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Query: UNIPROT:P06889 (Mol)
 630,302 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Bacterial nucleoid-associated proteins H-NS and Hha modulate gene expression in response to environmental factors. The N-terminal domain of H-NS is involved in homomeric and heteromeric protein-protein interactions. Homomeric interaction leads to the formation of dimers and higher oligomers. Heteromeric interactions with Hha-like proteins modify the modulatory properties of H-NS. In this study, we have used NMR and mutagenesis of the N-terminal domain of H-NS to identify the Hha-binding region around helices H1 and H2 of H-NS. Two conserved arginine residues, R12 and R15, located in the same side and in adjacent turns of helix H2 are shown to be involved in two different protein-protein interactions: R12 is essential for Hha binding and does not affect H-NS dimer formation, and R15 does not affect Hha binding but is essential for the proper folding of H-NS dimers. Our results demonstrate a close structural connection between Hha-H-NS interactions and H-NS dimerization that may be involved in a possible mechanism for the modulation of the H-NS regulatory activity by Hha.
J Mol Biol 2006 Jun 09
PMID:New roles for key residues in helices H1 and H2 of the Escherichia coli H-NS N-terminal domain: H-NS dimer stabilization and Hha binding. 1665 Apr 31

Based on the direct in situ mixing of the colors of different fluorochromes (fluorescein isothiocyanate, tetramethylrhodamine isothiocyanate, Cascade Blue) incorporated in sequential primed in situ labeling (PRINS) reactions, a new multicolor PRINS procedure is described, allowing the rapid and distinct in situ labeling of three or four human chromosomes. Each PRINS reaction consists of a unique 5-min step for annealing and elongation. In combination with the 0.5 M NaOH pretreatment for simultaneous in situ denaturation and decondensation of sperm nuclei, this technique has been adapted to human sperm nuclei for the direct assessment of aneuploidy.
Methods Mol Biol 2006
PMID:Analysis of sperm aneuploidy by PRINS. 1686 52

An ultrarapid three- and four-color primed in situ (PRINS) procedure has been developed for rapid chromosome identification and aneuploidy assessment on isolated cells. Based on the direct in situ mixing of fluorochromes (fluorescein isothiocyanate, tetramethylrhodamine isothiocyanate, Cascade Blue), this multicolor PRINS procedure is described on unfertilized human oocytes and isolated human blastomeres.
Methods Mol Biol 2006
PMID:PRINS as an efficient tool for aneuploidy assessment in human oocytes and preimplantation embryos. 1686 61

Understanding protein folding is one of the most challenging problems remaining in molecular biology. In this chapter, a highly parallel replica exchange molecular dynamics (REMD) method and its application to protein folding are described. The REMD method couples molecular dynamics trajectories with a temperature exchange Monte Carlo process for efficient sampling of the conformational space. A series of replicas are run in parallel at temperatures ranging from the desired temperature to a high temperature at which the replica can easily surmount the energy barriers. From time to time the configurations of neighboring replicas are exchanged and this exchange is accepted or rejected based on a Metropolis acceptance criterion that guarantees the detailed balance. Two example protein systems, one alpha-helix and one beta-hairpin, are used as case studies to demonstrate the power of the algorithm. Up to 64 replicas of solvated protein systems are simulated in parallel over a wide range of temperatures. The simulation results show that the combined trajectories in temperature and configurational space allow a replica to overcome free energy barriers present at low temperatures. These large-scale simulations also reveal detailed results on folding mechanisms, intermediate state structures, thermodynamic properties, and the temperature dependences for both protein systems.
Methods Mol Biol 2007
PMID:Replica exchange molecular dynamics method for protein folding simulation. 1695 25

Codistributed species may display either congruent phylogeographic patterns, indicating similar responses to a series of shared climatic and geologic events, or discordant patterns, indicating independent responses. This study compares the phylogeographic patterns of two similarly distributed salamander species within the Pacific Northwest of the United States: Cope's giant salamander (Dicamptodon copei) and Van Dyke's salamander (Plethodon vandykei). Previous studies of P. vandykei support two reciprocally monophyletic lineages corresponding to coastal populations, located from the Olympic Mountains to the mouth of the Columbia River, and inland populations within the Cascade Mountains. We hypothesized that D. copei would have a congruent phylogeographic pattern to P. vandykei due to similarity in distribution and dependence upon similar stream and stream-side habitats. We test this hypothesis by estimating the phylogeny of D. copei using approximately 1800bp of mitochondrial DNA and comparing it to that of P. vandykei. Sympatric populations of D. copei and of P. vandykei display an identical phylogeographic pattern, suggesting similar responses within their shared distribution. Populations of D. copei occurring outside the range of P. vandykei displayed high levels of genetic divergence from those sympatric to P. vandykei. Overall, phylogeographic patterns between the two species were ultimately incongruent due to the high divergence of these allopatric populations. These results provide an example of codistributed species displaying overall incongruent phylogeographic patterns while simultaneously displaying congruent patterns within portions of their shared geographic distribution. This pattern demonstrates that a simple dichotomy of congruent and incongruent phylogeographic patterns of codistributed species may be too simplistic and that more complex intermediate patterns can result even from minor differences in species' ranges.
Mol Phylogenet Evol 2007 May
PMID:Phylogeographic incongruence of codistributed amphibian species based on small differences in geographic distribution. 1711 14

Phosphodiesterase-5 (PDE-5) inhibitors including sildenafil and vardenafil induce powerful preconditioning-like cardioprotective effect against ischemia/reperfusion injury through opening of mitochondrial K(ATP) channels in the heart. The goal of these studies was to demonstrate the protective effect of sildenafil and vardenafil on reperfusion injury and to compare it with the antianginal vasodilator nitroglycerin (NTG). In addition, we determined the role of mitochondrial K(ATP) channels in protection. Adult male New Zealand white rabbits were anesthetized and subjected to ischemia by 30 min of coronary artery occlusion followed by 3 h of reperfusion. Seven groups were studied. 1-Controls; 2-Sildenafil (total dose: 0.71 mg/kg; i.v.) infused for 65 min starting 5 min before reperfusion; 3-Sildenafil+5-hydroxydecanoate (5-HD, blocker of mitochondrial K(ATP) channel, total dose: 5 mg/kg) administered as 2 bolus injections; 4-Vardenafil (total dose: 0.014 mg/kg; iv) administered as in group 2; 5-Vardenafil+5-HD administered as in group 3; 6-5-HD administered as two bolus injections and 7-Nitroglycerin (NTG, total dose: 2 microg kg(-1) min(-1)) administered as in group 2. Infarct size was reduced in sildenafil (19.19+/-1.3%) as well as vardenafil (17.0+/-2.0%) treated groups as compared to controls (33.8+/-1.7%). However, NTG failed to confer similar cardioprotection (31.5+/-0.8%). 5-HD blocked the cardioprotective effects of sildenafil and vardenafil as shown by an increase in infarct size (34.0+/-1.1% and 28.3+/-1.9%, respectively). Both sildenafil and vardenafil protect the ischemic myocardium against reperfusion injury through a mechanism dependent on mitochondrial K(ATP) channel opening.
J Mol Cell Cardiol 2007 Feb
PMID:Sildenafil and vardenafil but not nitroglycerin limit myocardial infarction through opening of mitochondrial K(ATP) channels when administered at reperfusion following ischemia in rabbits. 1715 8

Successful cloning by somatic cell nuclear transfer (SCNT) is thought to require reprogramming of a somatic nucleus to a state of restored totipotentiality [Dean, W., Santos, F., Reik, W., 2003. Epigenetic programming in early mammalian development and following somatic cell nuclear transfer. Semin. Cell. Dev. Biol. 14, 93-100; Jouneau, A., Renard, J.P., 2003. Reprogramming in nuclear transfer. Curr. Opin. Genet. Dev. 13, 486-491; ]. Though SCNT-induced reprogramming is reminiscent of the reprogramming that occurs after fertilization, reprogramming a differentiated nucleus to an embryonic state is delayed and incomplete in comparison (for review, see ). This is likely due to the existence of an epigenetic-based cellular memory, or program, that serves to regulate global patterns of gene expression, and is the basis of a genome defense mechanism that silences viruses and transposons. The mechanisms of this memory include CpG methylation and modification of histones. Recent evidence by Feng et al. [Feng, Y.-Q., Desprat, R., Fu, H., Olivier, E., Lin, C.M., Lobell, A., Gowda, S.N., Aladjem, M.I., Bouhasira, E.E., 2006. DNA methylation supports intrinsic epigenetic memory in mammalian cells. PLOS Genet. 2, 0461-0470], using a transgenic experimental system, indicates that these marks may be acquired in more than one order and thus, silent heterochromatic structure can be initiated by either methylation of CpG dinucleotides or by histone modifications. In this system, however, CpG methylation appears to differ from histone modifications because it bestows a persistent epigenetic, or cellular, memory. In other words, CpG methylation can independently confer cellular memory, whereas histone modifications appear to be limited in this capacity. Therefore, in the context of genomic reprogramming induced by SCNT, efficient demethylation is likely a key (if not the only) rate-limiting step to improving the efficiency and outcomes of SCNT cloning. This review discusses the possibility of targeting cellular memory, and in particular inducing demethylation of a somatic nucleus prior to nuclear transfer, to enable reprogramming events typically carried out by oocyte factors and thereby improve developmental competence of SCNT-reconstructed embryos. Several recent published reviews of SCNT, cellular reprogramming and genomic demethylation served as valuable sources for the authors and are recommended as supplemental reading. These include the following: Bird, A., 2002. DNA methylation patterns and epigenetic memory. Gen. Dev. 16, 6-21; Grafi, G., 2004. How cells dedifferentiate: a lesson from plants. Dev. Biol. 268, 1-6; Latham, K.E., 2005. Early and delayed aspects of nuclear reprogramming during cloning. Biol. Cell 97, 119-132; Lyko, F., Brown, R., 2005. DNA methyltransferase inhibitors and the development of epigenetic cancer therapies. J.Natl. Cancer Inst. 97, 1498-1506; Morgan, H.D., Santos, F., Green, K., Dean, W., Reik, W., 2005. Epigenetic reprogramming in mammals. Hum. Mol. Gen. 14, R47-R58; Szyf, M., 2005. DNA methylation and demethylation as targets for anticancer therapy. Biochemistry 70, 533-549; Buszczak, M., Spradling, A.C., 2006. Searching chromatin for stem cell identity. Cell 125, 233-236; Gurdon, J.B., 2006. From nuclear transfer to nuclear reprogramming: the reversal of cell differentiation. Annu. Rev. Cell. Dev. Biol. 22, 1-22; Yoo, C.B., Jones, P.A., 2006. Epigenetic therapy of cancer: past, present and future. Nat. Rev. 5, 37-50.
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PMID:Targeting cellular memory to reprogram the epigenome, restore potential, and improve somatic cell nuclear transfer. 1716 76

Bioactivation of nitroglycerin (GTN) into an activator of soluble guanylate cyclase (sGC) is essential for the vasorelaxant effect of the drug. Besides several enzymes that catalyze GTN bioactivation, the reaction with cysteine is the sole nonenzymatic mechanism known so far. Here we show that a reaction with ascorbate results in GTN bioactivation. In the absence of ascorbate, GTN did not affect the activity of purified sGC. However, the enzyme was activated to approximately 20% of maximal NO-stimulated activity by GTN in the presence of 10 mM ascorbate with an EC(50) value of 27.3 +/- 4.9 microM GTN. The EC(50) value of ascorbate was 0.11 +/- 0.011 mM. Activation of sGC was sensitive to oxyhemoglobin, superoxide, and a heme-site enzyme inhibitor. GTN had no effect when ascorbate was replaced by 1000 U of superoxide dismutase per milliliter. Ascorbate is known to reduce inorganic nitrite to NO. In the presence of 10 mM ascorbate, approximately 30 microM nitrite caused the same increase in sGC activity as 0.3 mM GTN. Determination of ascorbate-driven 1,2- and 1,3-glycerol dinitrate formation indicated that a 140 nM concentration of products was generated from 0.3 mM GTN within 10 min, excluding nitrite as a relevant intermediate. Our results suggest that a reaction between GTN and ascorbate or an ascorbate-derived species yields an activator of sGC with NO-like chemical properties. This reaction may contribute to GTN bioactivation in blood vessels under conditions of GTN tolerance and ascorbate supplementation.
Mol Pharmacol 2007 Jul
PMID:Bioactivation of nitroglycerin by ascorbate. 1744 67

Myocardial gene therapy continues to show promise as a tool for investigation and treatment of cardiac disease. Progress toward clinical approval has been slowed by limited in vivo delivery methods. We investigated the problem in a porcine model, with an objective of developing a method for high efficiency, homogeneous myocardial gene transfer that could be used in large mammals, and ultimately in humans. Eighty-one piglets underwent coronary catheterization for delivery of viral vectors into the left anterior descending artery and/or the great cardiac vein. The animals were followed for 5 or 28 days, and then transgene efficiency was quantified from histological samples. The baseline protocol included treatment with VEGF, nitroglycerin, and adenosine followed by adenovirus infusion into the LAD. Gene transfer efficiency varied with choice of viral vector, with use of VEGF, adenosine, or nitroglycerin, and with calcium concentration. The best results were obtained by manipulation of physical parameters. Simultaneous infusion of adenovirus through both left anterior descending artery and great cardiac vein resulted in gene transfer to 78+/-6% of myocytes in a larger target area. This method was well tolerated by the animals. We demonstrate targeted, homogeneous, high efficiency gene transfer using a method that should be transferable for eventual human usage.
J Mol Cell Cardiol 2007 May
PMID:Targeted high-efficiency, homogeneous myocardial gene transfer. 1748 13

Chronic administration of nitroglycerin (NTG) induces nitrate tolerance. Among possible underlying mechanisms, increased vascular production of reactive oxygen species (ROS) has emerged as a principal mechanism. Using cell culture and animal models of nitrate tolerance, we aimed to assess the impact of nitrates on NAD(P)H oxidases and aldehyde dehydrogenase 2 (ALDH2) expression. Rats and vascular smooth muscle cells were treated with NTG. Vascular reactivity was assessed by isometric tension studies. Superoxide was detected by dihydroethidium staining. Gene expression was measured by real-time polymerase chain reaction. NAD(P)H oxidase activity was measured using lucigenin-enhanced chemiluminescence. ALDH activity was measured biochemically, and NO consumption electrochemically. Nitrate tolerance was induced in rats by treatment with NTG for 3 days, and detected as impaired endothelium-dependent and -independent relaxation of aortic segments. Although superoxide production was increased in all aortic layers, expression of nox1, nox2 and nox4 was significantly decreased. Similarly, in vascular smooth muscle cells exposed to NTG for 6-24 h, NAD(P)H oxidase activity was increased, in spite of nox1 downregulation. In addition, expression and activity of ALDH-2 was decreased in nitrate-tolerant rings. Furthermore, exogenous addition of ALDH decreased superoxide generation in vitro and attenuated NO consumption in vascular smooth muscle cell homogenates. Our data suggest that in nitrate tolerance, activation of nox enzymes more than compensates for their downregulation, resulting in a net increase in superoxide and NO consumption. Furthermore, reduced ALDH-2 activity and expression leads to decreased NTG bioconversion. Therefore, both mechanisms reduce NO availability and impair vasorelaxation.
J Mol Cell Cardiol 2007 Jun
PMID:Increased superoxide production in nitrate tolerance is associated with NAD(P)H oxidase and aldehyde dehydrogenase 2 downregulation. 1749 33


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