Correlations between designability and various structural characteristics of protein lattice models

Using six kinds of lattice types (4 x 4, 5 x 5, and 6 x 6 square lattices; 3 x 3 x 3 cubic lattice; and 2+3+4+3+2 and 4+5+6+5+4 triangular lattices), three different size alphabets (HP, HNUP, and 20 letters), and two energy functions, the designability of protein structures is calculated based on random samplings of structures and common biased sampling (CBS) of protein sequence space. Then three quantities stability (average energy gap), foldability, and partnum of the structure, which are defined to elucidate the designability, are calculated. The authors find that whatever the type of lattice, alphabet size, and energy function used, there will be an emergence of highly designable (preferred) structure. For all cases considered, the local interactions reduce degeneracy and make the designability higher. The designability is sensitive to the lattice type, alphabet size, energy function, and sampling method of the sequence space. Compared with the random sampling method, both the CBS and the Metropolis Monte Carlo sampling methods make the designability higher. The correlation coefficients between the designability, stability, and foldability are mostly larger than 0.5, which demonstrate that they have strong correlation relationship. But the correlation relationship between the designability and the partnum is not so strong because the partnum is independent of the energy. The results are useful in practical use of the designability principle, such as to predict the protein tertiary structure.     

Acetylcholinesterase Inhibitory Activities of Essential Oils from Vietnamese Traditional Medicinal Plants

Essential oils are promising as environmentally friendly and safe sources of pesticides for human use. Furthermore, they are also of interest as aromatherapeutic agents in the treatment of Alzheimer’s disease, and inhibition of the enzyme acetylcholinesterase (AChE) has been evaluated as an important mechanism. The essential oils of some species in the genera Callicarpa, Premna, Vitex and Karomia of the family Lamiaceae were evaluated for inhibition of electric eel AChE using the Ellman method. The essential oils of Callicarpa candicans showed promising activity, with IC₅₀ values between 45.67 and 58.38 μg/mL. The essential oils of Callicarpa sinuata, Callicarpa petelotii, Callicarpa nudiflora, Callicarpa erioclona and Vitex ajugifolia showed good activity with IC₅₀ values between 28.71 and 54.69 μg/mL. The essential oils Vitex trifolia subsp. trifolia and Callicarpa rubella showed modest activity, with IC₅₀ values of 81.34 and 89.38, respectively. trans-Carveol showed an IC₅₀ value of 102.88 µg/mL. Molecular docking and molecular dynamics simulation were performed on the major components of the studied essential oils to investigate the possible mechanisms of action of potential inhibitors. The results obtained suggest that these essential oils may be used to control mosquito vectors that transmit pathogenic viruses or to support the treatment of Alzheimer’s disease.     

Optimization of Mulberry Extract Foam-Mat Drying Process Parameters

Mulberry powder was created from the extract using a foam-mat drying process. The studies aimed to evaluate the effects of egg albumin, carboxymethyl cellulose (CMC), digestion-resistant maltodextrin (DRM) contents, and whipping time (5 to 15 min) on the foam properties. The impact of different drying temperatures (60 to 75 °C) on the quality of the finished mulberry powder was also noted. The best foam expansion/stability value was determined using multiple regression models as a function of egg albumin, CMC, DRM, and whipping time. The results indicated that the main influencing factors for the foam properties were whipping time followed by egg albumin, CMC, and DRM. Optimum values of foam expansion and stability were achieved at 467.9% and 97.02%, respectively. The foam had a porous structure and good stability for subsequent drying, with optimal contents of egg albumin, CMC, and DRM used at 7.6%, 0.4%, and 2%, respectively, along with a whipping time of 14.5 min. The established models had a high coefficient of determination (R² > 0.9) and a high correlation between the predicted and observed values. Therefore, the model could be adjusted to determine the characteristics of the foam suitable for subsequent drying. The optimal values were then also verified. Minimal fluctuations (1.78–2.98%) between the experimental data and the optimal value were found. The drying temperature also significantly affected the quality of the mulberry powder. The foam was dried at 65 °C for 4 h to produce apowder with a beautiful light color (L* = 62.65), a characteristic purple-red color of mulberry (a* = 5.97). The moisture, water activity, and anthocyanin content of the finished mulberry powder were 4.57%, 0.3, and 5.4 mg/g, respectively.     

Morphology of {100} and {201} faces and the optical quality of KTiOPO4 crystals

Crystallography Reports - Potassium titanyl phosphate crystals up to 350 g in weight have been grown from a high-temperature solution in K4P2O7 by the flux method on a [100]-oriented seed. The...     

Electric fields drive bond homolysis

Electric fields have been used to control and direct chemical reactions in biochemistry and enzymatic catalysis, yet directly applying external electric fields to activate reactions in bulk solution and to characterize them ex situ remains a challenge. Here we utilize the scanning tunneling microscope-based break-junction technique to investigate the electric field driven homolytic cleavage of the radical initiator 4-(methylthio)benzoic peroxyanhydride at ambient temperatures in bulk solution, without the use of co-initiators or photochemical activators. Through time-dependent ex situ quantification by high performance liquid chromatography using a UV-vis detector, we find that the electric field catalyzes the reaction. Importantly, we demonstrate that the reaction rate in a field increases linearly with the solvent dielectric constant. Using density functional theory calculations, we show that the applied electric field decreases the dissociation energy of the O–O bond and stabilizes the product relative to the reactant due to their different dipole moments.

We demonstrate that electric fields can homolytically cleave a peroxide bond in different solvents with a rate that is proportional to the solvent dielectric constant.     

Ionic‐Liquid‐Derived,Water‐Soluble Ionic Cellulose

A new type of water‐soluble ionic cellulose was obtained by means of the dissolution of cellulose in dimethylimidazolium methylphosphite at elevated temperatures over 120 °C. FTIR spectroscopy, ¹H and ¹³C NMR spectroscopy, and elemental analysis results revealed that the repeating unit of the water‐soluble cellulose consists of a dialkylimidazolium cation and a phosphite anion bonded to cellulose. The degree of phosphorylation on the cellulose chain was between 0.4 and 1.3 depending on the reaction temperature and time. With an increasing degree of phosphorylation, water solubility was increased. Scanning electron microscopy and X‐ray diffraction analyses revealed that the cellulose crystalline phase in the parent crystalline cellulose changed to an amorphous phase upon transformation into ionic cellulose. Thermogravimetric analysis showed the prepared phosphorylated cellulose was stable over 250 °C and a substantial amount of residue remained at 500 °C.     

Reaktionen der Digalliumverbindung R2Ga–GaR2 [R = CH(SiMe3)2] mit Wasser und Carbonsäuren – Synthese von μ‐Hydroxo‐μ‐carboxylatodigallium‐Verbindungen unter Erhalt der Ga–Ga‐Bindungen

Treatment of the digallium compound R₂Ga–GaR₂ [ 1 , R = CH(SiMe₃)₂] with a broad variety of functionalized carboxylic acids in the presence of water yielded μ‐hydroxo‐μ‐carboxylatodigallium compounds ( 2 – 10 ) containing intact Ga–Ga bonds in high to moderate yields. The compounds form dimeric formula units in which the unsupported Ga–Ga bonds are bridged by two hydroxo and two carboxylato ligands. Each gallium atom is terminally coordinated by a bulky alkyl group. NMR spectroscopy revealed mixtures of two isomeric compounds in solution in all cases. The second component may show a different bridging mode with each Ga–Ga bond bridged by a bidentate carboxylato ligand to form Ga₂O₂C five‐membered heterocycles.     

Room Temperature Phosphorimetry as a New Spectrochemical Method of Analysis

Abstract

Luminescence spectroscopy has been extensively applied in the fields of clinical chemistry, biochemistry, and environmental chemistry. Proteins, nucleic acids, enzymes, drugs, and pollutants all show characteristic luminescence properties. The unexcelled sensitivity, selectivity, ease of sampling, and breadth of application of this method is of considerable interest to every analytical researcher and analyst. Whereas fluorimetry has become a well-established method for analysis [11, phosphorimetry has been used during the past decade only for a limited number of quantitative analyses, including the analysis of poly-nuclear aromatic compounds [2–41, coal tar fractions [5], air pollutants [6-8], impurities in petroleum fractions [9–111, detection of pesticides, and fungicides in foods [12–17], and the analysis of amino acids and pharmaceutical compounds in biological fluids [18–26]. Only recently has phosphorimetry been extensively developed into a practical qualitative and quantitative analytical method. Several papers have appeared in which the progress in instrumentation and methodology as well as the analytical uses of phosphorimetry were given [27–30]. In the 1960s the lack of use of phosphorimetry for quantitative analysis was primarily due to the great complexity and time needed to prepare and carry out an analysis at low temperature, and the poor precision and accuracy of measurements of snowed, opaque, or cracked inhomogeneous samples. In the early 1970s, improvements were achieved with techniques to enable the measurement of opaque matrices of organic solvents [31] and the development of time-resolved and phase-resolved phosphorimetry [32-361. However, in most phosphorimetric studies, the analysis still had to be performed using either low temperature rigid solvents of organic glasses, polymer matrices, or carefully degassed and purified solutions in order to minimize collisional triplet quenching. These requirements still are the main disadvantages which make this spectro-chemical method less-widely used than fluorimetry. Recently, the observed phenomenon of intense phosphorescence at room temperature (RTP) from ionic organic compounds adsorbed on a variety of supports, such as silica, alumina, paper, and asbestos [36, 37], has been proposed as a new analytical technique [38–42]. A large variety of ionic compounds of biological and clinical interest [38-40] has been investigated by this new method. The use of external heavy atom perturbers has also been investigated for the determination of trace nonionic compounds, such as the polyaromatic hydrocarbons [41]. Significant progress has been achieved with the development of a simple device for automated RTP measurement [42].