Decoding the intricate network of molecular interactions of a hyperstable engineered biocatalyst

Computational design of protein catalysts with enhanced stabilities for use in research and enzyme technologies is a challenging task. Using force-field calculations and phylogenetic analysis, we previously designed the haloalkane dehalogenase DhaA115 which contains 11 mutations that confer upon it outstanding thermostability (T_m = 73.5 °C; ΔT_m > 23 °C). An understanding of the structural basis of this hyperstabilization is required in order to develop computer algorithms and predictive tools. Here, we report X-ray structures of DhaA115 at 1.55 Å and 1.6 Å resolutions and their molecular dynamics trajectories, which unravel the intricate network of interactions that reinforce the αβα-sandwich architecture. Unexpectedly, mutations toward bulky aromatic amino acids at the protein surface triggered long-distance (∼27 Å) backbone changes due to cooperative effects. These cooperative interactions produced an unprecedented double-lock system that: (i) induced backbone changes, (ii) closed the molecular gates to the active site, (iii) reduced the volumes of the main and slot access tunnels, and (iv) occluded the active site. Despite these spatial restrictions, experimental tracing of the access tunnels using krypton derivative crystals demonstrates that transport of ligands is still effective. Our findings highlight key thermostabilization effects and provide a structural basis for designing new thermostable protein catalysts.

Illustration of cooperative thermostabilization effects of the double-lock system that: (i) induced backbone changes, (ii) closed the molecular gates, (iii) reduced the volumes of the main and slot access tunnels, and (iv) occluded the active site.     

Prebiotic Route to Thymine from Formamide—A Combined Experimental–Theoretical Study

Synthesis of RNA nucleobases from formamide is one of the recurring topics of prebiotic chemistry research. Earlier reports suggest that thymine, the substitute for uracil in DNA, may also be synthesized from formamide in the presence of catalysts enabling conversion of formamide to formaldehyde. In the current paper, we show that to a lesser extent conversion of uracil to thymine may occur even in the absence of catalysts. This is enabled by the presence of formic acid in the reaction mixture that forms as the hydrolysis product of formamide. Under the reaction conditions of our study, the disproportionation of formic acid may produce formaldehyde that hydroxymethylates uracil in the first step of the conversion process. The experiments are supplemented by quantum chemical modeling of the reaction pathway, supporting the plausibility of the mechanism suggested by Saladino and coworkers.     

Effect of Filtrated Osmotic Solution Based on Concentrated Chokeberry Juice and Mint Extract on the Drying Kinetics,Energy Consumption and Physicochemical Properties of Dried Apples

Background: Filtration of osmotic solution affects selective penetration during osmotic dehydration (OD), and after drying is finished, this can influence the chemical composition of the material, which is also modified by OD. Methods: Osmotic dehydration was carried out in filtrated and non-filtrated concentrated chokeberry juice with the addition of mint infusion. Then, this underwent convective drying, vacuum-microwave drying and combined convective pre-drying, followed by vacuum-microwave finishing drying. Drying kinetics were presented and mathematical models were selected. The specific energy consumption for each drying method was calculated and the energy efficiency was determined. Results and Discussion: The study revealed that filtration of osmotic solution did not have significant effect on drying kinetics; however, it affected selective penetration during OD. The highest specific energy consumption was obtained for the samples treated by convective drying (CD) (around 170 kJ·g⁻¹ fresh weight (fw)) and the lowest for the samples treated by vacuum-microwave drying (VMD) (around 30 kJ·g⁻¹ fw), which is due to the differences in the time of drying and when these methods are applied. Conclusions: Filtration of the osmotic solution can be used to obtain the desired material after drying and the VMD method is the most appropriate considering both phenolic acid content and the energy aspect of drying.     

The (010) Surface of the Al45Cr7 Complex Intermetallic Compound: Insights from Density Functional Theory

The Al₄₅Cr₇ compound is considered to exhibit an approximant structure of the icosahedral Al₄Cr phase. Its (010) surface has been investigated in detail using density functional calculations. Surface energy calculations show that the stable terminations result from a cleavage of the crystal between adjacent atomic planes, in agreement with the layered structure of the compound. The integrity of the icosahedral atomic arrangements (icosahedral clusters) found in the bulk structure, is predicted to be removed at the surface. This result is in contrast to what has been previously concluded for the (010) surface of the Al₁₃Fe₄ quasicrystal approximant. Our findings are discussed in relation to the bonding network in the compound, calculated using the Crystal Orbital Hamiltonian Population approach, as possible reasons for such contrasted behavior.     

Copper and Zinc as Potential Biomarkers of Mood Disorders and Pandemic Syndrome

The diagnosis of affective disorders has been the subject of constant research by clinicians from all over the world for many years. Making an appropriate diagnosis among patients suffering from mood disorders is sometimes problematic due to the personality-changing nature of patients and the similarity in the clinical picture of episodes in affective disorders. For this reason, there is a need to develop rapid and effective methods of determining biological markers that differentiate these diseases. The research was carried out with blood taken from 15 patients and 15 volunteers. The analysis of biological material for trace concentrations of zinc and copper was carried out with the use of ultrasensitive triple-quadrupole inductively coupled plasma mass spectrometry (TQ ICP-MS). The obtained results prove that the concentration of copper in the test group was lower than in the control group. For the zinc concentrations, the inverse relationship was observed. The group of patients was characterized by a higher concentration of this element than the group of healthy volunteers. Summarizing the obtained results and comparing them with the results of studies by other authors, it was found that zinc and copper may be potential biomarkers of affective disorders and pandemic syndrome.     

Influence of Plant Extract Addition to Marinades on Polycyclic Aromatic Hydrocarbon Formation in Grilled Pork Meat

Marinating is one of the most common methods of pre-processing meat. Appropriate selection of marinade ingredients can influence the physicochemical properties of the meat and can reduce the level of polycyclic aromatic hydrocarbons (PAHs) in the final product. The effects of the inclusion of natural plant extracts such as bay leaf (BL), black pepper (BP), turmeric (TU), jalapeno pepper (JP) and tamarind paste (TA) in marinades on the physicochemical properties of grilled pork neck were studied. The addition of spice extracts to marinades increased the proportion of colour components L* and b*. The use of TU, TA, JP, MX and C marinades lowered the hardness and pH of the meat. The highest phenolic compound levels were observed in the case of the mixture of all extracts (MX) and JP marinades, and the highest total antioxidant capacity was exhibited by the BL and MX marinades. The highest PAH content was recorded in the CON marinade (Σ12PAH 98.48 ± 0.81 µg/kg) and the lowest in the JP marinade (4.76 ± 0.08 µg/kg), which had the strongest, statistically significant reducing effect (95% reduction) on PAH levels. Analysis of correlation coefficients showed a relationship between the total antioxidant capacity of the marinades and the PAH content in grilled pork.     

Radiation-Induced Oxidation Reactions of 2-Selenouracil in Aqueous Solutions: Comparison with Sulfur Analog of Uracil

One-electron oxidation of 2-selenouracil (2-SeU) by hydroxyl (^●OH) and azide (^●N₃) radicals leads to various primary reactive intermediates. Their optical absorption spectra and kinetic characteristics were studied by pulse radiolysis with UV-vis spectrophotometric and conductivity detection and by the density functional theory (DFT) method. The transient absorption spectra recorded in the reactions of ^●OH with 2-SeU are dominated by an absorption band with an λ_max = 440 nm, the intensity of which depends on the concentration of 2-SeU and pH. Based on the combination of conductometric and DFT studies, the transient absorption band observed both at low and high concentrations of 2-SeU was assigned to the dimeric 2c-3e Se-Se-bonded radical in neutral form (2^●). The dimeric radical (2^●) is formed in the reaction of a selenyl-type radical (6^●) with 2-SeU, and both radicals are in equilibrium with K_eq = 1.3 × 10⁴ M⁻¹ at pH 4 (below the pK_a of 2-SeU). Similar equilibrium with K_eq = 4.4 × 10³ M⁻¹ was determined for pH 10 (above the pK_a of 2-SeU), which admittedly involves the same radical (6^●) but with a dimeric 2c-3e Se-Se bonded radical in anionic form (2^●−). In turn, at the lowest concentration of 2-SeU (0.05 mM) and pH 10, the transient absorption spectrum is dominated by an absorption band with an λ_max = 390 nm, which was assigned to the ^●OH adduct to the double bond at C5 carbon atom (3^●) based on DFT calculations. Similar spectral and kinetic features were also observed during the ^●N₃-induced oxidation of 2-SeU. In principle, our results mostly revealed similarities in one-electron oxidation pathways of 2-SeU and 2-thiouracil (2-TU). The major difference concerns the stability of dimeric radicals with a 2c-3e chalcogen-chalcogen bond in favor of 2-SeU.     

甘油氧化的光谱电化学傅里叶变换衰减全反射谱红外光谱薄膜流动池中硼酸镍层厚度的优化

在碱性甘油电氧化反应中,利用电化学傅里叶变换衰减全反射谱红外光谱法,研究了薄膜流动池中滴注硼酸镍催化剂负载量对玻碳电极性能的影响.连续操作的径向流动池包括一个位于内反射元件上方50μm的钻孔电极,可实现红外光谱分析.这是在确定条件下对电催化剂进行简便和可重复筛选的一个适合的方法,同时还提供了对复杂反应(如甘油氧化)产物选择性的检测.通过对泵送电解液进行更耗时的定量高效液相色谱分析,结果表明,衰减全反射红外光谱法可快速鉴定产物.在层流条件下,水中使用0.1 M甘油和1 M KOH,流速为5μL min-1时,甘油转化率较高.转化率和选择性取决于催化剂的负载量,负载量又决定了催化剂层的厚度和粗糙度.由于在更粗糙的膜中停留时间更长有利于再吸附和C-C键断裂,因此当负载量最高达210μg cm-2时,甘油转化率为73％且甲酸选择性接近80％.当最低负载量为13μg cm-2时,甘油转化率达到63％,甲酸选择性降至60％,相应地,C2物种(如乙醇酸盐)选择性较高,为8％.因此,只有催化剂负载量较低时才能形成几微米厚度范围内的薄膜,此时才适合进行优质催化剂的筛选.     

Isomerieverschiebung im Eu151

The isomer shift of the 21.7 keVγ transition in Eu¹⁵¹ has been studied for various divalent and trivalent europium compounds using the Mössbauer technique. Theγ energy is lower by up to 1.1·10^?6 eV in divalent compounds than in trivalent compounds. Using data from atomic spectroscopy it is estimated that the electron density at the nucleus is larger by about 1.9·10²⁶cm^?3 for the configuration 4f ⁶ than for 4f ⁷ due to different shielding of thes ² shells. The difference of the mean square radii of the 21.7 keV state and the ground state is thenδ〈r²〉=+0.03 fm². The measured isomer shift between trivalent and metallic europium and the relatives-electron densities in the rare earth metals measured by the positron annihilation rates are used to establish a calibration scheme for isomer shifts in rare earth metals. This calibration scheme is used to deduce a changeδ〈r ²〉=+0.005₅ fm² between the 26 keV state and the ground state of Dy¹⁶¹.