understood. In this work, we have utilized density functional theory (DFT) calculations to investigate the effect of anion ordering and exposed terminations on the electronic structures, optical absorption, water adsorption and the mechanisms of water oxidation and reduction reactions of SrTaO₂N. Our results indicate that cis configurations are more stable than trans configurations. The anion ordering has an important effect on the band gap and optical absorption coefficient. The terminations with exposed Ta atoms are more stable and have bigger work functions than those with exposed Sr atoms possibly due to the bonding ionicity and surface dipoles. The dissociative adsorption of water is energetically more favorable than the molecular adsorption on most surfaces. The highly active sites of hydrogen evolution reaction (HER) are the exposed nonmetal atoms. Terminations with exposed Sr and N atoms have lower overpotentials (0.70–0.77 V) of oxygen evolution reaction (OER) than others. They are comparable to the calculated results of common photocatalysts, such as Co₃O₄ and TiO₂. This study sheds light on the relationship between the termination structure with different anion orders and the photocatalysis-related properties of SrTaO₂N at a molecular level, which provides guidance for constructing highly active photocatalytic materials.     

Spatial structure of isoepoxyestafiatin

The spatial structure of the sesquiterpene lactone isoexpoxyestafiatin has been established by the x-ray method as 1,10ß;3,4-diepoxy-5,7,6H-11(13)en-6,12-olide.Translated from Khimiya Prirodnykh Soedinenii, Vol. 33, No. 1, pp. 66–67, January–February, 1997.     

Spatial structure of diacetyldihydroungminorine

The structure of diacetyldihydroungminorine, C₂₁H₂₅NO₇ (I), has been determined by the x-ray structural method: diffractometer, CuK radiation, 1278 reflections, R=0.089. An analysis has been made of the conformation of the (I) molecule in comparison with that observed for dihydrolycorine in solution and in the crystalline form. It was shown that the conformations of rings B, C, and D of the (I) molecule in the crystal and of dihydrolycorine in solution are identical. The lack of correspondence of the crystal-solution conformations in dihydrolycorine is connected with an inversion of the unshared electron pair of the nitrogen atom on the formation of a salt — the hydrobromide.Institute of Chemistry of Plant Substances, Uzbekistan Academy of Sciences, Tashkent. Translated from Khimiya Prirodnykh Soedinenii, No. 1, pp. 105–108, January–February, 1992.     

Spatial structure of cycleanine

Analysis of the PMR spectra of cycleanine in CDCl₃ (INDOR and double-resonance spectra) measured at various temperatures has shown that the cycleanine molecule exists in a stable symmetrical boat-like conformation for the macrocycle in which the tetrahydroisoquinoline rings acquire a distorted boat form, the benzyl groups are oriented axially, and the distance between them is the greatest. A comparison of the spectra of the cycleanine and its methiodide in CF₃COOH (double-resonance spectra) has shown that in solutions of cycleanine in the salt form there are molecules with axial and equatorial methyl groups at the nitrogen atoms (1:1). It has been shown with the aid of paramagnetic reagents that the main associating center in the cycleanine molecule is formed by the methoxy groups in position 7 and 7, which possess an increased electron density on their oxygen atoms because of their departure from the plane of conjugation with the aromatic ring of the isoquinoline nucleus.All-Union Scientific-Research Institute of Medicinal Plants, Moscow. Translated from Khimiya Prirodnykh Soedinenii, No. 1, pp. 60–66, January–February, 1980.     

Thickness-dependent ordering of water layers at the NaCl(100) surface

We have determined the ordering properties of water adsorbed at room temperature on the rock salt (100) surface under four different conditions: ultrahigh vacuum, dry nitrogen atmosphere, 45% and 75% relative humidity. Details of the atomic structure are determined for both sides of the solid-liquid interface. The top most layer of NaCl shows a small relaxation that changes from an expansion to a contraction with increasing humidity. Under all measured conditions water monolayers with different ordering properties are present at the interface. Surprisingly, we find that the amount of ordering in the first layer is increasing with increasing thickness of the water film. At a solid-liquid interface, the ordering appears to be correlated with the solubility.     

On the anisotropy of the intermolecucular potential of the CO2-Ne system in the repulsive short-range region

Ab-initio computations at the STO-3G level have been performed on CO₂-Ne. The short-range interactions are roughly proportional to Σ_ir_i^?12, where the r_i are the distances from neon to the atoms in CO₂. In this empirical approximation, the anisotropy effects are conveniently revealed by the proportionality coefficient whose value depends on the angle between the OCO and C-Ne axes.     

Spatial structure in the N-arylpiperazine series

Conclusions In the compounds examined, the angle of rotation of the plane of the aromatic ring relative to the unshared electron pair of the nitrogen atom is close to orthogonal, but in the o-fluoro-compound it is smaller.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 5, pp. 1317–1321, June, 1987.