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21.
《Bioorganic & medicinal chemistry》2016,24(20):4988-4997
The non-Boltzmann Bennett (NBB) free energy estimator method is applied to 21 molecules from the blind subset of the SAMPL4 challenge. When NBB is applied with the SMD implicit solvent model, and the OLYP/DZP level of quantum chemistry, highly accurate hydration free energy calculations are obtained with respect to experiment (RMSD = 0.89 kcal·mol−1). Other quantum chemical methods are also tested, and the effects of solvent model, density functional, basis set are explored in this benchmarking study, providing a framework for improvements in calculating hydration free energies. We provide a practical guide for using the best QM-NBB protocols that are consistently more accurate than either pure QM or pure MM alone. In situations where high accuracy hydration free energy predictions are needed, the QM-NBB method with SMD implicit solvent should be the first choice of quantum chemists. 相似文献
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M. Vidović F. Morina S. Milić‐Komić A. Vuleta B. Zechmann Lj. Prokić S. Veljović Jovanović 《Plant biology (Stuttgart, Germany)》2016,18(4):669-680
Hydrogen peroxide is an important signalling molecule, involved in regulation of numerous metabolic processes in plants. The most important sources of H2O2 in photosynthetically active cells are chloroplasts and peroxisomes. Here we employed variegated Pelargonium zonale to characterise and compare enzymatic and non‐enzymatic components of the antioxidative system in autotrophic and heterotrophic leaf tissues at (sub)cellular level under optimal growth conditions. The results revealed that both leaf tissues had specific strategies to regulate H2O2 levels. In photosynthetic cells, the redox regulatory system was based on ascorbate, and on the activities of thylakoid‐bound ascorbate peroxidase (tAPX) and catalase. In this leaf tissue, ascorbate was predominantly localised in the nucleus, peroxisomes, plastids and mitochondria. On the other hand, non‐photosynthetic cells contained higher glutathione content, mostly located in mitochondria. The enzymatic antioxidative system in non‐photosynthetic cells relied on the ascorbate–glutathione cycle and both Mn and Cu/Zn superoxide dismutase. Interestingly, higher content of ascorbate and glutathione, and higher activities of APX in the cytosol of non‐photosynthetic leaf cells compared to the photosynthetic ones, suggest the importance of this compartment in H2O2 regulation. Together, these results imply different regulation of processes linked with H2O2 signalling at subcellular level. Thus, we propose green‐white variegated leaves as an excellent system for examination of redox signal transduction and redox communication between two cell types, autotrophic and heterotrophic, within the same organ. 相似文献
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Wout Joseph Sam Aerts Matthias Vandenbossche Arno Thielens Luc Martens 《Bioelectromagnetics》2016,37(3):195-199
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《氨基酸和生物资源》2016,(3):16-20
建立2,4-二硝基氟苯柱前衍生化-反相高效液相色谱法测定绞股蓝茶叶中17种游离氨基酸的含量。以Phenomenex Gemini NX C18(4.6mm×250mm,5μm)为分析柱,采用梯度洗脱,流动相A为0.05mol·L-1乙酸钠(pH=6.4,含0.1%N,N-二甲基甲酰胺),流动相B为乙腈-水(1∶1,v/v),检测波长为360nm,柱温35℃;经方法学考察,该方法具有良好的稳定性和重现性。测定结果表明,绞股蓝茶叶中17种游离氨基酸总量为39.79mg·g-1,其中人体必需氨基酸占游离氨基酸总量的36.57%。从氨基酸含量考虑,绞股蓝茶叶具备一定的开发利用价值。 相似文献
27.
Thomas Simonson Shixin Ye‐Lehmann Zoltan Palmai Najette Amara Sandra Wydau‐Dematteis Erwan Bigan Karen Druart Clara Moch Pierre Plateau 《Proteins》2016,84(2):240-253
d ‐Amino acids are largely excluded from protein synthesis, yet they are of great interest in biotechnology. Unnatural amino acids have been introduced into proteins using engineered aminoacyl‐tRNA synthetases (aaRSs), and this strategy might be applicable to d ‐amino acids. Several aaRSs can aminoacylate their tRNA with a d ‐amino acid; of these, tyrosyl‐tRNA synthetase (TyrRS) has the weakest stereospecificity. We use computational protein design to suggest active site mutations in Escherichia coli TyrRS that could increase its d ‐Tyr binding further, relative to l ‐Tyr. The mutations selected all modify one or more sidechain charges in the Tyr binding pocket. We test their effect by probing the aminoacyl‐adenylation reaction through pyrophosphate exchange experiments. We also perform extensive alchemical free energy simulations to obtain l ‐Tyr/d ‐Tyr binding free energy differences. Agreement with experiment is good, validating the structural models and detailed thermodynamic predictions the simulations provide. The TyrRS stereospecificity proves hard to engineer through charge‐altering mutations in the first and second coordination shells of the Tyr ammonium group. Of six mutants tested, two are active towards d ‐Tyr; one of these has an inverted stereospecificity, with a large preference for d ‐Tyr. However, its activity is low. Evidently, the TyrRS stereospecificity is robust towards charge rearrangements near the ligand. Future design may have to consider more distant and/or electrically neutral target mutations, and possibly design for binding of the transition state, whose structure however can only be modeled. Proteins 2016; 84:240–253. © 2015 Wiley Periodicals, Inc. 相似文献
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The recent advent of dispersion-corrected density-functional theory (DFT) methods allows for quantitative modelling of molecular self-assembly processes, and we consider what is required to develop applications to the formation of large self-assembled monolayers (SAMs) on hydrophobic surfaces from organic solution. Focus is on application of the D3 dispersion correction of Grimme combined with the solvent dispersion model of Floris, Tomasi and Pascual–Ahuir to simulate observed scanning-tunnelling microscopy (STM) images of various polymorphs of tetraalkylporphyrin SAMs on highly oriented pyrolytic graphite surfaces. The most significant problem is identified as the need to treat SAM structures that are incommensurate with those of the substrate, providing a challenge to the use of traditional periodic-imaging boundary techniques. Using nearby commensurate lattices introduces non-systematic errors into calculated lattice constants and free energies of SAM formation that are larger than experimental uncertainties and polymorph differences. Developing non-periodic methods for polymorph interface simulation also remains a challenge. Despite these problems, existing methods can be used to interpret STM images and SAM atomic structures, distinguishing between multiple feasible polymorph types. They also provide critical insight into the factors controlling polymorphism. All this stems from a delicate balance that the intermolecular D3 and solvent Floris, Tomasi and Pascual–Ahuir corrections provide. Combined optimised treatments should yield fully quantitative approaches in the future. 相似文献
29.
To study population dynamics of Xanthomonas citri subsp. citri (Xcc) in citrus canker lesions on fruit, a needle‐free injector was used for infiltration of bacterial inoculum into fruit in situ on mature ‘Ruby Red’ grapefruit (Citrus paradisi Macf.) trees in Florida. Inoculations of Xcc at 105 colony‐forming units (cfu) per ml were conducted in 2012 and 2013 on attached fruit varying from 15 mm to 90 mm in diameter. Inoculations were repeated every 2–3 weeks until the fruit were no longer injectable. On fruit less than 40 mm in size, erumpent lesions formed within 2 weeks of inoculation and expanded 1–9 mm in diameter from 30 to 120 days postinoculation (dpi). Xcc populations in lesions were 6–8 log cfu per lesion at 30 dpi and maintained this population up to 90 dpi. By 120 dpi, Xcc populations declined 1–3 log units as rainfall and temperature decreased in September–October. Xcc populations declined to ~3 log cfu per lesion after 120 dpi in November 2012 and 2013, whereas the population resurged to 5 log cfu per lesion after 180 dpi in January–February 2014. 相似文献
30.
José Aldo Teixeira da Silva Erika Valente de Medeiros Jéssica Morais da Silva Dyana de A. Tenório Keila Aparecida Moreira Talita Camila Evaristo da Silva Nascimento Cristina Souza‐Motta 《Journal of Phytopathology》2016,164(11-12):1003-1011
Trichoderma has been used to manage a large number of pathogens, but there is a gap in the mechanisms used by these biocontrol agents regarding the physiological response of cassava plants (Manihot esculenta) when it is subjected to cassava root rot. The aims of this study were to investigate the antagonist activity of ten Trichoderma isolates against Fusarium solani on potato dextrose Agar (PDA), to quantify the chitinase production, to select and test in vivo the best isolate from each experiment and to assess the physiological response of cassava to the production of oxidative enzyme complex production (ascorbate peroxidase, catalase, peroxidase and polyphenol oxidase). All Trichoderma isolates have shown competitive capability against F. solani, and Trichoderma hamatum URM 6656 showed the highest inhibition of pathogen growth (88.91%). All isolates have shown chitinase activity, but Trichoderma aureoviride URM 5158 produced the highest amount of chitinase. T. hamatum URM 6656 and T. aureoviride URM 5158 were selected to be applied in vivo. The two Trichoderma strains reduced 64 and 60% of the disease severity in the shoot and 82 and 84% in the root. Cassava plants infected with Trichoderma have shown the highest peroxidase and ascorbate peroxidase production. Our results have indicated that T. aureoviride URM 5158 is an effective biocontrol agent against cassava root rot caused by F. solani, because it presented competitive antagonist capability in vitro, the highest chitinase production, and reduced the cassava root rot severity. The application of T. aureoviride has led to the maximum enzyme activity of reactive oxygen species group in cassava plants. 相似文献