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61.
The insect kinins are present in a wide variety of insects and function as potent diuretic peptides, though they are subject to rapid degradation by internal peptidases. Insect kinin analogs incorporating stereochemical variants of (2S,4S)-4-aminopyroglutamate (APy), a cis-peptide bond motif, demonstrate significant activity in a cricket diuretic assay. Insect kinin analogs containing (2R,4R)-APy, (2S,4R)-APy and (2S,4S)-APy are essentially equipotent on an insect diuretic assay, with EC(50) values of about 10(-7)M, whereas the (2R,4S)-APy analog is at least 10-fold more potent (EC(50) = 7 x 10(-9)M). Conformational studies in aqueous solution indicate that the (2R,4S)-APy analog is considerably more flexible than the other three variants, which may explain its greater potency. The work identifies the optimal stereochemistry for the APy scaffold with which to design biostable, peptidomimetic analogs with the potential to disrupt critical insect kinin-regulated processes in insects. 相似文献
62.
Fujarewicz K Kimmel M Lipniacki T Swierniak A 《IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM》2007,4(3):322-335
The paper concerns the problem of fitting mathematical models of cell signaling pathways. Such models frequently take the form of sets of nonlinear ordinary differential equations. While the model is continuous in time, the performance index used in the fitting procedure involves measurements taken at discrete time moments. Adjoint sensitivity analysis is a tool which can be used for finding the gradient of a performance index in the space of parameters of the model. In the paper, a structural formulation of adjoint sensitivity analysis called the generalized backpropagation through time (GBPTT) is used. The method is especially suited for hybrid, continuous-discrete time systems. As an example, we use the mathematical model NF-kappaB of the regulatory module, which plays a major role in the innate immune response in animals. 相似文献
63.
In vivo effects of lipopolysaccharide and TLR4 on platelet production and activity: implications for thrombotic risk. 总被引:2,自引:0,他引:2
Muthuvel Jayachandran Gregory J Brunn Krzysztof Karnicki Randall S Miller Whyte G Owen Virginia M Miller 《Journal of applied physiology》2007,102(1):429-433
Gram-negative bacteria release LPS, which activates Toll-like-receptor-4 (TLR4) in the host, initiating an inflammatory response to infection. Infection increases risk for thrombosis. Platelets contribute to defense from infection and to thrombosis. Experiments were designed to determine whether LPS, through TLR4 signaling, affects platelet phenotype. Platelet responses in wild-type (WT) mice and mice that lack the TLR4 gene (dTLR4) were compared following a single nonlethal injection of LPS (0.2 mg/kg iv). Compared with WT mice, mice without TLR4 had fewer circulating platelets with lower RNA content and were less responsive to thrombin-activated expression of P-selectin but were equally sensitive to aggregation or ATP secretion. One week following the LPS injection, the time it takes for the circulating platelet pool to turnover, the number of circulating platelets, thrombin-induced expression of P-selectin, and collagen-activated aggregation were increased comparably in both groups of mice. Therefore, the change of the platelet pool to an activated phenotype 1 wk after a single exposure to LPS appears to arise from a process that is independent of TLR4. The persistence of the effect 1 wk after the injection suggests that the changes reflect an action of LPS on megakaryocytes and their platelet progeny rather than on circulating platelets, which would have been cleared. 相似文献
64.
Sergey A. Samsonov Emilia A. Lubecka Krzysztof K. Bojarski Robert Ganzynkowicz Adam Liwo 《Biopolymers》2019,110(8):e23269
Heparin belongs to glycosaminoglycans (GAGs), a class of periodic linear anionic polysaccharides, which are functionally important components of the extracellular matrix owing to their interactions with various protein targets. Heparin is known to be involved in many cell signaling processes, while the experimental data available for heparin are significantly more abundant than for other GAGs. At the same time, the length and conformational flexibility of the heparin represent major challenges for its theoretical analysis. Coarse-grained (CG) approaches, which enable us to extend the size- and time-scale by orders of magnitude owing to reduction of system representation, appear, therefore, to be useful in simulating these systems. In this work, by using umbrella-sampling molecular dynamics simulations, we derived and parameterized the CG backbone-local potentials of heparin chains and the orientational potentials for the interactions of heparin with amino acid side chains to be further included in the physics-based Unified Coarse-Grained Model of biological macromolecules. With these potentials, simulations of extracellular matrix processes where both heparin and multiple proteins participate will be possible. 相似文献
65.
Magnetoreception is the ability of organisms to perceive magnetic fields in the surrounding environment and changes in its properties such as field direction, intensity and gradient, where the effect on organisms can manifest as an array of reactions. As the magnetic sense is found in many taxa, both evolutionarily young and old, it can be assumed that magnetoreception came into existence as one of the first sensory systems. Many studies on the effect of magnetic fields on fishes have considered both fishes that migrate for long distances and those that are more or less sedentary. Research has focused on tracing the perception of the geomagnetic field by fishes and understanding magnetic fields that are smaller and larger than the ambient Earth's geomagnetic field. The question of the effect of magnetic fields of values higher than the Earth's is gaining importance with the increasing effect of anthropogenic magnetic and electromagnetic fields in aquatic ecosystems. This review draws together the results of studies on the effect and reception of natural and human-generated magnetic fields on fishes at various stages of ontogeny, chronologically arranged from gametes, through embryonic development, embryonic and larval motor function, directional reactions of embryos and larvae, orientation of fishes, to the mechanisms of magnetic field reception. The present state of knowledge indicates a common nature of effect on various ontogenetic stages of fishes. However, understanding of the mechanisms of magnetic sense in fishes and its relevance for ecological outcomes highlights that further progress requires more detailed research. 相似文献
66.
Rafal Krela Elzbieta Poreba Martyna Weglewska Tomasz Skrzypczak Krzysztof Lesniewicz 《Biochimica et Biophysica Acta (BBA)/General Subjects》2019,1863(3):521-527
Background
During standard gene cloning, the recombinant protein appearing in bacteria as the result of expression leakage very often inhibits cell proliferation leading to blocking of the cloning procedure. Although different approaches can reduce transgene basal expression, the recombinant proteins, which even in trace amounts inhibit bacterial growth, can completely prevent the cloning process.Methods
Working to solve the problem of DNase II-like cDNA cloning, we developed a novel cloning approach. The method is based on separate cloning of the 5′ and 3′ fragments of target cDNA into a vector in such a way that the short Multiple Cloning Site insertion remaining between both fragments changes the reading frame and prevents translation of mRNA arising as a result of promoter leakage. Subsequently, to get the vector with full, uninterrupted Open Reading Frame, the Multiple Cloning Site insertion is removed by in vitro restriction/ligation reactions, utilizing the unique restriction site present in native cDNA.Results
Using this designed method, we cloned a coding sequence of AcDNase II that is extremely toxic for bacteria cells. Then, we demonstrated the usefulness of the construct prepared in this way for overexpression of AcDNase II in eukaryotic cells.Conclusions
The designed method allows cloning of toxic protein coding sequences that cannot be cloned by standard methods.General significance
Cloning of cDNAs encoding toxic proteins is still a troublesome problem that hinders the progress of numerous studies. The method described here is a convenient solution to cloning problems that are common in research on toxic proteins. 相似文献67.
J. Eduardo Fajardo Rojan Shrestha Nelson Gil Adam Belsom Silvia N. Crivelli Cezary Czaplewski Krzysztof Fidelis Sergei Grudinin Mikhail Karasikov Agnieszka S. Karczyńska Andriy Kryshtafovych Alexander Leitner Adam Liwo Emilia A. Lubecka Bohdan Monastyrskyy Guillaume Pagès Juri Rappsilber Adam K. Sieradzan Celina Sikorska Esben Trabjerg Andras Fiser 《Proteins》2019,87(12):1283-1297
With the advance of experimental procedures obtaining chemical crosslinking information is becoming a fast and routine practice. Information on crosslinks can greatly enhance the accuracy of protein structure modeling. Here, we review the current state of the art in modeling protein structures with the assistance of experimentally determined chemical crosslinks within the framework of the 13th meeting of Critical Assessment of Structure Prediction approaches. This largest-to-date blind assessment reveals benefits of using data assistance in difficult to model protein structure prediction cases. However, in a broader context, it also suggests that with the unprecedented advance in accuracy to predict contacts in recent years, experimental crosslinks will be useful only if their specificity and accuracy further improved and they are better integrated into computational workflows. 相似文献
68.
Davide Sala Yuanpeng Janet Huang Casey A. Cole David A. Snyder Gaohua Liu Yojiro Ishida G.V.T. Swapna Kelly P. Brock Chris Sander Krzysztof Fidelis Andriy Kryshtafovych Masayori Inouye Roberto Tejero Homayoun Valafar Antonio Rosato Gaetano T. Montelione 《Proteins》2019,87(12):1315-1332
CASP13 has investigated the impact of sparse NMR data on the accuracy of protein structure prediction. NOESY and 15N-1H residual dipolar coupling data, typical of that obtained for 15N,13C-enriched, perdeuterated proteins up to about 40 kDa, were simulated for 11 CASP13 targets ranging in size from 80 to 326 residues. For several targets, two prediction groups generated models that are more accurate than those produced using baseline methods. Real NMR data collected for a de novo designed protein were also provided to predictors, including one data set in which only backbone resonance assignments were available. Some NMR-assisted prediction groups also did very well with these data. CASP13 also assessed whether incorporation of sparse NMR data improves the accuracy of protein structure prediction relative to nonassisted regular methods. In most cases, incorporation of sparse, noisy NMR data results in models with higher accuracy. The best NMR-assisted models were also compared with the best regular predictions of any CASP13 group for the same target. For six of 13 targets, the most accurate model provided by any NMR-assisted prediction group was more accurate than the most accurate model provided by any regular prediction group; however, for the remaining seven targets, one or more regular prediction method provided a more accurate model than even the best NMR-assisted model. These results suggest a novel approach for protein structure determination, in which advanced prediction methods are first used to generate structural models, and sparse NMR data is then used to validate and/or refine these models. 相似文献
69.
Agnieszka Girstun Takao Ishikawa Krzysztof Staron 《Journal of cellular biochemistry》2019,120(7):11794-11808
Subnuclear localization of topoisomerase I (top I) is determined by its DNA relaxation activity and a net of its interactions with in majority unidentified nucleolar and nucleoplasmic elements. Here, we recognized SR protein SRSF1 (Serine/arginine-rich splicing factor 1, previously known as SF2/ASF) as a new element of the net. In HeLa cells, overexpression of SRSF1 recruited top I to the nucleoplasm whereas its silencing concentrated it in the nucleolus. Effect of SRSF1 was independent of top I relaxation activity and was the best pronounced for the mutant inactive in relaxation reaction. In HCT116 cells where top I was not released from the nucleolus upon halting relaxation activity, it was also not relocated by elevated level of SRSF1. Out of remaining SR proteins, SRSF5, SRSF7, and SRSF9 did not influence the localization of top I in HeLa cells whereas overexpression of SRSF2, SRSF3, SRSF6, and partly SRSF4 concentrated top I in the nucleolus, most possibly due to the reduction of the SRSF1 accessibility. Specific effect of SRSF1 was exerted because of its distinct RS domain. Silencing of SRSF1 compensated the deletion of the top I N-terminal region, individually responsible for nucleoplasmic localization of the mutant, and restored the wild-type phenotype of deletion mutant localization. SRSF1 was essential for the camptothecin-induced clearance from the nucleolus. These results suggest a possible role of SRSF1 in establishing partition of top I between the nucleolus and the nucleoplasm in some cell types with distinct combinations of SR proteins levels. 相似文献
70.
Mud (with or without Chironomus) taken from the bottom of a shallow (6 m) eutrophic reservoir, was maintained (about 3 weeks) in trays supported 30 cm and 70 cm above the bottom. At the end of the experiment it contained 7-9 times more Chironomus plumosus individuals than did the mud at the bottom. Numbers of young (≤12 mm) larvae were up to 18 times higher, and youngest (≤6 mm) larvae (absent in the bottom at the end of the experiment) were abundant. Such patterns were more evident at the higher (70 cm) than the lower (30 cm) level. Numbers of the oldest (≥18 mm) larvae at the higher level were only 6 times higher (whilst more than 8 times at the lower level) than at the bottom, probably due to quicker development and emergence in higher trays. So the production of the population increased with the increasing distance from the bottom. In the tray at the bottom (which could protrude 1–2 cm above it) numbers were twice those outside it, and the youngest larvae occurred. There was a slight current at the research site. Nevertheless, short time oxygen deficits occurred periodically, and were probably the main cause of considerable reductions in Chironomus numbers at the bottom during the experiment. 相似文献