Equivalent potential of water for the electronic structure of glycine

First-principles, all-electron, ab initio calculations have been performed to construct an equivalent potential of water for the electronic structure of glycine (Gly) in solution. The calculation involved three steps. The first step was to search for the minimum-energy geometric structure of the Gly + nH₂O system. The second step was to calculate the electronic structure of Gly with the potential of water molecules via the self-consistent cluster-embedding method (SCCE), based on the result obtained in the first step. The last step was to calculate the electronic structure of Gly with the potential of dipoles after replacing the water molecules with dipoles. The results show that the occupied molecular orbitals of Gly are raised by about 0.0524 Ry on average due to the effect of water. The effect of water can be simulated well using the dipole potential. The equivalent potential obtained can be applied directly to electronic structure calculations of proteins in solution using the SCCE method.     

Conformational control in structure-based drug design

In structure-based drug design, the basic goal is to design molecules that fit complementarily to a given binding pocket. Since such computationally modeled molecules may not adopt the intended bound conformation outside the binding pocket, one challenge is to ensure that the designed ligands adopt similar low energy conformations both inside and outside of the binding pocket. Computational chemistry methods and conformational preferences of small molecules from PDB and Cambridge Structural Database (CSD) can be used to predict the bound structures of the designed molecules. Herein, we review applications of conformational control in structure-based drug design using selected examples from the recent medicinal chemistry literature. The main purpose is to highlight some intriguing conformational features that can be applied to other drug discovery programs.     

Evaluation of the predatory mite Amblyseius hainanensis (Acari: Phytoseiidae) and artificial rainfall for the management of Brevipalpus obovatus (Acari: Tenuipalpidae)

Brevipalpus obovatus Donnadieu is an important pest mite on tea plants in South China. In the current study, predatory mites of B. obovatus in the tea gardens of Guangzhou were extensively surveyed. In total, 13 species of predatory mites (four families with seven genera) were recorded. The population proportion of Amblyseius hainanensis Wu et Qian was the highest (68.6?%), followed by that of Anystis baccarum (L.) (8.4?%) and A. theae Wu (6.3?%). The effects of starvation time, habitat size and pest population density on the predatory efficiency of the most dominant species, A. hainanensis, feeding on B. obovatus were assessed. In addition, the effectiveness of artificial rainfall in reducing B. obovatus populations was evaluated. After starvation for 48?h, the predatory efficiency of A. hainanensis was significantly higher than those that had been starved for 24 or 72?h when 30-50 B. obovatus eggs were made available. The predation of A. hainanensis on B. obovatus also increased with increasing prey density. The number of prey attacked by A. hainanensis in a 3.2?cm(2) habitat was significantly higher than in a 6.3?cm(2) habitat. The average predation of A. hainanensis was 31.7 eggs per day when offered 100 B. obovatus eggs on a tea leaf. This decreased to 17.8 eggs per day when four A. hainanensis shared 100 B. obovatus eggs. B. obovatus populations can be reduced by artificial rainfall, with the reduction affected by rainfall intensity. With an intensity of 40?mm in 15?min, 90.2?% mortality of B. obovatus occurred; lower mortalities were recorded (13.3 and 29.8?%) when the intensity was 2 or 4?mm in 15?min. Combination of the predatory mite A. hainanensis and artificial rainfall for the integrated pest management of B. obovatus is discussed.     

Increasing in vitro microrhizome production of ginger (Zingiber officinale Roscoe)

In this study, using the quadratic saturation 310 D-optimal design method, we examined the effect of kinetin (KT), gibberellic acid (GA), and naphthalene acetic acid (NAA) on microrhizome production in ginger. The effect of GA on rhizome induction was larger than that of KT or NAA. Using simulation and optimality selection for tissue culture, we found that concentrations of GA, KT, and NAA of 1.33–2.35, 0.49–0.66, and 0.62 g/l, respectively, gave a microrhizome weight of over 0.25 g. The optimal conditions for microrhizome production were 80 g/l sucrose, 2 × MS macro-elements, and 1 × MS micro-elements, with a photoperiod of 24L:0D (light/dark). At the same time, 100% survival could be achieved on transfer of the in vitro ginger plantlets with microrhizomes to soil.     

Classification of subcellular location by comparative proteomic analysis of native and density-shifted lysosomes

One approach to the functional characterization of the lysosome lies in the use of proteomic methods to identify proteins in subcellular fractions enriched for this organelle. However, distinguishing between true lysosomal residents and proteins from other cofractionating organelles is challenging. To this end, we implemented a quantitative mass spectrometry approach based on the selective decrease in the buoyant density of liver lysosomes that occurs when animals are treated with Triton-WR1339. Liver lysosome-enriched preparations from control and treated rats were fractionated by isopycnic sucrose density gradient centrifugation. Tryptic peptides derived from gradient fractions were reacted with isobaric tag for relative and absolute quantitation eight-plex labeling reagents and analyzed by two-dimensional liquid chromatography matrix-assisted laser desorption ionization time-of-flight MS. Reporter ion intensities were used to generate relative protein distribution profiles across both types of gradients. A distribution index was calculated for each identified protein and used to determine a probability of lysosomal residence by quadratic discriminant analysis. This analysis suggests that several proteins assigned to the lysosome in other proteomics studies are not true lysosomal residents. Conversely, results support lysosomal residency for other proteins that are either not or only tentatively assigned to this location. The density shift for two proteins, Cu/Zn superoxide dismutase and ATP-binding cassette subfamily B (MDR/TAP) member 6, was corroborated by quantitative Western blotting. Additional balance sheet analyses on differential centrifugation fractions revealed that Cu/Zn superoxide dismutase is predominantly cytosolic with a secondary lysosomal localization whereas ATP-binding cassette subfamily B (MDR/TAP) member 6 is predominantly lysosomal. These results establish a quantitative mass spectrometric/subcellular fractionation approach for identification of lysosomal proteins and underscore the necessity of balance sheet analysis for localization studies.     

血清S-100B蛋白和NSE含量变化评估脑损伤程度的意义

目的探讨颅脑损伤后血清S-100B蛋白、神经元特异性烯醇化酶(NSE)水平变化及其在损伤程度的临床意义。方法采用酶联免疫测定法检测90例颅脑损伤患者入院时及入院后6、12、24h和3、7天血清S-100B蛋白、NSE水平,并分析其与颅脑损伤严重程度的关系。同时选择30例健康体检者作为对照组进行比较分析。结果颅脑损伤后血清S-100B蛋白、NSE水平较对照组明显升高(P0.05或P0.01);重型组患者的血清S-100B蛋白和NSE水平明显高于轻、中型组患者(P0.05或P0.01);动态检测结果显示,血清S-100B蛋白在伤后12h达峰值(P0.05),NSE含量在伤后24h达峰值(P0.05),然后缓慢下降。GCS评分与S-100B、NSE浓度呈负相关(分别为r=-0.814,P0.01;r=-0.726,P0.05)。结论颅脑损伤后血清S-100B蛋白、NSE水平升高,其与脑损伤程度有较好的相关性,2种标记物水平对颅脑损伤程度有较高的评估价值。     

A Strategy for Sensitive,Large Scale Quantitative Metabolomics

Metabolite profiling has been a valuable asset in the study of metabolism in health and disease. However, current platforms have different limiting factors, such as labor intensive sample preparations, low detection limits, slow scan speeds, intensive method optimization for each metabolite, and the inability to measure both positively and negatively charged ions in single experiments. Therefore, a novel metabolomics protocol could advance metabolomics studies. Amide-based hydrophilic chromatography enables polar metabolite analysis without any chemical derivatization. High resolution MS using the Q-Exactive (QE-MS) has improved ion optics, increased scan speeds (256 msec at resolution 70,000), and has the capability of carrying out positive/negative switching. Using a cold methanol extraction strategy, and coupling an amide column with QE-MS enables robust detection of 168 targeted polar metabolites and thousands of additional features simultaneously.  Data processing is carried out with commercially available software in a highly efficient way, and unknown features extracted from the mass spectra can be queried in databases.     

AMPK regulates homeostasis of invasion and viability in trophoblasts by redirecting glucose metabolism: Implications for pre‐eclampsia

Pre‐eclampsia (PE) is deemed an ischemia‐induced metabolic disorder of the placenta due to defective invasion of trophoblasts during placentation; thus, the driving role of metabolism in PE pathogenesis is largely ignored. Since trophoblasts undergo substantial glycolysis, this study aimed to investigate its function and regulatory mechanism by AMPK in PE development. Metabolomics analysis of PE placentas was performed by gas chromatography–mass spectrometry (GC–MS). Trophoblast‐specific AMPKα1‐deficient mouse placentas were generated to assess morphology. A mouse PE model was established by Reduced Uterine Perfusion Pressure, and placental AMPK was modulated by nanoparticle‐delivered A769662. Trophoblast glucose uptake was measured by 2‐NBDG and 2‐deoxy‐d‐[³H] glucose uptake assays. Cellular metabolism was investigated by the Seahorse assay and GC–MS.PE complicated trophoblasts are associated with AMPK hyperactivation due not to energy deficiency. Thereafter, AMPK activation during placentation exacerbated PE manifestations but alleviated cell death in the placenta. AMPK activation in trophoblasts contributed to GLUT3 translocation and subsequent glucose metabolism, which were redirected into gluconeogenesis, resulting in deposition of glycogen and accumulation of phosphoenolpyruvate; the latter enhanced viability but compromised trophoblast invasion. However, ablation of AMPK in the mouse placenta resulted in decreased glycogen deposition and structural malformation. These data reveal a novel homeostasis between invasiveness and viability in trophoblasts, which is mechanistically relevant for switching between the ‘go’ and ‘grow’ cellular programs.

Pre‐eclampsia (PE) is associated with trophoblast AMPK hyperactivation, presumably due to LKB1 phosphorylation, and glucose uptake is consequently increased via trafficking of GLUT3 from the cytosol to the plasma membrane. Such translocation enhances glycolytic flux and redirects glucose metabolic intermediates into gluconeogenesis, resulting in PEP accumulation, which not only benefits cell survival but also suppresses invasion by repressing MMPs, and thus in turn modulates switching between the ‘go’ and ‘grow’ cellular programs.