Water regulation of actinomycin-D binding to DNA: the interplay among drug affinity, DNA long-range conformation, and hydration

Actiaomycin-D (actD) binds to natural DNA at two different classes of binding sites, weak and strong. The affinity for these sites is highly dependent on DNA se(sequence and solution conditions, and the interaction appears to be purely entropic driven Although the entropic character of this reaction has been attributed to the release of water molecules upon drug to DNA complex formation, the mechanism by which hydration regulates actD binding and discrimination between different classes of binding sites on natural DNA is still unknown. In this work, we investigate the role of hydration on this reaction using the osmotic stress method. We skew that the decrease of solution water activity, due to the addition of sucrose, glycerol ethylene glycol, and betaine, favors drug binding to the strong binding sites on DNA by increasing both the apparent binding affinity Delta G, and the number of DNA base pairs apparently occupied by the bound drug n(bp/actD). These binding parameters vary linearly with the logarithm of the molar fraction of water in solution log(X-w), which indicates the contribution of water binding to the energetic of the reaction. It is demonstrated that the hydration change measured upon binding increases proportionally to the apparent size of the binding site n(bp/uctD). This indicates that n(bp/actD) measured from the Scatchard plod is a measure of the size of the DNA molecule changing conformation due to ligand binding. We also find that the contribution of DNA deformation, gauged by n(bp/act) to the total free energy of binding Delta G, is given by Delta G = Delta G(local) + n(bp/actD) x delta G(DNA), where Delta G(local), = -8020 +/- 51 cal/mol of actD bound and delta G(DNa) = -24.1 +/- 1.7cal/mol of base pair at 25 degrees C. We interpret Delta G(local), as the energetic contribution due to the direct interactions of actD with the actual tetranucleotide binding site, and it n(bp/actB) X delta G(DNA) as that due to change inconformation, induced by binding, of it n(bp/actD) DNA base pairs flanking the local site. This interpretation is supported by the agreement found between the value of delta G(DNA) and the torsional free energy change measured independently. We conclude suggesting an allosteric model for ligand binding to DNA, such that the increase in binding affinity is achieved by increasing the relaxation of the unfavorable free energy of binding storage at the local site through a larger number of DNA base pairs. The new aspect on this model is that the size of the complex is not fixed but determined by solutions conditions, such as water activity, which modulate the energetic barrier to change helix conformation. These results may suggest that long-range allosteric transitions of duplex DNA are involved in the inhibition of RNA synthesis by actD, and more generally, in the regulation of transcription. (C) 2000 John Wiley & Sons, Inc.

Anoplin, a novel antimicrobial peptide from the venom of the solitary wasp Anoplius samariensis

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The effect of bovine interferon-alpha I1 on pregnancy rate in heifers.

Bovine interferon-alpha I1 (bIFN-alpha) may be useful for enhancing fertility in sheep and cattle because it has extensive sequence homology with ovine and bovine trophoblast protein-1 and, like those proteins, extends corpus luteum lifespan. To test the effectiveness of bIFN-alpha to enhance fertility, several experiments were performed in which inseminated heifers were given i.m. injections of bIFN-alpha approximately at the time of embryo-mediated signals that result in maintenance of the corpus luteum. In Exp. 1, heifers given 20 mg of bIFN-alpha daily from d 14 to 17 tended (P less than .07) to have lower pregnancy rates at d 110 to 112 of gestation (36/75; 48% vs 43/72; 60%). Similar results were obtained in Exp. 2 when heifers received a single injection of 40 mg of bIFN-alpha or placebo at d 13 after estrus; pregnancy rates at d 42 were 39/104 (38%) for bIFN-alpha and 47/98 (48%) for placebo. In Exp. 3, heifers were given gradually increasing doses of bIFN-alpha or placebo from d 11 to 19, because such a regimen had been shown to reduce the number of heifers experiencing hyperthermia after bIFN-alpha injection. Pregnancy rates were 42/95 (44%) for bIFN-alpha and 62/111 (56%) for placebo. Across all three experiments, pregnancy rates were lower (P less than .01) for heifers treated with bIFN-alpha (117/274; 43%) than for heifers treated with placebo (152/281; 54%). In conclusion, these results demonstrate that, under the administration systems used, bIFN-alpha does not increase pregnancy rate, but rather tends to reduce it.

Structures of the noncovalent complexes of human and bovine prothrombin fragment 2 with human PPACK-thrombin

Both human and bovine prothrombin fragment 2 (the second kringle) have been cocrystallized separately with human PPACK (D-Phe-Pro-Arg)-thrombin, and the structures of these noncovalent complexes have been determined and refined (R = 0.155 and 0.157, respectively) at 3.3-Å resolution using X-ray crystallographic methods. The kringles interact with thrombin at a site that has previously been proposed to be the heparin binding region. The latter is a highly electropositive surface near the C-terminal helix of thrombin abundant in arginine and lysine residues. These form salt bridges with acidic side chains of kringle 2. Somewhat unexpectedly, the negative groups of the kringle correspond to an enlarged anionic center of the lysine binding site of lysine binding kringles such as plasminogens K1 and K4 and TPA K2. The anionic motif is DGDEE in prothrombin kringle 2. The corresponding cationic center of the lysine binding site region has an unfavorable Arg70Asp substitution, but Lys35 is conserved. However, the folding of fragment 2 is different from that of prothrombin kringle 1 and other kringles: the second outer loop possesses a distorted two-turn helix, and the hairpin β-turn of the second inner loop pivots at Val64 and Asp70 by 60°. Lys35 is located on a turn of the helix, which causes it to project into solvent space in the fragment 2-thrombin complex, thereby devastating any vestige of the cationic center of the lysine binding site. Since fragment 2 has not been reported to bind lysine, it most likely has a different inherent folding conformation for the second outer loop, as has also been observed to be the case with TPA K2 and the urokinase kringle. The movement of the Val64-Asp70 β-turn is most likely a conformational change accompanying complexation, which reveals a new heretofore unsuspected flexibility in kringles. The fragment 2-thrombin complex is only the second cassette module-catalytic domain structure to be determined for a multidomain blood protein and only the third domain-domain interaction to be described among such proteins, the others being factor Xa without a Gla domain and Ca2+ prothrombin fragment 1 with a Gla domain and a kringle. © 1993 American Chemical Society.

Hepatogenous photosensitization of ruminants by Brachiaria decumbens and Panicum dichotomiflorum in the absence of sporidesmin: Lithogenic saponins may be responsible

As part of a study of plants involved in crystal-associated hepatogenous photosensitization diseases, samples of Brachiaria decumbens and Panicum dichotomiflorum on which cattle and goats had recently been photosensitized were analyzed. The level of saponins associated with these photosensitization outbreaks were determined by GC-MS. Only low levels of Pithomyces chartarum spores were present on the B decumbens, and all isolates obtained failed to produce sporidesmin.

Estimativa do tamanho das fêmeas com ovos de Moina minuta Hansen, 1899 (Cladocera, Crustacea) no lago Amapá, Rio Branco, Estado do Acre Brasil

Moina minuta, a tropical species of Cladocera, was selected for the study of medium size at maturity and female egg production, due to its abundance and frequency in samples during low-water season in 1997 and high-water season in 1998, in Amapá Lake, Western Amazônia. The primiparous female had a size of 330 μm and 340 μm in low and high water, respectively. Moina individuals reached maximum size during high water (595μm). The medium size of the ovigerous females, in low water was 501 μm, producing an average of 4.41 eggs/female, while in high water, it was 533μm, with an average egg production of 4.84 eggs/female. The results, analyzed by the t test and Fischer's F test, showed that there were no statistical differences in size among individuals (t= -10.69, F=1.20 and P>0.1227), nor among ovigerous females (t= -4.45, F=1.02 and P>0.8906), considering the two seasons.

Measurement of the charge ratio of atmospheric muons with the CMS detector

We present a measurement of the ratio of positive to negative muon fluxes from cosmic ray interactions in the atmosphere, using data collected by the CMS detector both at ground level and in the underground experimental cavern at the CERN LHC. Muons were detected in the momentum range from 5 GeV/. c to 1 TeV/. c. The surface flux ratio is measured to be 1.2766±0.0032(stat.)±0.0032(syst.), independent of the muon momentum, below 100 GeV/. c. This is the most precise measurement to date. At higher momenta the data are consistent with an increase of the charge ratio, in agreement with cosmic ray shower models and compatible with previous measurements by deep-underground experiments. © 2010.

Measurement of the muon stopping power in lead tungstate

A large sample of cosmic ray events collected by the CMS detector is exploited to measure the specific energy loss of muons in the lead tungstate (PbWO4) of the electromagnetic calorimeter. The measurement spans a momentum range from 5 GeV/c to 1 TeV/c. The results are consistent with the expectations over the entire range. The calorimeter energy scale, set with 120 GeV/c electrons, is validated down to the sub-GeV region using energy deposits, of order 100 MeV, associated with low-momentum muons. The muon critical energy in PbWO4 is measured to be 160+5 -68 GeV, in agreement with expectations. This is the first experimental determination of muon critical energy. © 2010 IOP Publishing Ltd and SISSA.

Commissioning of the CMS experiment and the cosmic run at four tesla

The CMS Collaboration conducted a month-long data-taking exercise known as the Cosmic Run At Four Tesla in late 2008 in order to complete the commissioning of the experiment for extended operation. The operational lessons resulting from this exercise were addressed in the subsequent shutdown to better prepare CMS for LHC beams in 2009. The cosmic data collected have been invaluable to study the performance of the detectors, to commission the alignment and calibration techniques, and to make several cosmic ray measurements. The experimental setup, conditions, and principal achievements from this data-taking exercise are described along with a review of the preceding integration activities. © 2010 IOP Publishing Ltd and SISSA.

Performance of the CMS Level-1 trigger during commissioning with cosmic ray muons and LHC beams

The CMS Level-1 trigger was used to select cosmic ray muons and LHC beam events during data-taking runs in 2008, and to estimate the level of detector noise. This paper describes the trigger components used, the algorithms that were executed, and the trigger synchronisation. Using data from extended cosmic ray runs, the muon, electron/photon, and jet triggers have been validated, and their performance evaluated. Efficiencies were found to be high, resolutions were found to be good, and rates as expected. © 2010 IOP Publishing Ltd and SISSA.

Performance of the CMS drift-tube chamber local trigger with cosmic rays

The performance of the Local Trigger based on the drift-tube system of the CMS experiment has been studied using muons from cosmic ray events collected during the commissioning of the detector in 2008. The properties of the system are extensively tested and compared with the simulation. The effect of the random arrival time of the cosmic rays on the trigger performance is reported, and the results are compared with the design expectations for proton-proton collisions and with previous measurements obtained with muon beams. © 2010 IOP Publishing Ltd and SISSA.

Fine synchronization of the CMS muon drift-tube local trigger using cosmic rays

The CMS experiment uses self-triggering arrays of drift tubes in the barrel muon trigger to perform the identification of the correct bunch crossing. The identification is unique only if the trigger chain is correctly synchronized. In this paper, the synchronization performed during an extended cosmic ray run is described and the results are reported. The random arrival time of cosmic ray muons allowed several synchronization aspects to be studied and a simple method for the fine synchronization of the Drift Tube Local Trigger at LHC to be developed. © 2010 IOP Publishing Ltd and SISSA.

Commissioning of the CMS High-Level Trigger with cosmic rays

The CMS High-Level Trigger (HLT) is responsible for ensuring that data samples with potentially interesting events are recorded with high efficiency and good quality. This paper gives an overview of the HLT and focuses on its commissioning using cosmic rays. The selection of triggers that were deployed is presented and the online grouping of triggered events into streams and primary datasets is discussed. Tools for online and offline data quality monitoring for the HLT are described, and the operational performance of the muon HLT algorithms is reviewed. The average time taken for the HLT selection and its dependence on detector and operating conditions are presented. The HLT performed reliably and helped provide a large dataset. This dataset has proven to be invaluable for understanding the performance of the trigger and the CMS experiment as a whole. © 2010 IOP Publishing Ltd and SISSA.