Impact of Noncovalent Sulfur–Fluorine Interaction Position on Properties,Structures, and Photovoltaic Performance in Naphthobisthiadiazole‐Based Semiconducting Polymers

Controlling the energetics and backbone order of semiconducting polymers is essential for the performance improvement of polymer‐based solar cells. The use of fluorine as the substituent for the backbone is known to effectively deepen the molecular orbital energy levels and coplanarize the backbone by noncovalent interactions with sulfur of the thiophene ring. In this work, novel semiconducting polymers are designed and synthesized based on difluoronaphthobisthiadiazole (FNTz) as a new family of naphthobisthiadiazole (NTz)–quaterthiophene copolymer systems, which are one of the highest performing polymers in solar cells. The effect of the fluorination position on the energetics and backbone order is systematically studied. It is found that the dependence of the solar cell fill factor on the active layer thickness is very sensitive to the fluorination position. It is thus further investigated and discussed how the structural features of the polymers influence the photovoltaic parameters as well as the diode characteristics and bimolecular recombination. Further, the polymer with fluorine on both the naphthobisthiadiazole and quaterthiophene moieties exhibits a quite high power conversion efficiency of 10.8% in solar cells in combination with a fullerene. It is believed that the results would offer new insights into the development of semiconducting polymers.     

Plasminogen binding with decapeptide and polypeptide fragments of streptokinase

The plasminogen binding with streptokinase decapeptides, modeling the primary structure of molecule, and chymotryptic fragments of streptokinase have been investigated. The immunoenzymatic assay has shown that plasminogen binds to all streptokinase fragments with the decreasing affinity in the set of fragments: 36 > 30 > 17 > 7 > 11 kDa. Location of the binding sites in streptokinase primary structure was performed using the immobilized decapeptides on plastic pins adopted to IEA. In the presence of 10 mM 6-aminohexanoic acid 11 sites for human Glu- and mini-plasminogens, pig and bovine plasminogens binding have been found. They were of the same location for human, bovine and pig plasminogens. 3 sites were located in plasminogen alpha-domain--T43-A72, N113-T126, Q133-V158, 5 sites in beta-domain--T163-L188, A203-S222, Q239-I264, Y275-L294, T315-L340, and 3 sites in gamma-domain--T361-R362, N377-E392, T397-N410. Participation of linear part of streptokinase polypeptide chain in plasminogen--streptokinase complex formation is suggested.     

Effect of forskolin and quinacrine on leukocyte functions under the effect of low-dose radiation

The adenylate cyclase and phospholipase A2 incorporation in the functional responses as well as lipid peroxidation processes and glutathione system homeostasis of animal leukocytes to small doses of ionizing radiation (1-100 mGy) have been estimated. The cells were irradiated by introduction of radioactive isotope 14C-leucine into the incubation medium. It is established that the ionizing radiation has different effects on the modification of cellular functions by the agents, which change adenylate cyclase and phospholipase A2 activity. Neutralization of stimulative irradiation effect on chemokinesis of polymorphonuclear leukocytes by quinacrine (the inhibitor of phospholipase A2) indicates for certain, that metabolism of eicosanoids takes immediate part in the cell response to ionizing radiation. Apparently, adenylate cyclase has no influence on this process, where at indicates the lack of influence of forskolin (the stimulator of adenylate cyclase) on the spontaneous motility, and on the radiation action on this leukocyte function. Rosette forming ability of lymphocytes is regulated by both enzymes because it is modified both by the inhibitor of phospholipase A2, and by the adenylate cyclase stimulant. In this case it is impossible to exclude the action of ionizing radiation both through the adenylate cyclase cascade, and through the eicosanoid metabolism. In all the concentration range the radionuclides do not affect the studied biochemical indexes of the cell, but change the action of the modifiers.     

The cytotoxic effect of heavy metals on an L-cell culture

The dependence of some parameters of L-cells culture viability on different concentrations of heavy metals was studied. Considerable cytotoxic effect of low concentrations of nickel (0.025 mcg/ml) and lead (0.05 mcg/ml) was shown. Copper and chrome at concentrations of 0.25-0.5 mcg/ml promote cells proliferation between third and fifth days of cultivation. Nickel at concentration 0.025 mcg/ml and lead at all investigated concentrations synchronize cells division in culture. Increasing of giant polynucleas cells level in culture was characteristic for investigated metals. The maximum levels of this type cells were caused by the action of nickel, chrome and copper.     

Profile-based string kernels for remote homology detection and motif extraction

We introduce novel profile-based string kernels for use with support vector machines (SVMs) for the problems of protein classification and remote homology detection. These kernels use probabilistic profiles, such as those produced by the PSI-BLAST algorithm, to define position-dependent mutation neighborhoods along protein sequences for inexact matching of k-length subsequences ("k-mers") in the data. By use of an efficient data structure, the kernels are fast to compute once the profiles have been obtained. For example, the time needed to run PSI-BLAST in order to build the profiles is significantly longer than both the kernel computation time and the SVM training time. We present remote homology detection experiments based on the SCOP database where we show that profile-based string kernels used with SVM classifiers strongly outperform all recently presented supervised SVM methods. We further examine how to incorporate predicted secondary structure information into the profile kernel to obtain a small but significant performance improvement. We also show how we can use the learned SVM classifier to extract "discriminative sequence motifs"--short regions of the original profile that contribute almost all the weight of the SVM classification score--and show that these discriminative motifs correspond to meaningful structural features in the protein data. The use of PSI-BLAST profiles can be seen as a semi-supervised learning technique, since PSI-BLAST leverages unlabeled data from a large sequence database to build more informative profiles. Recently presented "cluster kernels" give general semi-supervised methods for improving SVM protein classification performance. We show that our profile kernel results also outperform cluster kernels while providing much better scalability to large datasets.     

Semi-supervised protein classification using cluster kernels

MOTIVATION: Building an accurate protein classification system depends critically upon choosing a good representation of the input sequences of amino acids. Recent work using string kernels for protein data has achieved state-of-the-art classification performance. However, such representations are based only on labeled data--examples with known 3D structures, organized into structural classes--whereas in practice, unlabeled data are far more plentiful. RESULTS: In this work, we develop simple and scalable cluster kernel techniques for incorporating unlabeled data into the representation of protein sequences. We show that our methods greatly improve the classification performance of string kernels and outperform standard approaches for using unlabeled data, such as adding close homologs of the positive examples to the training data. We achieve equal or superior performance to previously presented cluster kernel methods and at the same time achieving far greater computational efficiency. AVAILABILITY: Source code is available at www.kyb.tuebingen.mpg.de/bs/people/weston/semiprot. The Spider matlab package is available at www.kyb.tuebingen.mpg.de/bs/people/spider. SUPPLEMENTARY INFORMATION: www.kyb.tuebingen.mpg.de/bs/people/weston/semiprot.     

An intramolecular interaction between SH2-kinase linker and kinase domain is essential for the catalytic activity of protein-tyrosine kinase-6

Protein-tyrosine kinase-6 (PTK6, also known as Brk) is a non-receptor tyrosine kinase that contains SH3, SH2, and catalytic (Kinase) domains. We have identified an intramolecular interaction between the linker (Linker) region connecting the SH2 and Kinase domains and the Kinase domain. Residue Trp-184 within the Linker region is essential for the Linker-Kinase interaction but not for the Linker-SH3 interaction. A recombinant PTK6 Kinase domain connected to the Linker region had catalytic activity in terms of autophosphorylation, phosphorylation of a PTK6 substrate, BKS, and phosphorylation of an oligopeptide substrate, whereas the Kinase domain itself, or one connected to a Linker region containing a W184A substitution, did not. The introduction of the W184A mutation into PTK6 also abrogated autophosphorylation and phosphorylation of another PTK6 substrate, Sam68, as well as phosphorylation of intracellular proteins. It also abolished the ability of PTK6 to promote proliferation and prevent apoptosis of HEK 293 cells, as well as to permit anchorage-independent colony formation. Therefore, unlike Src family members, in which the Linker-Kinase interaction inhibits catalytic activity, in PTK6 this interaction has an essential positive role.