Role of phospholipase Cgamma-induced activation of protein kinase Cepsilon (PKCepsilon) and PKCbetaI in epidermal growth factor-mediated protection of tight junctions from acetaldehyde in Caco-2 cell monolayers

Epidermal growth factor (EGF) protects the intestinal epithelial tight junctions from acetaldehyde-induced insult. The role of phospholipase Cgamma (PLCgamma) and protein kinase C (PKC) isoforms in the mechanism of EGF-mediated protection of tight junction from acetaldehyde was evaluated in Caco-2 cell monolayers. EGF-mediated prevention of acetaldehyde-induced decrease in transepithelial electrical resistance and an increase in inulin permeability, and subcellular redistribution of occludin and ZO-1 was attenuated by reduced expression of PLCgamma1 by short hairpin RNA. EGF induced a rapid activation of PLCgamma1 and PLC-dependent membrane translocation of PKCepsilon and PKCbetaI. Inhibition of PKC activity or selective interference of membrane translocation of PKCepsilon and PKCbetaI by RACK interference peptides attenuated EGF-mediated prevention of acetaldehyde-induced increase in inulin permeability and redistribution of occludin and ZO-1. BAPTA-AM and thapsigargin blocked EGF-induced membrane translocation of PKCbetaI and attenuated EGF-mediated prevention of acetaldehyde-induced disruption of tight junctions. EGF-induced translocation of PKCepsilon and PKCbetaI was associated with organization of F-actin near the perijunctional region. This study shows that PLCgamma-mediated activation of PKCepsilon and PKCbetaI and intracellular calcium is involved in EGF-mediated protection of tight junctions from acetaldehyde-induced insult.     

Postconditioning fails to improve no reflow or alter infarct size in an open-chest rabbit model of myocardial ischemia-reperfusion

Postconditioning (PoC) with brief intermittent ischemia after myocardial reperfusion has been shown to lessen some elements of postischemic injury including arrhythmias and, in some studies, the size of myocardial infarction. We hypothesized that PoC could improve reflow to the risk zone after reperfusion. Anesthetized, open-chest rabbits were subjected to 30 min of coronary artery occlusion followed by 3 h of reperfusion. In protocol 1, rabbits were randomly assigned to the control group (n = 10, no further intervention after reperfusion) or to the PoC group, which consisted of four cycles of 30-s reocclusions with 30 s of reperfusion in between starting at 30 s after the initial reperfusion (4 x 30/30, n = 10). In protocol 2, rabbits were assigned to the control group (n = 7) or the PoC group, which received PoC consisting of four cycles of 60-s intervals of ischemia and reperfusion starting at 30 s after the initial reperfusion (4 x 60/60, n = 7). No reflow was determined by injecting thioflavine S (a fluorescent marker of capillary perfusion), risk zone by blue dye, and infarct size by triphenyltetrazolium chloride. In protocol 1, there were no statistical differences in hemodynamics, ischemic risk zone, or infarct size (35 +/- 6% of the risk zone in the PoC group vs. 29 +/- 4% in the control group, P = 0.38) between the groups. Similarly, in protocol 2, PoC failed to reduce infarct size compared with the control group (45 +/- 4% of the risk zone in the PoC group vs. 42 +/- 6% in the control group, P = 0.75). There was a strong correlation in both protocols between the size of the necrotic zone and the portion of the necrotic zone that contained an area of no reflow. However, PoC did not affect this relationship. PoC did not reduce infarct size in this model, nor did it reduce the extent of the anatomic zone of no reflow, suggesting that this intervention may not impact postreperfusion microvascular damage due to ischemia.     

Synthesis of a novel plant growth promoter from gallic acid

Gallic acid has been modified to naphthophenone derivatives with esterified fatty acid side chain. Compound 12, an ethyl crotonate ester of naphthophenone derivative has shown potent auxin like growth promoter activity. This is the first example of naphthophenone derivatives with plant growth promoting activity.     

Wetland flux controls: how does interacting water table levels and temperature influence carbon dioxide and methane fluxes in northern Wisconsin?

Wetlands play a disproportionately large role in global terrestrial carbon stocks, and from 1 year to the next individual wetlands can fluctuate between carbon sinks and sources depending on factors such as hydrology, temperature, and land use. Although much research has been done on short-term seasonal to annual wetland biogeochemical cycles, there is a lack of experimental evidence concerning how the reversibility of wetland hydrological changes will influence these cycles over longer time periods. Five years of drought-induced declining water table at Lost Creek, a shrub fen wetland in northern Wisconsin, coincided with increased ecosystem respiration (R_eco) and gross primary production (GPP) as derived from long-term eddy covariance observations. Since then, however, the average water table level at this site has increased, providing a unique opportunity to explore how wetland carbon fluxes are affected by interannual air temperature differences as well as changing water table levels. Water table level, as measured by water discharge, was correlated with R_eco and GPP at interannual time scales. However, air temperature had a strong correlation with R_eco, GPP, and net ecosystem productivity (NEP) at monthly time scales and correlated with NEP at inter-annual time scales. Methane flux was strongly temperature-controlled at seasonal time scales, increasing an order of magnitude from April to July. Annual methane emissions were 51 g C m^?2. Our results demonstrate that over multi-year timescales, water table fluctuations can have limited effects on wetland net carbon fluxes and instead at Lost Creek annual temperature is the best predictor of interannual variation.     

β-Alanine suppresses heat inactivation of lactate dehydrogenase

β-Alanine exhibits neurotransmitter activity and is a component of the anti-glycation agent carnosine. We propose that β-alanine may have additional properties which may be of physiological significance. Interestingly, stress modulates the level of β-alanine, which regulates excitotoxicity responses and prevents neuronal cell death. We hypothesize that β-alanine's protective role may involve preservation of enzyme structure and function, suggesting that β-alanine may act as a chemical chaperone. We used light scattering, enzyme activity and intrinsic fluorescence to monitor heat-induced changes in lactate dehydrogenase (LDH) in the presence and absence of β-alanine. We observed that β-alanine suppressed heat-induced LDH inactivation, prevented LDH aggregation, ameliorated the decrease in intrinsic fluorescence and reactivated thermally denatured LDH. These observations support the hypothesis that β-alanine has chaperone-like activity and may play a cellular role in the preservation of enzyme function.     

DINC: A new AutoDock-based protocol for docking large ligands

Background

Using the popular program AutoDock, computer-aided docking of small ligands with 6 or fewer rotatable bonds, is reasonably fast and accurate. However, docking large ligands using AutoDock's recommended standard docking protocol is less accurate and computationally slow.

Results

In our earlier work, we presented a novel AutoDock-based incremental protocol (DINC) that addresses the limitations of AutoDock's standard protocol by enabling improved docking of large ligands. Instead of docking a large ligand to a target protein in one single step as done in the standard protocol, our protocol docks the large ligand in increments. In this paper, we present three detailed examples of docking using DINC and compare the docking results with those obtained using AutoDock's standard protocol. We summarize the docking results from an extended docking study that was done on 73 protein-ligand complexes comprised of large ligands. We demonstrate not only that DINC is up to 2 orders of magnitude faster than AutoDock's standard protocol, but that it also achieves the speed-up without sacrificing docking accuracy. We also show that positional restraints can be applied to the large ligand using DINC: this is useful when computing a docked conformation of the ligand. Finally, we introduce a webserver for docking large ligands using DINC.

Conclusions

Docking large ligands using DINC is significantly faster than AutoDock's standard protocol without any loss of accuracy. Therefore, DINC could be used as an alternative protocol for docking large ligands. DINC has been implemented as a webserver and is available at http://dinc.kavrakilab.org. Applications such as therapeutic drug design, rational vaccine design, and others involving large ligands could benefit from DINC and its webserver implementation.

     

Comparative analysis of binding sites of human meprins with hydroxamic acid derivative by molecular dynamics simulation study

Meprins are complex and highly glycosylated multi-domain enzymes that require post-translational modifications to reach full activity. Meprins are metalloproteases of the astacin family characterized by a conserved zinc-binding motif (HExxHxxGFxHExxRxDR). Human meprin-α and -β protease subunits are 55% identical at the amino acid level, however the substrate and peptide bond specificities vary markedly. Current work focuses on the critical amino acid residues in the non-primed subsites of human meprins-α and -β involved in inhibitor/ligand binding. To compare the molecular events underlying ligand affinity, homology modeling of the protease domain of humep-α and -β based on the astacin crystal structure followed by energy minimization and molecular dynamics simulation of fully solvated proteases with inhibitor Pro-Leu-Gly-hydroxamate in S subsites were performed. The solvent accessible surface area curve shows a decrease in solvent accessibility values at specific residues upon inhibitor binding. The potential energy, total energy, H-bond interactions, root mean square deviation and root mean square fluctuation plot reflect the subtle differences in the S subsite of the enzymes which interact with different residues at P site of the inhibitor.