Major house dust mite allergen, Der p I, activates phospholipase D in human peripheral blood mononuclear cells from allergic patients: involvement of protein kinase C

The major house-dust-mite allergen, Der p I, stimulates the phospholipase D (PLD) in peripheral blood mononuclear cells (PBMC) from allergic patients with maximal responses after 30 min exposure. At 30 min, Der p I stimulated PLD activity by 1.4-fold in mild, 1.6-fold in moderate and 2-fold in severe allergic patients over control values (p < 0.05). When the cells were pretreated for 24 h with phorbol myristate acetate to down-regulate protein kinase C (PKC), PLD stimulation by Der p I was largely abolished. These results indicate that in PBMC from allergic patients, Der p I can stimulate PLD activity, and that PKC activation is involved in this stimulation.     

Involvement of protein kinase C pathway in UVC-stimulated phospholipase D2 activity in Vero 76 cells

Phospholipase D (PLD) activity is known to be related to oxidant-induced cellular signaling and membrane disturbance. Previously, an induction of PLD activity in various cell lines by X-ray irradiation was observed. In this study, we examined the effect of UVC radiation on the PLD activity in Vero 76 cells. At a dose of 10 kJ/m2 of UVC irradiation, the PLD activity was stimulated approximately 10-fold over the basal activity. This UVC-induced PLD activity was found to be dependent on the presence of extracellular calcium and was inhibited by catalase as well as amifostine-an intracellular thiol antioxidant. Pretreatments with Ro32-0432-a selective inhibitor of protein kinase C (PKC)-and downregulation of PKC by preincubation of phorbol 12-myristate 13-acetate significantly inhibited the UVC-induced PLD activity. UVC-stimulated PLD activity was observed only in murine PLD2 (mPLD2)-transfected Vero 76 cells and not in human PLD1 (hPLD1)-transfected cells. Transient incorporation of PKC with mPLD2 and the phosphorylation of mPLD2 by a and b forms of PKC by UVC irradiation were observed. These results suggest that the UVC-stimulated PLD activity in Vero 76 cells is mediated through transient phosphorylation of PLD2 by the translocation of PKC to PLD2.     

离子交换介孔分子筛DEAE-SBA-15的制备及其用于分离纯化粉尘螨主要变应原Derf2

通过3-含氧缩水甘油基-丙基-三甲氧基硅烷(GPTS)将二乙胺基乙基(DEAE)嫁接在介孔分子筛SBA-15的表面,制得弱阴离子交换层析剂DEAE-SBA-15,使其既具有分子筛作用,又具有离子交换作用的特点.经DEAE-SBA-15层析后,从粉尘螨代谢培养基中获得单一的洗脱峰,SDS-PAGE显示一条谱带,其相对分子质量为14000,表明经分离纯化所得到的蛋白质是粉尘螨主要变应原Derf2.对螨性哮喘患者皮肤点刺试验表明,所得Derf2仍具有变应原活性,且仅通过一次柱色谱即得Derf2,表明DEAE-SBA-15是一种较好的离子交换层析剂.     

The regulation of protein synthesis and translation factors by CD3 and CD28 in human primary T lymphocytes

Background  

Activation of human resting T lymphocytes results in an immediate increase in protein synthesis. The increase in protein synthesis after 16–24 h has been linked to the increased protein levels of translation initiation factors. However, the regulation of protein synthesis during the early onset of T cell activation has not been studied in great detail. We studied the regulation of protein synthesis after 1 h of activation using αCD3 antibody to stimulate the T cell receptor and αCD28 antibody to provide the co-stimulus.     

Preparative electroelution of specific protein antigens from MicoplasmaPneumoniae: use in an enazyme-linked immunosorbent assay (Ellisa)

A rapid, simple and preparative method is described for the recovery of the seven highest molecular weight proteins (HMWP) from Mycoplasma pneumoniae membrane. The yield of proteins obtained was approximately 90%. The method involved the separation of M. pneumoniae proteins by socium dodecyl sulphate polycrylamide gel electrophoresis (SDS-PAGE), followed by electroelution of HMWP.These eluted antigens were used in an ELISA to measure IgG antibodies in sera 9 blood donors and 9 patients with M. pneumoniae infection.The specificity fo M. pneumoniae HMWP was examined by competition ELISA and immunoblotting with different mycoplasma species encountered in teh respiratory tract.     

The role of human in the loop: lessons from D3R challenge 4

The rapid development of new machine learning techniques led to significant progress in the area of computer-aided drug design. However, despite the enormous predictive power of new methods, they lack explainability and are often used as black boxes. The most important decisions in drug discovery are still made by human experts who rely on intuitions and simplified representation of the field. We used D3R Grand Challenge 4 to model contributions of human experts during the prediction of the structure of protein–ligand complexes, and prediction of binding affinities for series of ligands in the context of absence or abundance of experimental data. We demonstrated that human decisions have a series of biases: a tendency to focus on easily identifiable protein–ligand interactions such as hydrogen bonds, and neglect for a more distributed and complex electrostatic interactions and solvation effects. While these biases still allow human experts to compete with blind algorithms in some areas, the underutilization of the information leads to significantly worse performance in data-rich tasks such as binding affinity prediction.     

Comparison of 1D a 2D ITP-MS performance parameters and application possibilities: Ultratrace determination of B vitamins in human urine

The possibility to investigate analytes at ultra-low concentration levels still remains a hot topic in bioanalysis. In this area, various preconcentration techniques are an integral part of analytical procedures. When applying electromigration separation techniques, an isotachophoresis has been advantageously employed many times for this purpose. To solve current biomedical tasks effectively, an advanced two-dimensional isotachophoretic instrument (in a hydrodynamically closed separation system with an enhanced sample load capacity) hyphenated with mass spectrometry (ITP-ITP-MS) has been proposed by Foret and coworkers. As a continuation, this work represents the first study dealing with a full validation of an ITP-ITP-MS method. In order to see the benefits of an online ITP sample pretreatment (preconcentration and clean-up) on the performance parameters, the developed 2D ITP-MS method was compared with a corresponding 1D ITP-MS method. Application potentialities of the compared methods were demonstrated via a determination of two B vitamins, namely thiamine and pyridoxine, in human urine samples. The developed 2D ITP-MS method showed its enhanced effectivity and usefulness for a routine biomedical use (here, a reliable screening of trace B vitamins in human urine without an offline sample preparation).     

SFE-CO2 extract from Typhonium giganteum Engl. tubers, induces apoptosis in human hepatoma SMMC-7721 cells involvement of a ROS-mediated mitochondrial pathway

Typhonium giganteum Engl. (BaiFuzi) is one of the herbs commonly used in traditional Chinese medicine against cancer. In our previous studies, 37 compounds were identified the SFE-CO(2) (supercritical fluid extraction with CO(2)) extract by GC-MS, including the four major components [β-sitosterol (40.22%), campesterol (18.45%), n-hexadecanoic acid (9.52%) and (Z,Z)-9,12-octadecadienoic acid (8.15%)]. The anti-cancer mechanisms of the SFE-CO(2 )extract from T. giganteum Engl. tubers have not been reported as yet. In this paper, the molecular mechanisms of the SFE-CO(2) extract-mediated apoptosis in SMMC-7721 cells were further examined. SFE-CO(2) extract inhibited the growth of SMMC-7721 cells in a time- and dose-dependent manner, arrested the cell cycle in the S phase and G2/M phase, and induced apoptosis. In addition, reactive oxygen species (ROS) increase, reduction of mitochondrial membrane potential, a rise in intracellular calcium levels were found in SMMC-7721 cells after treated with the extract. Western blot analysis showed that the extract caused down-regulation of Bcl-2 expression, and up-regulation of Bax expression. Moreover, caspase-3 and caspase-9 protease activity significantly increased in a dose-dependent manner. Collectively, our results showed that the SFE-CO(2) extract from T. giganteum Engl. tubers induces apoptosis in SMMC-7721 cells involving a ROS-mediated mitochondrial signalling pathway.     

Solid-state NMR spectroscopy of human immunodeficiency virus fusion peptides associated with host-cell-like membranes: 2D correlation spectra and distance measurements support a fully extended conformation and models for specific antiparallel strand registries

The human immunodeficiency virus (HIV) is "enveloped" by a membrane, and infection of a host cell begins with fusion between viral and target cell membranes. Fusion is catalyzed by the HIV gp41 protein which contains a functionally critical approximately 20-residue apolar "fusion peptide" (HFP) that associates with target cell membranes. In this study, chemically synthesized HFPs were associated with host-cell-like membranes and had "scatter-uniform" labeling (SUL), that is, only one residue of each amino acid type was U-(13)C, (15)N labeled. For the first sixteen HFP residues, an unambiguous (13)C chemical shift assignment was derived from 2D (13)C/(13)C correlation spectra with short mixing times, and the shifts were consistent with continuous beta-strand conformation. (13)C-(13)C contacts between residues on adjacent strands were derived from correlation spectra with long mixing times and suggested close proximity of the following residues: Ala-6/Gly-10, Ala-6/Phe-11, and Ile-4/Gly-13. Specific antiparallel beta-strand registries were further tested using a set of HFPs that were (13)CO-labeled at Ala-14 and (15)N-labeled at either Val-2, Gly-3, Ile-4, or Gly-5. The solid-state NMR data were fit with 50-60% population of antiparallel HFP with either Ala-14/Gly-3 or Ala-14/Ile-4 registries and 40-50% population of structures not specified by the NMR experiments. The first two registries correlated with intermolecular hydrogen bonding of 15-16 apolar N-terminal residues and this hydrogen-bonding pattern would be consistent with a predominant location of these residues in the hydrophobic membrane interior. To our knowledge, these results provide the first residue-specific structural models for membrane-associated HFP in its beta-strand conformation.     

Identification of four novel phosphorylation sites in estrogen receptor α: impact on receptor-dependent gene expression and phosphorylation by protein kinase CK2

Background

Human S100A12 is a member of the S100 family of EF-hand calcium-modulated proteins that are associated with many diseases including cancer, chronic inflammation and neurological disorders. S100A12 is an important factor in host/parasite defenses and in the inflammatory response. Like several other S100 proteins, it binds zinc and copper in addition to calcium. Mechanisms of zinc regulation have been proposed for a number of S100 proteins e.g. S100B, S100A2, S100A7, S100A8/9. The interaction of S100 proteins with their targets is strongly dependent on cellular microenvironment.

Results

The aim of the study was to explore the factors that influence S100A12 oligomerization and target interaction. A comprehensive series of biochemical and biophysical experiments indicated that changes in the concentration of calcium and zinc led to changes in the oligomeric state of S100A12. Surface plasmon resonance confirmed that the presence of both calcium and zinc is essential for the interaction of S100A12 with one of its extracellular targets, RAGE – the Receptor for Advanced Glycation End products. By using a single-molecule approach we have shown that the presence of zinc in tissue culture medium favors both the oligomerization of exogenous S100A12 protein and its interaction with targets on the cell surface.

Conclusion

We have shown that oligomerization and target recognition by S100A12 is regulated by both zinc and calcium. Our present work highlighted the potential role of calcium-binding S100 proteins in zinc metabolism and, in particular, the role of S100A12 in the cross talk between zinc and calcium in cell signaling.     

Differences in the low-energy collision-activated dissociation of carboxylate anions from structurally similar prostaglandins: E2, F2α, D2, and DHKF2α

Some intriguing discoveries were made concerning the collision-activated dissociation behavior of the derivatized carboxylate anions of PGE₂ and PGF_2α. The carboxylate anion [MPFB]^? formed from electron-capture negative chemical ionization of the pentafluorobenzyl ester-trimethylsilyl derivative of PGF_2α showed little fragmentation under typical collision gas pressures and energies (<2.0 mtorr N₂ and <20 eV). In contrast, the daughter spectra of the carboxylate anion of the methoxime-pentafluorobenzyl ester-trimethylsilyl derivative of PGE₂ produced many intense fragments under the same conditions.     

Temperature modulated differential scanning calorimetry (TMDSC) in the region of phase transitions. Part 2: some specific results from polymers

By means of four different examples (pressure crystallised, gel crystallised, nascent and highly stretched polyethylenes (PEs)) it is shown that temperature modulated DSC offers advantages against common DSC. It is possible to see dynamic processes inside the sample during melting. This way we found (i) that during melting of high pressure crystallised PE the so-called ₂-process (known from DMA) takes place, (ii) the lamellae doubling in gel crystallised UHMWPE can be seen in TMDSC signals, though no balance heat flow rate is visible in the common DSC, (iii) the same is true for the recrystallisation in nascent and highly stretched PE many degrees before the melting peak appears. To separate these results from the measured curves the knowledge of the heat transport into and within the sample is needed. A simple low pass filter model has proved its worth for this purpose.     

Antisymmetric exchange in [2Fe-2S]1+ clusters: EPR of the Rieske protein from Thermus thermophilus at pH 14

[2Fe-2S] clusters found in the xanthine oxidase family of proteins exhibit an S = 1/2 EPR feature, called signal II, for which one g-value is significantly above g = 2.0. The g-values of signal II cannot be explained with the standard spin coupling model that has been so successful in describing the g = 1.94 signals of [2Fe-2S] ferredoxins. We have studied the EPR spectra of the Rieske protein from Thermus thermophilus at pH 14 and observed a signal II-type EPR spectrum, with g-values at 1.81, 1.94, and 2.14. It is shown that the g-values of signal II can be explained by including an antisymmetric exchange term, d.S1xS2, in the spin Hamiltonian. The presence of this term is sensed by EPR if the isotropic exchange coupling constant J is sufficiently small. For the Rieske protein we determined J = 43 cm-1 which is at least 4 times smaller than the J values reported for [2Fe-2S] clusters that yield standard g = 1.94 signals.     

Structure elucidation from 2D NMR spectra using the StrucEluc expert system: detection and removal of contradictions in the data

The elucidation of chemical structures from 2D NMR data commonly utilizes a combination of COSY, HMQC/HSQC, and HMBC data. Generally COSY connectivities are assumed to mostly describe the separation of protons that are separated by 1 skeletal bond (3JHH), while HMBC connectivities represent protons separated from carbon atoms by 1 to 2 skeletal bonds (2JCH and 3JCH). Obviously COSY and HMBC connectivities of lengths greater than those described have been detected. Though experimental techniques have recently been described to aid in the identification of the nature of the couplings the detection of whether a coupling is 2-bond or greater still remains a challenge in most laboratories. In the StrucEluc software system the common lengths of the connectivities, 1-bond for COSY and 1- or 2-bond for HMBC, derived from 2D NMR data are set as the default. Therefore, in the presence of any extended connectivities contradictions can appear in the 2D NMR data. In this article, algorithmic methods for the detection and removal of contradictions in 2D NMR data that have been developed in support of StrucEluc are described. The methods are based on the analysis of molecular connectivity diagrams, MCDs. These methods have been implemented in the StrucEluc system and tested by solving 50 structural problems with 2D NMR spectral data containing contradictions. The presence of contradictions was detected by the algorithm in 90% of the cases, and the contradictions were automatically removed in approximately 50% of the problems. A method of "fuzzy" structure generation in the presence of contradictions has been suggested and successfully tested in this work. This work will demonstrate examples of the application of developed methods to a number of structural problems.     

Workflows and performances in the ranking prediction of 2016 D3R Grand Challenge 2: lessons learned from a collaborative effort

The 2016 D3R Grand Challenge 2 includes both pose and affinity or ranking predictions. This article is focused exclusively on affinity predictions submitted to the D3R challenge from a collaborative effort of the modeling and informatics group. Our submissions include ranking of 102 ligands covering 4 different chemotypes against the FXR ligand binding domain structure, and the relative binding affinity predictions of the two designated free energy subsets of 15 and 18 compounds. Using all the complex structures prepared in the same way allowed us to cover many types of workflows and compare their performances effectively. We evaluated typical workflows used in our daily structure-based design modeling support, which include docking scores, force field-based scores, QM/MM, MMGBSA, MD-MMGBSA, and MacroModel interaction energy estimations. The best performing methods for the two free energy subsets are discussed. Our results suggest that affinity ranking still remains very challenging; that the knowledge of more structural information does not necessarily yield more accurate predictions; and that visual inspection and human intervention are considerably important for ranking. Knowledge of the mode of action and protein flexibility along with visualization tools that depict polar and hydrophobic maps are very useful for visual inspection. QM/MM-based workflows were found to be powerful in affinity ranking and are encouraged to be applied more often. The standardized input and output enable systematic analysis and support methodology development and improvement for high level blinded predictions.     

Protein Alpha Shape Similarity Analysis (PASSA): a new method for mapping protein binding sites. Application in the design of a selective inhibitor of tyrosine kinase 2

We have developed a method that we have called Protein Alpha Shape Similarity Analysis (PASSA), that identifies interaction sites that can be utilised to achieve selectivity towards a protein. We have shown that this method is able to identify residues of tyrosine kinases that interact with known selective inhibitors using the following test cases: Abelson (Abl) kinase in complex with STI-571 and Janus kinase 2 (Jak2) in complex with AG-490. The 3D structures of the tyrosine kinase domains of Tyrosine kinase 2 (Tyk2) and Jak2 have been predicted by homology modelling. Computational docking of AG-490 and a set of tyrphostins known not to inhibit Jak2 indicated that our homology models are able to separate inhibitors from non-inhibitors. PASSA has also been used to identify unique properties of Tyk2. According to our results, interactions with hydrogen acceptors and donors on the following residues can be utilised to achieve selectivity towards Tyk2: Y955, E1053, D1062 and S1063. These residues are placed close to non-conserved hydrophobic pockets. The PASSA results, together with results from Multiple Copy Simultaneous Search (MCSS) were used to suggest functional groups of a selective Tyk2 inhibitor.