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1.
Klara Markova Klaudia Chmelova Srgio M. Marques Philippe Carpentier David Bednar Jiri Damborsky Martin Marek 《Chemical science》2020,11(41):11162
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 (Tm = 73.5 °C; ΔTm > 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. 相似文献
2.
Lipophilicity study of eight cephalosporins by reversed‐phase thin‐layer chromatographic method
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Monika Dąbrowska Łukasz Komsta Jan Krzek Kinga Kokoszka 《Biomedical chromatography : BMC》2015,29(11):1759-1768
The lipophilicity (RM0) and specific hydrophobic surface area for the representatives of four generation cephalosporins have been determined by reversed‐phase thin‐layer chromatography, and the effect of different mobile‐phase modifiers (such as methanol, acetonitrile, acetone, 1,4‐dioxane and 2‐propanol) on the retention has been studied. The compounds studied showed typical retention behavior; their RM values decreased linearly with increasing concentration of the organic modifier in the eluent. The linear correlations between the volume fraction of the organic solvent and the RM values over a limited range were established for each solute, resulting in high values of correlation coefficients (>0.95 in most cases). RM values were determined by various concentrations of organic modifier, and the correlation obtained was extrapolated to 0% of organic modifier. Chromatographically established logP (RM0) parameters were compared with computationally calculated partition coefficients values (AClogP, ALOGP, KOWWIN, ALOGPs, XLOGP2, MLOGP and XLOGP3) and experimental octanol–water logP values (measured by the shake flask method). The received results demonstrate that RP‐TLC may be a good alternative technique for analytics in describing the lipophilic nature of investigated cephalosporins as well as the activity. Copyright © 2015 John Wiley & Sons, Ltd. 相似文献
3.
Luk Petera Klaudia Mrazikova Lukas Nejdl Kristyna Zemankova Marketa Vaculovicova Adam Pastorek Svatopluk Civis Petr Kubelik Alan Heays Giuseppe Cassone Jiri Sponer Martin Ferus Judit Sponer 《Molecules (Basel, Switzerland)》2021,26(8)
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. 相似文献
4.
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. 相似文献
5.
Berenika Kokoszka Nina K. Jarrah Cong Liu Prof. Dr. David T. Moore Prof. Dr. Kai Landskron 《Angewandte Chemie (International ed. in English)》2014,53(14):3698-3701
An electrical effect, the supercapacitive swing adsorption (SSA) effect is reported, which allows for reversible adsorption and desorption of carbon dioxide by capacitive charge and discharge of electrically conducting porous carbon materials. The SSA effect can be observed when an electrically conducting, nanoporous carbon material is brought into contact with carbon dioxide gas and an aqueous electrolyte. Charging the supercapacitor electrodes initiates the spontaneous organization of electrolyte ions into an electric double layer at the surface of each porous electrode. The presence of this double layer leads to reversible, selective uptake and release of the CO2 as the supercapacitor is charged and discharged. 相似文献
6.
Magdalena
widro Klaudia Ordon Magorzata Herman Dominika Dudek Renata Wietecha-Posuszny 《Molecules (Basel, Switzerland)》2022,27(1)
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. 相似文献
7.
Anna Onopiuk Klaudia Koodziejczak Monika Marcinkowska-Lesiak Iwona Wojtasik-Kalinowska Arkadiusz Szpicer Adrian Stelmasiak Andrzej Poltorak 《Molecules (Basel, Switzerland)》2022,27(1)
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. 相似文献
8.
Konrad Skotnicki Ireneusz Janik Klaudia Sadowska Grazyna Leszczynska Krzysztof Bobrowski 《Molecules (Basel, Switzerland)》2022,27(1)
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 λmax = 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 Keq = 1.3 × 104 M−1 at pH 4 (below the pKa of 2-SeU). Similar equilibrium with Keq = 4.4 × 103 M−1 was determined for pH 10 (above the pKa 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 λmax = 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. 相似文献
9.
Using computationally efficient wavelet methods, we study two nonlinear models of financial returns {r
t
}: linear ARCH (LARCH) and fractionally integrated GARCH (FIGARCH). We estimate the tail index α and the long memory parameter d of the squared returns Xt = rt2{X_t= r_t^2} of LARCH, and of the powers X
t
= |r
t
|
p
of FIGARCH. We find that the X
t
have infinite variance and long memory, and show how the estimates of α and d depend on the model parameters. These relationships are determined empirically, as the setting is quite complex, and no suitable
theory has been developed so far. In particular, we provide empirical relationships between the estimates [^(d)]{\hat d} and the difference parameters in LARCH and FIGARCH. Our computational work uncovers tail and memory properties of LARCH and
FIGARCH for practically relevant parameter ranges, and provides some guidance on modeling returns on speculative assets including
FX rates, stocks and market indices. 相似文献
10.