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1.
Summary The feasibility of determining the relative populations of multi-conformer structures from NOE-derived distances alone is assessed. Without cross-validation of the NOE restraints, any population ratio can be refined to a similar quality of the fit. Complete cross-validation provides a less biased measure of fit and allows the estimation of the correct population ratio when used in conjunction with very tight distance restraints. With the qualitative distance restraints most commonly used in NMR structure determination, cross-validation is unsuccessful in providing the correct answer. Other experimental sources are therefore needed to determine relative populations of multi-conformer structures.To whom correspondence should be addressed. 相似文献
2.
Kristen M. Varney Alexandre M. J. J. Bonvin Marzena Pazgier Jakob Malin Wenbo Yu Eugene Ateh Taiji Oashi Wuyuan Lu Jing Huang Marlies Diepeveen-de Buin Joseph Bryant Eefjan Breukink Alexander D. MacKerell Jr Erik P. H. de Leeuw 《PLoS pathogens》2013,9(11)
We have previously reported on the functional interaction of Lipid II with human alpha-defensins, a class of antimicrobial peptides. Lipid II is an essential precursor for bacterial cell wall biosynthesis and an ideal and validated target for natural antibiotic compounds. Using a combination of structural, functional and in silico analyses, we present here the molecular basis for defensin-Lipid II binding. Based on the complex of Lipid II with Human Neutrophil peptide-1, we could identify and characterize chemically diverse low-molecular weight compounds that mimic the interactions between HNP-1 and Lipid II. Lead compound BAS00127538 was further characterized structurally and functionally; it specifically interacts with the N-acetyl muramic acid moiety and isoprenyl tail of Lipid II, targets cell wall synthesis and was protective in an in vivo model for sepsis. For the first time, we have identified and characterized low molecular weight synthetic compounds that target Lipid II with high specificity and affinity. Optimization of these compounds may allow for their development as novel, next generation therapeutic agents for the treatment of Gram-positive pathogenic infections. 相似文献
3.
CCL18 has been reported to be present constitutively at high levels in the circulation, and is further elevated during inflammatory diseases. Since it is a rather poor chemoattractant, we wondered if it may have a regulatory role. CCL18 has been reported to inhibit cellular recruitment mediated by CCR3, and we have shown that whilst it is a competitive functional antagonist as assessed by Schild plot analysis, it only binds to a subset of CCR3 receptor populations. We have extended this inhibitory activity to other receptors and have shown that CCL18 is able to inhibit CCR1, CCR2, CCR4 and CCR5 mediated chemotaxis, but has no effect on CCR7 and CCR9, nor the CXC receptors that we have tested. Whilst CCL18 is able to bind to CCR3, it does not bind to the other receptors that it inhibits. We therefore tested the hypothesis that it may displace glycosaminoglycan (GAG) chemokines bound either in cis- on the leukocyte, or in trans-presentation on the endothelial surface, thereby inhibiting the recruitment of leukocytes into the site of inflammation. We show that CCL18 selectivity displaces heparin bound chemokines, and that chemokines from all four chemokine sub-classes displace cell bound CCL18. We propose that CCL18 has regulatory properties inhibiting chemokine function when GAG-mediated presentation plays a role in receptor activation. 相似文献
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The effect of food deprivation on ova transport, hormonal profiles and metabolic changes was studied in 20 crossbred multiparous
sows during their second oestrus after weaning. To determine the time of ovulation, transrectal ultrasonographic examination
was performed. The sows were divided into 2 groups, one control group (C-group), which was fed according to Swedish standards,
and one experimental group (E-group). The E-group sows were deprived of food from the first morning meal after ovulation until
slaughter. Blood samples were collected every second hour from about 12 h before expected ovulation in the second oestrus
after weaning until slaughter and were analysed for progesterone, prostaglandin F2α-metabolite, insulin, glucose, free fatty acids and triglycerides. All sows were slaughtered approximately 48 h after ovulation
and the genital tract was recovered. The isthmic part of the oviduct was divided into 3 equally long segments and flushed
separately with phosphate buffered saline (PBS). Uterine horns were also flushed with PBS. A significantly greater number
of ova were found in the first and second part of the isthmus in the E-group (p = 0.05) while in the C-group most of the ova
were found in the third part of the isthmus or the uterus (p = 0.01). The level of prostaglandin F2α-metabolite was significantly higher in the E-group compared with the C-group. The concentration of progesterone increased
in both groups after ovulation but there were no significant differences between the groups. The other blood parameters showed
that the food-deprived sows were in a catabolic state. The 48 h period of fasting results, directly or indirectly in an delayed
ova transport, which may be due to a delayed relaxation in the smooth circular muscle layer of the isthmus. 相似文献
6.
de Vries SJ van Dijk AD Krzeminski M van Dijk M Thureau A Hsu V Wassenaar T Bonvin AM 《Proteins》2007,69(4):726-733
Here we present version 2.0 of HADDOCK, which incorporates considerable improvements and new features. HADDOCK is now able to model not only protein-protein complexes but also other kinds of biomolecular complexes and multi-component (N > 2) systems. In the absence of any experimental and/or predicted information to drive the docking, HADDOCK now offers two additional ab initio docking modes based on either random patch definition or center-of-mass restraints. The docking protocol has been considerably improved, supporting among other solvated docking, automatic definition of semi-flexible regions, and inclusion of a desolvation energy term in the scoring scheme. The performance of HADDOCK2.0 is evaluated on the targets of rounds 4-11, run in a semi-automated mode using the original information we used in our CAPRI submissions. This enables a direct assessment of the progress made since the previous versions. Although HADDOCK performed very well in CAPRI (65% and 71% success rates, overall and for unbound targets only, respectively), a substantial improvement was achieved with HADDOCK2.0. 相似文献
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9.
Identifying resuspended particles using isotope ratios 总被引:3,自引:2,他引:3
Three simple methods were developed to estimate the proportion of particles in lake water derived from resuspended material. These techniques use the different distributions of long and short-lived radioisotopes sorbed onto particles and were tested in the three basins of Lake Erie using 7Be, 137Cs and 210Po/210Pb.While the concentration of 210Po on particles did not vary significantly in the lake, resuspended particles were characterized by high concentrations of 137Cs and low concentrations of 7Be. The distribution of these radioisotopes is consistent with a simple mixing model in which the fraction of particles in the lake water derived from resuspension ranged from 8% to about 100%. Higher concentrations of resuspended particles were found in deeper samples from the nepheloid layer and in the shallow western basin where thermal stratification was very weak. 相似文献
10.
Juan Manuel Herrero-Medrano Hendrik-Jan Megens Martien AM Groenen Mirte Bosse Miguel Pérez-Enciso Richard PMA Crooijmans 《BMC genomics》2014,15(1)