Stabilization of Haloalkane Dehalogenase Structure by Interfacial Interaction with Ionic Liquids

Ionic liquids attracted interest as green alternatives to replace conventional organic solvents in protein stability studies. They can play an important role in the stabilization of enzymes such as haloalkane dehalogenases that are used for biodegradation of warfare agents and halogenated environmental pollutants. Three-dimensional crystals of haloalkane dehalogenase variant DhaA80 (T148L+G171Q+A172V+C176F) from Rhodococcus rhodochrous NCIMB 13064 were grown and soaked with the solutions of 2-hydroxyethylammonium acetate and 1-butyl-3-methylimidazolium methyl sulfate. The objective was to study the structural basis of the interactions between the ionic liquids and the protein. The diffraction data were collected for the 1.25 angstrom resolution for 2-hydroxyethylammonium acetate and 1.75 angstrom resolution for 1-butyl-3-methylimidazolium methyl sulfate. The structures were used for molecular dynamics simulations to study the interactions of DhaA80 with the ionic liquids. The findings provide coherent evidence that ionic liquids strengthen both the secondary and tertiary protein structure due to extensive hydrogen bond interactions

Substituent Effect on Porphyrin Film-Gas Interaction by Optical Waveguide: Spectrum Analysis and Molecular Dynamic Simulation

Substituent effect on optical gas sensing performance in porphyrin-based optical waveguide detection system was studied by molecular dynamics simulation (MDS), absorption/emission spectrum analysis, and optical waveguide (OWG) detection. The affinities of porphyrin with seven types of substituents (–H, –OH, –tBu, –COOH, –NH2, –OCH3, –SO3−) on para position of meso-phenyl porphyrin toward gas molecules in adsorption process were studied in different size of boxes with the same pressure and concentration. Analyte gases (CO2, H2S, HCl, NO2) were exposed to porphyrin film in absorption spectrophotometer, and in OWG with evanescent field excited by a guiding laser light with 670 nm wavelength. The extent of interaction between host molecule and the guest analytes was analyzed by the number of gas molecules in vicinity of 0.3 nm around substituents of porphyrin molecules. Optical waveguide results reveal that sulfonate porphyrin is mostly responsive to hydrochloride, hydrosulfide gas and nitrogen dioxide gases with strong response intensity. Molecular dynamics and spectral analysis provide objective information about the molecular state and sensing properties. Molecular rearrangements induced by gas exposure was studied by spectral analysis and surface morphology before and after gas exposure taking hydrosulfide gas as an example. Film-gas interaction mechanism was discussed in terms of each gas and substituent group characters

Propensity of formate, acetate, benzoate, and phenolate for the aqueous solution/vapor interface: Surface tension measurements and molecular dynamics simulations,

The properties of aliph. and arom. carboxylates and phenolate-mimicking functional groups of humic acid are discussed with regard to their behavior in aq. solns. close to the surface. Both surface tension measurements and MD simulations confirm that Na formate behaves in accord with the classical theory of surfaces of electrolytes, whereas NaOAc and, much more pronounced, NaOBz and Na phenolate show a more hydrotropic behavior with surface active anions. Further to the surface tension data, the MD results suggest that these hydrotropes are highly oriented at the soln.-vapor interface

Propensity of citric, maleic, oxalic and succnic acids for the acquous solution- vapour interface : Surface tension measurment and molecular dynamics simulations

Behaviour of oxalic, citric, succinic, and maleic acids at the air/water interface is characterized and quantified by surface tension measurements in a broad concentration range and molecular dynamics simulations in slab geometry employing a polarizable force field. The relative order of surface propensities of these atmospherically relevant acids is established in this study with results being also in a very good agreement with previous measurements

The C-terminal basic residues contribute to the chemical- and voltage-dependent activation of TRPA1

The ankyrin transient receptor potential channel TRPA1 is a non-selective cationic channel that is expressed by sensory neurons, where it can be activated by pungent chemicals, such as AITC (allyl isothiocyanate), cinnamon or allicin, by deep cooling (<18 °C) or highly depolarizing voltages (>+100 mV). From the cytoplasmic side, this channel can be regulated by negatively charged ligands such as phosphoinositides or inorganic polyphosphates, most likely through an interaction with as yet unidentified positively charged domain(s). In the present study, we mutated 27 basic residues along the C-terminal tail of TRPA1, trying to explore their role in AITC- and voltage-dependent gating. In the proximal part of the C-terminus, the function-affecting mutations were at Lys969, Arg975, Lys988 and Lys989. A second significant region was found in the predicted helix, centred around Lys1048 and Lys1052, in which single alanine mutations completely abolished AITC- and voltage-dependent activation. In the distal portion of the C-terminus, the charge neutralizations K1092A and R1099A reduced the AITC sensitivity, and, in the latter mutant, increased the voltage-induced steady-state responses. Taken together, our findings identify basic residues in the C-terminus that are strongly involved in TRPA1 voltage and chemical sensitivity, and some of them may represent possible interaction sites for negatively charged molecules that are generally considered to modulate TRPA1

Electronic structure, chemical bonding features, and electron charge density of the double-cubane single crystal [Sb7S8Br2](AlCl4)3

The present calculations were performed using all-electron full potential linearized augmented plane wave method based on the density functional theory. We have optimized the structure of the double-cubane single crystal [Sb7S8Br2](AlCl4)3, starting with the x-ray diffraction data Zhang et al., [J. Am. Chem. Soc. 131, 9896 (2009)] , by minimization of the forces (1 mRy/au) acting on the atoms, keeping the lattice parameters fixed at the experimental values. Our calculations show that [Sb7S8Br2](AlCl4)3 possesses a wide indirect energy band gap of about 1.6 eV (2.03 eV) using local density approximation (Engel–Vosko generalized gradient approximation) exchange correlation potentials. To describe the bonding properties we have evaluated the electronic charge space density contour in four planes-namely (001), (110), (100), and (010) which show that this compound possesses a considerable anisotropy. The contour plot shows partial ionic and strong covalent bonding between S–Sb, Al–Cl, S–Br, S–S, Cl–Cl, and Sb–Br atoms