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Sample records for affect stability binding

  1. Stability of the octameric structure affects plasminogen-binding capacity of streptococcal enolase.

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    Amanda J Cork

    Full Text Available Group A Streptococcus (GAS is a human pathogen that has the potential to cause invasive disease by binding and activating human plasmin(ogen. Streptococcal surface enolase (SEN is an octameric α-enolase that is localized at the GAS cell surface. In addition to its glycolytic role inside the cell, SEN functions as a receptor for plasmin(ogen on the bacterial surface, but the understanding of the molecular basis of plasmin(ogen binding is limited. In this study, we determined the crystal and solution structures of GAS SEN and characterized the increased plasminogen binding by two SEN mutants. The plasminogen binding ability of SENK312A and SENK362A is ~2- and ~3.4-fold greater than for the wild-type protein. A combination of thermal stability assays, native mass spectrometry and X-ray crystallography approaches shows that increased plasminogen binding ability correlates with decreased stability of the octamer. We propose that decreased stability of the octameric structure facilitates the access of plasmin(ogen to its binding sites, leading to more efficient plasmin(ogen binding and activation.

  2. COX7A2L Is a Mitochondrial Complex III Binding Protein that Stabilizes the III2+IV Supercomplex without Affecting Respirasome Formation.

    Science.gov (United States)

    Pérez-Pérez, Rafael; Lobo-Jarne, Teresa; Milenkovic, Dusanka; Mourier, Arnaud; Bratic, Ana; García-Bartolomé, Alberto; Fernández-Vizarra, Erika; Cadenas, Susana; Delmiro, Aitor; García-Consuegra, Inés; Arenas, Joaquín; Martín, Miguel A; Larsson, Nils-Göran; Ugalde, Cristina

    2016-08-30

    Mitochondrial respiratory chain (MRC) complexes I, III, and IV associate into a variety of supramolecular structures known as supercomplexes and respirasomes. While COX7A2L was originally described as a supercomplex-specific factor responsible for the dynamic association of complex IV into these structures to adapt MRC function to metabolic variations, this role has been disputed. Here, we further examine the functional significance of COX7A2L in the structural organization of the mammalian respiratory chain. As in the mouse, human COX7A2L binds primarily to free mitochondrial complex III and, to a minor extent, to complex IV to specifically promote the stabilization of the III2+IV supercomplex without affecting respirasome formation. Furthermore, COX7A2L does not affect the biogenesis, stabilization, and function of the individual oxidative phosphorylation complexes. These data show that independent regulatory mechanisms for the biogenesis and turnover of different MRC supercomplex structures co-exist.

  3. COX7A2L Is a Mitochondrial Complex III Binding Protein that Stabilizes the III2+IV Supercomplex without Affecting Respirasome Formation

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    Rafael Pérez-Pérez

    2016-08-01

    Full Text Available Mitochondrial respiratory chain (MRC complexes I, III, and IV associate into a variety of supramolecular structures known as supercomplexes and respirasomes. While COX7A2L was originally described as a supercomplex-specific factor responsible for the dynamic association of complex IV into these structures to adapt MRC function to metabolic variations, this role has been disputed. Here, we further examine the functional significance of COX7A2L in the structural organization of the mammalian respiratory chain. As in the mouse, human COX7A2L binds primarily to free mitochondrial complex III and, to a minor extent, to complex IV to specifically promote the stabilization of the III2+IV supercomplex without affecting respirasome formation. Furthermore, COX7A2L does not affect the biogenesis, stabilization, and function of the individual oxidative phosphorylation complexes. These data show that independent regulatory mechanisms for the biogenesis and turnover of different MRC supercomplex structures co-exist.

  4. Changes to gonadotropin-releasing hormone (GnRH) receptor extracellular loops differentially affect GnRH analog binding and activation: evidence for distinct ligand-stabilized receptor conformations.

    Science.gov (United States)

    Pfleger, Kevin D G; Pawson, Adam J; Millar, Robert P

    2008-06-01

    GnRH and its structural variants bind to GnRH receptors from different species with different affinities and specificities. By investigating chimeric receptors that combine regions of mammalian and nonmammalian GnRH receptors, a greater understanding of how different domains influence ligand binding and receptor activation can be achieved. Using human-catfish and human-chicken chimeric receptors, we demonstrate the importance of extracellular loop conformation for ligand binding and agonist potency, providing further evidence for GnRH and GnRH II stabilization of distinct active receptor conformations. We demonstrate examples of GnRH receptor gain-of-function mutations that apparently improve agonist potency independently of affinity, implicating a role for extracellular loops in stabilizing the inactive receptor conformation. We also show that entire extracellular loop substitution can overcome the detrimental effects of localized mutations, thereby demonstrating the importance of considering the conformation of entire domains when drawing conclusions from point-mutation studies. Finally, we present evidence implicating the configuration of extracellular loops 2 and 3 in combination differentiating GnRH analog binding modes. Because there are two endogenous forms of GnRH ligand but only one functional form of full-length GnRH receptor in humans, understanding how GnRH and GnRH II can elicit distinct functional effects through the same receptor is likely to provide important insights into how these ligands can have differential effects in both physiological and pathological situations. PMID:18356273

  5. Stabilized sulfur binding using activated fillers

    Energy Technology Data Exchange (ETDEWEB)

    Kalb, Paul D.; Vagin, Vyacheslav P.; Vagin, Sergey P.

    2015-07-21

    A method of making a stable, sulfur binding composite comprising impregnating a solid aggregate with an organic modifier comprising unsaturated hydrocarbons with at least one double or triple covalent bond between adjacent carbon atoms to create a modifier-impregnated aggregate; heating and drying the modifier-impregnated aggregate to activate the surface of the modifier-impregnated aggregate for reaction with sulfur.

  6. Alcohol Binding to the Odorant Binding Protein LUSH: Multiple Factors Affecting Binding Affinities

    OpenAIRE

    Ader, Lauren; Jones, David N. M.; Lin, Hai

    2010-01-01

    Density function theory (DFT) calculations have been carried out to investigate the binding of alcohols to the odorant binding protein LUSH from Drosophila melanogaster. LUSH is one of the few proteins known to bind to ethanol at physiologically relevant concentrations and where high-resolution structural information is available for the protein bound to alcohol at these concentrations. The structures of the LUSH–alcohol complexes identify a set of specific hydrogen-bonding interactions as cr...

  7. Stability and Sugar Recognition Ability of Ricin-Like Carbohydrate Binding Domains

    Energy Technology Data Exchange (ETDEWEB)

    Yao, Jianzhuang [ORNL; Nellas, Ricky B [ORNL; Glover, Mary M [ORNL; Shen, Tongye [ORNL

    2011-01-01

    Lectins are a class of proteins known for their novel binding to saccharides. Understanding this sugar recognition process can be crucial in creating structure-based designs of proteins with various biological roles. We focus on the sugar binding of a particular lectin, ricin, which has two -trefoil carbohydrate-binding domains (CRDs) found in several plant protein toxins. The binding ability of possible sites of ricin-like CRD has been puzzling. The apo and various (multiple) ligand-bound forms of the sugar-binding domains of ricin were studied by molecular dynamics simulations. By evaluating structural stability, hydrogen bond dynamics, flexibility, and binding energy, we obtained a detailed picture of the sugar recognition of the ricin-like CRD. Unlike what was previously believed, we found that the binding abilities of the two known sites are not independent of each other. The binding ability of one site is positively affected by the other site. While the mean positions of different binding scenarios are not altered significantly, the flexibility of the binding pockets visibly decreases upon multiple ligand binding. This change in flexibility seems to be the origin of the binding cooperativity. All the hydrogen bonds that are strong in the monoligand state are also strong in the double-ligand complex, although the stability is much higher in the latter form due to cooperativity. These strong hydrogen bonds in a monoligand state are deemed to be the essential hydrogen bonds. Furthermore, by examining the structural correlation matrix, the two domains are structurally one entity. Galactose hydroxyl groups, OH4 and OH3, are the most critical parts in both site 1 and site 2 recognition.

  8. Stability of Facial Affective Expressions in Schizophrenia

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    H. Fatouros-Bergman

    2012-01-01

    Full Text Available Thirty-two videorecorded interviews were conducted by two interviewers with eight patients diagnosed with schizophrenia. Each patient was interviewed four times: three weekly interviews by the first interviewer and one additional interview by the second interviewer. 64 selected sequences where the patients were speaking about psychotic experiences were scored for facial affective behaviour with Emotion Facial Action Coding System (EMFACS. In accordance with previous research, the results show that patients diagnosed with schizophrenia express negative facial affectivity. Facial affective behaviour seems not to be dependent on temporality, since within-subjects ANOVA revealed no substantial changes in the amount of affects displayed across the weekly interview occasions. Whereas previous findings found contempt to be the most frequent affect in patients, in the present material disgust was as common, but depended on the interviewer. The results suggest that facial affectivity in these patients is primarily dominated by the negative emotions of disgust and, to a lesser extent, contempt and implies that this seems to be a fairly stable feature.

  9. Proteolytically stabilizing fibronectin without compromising cell and gelatin binding activity.

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    Zhang, Chen; Ramanathan, Anand; Karuri, Nancy Wangechi

    2015-01-01

    Excessive proteolytic degradation of fibronectin (FN) has been implicated in impaired tissue repair in chronic wounds. We previously reported two strategies for stabilizing FN against proteolytic degradation; the first conjugated polyethylene glycol (PEG) through cysteine residues and the second conjugated PEG chains of varying molecular weight on lysine residues. PEGylation of FN via lysine residues resulted in increased resistance to proteolysis with increasing PEG size, but an overall decrease in biological activity, as characterized by cell and gelatin binding. Our latest method to stabilize FN against proteolysis masks functional regions in the protein during lysine PEGylation. FN is PEGylated while it is bound to gelatin Sepharose beads with 2, 5, and 10 kDa PEG precursors. This results in partially PEGylated FN that is more stable than native FN and whose proteolytic stability increases with PEG molecular weight. Unlike completely PEGylated FN, partially PEGylated FN has cell adhesion, gelatin binding, and matrix assembly responses that are comparable to native FN. This is new evidence of how PEGylation variables can be used to stabilize FN while retaining its activity. The conjugates developed herein can be used to dissect molecular mechanisms mediated by FN stability and functionality, and address the problem of FN degradation in chronic wounds.

  10. Binding energy and stability of heavy and superheavy nuclei

    OpenAIRE

    Kolesnikov, N.N.

    2012-01-01

    Three different ways for description of binding energy of superheavy nuclei are discussed. First, one can consider superheavy nuclei as a part of a whole system of nuclei for which a global mass formula is found. Another way is the detailed local description of energy of superheavy nuclei taking into account the effects of shells and subshells. The third way of description, applied for nuclei in the region limited by principal magic numbers, is attached to the beta-stability line.

  11. Mouthrinses affect color stability of composite

    Science.gov (United States)

    Baig, Arshia Rashid; Shori, Deepa Deepak; Shenoi, Pratima Ramakrishna; Ali, Syed Navid; Shetti, Sanjay; Godhane, Alkesh

    2016-01-01

    Aim: The aim of this study is to evaluate the effect of alcohol and nonalcohol containing mouth rinses on the color stability of a nanofilled resin composite restorative material. Materials and Methods: A total of 120 samples of a nanofilled resin composite material (Tetric N-Ceram, Ivoclar Vivadent AG, FL-9494 Schaan/Liechtenstein) were prepared and immersed in distilled water for 24 h. Baseline color values were recorded using Color Spectrophotometer 3600d (Konica Minolta, Japan). Samples were then randomly distributed into six groups: Group I - distilled water (control group), Group II - Listerine, Group III - Eludril, Group IV - Phosflur, Group V - Amflor, and Group VI - Rexidin. The postimmersion color values of the samples were then recorded, respectively. Results: Significant reduction in the mean color value (before and after immersion) was observed in nonalcohol containing mouth rinses (P resin composite restorative material, but the color shift was dependent on the material and the mouthrinse used. Group VI (Rexidin) showed maximum color change. PMID:27563186

  12. Effects of spermine binding on Taxol-stabilized microtubules

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    Cheng, Shengfeng; Regmi, Chola

    Previous studies have shown that polyamines such as spermine present in cells at physiological concentrations can facilitate the polymerization of tubulins into microtubules (MTs). A recent experiment demonstrates that in the presence of high-concentration spermine, Taxol-stabilized MTs undergo a shape transformation into inverted tubulin tubules (ITTs), the outside surface of which corresponds to the inside surface of a regular MT. However, the molecular mechanism underlying the shape transformation of MTs into ITTs is unclear. We perform all atom molecular dynamics simulations on Taxol-stabilized MT sheets containing two protofilaments surrounded by spermine ions. The spermine concentration is varied from 0 to 25mM to match the range probed experimentally. We identify important spermine binding regions on the MT surface and the influence of the spermine binding on the structure and dynamics of MTs. In contrast to Taxol, our results show that spermine binding seems to decrease the flexibility of tubulin proteins, resulting in weaker tubulin-tubulin contacts and promoting the bending of protofilaments into curved protofilaments, inverted rings, and eventually inverted tubules.

  13. Stage structure alters how complexity affects stability of ecological networks

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    Rudolf, V.H.W.; Lafferty, Kevin D.

    2011-01-01

    Resolving how complexity affects stability of natural communities is of key importance for predicting the consequences of biodiversity loss. Central to previous stability analysis has been the assumption that the resources of a consumer are substitutable. However, during their development, most species change diets; for instance, adults often use different resources than larvae or juveniles. Here, we show that such ontogenetic niche shifts are common in real ecological networks and that consideration of these shifts can alter which species are predicted to be at risk of extinction. Furthermore, niche shifts reduce and can even reverse the otherwise stabilizing effect of complexity. This pattern arises because species with several specialized life stages appear to be generalists at the species level but act as sequential specialists that are hypersensitive to resource loss. These results suggest that natural communities are more vulnerable to biodiversity loss than indicated by previous analyses.

  14. Helix A Stabilization Precedes Amino-terminal Lobe Activation upon Calcium Binding to Calmodulin

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    Chen, Baowei [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Lowry, David [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Mayer, M. Uljana [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Squier, Thomas C. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2008-08-09

    The structural coupling between opposing domains of CaM was investigated using the conformationally sensitive biarsenical probe 4,5-bis(1,3,2-dithioarsolan-2-yl)-resorufin (ReAsH), which upon binding to an engineered tetracysteine binding motif near the end of helix A (Thr-5 to Phe-19) becomes highly fluorescent. Changes in conformation and dynamics are reflective of the native CaM structure, as there is no change in the 1H-15N HSQC NMR spectrum in comparison to wild-type CaM. We find evidence of a conformational intermediate associated with CaM activation, where calcium occupancy of sites in the amino-terminal and carboxyl-terminal lobes of CaM differentially affect the fluorescence intensity of bound ReAsH. Insight into the structure of the conformational intermediate is possible from a consideration of calcium-dependent changes in rates of ReAsH binding and helix A mobility, which respectively distinguish secondary structural changes associated with helix A stabilization from the tertiary structural reorganization of the amino-terminal lobe of CaM necessary for high-affinity binding to target proteins. Helix A stabilization is associated with calcium occupancy of sites in the carboxyl-terminal lobe (Kd = 0.36 ± 0.04 μM), which results in a reduction in the rate of ReAsH binding from 4900 M-1 sec-1 to 370 M-1 sec-1. In comparison, tertiary structural changes involving helix A and other structural elements in the amino-terminal lobe requires calcium-occupancy of amino-terminal sites (Kd = 18 ± 3 μM). Observed secondary and tertiary structural changes involving helix A in response to the sequential calcium occupancy of carboxyl- and amino-terminal lobe calcium binding sites suggest an important involvement of helix A in mediating the structural coupling between the opposing domains of CaM. These results are discussed in terms of a model in which carboxyl-terminal lobe calcium activation induces

  15. Factors affecting the stability of chloroplast membranes in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Takaoki, T.; Torres-Pereira, J.; Packer, L.

    1974-01-01

    Factors which affect the stability of light-induced atebrin fluorescence quenching activity in chloroplast membranes, a measure of the electron transport dependent formation of energy-linked H/sup +/ gradients, were investigated in vitro. Class II spinach chloroplast membranes were isolated and stored at 0 to 4/sup 0/C and aliquots were subsequently tested for their retention of energizing capacity. The main factors which increase the stability of this activity were found to be (a) isolation in a potassium-containing medium but storage in a sucrose medium containing a low concentration of electrolytes; (b) the presence of butylated hydroxytoluene (an antioxidant), and a protein such as bovine serum albumin to remove free fatty acids in the medium during storage. Under these conditions, the energization capacity of chloroplasts is retained for more than 40 days.

  16. Radioiodination of chicken luteinizing hormone without affecting receptor binding potency

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    Kikuchi, M.; Ishii, S. (Waseda Univ., Tokyo (Japan))

    1989-12-01

    By improving the currently used lactoperoxidase method, we were able to obtain radioiodinated chicken luteinizing hormone (LH) that shows high specific binding and low nonspecific binding to a crude plasma membrane fraction of testicular cells of the domestic fowl and the Japanese quail, and to the ovarian granulosa cells of the Japanese quail. The change we made from the original method consisted of (1) using chicken LH for radioiodination that was not only highly purified but also retained a high receptor binding potency; (2) controlling the level of incorporation of radioiodine into chicken LH molecules by employing a short reaction time and low temperature; and (3) fractionating radioiodinated chicken LH further by gel filtration using high-performance liquid chromatography. Specific radioactivity of the final {sup 125}I-labeled chicken LH preparation was 14 microCi/micrograms. When specific binding was 12-16%, nonspecific binding was as low as 2-4% in the gonadal receptors. {sup 125}I-Labeled chicken LH was displaced by chicken LH and ovine LH but not by chicken follicle-stimulating hormone. The equilibrium association constant of quail testicular receptor was 3.6 x 10(9) M-1. We concluded that chicken LH radioiodinated by the present method is useful for studies of avian LH receptors.

  17. The stability of triplex DNA is affected by the stability of the underlying duplex

    OpenAIRE

    Rusling, David A.; Rachwal, Phillip A.; Brown, Tom; Fox, Keith R.

    2009-01-01

    Abstract We have studied the formation of DNA triple helices in different sequence contexts and show that, for the most stable triplexes, their apparent stability is affected by the stability of the underlying duplex. For a 14-mer parallel triplex-forming oligonucleotide (generating C+.GC and T.AT triplets) at pH 5.0 the Tm is more than 10?C lower with an intermolecular 14-mer duplex target, than it is with an intramolecular duplex, or one which is flanked by 6 GC base pairs at eit...

  18. The Stability of Unsaturated Soil Slope Affected by Rainfall Seeping

    Institute of Scientific and Technical Information of China (English)

    Zhang Shilin; Wang Guochen; Shao Longtan

    2007-01-01

    Because rainfall seeping makes losing stability of unsaturated soil slope, and arouses great loss to production and human being safety, the stability of unsaturated soil slope has been researched by many scholars recently. This article mainly uses the model for the prediction of shear strength with respect to soil suction, developed by Vanapalli and Fredlund to formulate rainfall seeping how to affect the stability of unsaturated soil slope. Firstly, volumetric water content of unsaturated soil slope changes with rainfall duration, and effective saturation changes with its volumetric water content. Secondly, soil volume weight changes with its volumetric water content. Thirdly, matric suction also changes with its volumetric water content. According to these causes, this article researches how much they make the contribution to the minimum safety coefficient respectively. At last, these factors roundly considered, this article gets the rule of minimum safety coefficient of unsaturated soil slope with rainfall duration that is minimum safety coefficient gradually increasing firstly, then decreasing that is composed of two sectors, first is slowly decreasing, then is fast decreasing after some value.

  19. Probing the binding of trypsin to glutathione-stabilized gold nanoparticles in aqueous solution.

    Science.gov (United States)

    Wang, Gongke; Liu, Xingbing; Yan, Changling; Bai, Guangyue; Lu, Yan

    2015-11-01

    We investigate the interaction of trypsin with glutathione-stabilized Au nanoparticles (NPs) using fluorescence, synchronous fluorescence and ultraviolet (UV) absorption spectroscopy. We find that trypsin binds strongly to the Au NPs with a static quenching mechanism, and that the interaction is characteristic of positive cooperative binding. Furthermore, we determine the binding constants and the thermodynamic parameters, which suggest that the main binding forces between the glutathione-stabilized Au NPs and trypsin are electrostatic interactions and hydrogen bonding. Analysis of UV-vis absorption spectra suggests that aggregation of the Au NPs occurs in the trypsin/Au NPs system, which significantly alters the conformation of the protein.

  20. Protein-binding RNA aptamers affect molecular interactions distantly from their binding sites

    DEFF Research Database (Denmark)

    Dupont, Daniel M; Thuesen, Cathrine K; Bøtkjær, Kenneth A;

    2015-01-01

    Nucleic acid aptamer selection is a powerful strategy for the development of regulatory agents for molecular intervention. Accordingly, aptamers have proven their diligence in the intervention with serine protease activities, which play important roles in physiology and pathophysiology. Nonetheless...... potential, both binding to the serine protease urokinase-type plasminogen activator (uPA). We determine the subsequent impact of aptamer binding on the well-established molecular interactions (plasmin, PAI-1, uPAR, and LRP-1A) controlling uPA activities. One of the aptamers (upanap-126) binds to the area...... around the C-terminal α-helix in pro-uPA, while the other aptamer (upanap-12) binds to both the β-hairpin of the growth factor domain and the kringle domain of uPA. Based on the mapping studies, combined with data from small-angle X-ray scattering analysis, we construct a model for the upanap-12:pro...

  1. Protein-binding RNA aptamers affect molecular interactions distantly from their binding sites.

    Directory of Open Access Journals (Sweden)

    Daniel M Dupont

    Full Text Available Nucleic acid aptamer selection is a powerful strategy for the development of regulatory agents for molecular intervention. Accordingly, aptamers have proven their diligence in the intervention with serine protease activities, which play important roles in physiology and pathophysiology. Nonetheless, there are only a few studies on the molecular basis underlying aptamer-protease interactions and the associated mechanisms of inhibition. In the present study, we use site-directed mutagenesis to delineate the binding sites of two 2´-fluoropyrimidine RNA aptamers (upanap-12 and upanap-126 with therapeutic potential, both binding to the serine protease urokinase-type plasminogen activator (uPA. We determine the subsequent impact of aptamer binding on the well-established molecular interactions (plasmin, PAI-1, uPAR, and LRP-1A controlling uPA activities. One of the aptamers (upanap-126 binds to the area around the C-terminal α-helix in pro-uPA, while the other aptamer (upanap-12 binds to both the β-hairpin of the growth factor domain and the kringle domain of uPA. Based on the mapping studies, combined with data from small-angle X-ray scattering analysis, we construct a model for the upanap-12:pro-uPA complex. The results suggest and highlight that the size and shape of an aptamer as well as the domain organization of a multi-domain protein such as uPA, may provide the basis for extensive sterical interference with protein ligand interactions considered distant from the aptamer binding site.

  2. Surface modification of layered silicates. II. Factors affecting thermal stability

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    Mittal, Vikas

    2012-12-01

    Different aluminosilicates, such as montmorillonite, vermiculite and mica, were surface-treated with a variety of organic modifiers to quantify factors affecting the thermal stability of the modified fillers. Montmorillonites with different cation exchange capacities were also used. Thermal characterisation was carried out via high resolution thermogravimetric analysis and the results were correlated with X-ray diffraction measurements. Modified substrates, such as montmorillonite, vermiculite and mica, differed in their thermal behaviour even when modified with the same surface modifiers. Phosphonium-based modifiers were the most thermally stable, compared to pyridinium and ammonium ions. Mixed brushes from the modifiers also influenced the thermal behaviour of the modified substrates. When further modified using physical adsorption or chemical reactions on the surface, the modified minerals also displayed alterations in the thermal behaviour of the fillers. The results can be used as a guide for the selection of surface modifiers in the nanocomposite synthesis process where compounding of the filler with the polymer at high temperature and shear is required.

  3. Surface modification of layered silicates. I. Factors affecting thermal stability

    Science.gov (United States)

    Mittal, Vikas

    2012-12-01

    The resistance of modification molecules bound to montmorillonite platelet surfaces towards structural damage at high temperature is a major parameter guiding the formation of optimal interface between the filler and polymer phases in a nanocomposite material. As nanocomposites are generated by melt-blending of modified mineral and polymer, it is necessary to quantify the thermal resistance of the filler surface modification at the compounding conditions because different modifications differ in chain length, chemical structure, chain density, and thermal performance. A number of different alkyl ammonium modifications were exchanged on the montmorillonites with cation exchange capacities in the range 680-900 µequiv. g-1 and their thermal behaviour was characterised using high resolution thermogravimetric analysis. Quantitative comparisons between different modified minerals were achieved by comparing temperature at 10% weight loss as well peak degradation temperature. Various factors affecting thermal stability, such as length and density (or number) of alkyl chains in the modification, presence of excess modification molecules on the filler surface, the chemical structure of the surface modifications, etc. were studied. The TGA findings were also correlated with X-ray diffraction of the modified platelets.

  4. Spastin binds to lipid droplets and affects lipid metabolism.

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    Chrisovalantis Papadopoulos

    2015-04-01

    Full Text Available Mutations in SPAST, encoding spastin, are the most common cause of autosomal dominant hereditary spastic paraplegia (HSP. HSP is characterized by weakness and spasticity of the lower limbs, owing to progressive retrograde degeneration of the long corticospinal axons. Spastin is a conserved microtubule (MT-severing protein, involved in processes requiring rearrangement of the cytoskeleton in concert to membrane remodeling, such as neurite branching, axonal growth, midbody abscission, and endosome tubulation. Two isoforms of spastin are synthesized from alternative initiation codons (M1 and M87. We now show that spastin-M1 can sort from the endoplasmic reticulum (ER to pre- and mature lipid droplets (LDs. A hydrophobic motif comprised of amino acids 57 through 86 of spastin was sufficient to direct a reporter protein to LDs, while mutation of arginine 65 to glycine abolished LD targeting. Increased levels of spastin-M1 expression reduced the number but increased the size of LDs. Expression of a mutant unable to bind and sever MTs caused clustering of LDs. Consistent with these findings, ubiquitous overexpression of Dspastin in Drosophila led to bigger and less numerous LDs in the fat bodies and increased triacylglycerol levels. In contrast, Dspastin overexpression increased LD number when expressed specifically in skeletal muscles or nerves. Downregulation of Dspastin and expression of a dominant-negative variant decreased LD number in Drosophila nerves, skeletal muscle and fat bodies, and reduced triacylglycerol levels in the larvae. Moreover, we found reduced amount of fat stores in intestinal cells of worms in which the spas-1 homologue was either depleted by RNA interference or deleted. Taken together, our data uncovers an evolutionarily conserved role of spastin as a positive regulator of LD metabolism and open up the possibility that dysfunction of LDs in axons may contribute to the pathogenesis of HSP.

  5. Arabidopsis AtADF1 is Functionally Affected by Mutations on Actin Binding Sites

    Institute of Scientific and Technical Information of China (English)

    Chun-Hai Dong; Wei-Ping Tang; Jia-Yao Liu

    2013-01-01

    The plant actin depolymerizing factor (ADF) binds to both monomeric and filamentous actin,and is directly involved in the depolymerization of actin filaments.To better understand the actin binding sites of the Arabidopsis thaliana L.AtADF1,we generated mutants of AtADF1 and investigated their functions in vitro and in vivo.Analysis of mutants harboring amino acid substitutions revealed that charged residues (Arg98 and Lys100) located at the α-helix 3 and forming an actin binding site together with the N-terminus are essential for both G-and F-actin binding.The basic residues on the β-strand 5 (K82/A) and the α-helix 4 (R135/A,R137/A) form another actin binding site that is important for F-actin binding.Using transient expression of CFP-tagged AtADF1 mutant proteins in onion (Allium cepa) peel epidermal cells and transgenic Arabidopsis thaliana L.plants overexpressing these mutants,we analyzed how these mutant proteins regulate actin organization and affect seedling growth.Our results show that the ADF mutants with a lower affinity for actin filament binding can still be functional,unless the affinity foractin monomers is also affected.The G-actin binding activity of the ADF plays an essential role in actin binding,depolymerization of actin polymers,and therefore in the control of actin organization.

  6. STN1 OB Fold Mutation Alters DNA Binding and Affects Selective Aspects of CST Function

    Science.gov (United States)

    Bhattacharjee, Anukana; Stewart, Jason; Chaiken, Mary; Price, Carolyn M.

    2016-01-01

    Mammalian CST (CTC1-STN1-TEN1) participates in multiple aspects of telomere replication and genome-wide recovery from replication stress. CST resembles Replication Protein A (RPA) in that it binds ssDNA and STN1 and TEN1 are structurally similar to RPA2 and RPA3. Conservation between CTC1 and RPA1 is less apparent. Currently the mechanism underlying CST action is largely unknown. Here we address CST mechanism by using a DNA-binding mutant, (STN1 OB-fold mutant, STN1-OBM) to examine the relationship between DNA binding and CST function. In vivo, STN1-OBM affects resolution of endogenous replication stress and telomere duplex replication but telomeric C-strand fill-in and new origin firing after exogenous replication stress are unaffected. These selective effects indicate mechanistic differences in CST action during resolution of different replication problems. In vitro binding studies show that STN1 directly engages both short and long ssDNA oligonucleotides, however STN1-OBM preferentially destabilizes binding to short substrates. The finding that STN1-OBM affects binding to only certain substrates starts to explain the in vivo separation of function observed in STN1-OBM expressing cells. CST is expected to engage DNA substrates of varied length and structure as it acts to resolve different replication problems. Since STN1-OBM will alter CST binding to only some of these substrates, the mutant should affect resolution of only a subset of replication problems, as was observed in the STN1-OBM cells. The in vitro studies also provide insight into CST binding mechanism. Like RPA, CST likely contacts DNA via multiple OB folds. However, the importance of STN1 for binding short substrates indicates differences in the architecture of CST and RPA DNA-protein complexes. Based on our results, we propose a dynamic DNA binding model that provides a general mechanism for CST action at diverse forms of replication stress. PMID:27690379

  7. Thermal stability and binding energetics of thymidylate synthase ThyX.

    Science.gov (United States)

    Krumova, Sashka; Todinova, Svetla; Tileva, Milena; Bouzhir-Sima, Latifa; Vos, Marten H; Liebl, Ursula; Taneva, Stefka G

    2016-10-01

    The bacterial thymidylate synthase ThyX is a multisubstrate flavoenzyme that takes part in the de novo synthesis of thymidylate in a variety of microorganisms. Herein we study the effect of FAD and dUMP binding on the thermal stability of wild type (WT) ThyX from the mesophilic Paramecium bursaria chlorella virus-1 (PBCV-1) and from the thermophilic bacterium Thermotoga maritima (TmThyX), and from two variants of TmThyX, Y91F and S88W, using differential scanning calorimetry. The energetics underlying these processes was characterized by isothermal titration calorimetry. The PBCV-1 protein is significantly less stable against the thermal challenge than the TmThyX WT. FAD exerted stabilizing effect greater for PBCV-1 than for TmThyX and for both mutants, whereas binding of dUMP to FAD-loaded proteins stabilized further only TmThyX. Different thermodynamic signatures describe the FAD binding to the WT ThyX proteins. While TmThyX binds FAD with a low μM binding affinity in a process characterized by a favorable entropy change, the assembly of PBCV-1 with FAD is governed by a large enthalpy change opposed by an unfavorable entropy change resulting in a relatively strong nM binding. An enthalpy-driven formation of a high affinity ternary ThyX/FAD/dUMP complex was observed only for TmThyX. PMID:27268384

  8. Ca2+ and Mg2+ binding induce conformational stability of Calfumirin-1 from Dictyostelium discoideum

    Indian Academy of Sciences (India)

    Bairagi C Mallick; Sa-Ouk Kang; Suman Jha

    2014-05-01

    The apo-Calfumirin-1 (CAF-1) binds to Ca2+ with high affinity and also to Mg2+ with high positive cooperativity. The thermal unfolding curves of wtCAF-1 monitored at neutral pH by CD spectroscopy are reversible and show different thermal stabilities in the absence or presence of Ca2+ and Mg2+ ions. Metalfree wtCAF-1 shows greater thermal stability than EF-IV mutant protein. We observed that GdnHCl-induced unfolding of apo-wtCAF-1 monitored by CD and fluorescence spectroscopies increases co-operative folding with approximately same C values. Binding of Ca2+ and Mg2+ ions to CAF-1 dramatically altered the fluorescence and CD spectra, indicating metal ion-induced conformational changes both in the wild-type and mutant proteins. The hydrophobic probe, ANS is used to observe alteration in surface hydrophobicity of the protein in different ligation states. In apo-wtCAF-1, the exposed hydrophobic surfaces are able to bind ANS which is in contrast to the unfolded or the metal ions ligated conformations. Isothermal titration calorimetry (ITC) resultsshow two possible independent binding sites of comparable affinity for the metal ions. However, their binding to the EF-IV E helix-loop-F helix mutant apo-protein happens with different affinities. The present study demonstrates that Ca2+ or Mg2+ binding plays a possible role in the conformational stability of the protein.

  9. DNA binding during expanded bed adsorption and factors affecting adsorbent aggregation

    DEFF Research Database (Denmark)

    Arpanaei, Ayyoob; Mathiasen, N.; Hobley, Timothy John

    2008-01-01

    tolerance of anion exchangers when binding DNA. However, more importantly. with the adsorbents examined here. attempts to reduce bed aggregation by feedstock conditioning with added salt may increase DNA binding leading to a reduction in expanded bed adsorption performance compromising protein capture...... ligand densities to be examined. Very high dynamic binding capacities at 10% breakthrough were found in the absence of added salt. However, the highest binding capacities (similar to 10 and similar to 19mg DNA ml(-1) gel) were found in buffers containing added salt at concentrations of either 0.25 or 0......) even though the dynamic binding capacity was reduced as DNA concentration was increased. The extent of bed contraction during DNA loading was found to be a function of added salt concentration and ligand density of the adsorbent. The results imply that ligand density significantly affects the salt...

  10. A Novel Role of Vimentin Filaments: Binding and Stabilization of Collagen mRNAs ▿

    OpenAIRE

    Azariyas A Challa; Stefanovic, Branko

    2011-01-01

    The stem-loop in the 5′ untranslated region (UTR) of collagen α1(I) and α2(I) mRNAs (5′SL) is the key element regulating their stability and translation. Stabilization of collagen mRNAs is the predominant mechanism for high collagen expression in fibrosis. LARP6 binds the 5′SL of α1(I) and α2(I) mRNAs with high affinity. Here, we report that vimentin filaments associate with collagen mRNAs in a 5′SL- and LARP6-dependent manner and stabilize collagen mRNAs. LARP6 interacts with vimentin filame...

  11. Distinct pose of discodermolide in taxol binding pocket drives a complementary mode of microtubule stabilization.

    Science.gov (United States)

    Khrapunovich-Baine, Marina; Menon, Vilas; Verdier-Pinard, Pascal; Smith, Amos B; Angeletti, Ruth Hogue; Fiser, Andras; Horwitz, Susan Band; Xiao, Hui

    2009-12-15

    The microtubule cytoskeleton has proven to be an effective target for cancer therapeutics. One class of drugs, known as microtubule stabilizing agents (MSAs), binds to microtubule polymers and stabilizes them against depolymerization. The prototype of this group of drugs, Taxol, is an effective chemotherapeutic agent used extensively in the treatment of human ovarian, breast, and lung carcinomas. Although electron crystallography and photoaffinity labeling experiments determined that the binding site for Taxol is in a hydrophobic pocket in beta-tubulin, little was known about the effects of this drug on the conformation of the entire microtubule. A recent study from our laboratory utilizing hydrogen-deuterium exchange (HDX) in concert with various mass spectrometry (MS) techniques has provided new information on the structure of microtubules upon Taxol binding. In the current study we apply this technique to determine the binding mode and the conformational effects on chicken erythrocyte tubulin (CET) of another MSA, discodermolide, whose synthetic analogues may have potential use in the clinic. We confirmed that, like Taxol, discodermolide binds to the taxane binding pocket in beta-tubulin. However, as opposed to Taxol, which has major interactions with the M-loop, discodermolide orients itself away from this loop and toward the N-terminal H1-S2 loop. Additionally, discodermolide stabilizes microtubules mainly via its effects on interdimer contacts, specifically on the alpha-tubulin side, and to a lesser extent on interprotofilament contacts between adjacent beta-tubulin subunits. Also, our results indicate complementary stabilizing effects of Taxol and discodermolide on the microtubules, which may explain the synergy observed between the two drugs in vivo.

  12. Investigating the linkage between disease-causing amino acid variants and their effect on protein stability and binding.

    Science.gov (United States)

    Peng, Yunhui; Alexov, Emil

    2016-02-01

    Single amino acid variations (SAV) occurring in human population result in natural differences between individuals or cause diseases. It is well understood that the molecular effect of SAV can be manifested as changes of the wild type characteristics of the corresponding protein, among which are the protein stability and protein interactions. Typically the effect of SAV on protein stability and interactions was assessed via the changes of the wild type folding and binding free energies. However, in terms of SAV affecting protein functionally and disease susceptibility, one wants to know to what extend the wild type function is perturbed by the SAV. Here it is demonstrated that relative, rather than the absolute, change of the folding and binding free energy serves as a good indicator for SAV association with disease. Using HumVar as a source for disease-causing SAV and experimentally determined free energy changes from ProTherm and SKEMPI databases, correlation coefficients (CC) between the disease index (Pd) and relative folding (Ppr,f) and binding (Ppr,b) probability indexes, respectively, was achieved. The obtained CCs demonstrated the applicability of the proposed approach and it served as good indicator for SAV association with disease. PMID:26650512

  13. Seasonal difference in brain serotonin transporter binding predicts symptom severity in patients with seasonal affective disorder

    DEFF Research Database (Denmark)

    Mc Mahon, Brenda; Andersen, Sofie B; Madsen, Martin K.;

    2016-01-01

    between summer and winter (P sex- (P = 0.02) and genotype- (P = 0.04) dependent. In the patients with seasonal affective disorder, the seasonal change in serotonin transporter binding was positively associated with change in depressive symptom...... to the environmental stress of winter, especially in individuals with high predisposition to affective disorders.media-1vid110.1093/brain/aww043_video_abstractaww043_video_abstract....

  14. Seasonal difference in brain serotonin transporter binding predicts symptom severity in patients with seasonal affective disorder.

    Science.gov (United States)

    Mc Mahon, Brenda; Andersen, Sofie B; Madsen, Martin K; Hjordt, Liv V; Hageman, Ida; Dam, Henrik; Svarer, Claus; da Cunha-Bang, Sofi; Baaré, William; Madsen, Jacob; Hasholt, Lis; Holst, Klaus; Frokjaer, Vibe G; Knudsen, Gitte M

    2016-05-01

    Cross-sectional neuroimaging studies in non-depressed individuals have demonstrated an inverse relationship between daylight minutes and cerebral serotonin transporter; this relationship is modified by serotonin-transporter-linked polymorphic region short allele carrier status. We here present data from the first longitudinal investigation of seasonal serotonin transporter fluctuations in both patients with seasonal affective disorder and in healthy individuals. Eighty (11)C-DASB positron emission tomography scans were conducted to quantify cerebral serotonin transporter binding; 23 healthy controls with low seasonality scores and 17 patients diagnosed with seasonal affective disorder were scanned in both summer and winter to investigate differences in cerebral serotonin transporter binding across groups and across seasons. The two groups had similar cerebral serotonin transporter binding in the summer but in their symptomatic phase during winter, patients with seasonal affective disorder had higher serotonin transporter than the healthy control subjects (P = 0.01). Compared to the healthy controls, patients with seasonal affective disorder changed their serotonin transporter significantly less between summer and winter (P sex- (P = 0.02) and genotype- (P = 0.04) dependent. In the patients with seasonal affective disorder, the seasonal change in serotonin transporter binding was positively associated with change in depressive symptom severity, as indexed by Hamilton Rating Scale for Depression - Seasonal Affective Disorder version scores (P = 0.01). Our findings suggest that the development of depressive symptoms in winter is associated with a failure to downregulate serotonin transporter levels appropriately during exposure to the environmental stress of winter, especially in individuals with high predisposition to affective disorders.media-1vid110.1093/brain/aww043_video_abstractaww043_video_abstract. PMID:26994750

  15. How the spatial variation of tree roots affects slope stability

    Science.gov (United States)

    Mao, Zhun; Stokes, A.; Jourdan, C.; Rey, H.; Courbaud, B.; Saint-André, L.

    2010-05-01

    It is now widely recognized that plant roots can reinforce soil against shallow mass movement. Although studies on the interactions between vegetation and slope stability have significantly augmented in recent years, a clear understanding of the spatial dynamics of root reinforcement (through additional cohesion by roots) in subalpine forest is still limited, especially with regard to the roles of different forest management strategies or ecological landscapes. The architecture of root systems is important for soil cohesion, but in reality it is not possible to measure the orientation of each root in a system. Therefore, knowledge on the effect of root orientation and anisotropy on root cohesion on the basis of in situ data is scanty. To determine the effect of root orientation in root cohesion models, we investigated root anisotropy in two mixed, mature, naturally regenerated, subalpine forests of Norway spruce (Picea abies), and Silver fir (Abies alba). Trees were clustered into islands, with open spaces between each group, resulting in strong mosaic heterogeneity within the forest stand. Trenches within and between clusters of trees were dug and root distribution was measured in three dimensions. We then simulated the influence of different values for a root anisotropy correction factor in forests with different ecological structures and soil depths. Using these data, we have carried out simulations of slope stability by calculating the slope factor of safety depending on stand structure. Results should enable us to better estimate the risk of shallow slope failure depending on the type of forest and species.

  16. The constant region affects antigen binding of antibodies to DNA by altering secondary structure.

    Science.gov (United States)

    Xia, Yumin; Janda, Alena; Eryilmaz, Ertan; Casadevall, Arturo; Putterman, Chaim

    2013-11-01

    We previously demonstrated an important role of the constant region in the pathogenicity of anti-DNA antibodies. To determine the mechanisms by which the constant region affects autoantibody binding, a panel of isotype-switch variants (IgG1, IgG2a, IgG2b) was generated from the murine PL9-11 IgG3 autoantibody. The affinity of the PL9-11 antibody panel for histone was measured by surface plasmon resonance (SPR). Tryptophan fluorescence was used to determine wavelength shifts of the antibody panel upon binding to DNA and histone. Finally, circular dichroism spectroscopy was used to measure changes in secondary structure. SPR analysis revealed significant differences in histone binding affinity between members of the PL9-11 panel. The wavelength shifts of tryptophan fluorescence emission were found to be dependent on the antibody isotype, while circular dichroism analysis determined that changes in antibody secondary structure content differed between isotypes upon antigen binding. Thus, the antigen binding affinity is dependent on the particular constant region expressed. Moreover, the effects of antibody binding to antigen were also constant region dependent. Alteration of secondary structures influenced by constant regions may explain differences in fine specificity of anti-DNA antibodies between antibodies with similar variable regions, as well as cross-reactivity of anti-DNA antibodies with non-DNA antigens.

  17. Antibacterial surfaces by adsorptive binding of polyvinyl-sulphonate-stabilized silver nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Vasilev, Krasimir; Sah, Vasu R; Goreham, Renee V; Short, Robert D [Mawson Institute, University of South Australia, Mawson Lakes Campus, Mawson Lakes, Adelaide, SA 5095 (Australia); Ndi, Chi; Griesser, Hans J, E-mail: Krasimir.vasilev@unisa.edu.au [Ian Wark Research Institute, University of South Australia, Mawson Lakes, Adelaide, SA 5095 (Australia)

    2010-05-28

    This paper presents a novel and facile method for the generation of efficient antibacterial coatings which can be applied to practically any type of substrate. Silver nanoparticles were stabilized with an adsorbed surface layer of polyvinyl sulphonate (PVS). This steric layer provided excellent colloidal stability, preventing aggregation over periods of months. PVS-coated silver nanoparticles were bound onto amine-containing surfaces, here produced by deposition of an allylamine plasma polymer thin film onto various substrates. SEM imaging showed no aggregation upon surface binding of the nanoparticles; they were well dispersed on amine surfaces. Such nanoparticle-coated surfaces were found to be effective in preventing attachment of Staphylococcus epidermidis bacteria and also in preventing biofilm formation. Combined with the ability of plasma polymerization to apply the thin polymeric binding layer onto a wide range of materials, this method appears promising for the fabrication of a wide range of infection-resistant biomedical devices.

  18. Lamb meat colour stability as affected by dietary tannins

    Directory of Open Access Journals (Sweden)

    Pietro Pennisi

    2010-01-01

    Full Text Available Twenty-one male Comisana lambs were divided into three groups at 45 days of age and were individually penned for 60 days. Seven lambs were fed a concentrate-based diet (C, seven lambs received the same concentrate with the addiction of tannins from quebracho (Schinopsis lorentzii; T, whereas the remaining animals were fed exclusively fresh vetch (Vicia sativa; H. Colour descriptors (a*, b* and H* and metmyoglobin (MMb percentages were measured on minced semimembranosus muscle over 14 days of refrigerated storage in a high oxygen atmosphere. Regardless of dietary treatment, meat redness decreased, while yellowness and hue angle increased (P < 0.001 over storage duration. However, higher a* values, lower b* values and lower H* values were observed in meat from both H- and T-fed animals as compared to meat from C-fed lambs (P = 0.012; P = 0.02; P = 0.003, respectively. Metmyoglobin formation increased over time (P < 0.001, but H diet resulted in lower metmyoglobin percentages than C diet (P = 0.007. We conclude that the inclusion of tannins into the concentrate improved meat colour stability compared to a tannin-free concentrate. Moreover, the protective effect of tannins against meat discolouration was comparable to that obtained by feeding lambs fresh herbage.

  19. Sulfatide-Hsp70 Interaction Promotes Hsp70 Clustering and Stabilizes Binding to Unfolded Protein

    Directory of Open Access Journals (Sweden)

    Yoichiro Harada

    2015-05-01

    Full Text Available The 70-kDa heat shock protein (Hsp70, one of the major stress-inducible molecular chaperones, is localized not only in the cytosol, but also in extracellular milieu in mammals. Hsp70 interacts with various cell surface glycolipids including sulfatide (3'-sulfogalactosphingolipid. However, the molecular mechanism, as well as the biological relevance, underlying the glycolipid-Hsp70 interaction is unknown. Here we report that sulfatide promotes Hsp70 oligomerization through the N-terminal ATPase domain, which stabilizes the binding of Hsp70 to unfolded protein in vitro. We find that the Hsp70 oligomer has apparent molecular masses ranging from 440 kDa to greater than 669 kDa. The C-terminal peptide-binding domain is dispensable for the sulfatide-induced oligomer formation. The oligomer formation is impaired in the presence of ATP, while the Hsp70 oligomer, once formed, is unable to bind to ATP. These results suggest that sulfatide locks Hsp70 in a high-affinity state to unfolded proteins by clustering the peptide-binding domain and blocking the binding to ATP that induces the dissociation of Hsp70 from protein substrates.

  20. Gemini surfactants affect the structure, stability, and activity of ribonuclease Sa.

    Science.gov (United States)

    Amiri, Razieh; Bordbar, Abdol-Khalegh; Laurents, Douglas V

    2014-09-11

    Gemini surfactants have important advantages, e.g., low micromolar CMCs and slow millisecond monomer ↔ micelle kinetics, for membrane mimetics and for delivering nucleic acids for gene therapy or RNA silencing. However, as a prerequisite, it is important to characterize interactions occurring between Gemini surfactants and proteins. Here NMR and CD spectroscopies are employed to investigate the interactions of cationic Gemini surfactants with RNase Sa, a negatively charged ribonuclease. We find that RNase Sa binds Gemini surfactant monomers and micelles at pH values above 4 to form aggregates. Below pH 4, where the protein is positively charged, these aggregates dissolve and interactions are undetectable. Thermal denaturation experiments show that surfactant lowers RNase Sa's conformational stability, suggesting that surfactant binds the protein's denatured state preferentially. Finally, Gemini surfactants were found to bind RNA, leading to the formation of large complexes. Interestingly, Gemini surfactant binding did not prevent RNase Sa from cleaving RNA. PMID:25133582

  1. Thermodynamic stability and retinol binding property of {beta}-lactoglobulin in the presence of cationic surfactants

    Energy Technology Data Exchange (ETDEWEB)

    Sahihi, M. [Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111 (Iran, Islamic Republic of); Bordbar, A.K., E-mail: bordbar@chem.ui.ac.ir [Department of Chemistry, University of Isfahan, Isfahan 81746-73441 (Iran, Islamic Republic of); Ghayeb, Y. [Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111 (Iran, Islamic Republic of)

    2011-08-15

    Highlights: > The stability parameters of {beta}-lactoglobulin, BLG, in the presence of C{sub n}TAB have been evaluated. > Rising in hydrocarbon chain length increases the denaturating power of surfactants. > C{sub n}TAB enhances the retinol binding affinity of BLG in all of its concentration range. - Abstract: In this work the stability parameters of bovine {beta}-lactoglobulin, variant A (BLG-A), with regard to their transition curves induced by dodecyltrimethylammonium bromide (C{sub 12}TAB), tetradecyltrimethylammonium bromide (C{sub 14}TAB) and hexadecyltrimethylammonium bromide (C{sub 16}TAB) as cationic surfactants, were determined at 298 K. For each transition curve, the conventional method of analysis which assumes a linear concentration dependence of the pre- and post-transition base lines, gave the most realistic values for {Delta}G{sub D}(H{sub 2}O). The results represent the increase in the denaturating power of surfactants with an increase in hydrocarbon chain length. The value of about 22.27 kJ . mol{sup -1} was obtained for {Delta}G{sub D}(H{sub 2}O) from transition curves. Subsequently, the retinol binding property of BLG as its functional indicator was investigated in the presence of these surfactants using the spectrofluorimeter titration method. The results represent the substantial enhancement of retinol binding affinity of BLG in the presence of these surfactants.

  2. Dermal nanocrystals from medium soluble actives - physical stability and stability affecting parameters.

    Science.gov (United States)

    Zhai, Xuezhen; Lademann, Jürgen; Keck, Cornelia M; Müller, Rainer H

    2014-09-01

    Nanocrystals are meanwhile applied to increase the dermal penetration of drugs, but were applied by now only to poorly soluble drugs (e.g. 1-10 μg/ml). As a new concept nanocrystals from medium soluble actives were produced, using caffeine as model compound (solubility 16 mg/ml at 20 °C). Penetration should be increased by (a) further increase in solubility and (b) mainly by increased hair follicle targeting of nanocrystals compared to pure solution. Caffeine nanocrystal production in water lead to pronounced crystal growth. Therefore the stability of nanocrystals in water-ethanol (1:9) and ethanol-propylene glycol (3:7) mixtures with lower dielectric constant D was investigated, using various stabilizers. Both mixtures in combination with Carbopol 981 (non-neutralized) yielded stable nanosuspensions over 2 months at 4 °C and room temperature. Storage at 40 °C lead to crystal growth, attributed to too strong solubility increase, supersaturation and Ostwald ripening effects. Stability of caffeine nanocrystals at lower temperatures could not only be attributed to lower solubility, because the solubilities of caffeine in mixtures and in water are not that much different. Other effects such as quantified by reduced dielectric constant D, and specific interactions between dispersion medium and crystal surface seem to play a role. With the 2 mixtures and Carbopol 981, a basic formulation composition for this type of nanocrystals has been established, to be used in the in vivo proof of principle of the new concept. PMID:25016978

  3. Dermal nanocrystals from medium soluble actives - physical stability and stability affecting parameters.

    Science.gov (United States)

    Zhai, Xuezhen; Lademann, Jürgen; Keck, Cornelia M; Müller, Rainer H

    2014-09-01

    Nanocrystals are meanwhile applied to increase the dermal penetration of drugs, but were applied by now only to poorly soluble drugs (e.g. 1-10 μg/ml). As a new concept nanocrystals from medium soluble actives were produced, using caffeine as model compound (solubility 16 mg/ml at 20 °C). Penetration should be increased by (a) further increase in solubility and (b) mainly by increased hair follicle targeting of nanocrystals compared to pure solution. Caffeine nanocrystal production in water lead to pronounced crystal growth. Therefore the stability of nanocrystals in water-ethanol (1:9) and ethanol-propylene glycol (3:7) mixtures with lower dielectric constant D was investigated, using various stabilizers. Both mixtures in combination with Carbopol 981 (non-neutralized) yielded stable nanosuspensions over 2 months at 4 °C and room temperature. Storage at 40 °C lead to crystal growth, attributed to too strong solubility increase, supersaturation and Ostwald ripening effects. Stability of caffeine nanocrystals at lower temperatures could not only be attributed to lower solubility, because the solubilities of caffeine in mixtures and in water are not that much different. Other effects such as quantified by reduced dielectric constant D, and specific interactions between dispersion medium and crystal surface seem to play a role. With the 2 mixtures and Carbopol 981, a basic formulation composition for this type of nanocrystals has been established, to be used in the in vivo proof of principle of the new concept.

  4. Conformational stability and aggregation of therapeutic monoclonal antibodies studied with ANS and Thioflavin T binding.

    Science.gov (United States)

    Kayser, Veysel; Chennamsetty, Naresh; Voynov, Vladimir; Helk, Bernhard; Trout, Bernhardt L

    2011-01-01

    Characterization of aggregation profiles of monoclonal antibodies (mAb) is gaining importance because an increasing number of mAb-based therapeutics are entering clinical studies and gaining marketing approval. To develop a successful formulation, it is imperative to identify the critical biochemical properties of each potential mAb drug candidate. We investigated the conformational change and aggregation of a human IgG1 using external dye-binding experiments with fluorescence spectroscopy and compared the aggregation profiles obtained to the results of size-exclusion chromatography. We show that using an appropriate dye at selected mAb concentration, unfolding or aggregation can be studied. In addition, dye-binding experiments may be used as conventional assays to study therapeutic mAb stability. PMID:21540645

  5. Self-peptides with intermediate capacity to bind and stabilize MHC class I molecules may be immunogenic

    DEFF Research Database (Denmark)

    Andersen, M L M; Ruhwald, Morten; Nissen, M H;

    2003-01-01

    Thirty self-peptides were selected on the basis of their predicted binding to H-2b molecules. The binding of peptides was ascertained experimentally by biochemical (KD measurements) and cellular [major histocompatibility complex class I (MHC-I) stabilization] assays. A weak, but significant, corr...

  6. Enhanced exo-inulinase activity and stability by fusion of an inulin-binding module.

    Science.gov (United States)

    Zhou, Shun-Hua; Liu, Yuan; Zhao, Yu-Juan; Chi, Zhe; Chi, Zhen-Ming; Liu, Guang-Lei

    2016-09-01

    In this study, an inulin-binding module from Bacillus macerans was successfully fused to an exo-inulinase from Kluyveromyces marxianus, creating a hybrid functional enzyme. The recombinant exo-inulinase (rINU), the hybrid enzyme (rINUIBM), and the recombinant inulin-binding module (rIBM) were, respectively, heterologously expressed and biochemically characterized. It was found that both the inulinase activity and the catalytic efficiency (k cat/K m(app)) of the rINUIBM were considerably higher than those of rINU. Though the rINU and the rINUIBM shared the same optimum pH of 4.5, the optimum temperature of the rINUIBM (60 °C) was 5 °C higher than that of the rINU. Notably, the fused IBM significantly enhanced both the pH stability and the thermostability of the rINUIBM, suggesting that the rINUIBM obtained would have more extensive potential applications. Furthermore, the fusion of the IBM could substantially improve the inulin-binding capability of the rINUIBM, which was consistent with the determination of the K m(app). This meant that the fused IBM could play a critical role in the recognition of polysaccharides and enhanced the hydrolase activity of the associated inulinase by increasing enzyme-substrate proximity. Besides, the extra supplement of the independent non-catalytic rIBM could also improve the inulinase activity of the rINU. However, this improvement was much better in case of the fusion. Consequently, the IBM could be designated as a multifunctional domain that was responsible for the activity enhancement, the stabilization, and the substrate binding of the rINUIBM. All these features obtained in this study make the rINUIBM become an attractive candidate for an efficient inulin hydrolysis.

  7. Radiation effects on the stability of benzimidazole, which directly affects the stability of human DNA

    International Nuclear Information System (INIS)

    As all of us know that DNA is the genetic material and that is therefore stood at the very center of the study of life. Among the four important nitrogenous bases found in DNA one is purine which is nothing but a benzimidazole structure substituted by two nitrogens at 1 and 3 positions. Denaturation and renaturation duo to radiation are the two important incidents in DNA life which are the reason of many diseases and also the remedy of many diseases. These two incidents occur due to environmental effect on the parent part of DNA such as purine or we may say that benzimidazole structure. Since benzimidazole is an important part of human DNA structure so its response on different environment causes e huge effect on human gen. To study such response different types of benzimidazole molecules have been studied and two of such benzimidazole molecules are 2-Acetyl Benzomidazole (2ABI) and 2-Benzoyl Benzimidazole (2BBI). Usually these molecules show excited state proton transfer characteristics in polar and nonpolar environment. Proton transfer effect is very important behavior in DNA bases which is the fundamental phenomenon of different drug designing. To control such effect or to produce the effect as much as we want we have tried to restrict the molecule in different nano cavities. Michroheterogeneous media such as micelles as usual has enormous environmental effect on charge transfer phenomenon. The specialty of this media is that they have an ability to concentrate guest molecules into relatively small effective volumes and then to promote the re-encounter of such molecules. This property also makes micelles a good device for inducing efficient electrostatic interactions between the micelle head groups and the guest molecules. This electrostatic interaction has a direct effect on the stability of 2ABI and 2BBI molecule in ground state as well as in excited state due to micellization and this stability has enormous effect on human gene stability. (authors)

  8. Methodical design for stability assessments of permafrost-affected high-mountain rock walls

    OpenAIRE

    Fischer, L.; C. Huggel

    2008-01-01

    Slope stability of steep rock walls in glacierised and permafrost-affected high-mountain regions is influenced by a number of different factors and processes. For an integral assessment of slope stability, a better understanding of the predisposing factors is particularly important, especially in view of rapid climate-related changes. This study introduces a methodical design that includes suitable methods and techniques for investigations of different predisposing factors in high-mountain ro...

  9. Using DNA duplex stability information for transcription factor binding site discovery.

    Science.gov (United States)

    Gordân, Raluca; Hartemink, Alexander J

    2008-01-01

    Transcription factor (TF) binding site discovery is an important step in understanding transcriptional regulation. Many computational tools have already been developed, but their success in detecting TF motifs is still limited. We believe one of the main reasons for the low accuracy of current methods is that they do not take into account the structural aspects of TF-DNA interaction. We have previously shown that knowledge about the structural class of the TF and information about nucleosome occupancy can be used to improve motif discovery. Here, we demonstrate the benefits of using information about the DNA double-helical stability for motif discovery. We notice that, in general, the energy needed to destabilize the DNA double helix is higher at TF binding sites than at random DNA sites. We use this information to derive informative positional priors that we incorporate into a motif finding algorithm. When applied to yeast ChIP-chip data, the new informative priors improve the performance of the motif finder significantly when compared to priors that do not use the energetic stability information.

  10. Hand Proximity Differentially Affects Visual Working Memory for Color and Orientation in a Binding Task

    Directory of Open Access Journals (Sweden)

    Shane P. Kelly

    2014-04-01

    Full Text Available Observers determined whether two sequentially presented arrays of six lines were the same or different. Differences, when present, involved either a swap in the color of two lines or a swap in the orientation of two lines. Thus, accurate change detection required the binding of color and orientation information for each line within visual working memory. Holding viewing distance constant, the proximity of the arrays to the hands was manipulated. Placing the hands near the to-be-remembered array decreased participants’ ability to remember color information, but increased their ability to remember orientation information. This pair of results indicates that hand proximity differentially affects the processing of various types of visual information, a conclusion broadly consistent with functional and anatomical differences in the magnocellular and parvocellular pathways. It further indicates that hand proximity affects the likelihood that various object features will be encoded into integrated object files.

  11. Hand proximity differentially affects visual working memory for color and orientation in a binding task.

    Science.gov (United States)

    Kelly, Shane P; Brockmole, James R

    2014-01-01

    Observers determined whether two sequentially presented arrays of six lines were the same or different. Differences, when present, involved either a swap in the color of two lines or a swap in the orientation of two lines. Thus, accurate change detection required the binding of color and orientation information for each line within visual working memory. Holding viewing distance constant, the proximity of the arrays to the hands was manipulated. Placing the hands near the to-be-remembered array decreased participants' ability to remember color information, but increased their ability to remember orientation information. This pair of results indicates that hand proximity differentially affects the processing of various types of visual information, a conclusion broadly consistent with functional and anatomical differences in the magnocellular and parvocellular pathways. It further indicates that hand proximity affects the likelihood that various object features will be encoded into integrated object files. PMID:24795671

  12. Deactivation of ferrylmyoglobin by vanillin as affected by vanillin binding to β-lactoglobulin.

    Science.gov (United States)

    Libardi, Silvia Helena; Borges, Júlio C; Skibsted, Leif H; Cardoso, Daniel R

    2011-06-01

    Vanillin was found to be efficient as a deactivator of ferrylmyoglobin with a second-order rate constant of k(2) = 57 ± 1 L mol(-1) s(-1) for reduction to metmyoglobin with ΔH(‡) = 58.3 ± 0.3 kJ mol(-1) and ΔS(‡) = -14 ± 1 J mol(-1) K(-1) in aqueous pH 7.4 solution at 25 °C. Binding to β-lactoglobulin (βLG) was found to affect the reactivity of vanillin at 25 °C only slightly to k(2) = 48 ± 2 L mol(-1) s(-1) (ΔH(‡) = 68.4 ± 0.4 kJ mol(-1) and ΔS(‡) = 17 ± 1 J mol(-1) K(-1)) for deactivation of ferrylmyoglobin. Binding of vanillin to βLG was found to have a binding stoichiometry vanillin/βLG > 10 with K(A) = 6 × 10(2) L mol(-1) and an apparent total ΔH° of approximately -38 kJ mol(-1) and ΔS° = -55.4 ± 4 J mol(-1) K(-1) at 25 °C and ΔC(p, obs) = -1.02 kJ mol(-1) K(-1) indicative of increasing ordering in the complex, as determined by isothermal titration microcalorimetry. From tryptophan fluorescence quenching for βLG by vanillin, approximately one vanillin was found to bind to each βLG far stronger with K(A) = 5 × 10(4) L mol(-1) and a ΔH° = -10.2 kJ mol(-1) and ΔS° = 55 J mol(-1) K(-1) at 25 °C. The kinetic entropy/enthalpy compensation effect seen for vanillin reactivity by binding to βLG is concluded to relate to the weakly bound vanillin oriented through hydrogen bonds on the βLG surface with the phenolic group pointing toward the solvent, in effect making both ΔH(‡) and ΔS(‡) more positive. The more strongly bound vanillin capable of tryptophan quenching in the βLG calyx seems less or nonreactive.

  13. An epigenetic regulator emerges as microtubule minus-end binding and stabilizing factor in mitosis.

    Science.gov (United States)

    Meunier, Sylvain; Shvedunova, Maria; Van Nguyen, Nhuong; Avila, Leonor; Vernos, Isabelle; Akhtar, Asifa

    2015-01-01

    The evolutionary conserved NSL complex is a prominent epigenetic regulator controlling expression of thousands of genes. Here we uncover a novel function of the NSL complex members in mitosis. As the cell enters mitosis, KANSL1 and KANSL3 undergo a marked relocalisation from the chromatin to the mitotic spindle. By stabilizing microtubule minus ends in a RanGTP-dependent manner, they are essential for spindle assembly and chromosome segregation. Moreover, we identify KANSL3 as a microtubule minus-end-binding protein, revealing a new class of mitosis-specific microtubule minus-end regulators. By adopting distinct functions in interphase and mitosis, KANSL proteins provide a link to coordinate the tasks of faithful expression and inheritance of the genome during different phases of the cell cycle.

  14. Human single-stranded DNA binding proteins: guardians of genome stability

    Institute of Scientific and Technical Information of China (English)

    Yuanzhong Wu; Jinping Lu; Tiebang Kang

    2016-01-01

    Single-stranded DNA-binding proteins (SSBs) are essential for maintaining the integrity of the genome in all organisms.All processes related to DNA,such as replication,excision,repair,and recombination,require the participation of SSBs whose oligonucleotideaoligosaccharide-binding (OB)-fold domain is responsible for the interaction with single-stranded DNA (ssDNA).For a long time,the heterotrimeric replication protein A (RPA) complex was believed to be the only nuclear SSB in eukanyotes to participate in ssDNA processing,while mitochondrial SSBs that are consewed with prokaryotic SSBs were shown to be essential for maintaining genome stability in eukaryotic mitochondria.In recent years,two new proteins,hSSB1 and hSSB2 (human SSBs 1/2),were identified and have better sequence similarity to bacterial and archaeal SSBs than RPA.This review summarizes the current understanding of these human SSBs in DNA damage repair and in cell-cycle checkpoint activation following DNA damage,as well as their relationships with cancer.

  15. Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site

    Science.gov (United States)

    Liu, Chuang; Perilla, Juan R.; Ning, Jiying; Lu, Manman; Hou, Guangjin; Ramalho, Ruben; Himes, Benjamin A.; Zhao, Gongpu; Bedwell, Gregory J.; Byeon, In-Ja; Ahn, Jinwoo; Gronenborn, Angela M.; Prevelige, Peter E.; Rousso, Itay; Aiken, Christopher; Polenova, Tatyana; Schulten, Klaus; Zhang, Peijun

    2016-03-01

    The host cell factor cyclophilin A (CypA) interacts directly with the HIV-1 capsid and regulates viral infectivity. Although the crystal structure of CypA in complex with the N-terminal domain of the HIV-1 capsid protein (CA) has been known for nearly two decades, how CypA interacts with the viral capsid and modulates HIV-1 infectivity remains unclear. We determined the cryoEM structure of CypA in complex with the assembled HIV-1 capsid at 8-Å resolution. The structure exhibits a distinct CypA-binding pattern in which CypA selectively bridges the two CA hexamers along the direction of highest curvature. EM-guided all-atom molecular dynamics simulations and solid-state NMR further reveal that the CypA-binding pattern is achieved by single-CypA molecules simultaneously interacting with two CA subunits, in different hexamers, through a previously uncharacterized non-canonical interface. These results provide new insights into how CypA stabilizes the HIV-1 capsid and is recruited to facilitate HIV-1 infection.

  16. Effects of ligand binding on the mechanical stability of protein GB1 studied by steered molecular dynamics simulation.

    Science.gov (United States)

    Su, Ji-Guo; Zhao, Shu-Xin; Wang, Xiao-Feng; Li, Chun-Hua; Li, Jing-Yuan

    2016-08-01

    Regulation of the mechanical properties of proteins plays an important role in many biological processes, and sheds light on the design of biomaterials comprised of protein. At present, strategies to regulate protein mechanical stability focus mainly on direct modulation of the force-bearing region of the protein. Interestingly, the mechanical stability of GB1 can be significantly enhanced by the binding of Fc fragments of human IgG antibody, where the binding site is distant from the force-bearing region of the protein. The mechanism of this long-range allosteric control of protein mechanics is still elusive. In this work, the impact of ligand binding on the mechanical stability of GB1 was investigated using steered molecular dynamics simulation, and a mechanism underlying the enhanced protein mechanical stability is proposed. We found that the external force causes deformation of both force-bearing region and ligand binding site. In other words, there is a long-range coupling between these two regions. The binding of ligand restricts the distortion of the binding site and reduces the deformation of the force-bearing region through a long-range allosteric communication, which thus improves the overall mechanical stability of the protein. The simulation results are very consistent with previous experimental observations. Our studies thus provide atomic-level insights into the mechanical unfolding process of GB1, and explain the impact of ligand binding on the mechanical properties of the protein through long-range allosteric regulation, which should facilitate effective modulation of protein mechanical properties. PMID:27444879

  17. Effects of ligand binding on the mechanical stability of protein GB1 studied by steered molecular dynamics simulation.

    Science.gov (United States)

    Su, Ji-Guo; Zhao, Shu-Xin; Wang, Xiao-Feng; Li, Chun-Hua; Li, Jing-Yuan

    2016-08-01

    Regulation of the mechanical properties of proteins plays an important role in many biological processes, and sheds light on the design of biomaterials comprised of protein. At present, strategies to regulate protein mechanical stability focus mainly on direct modulation of the force-bearing region of the protein. Interestingly, the mechanical stability of GB1 can be significantly enhanced by the binding of Fc fragments of human IgG antibody, where the binding site is distant from the force-bearing region of the protein. The mechanism of this long-range allosteric control of protein mechanics is still elusive. In this work, the impact of ligand binding on the mechanical stability of GB1 was investigated using steered molecular dynamics simulation, and a mechanism underlying the enhanced protein mechanical stability is proposed. We found that the external force causes deformation of both force-bearing region and ligand binding site. In other words, there is a long-range coupling between these two regions. The binding of ligand restricts the distortion of the binding site and reduces the deformation of the force-bearing region through a long-range allosteric communication, which thus improves the overall mechanical stability of the protein. The simulation results are very consistent with previous experimental observations. Our studies thus provide atomic-level insights into the mechanical unfolding process of GB1, and explain the impact of ligand binding on the mechanical properties of the protein through long-range allosteric regulation, which should facilitate effective modulation of protein mechanical properties.

  18. Emulsifier type, metal chelation and pH affect oxidative stability of n-3-enriched emulsions

    DEFF Research Database (Denmark)

    Haahr, Anne-Mette; Jacobsen, Charlotte

    2008-01-01

    Recent research has shown that the oxidative stability of oil-in-water emulsions is affected by the type of surfactant used as emulsifier. The aim of this study was to evaluate the effect of real food emulsifiers as well as metal chelation by EDTA and pH on the oxidative stability of a 10% n-3...... to their ability to chelate iron, scavenge free radicals, interfere with interactions between the lipid hydroperoxides and iron as well as to form a physical harrier around the oil droplets....

  19. Study on the Gas Phase Stability of Heme-binding Pocket in Cytochrome Tb5 and Its Mutants by Electrospray Mass Spectrometry

    Institute of Scientific and Technical Information of China (English)

    YU,Chong-Tian(余翀天); GUO,Yin-Long(郭寅龙); L(U),Long(吕龙); WANG,Yun-Hua(王韵华); YAO,Ping(姚萍); HUANG,Zhong-Xian(黄仲贤)

    2002-01-01

    To ehucidate the effect of various amino acid residues on the heme-binding pocket in cytochrome Tbs, several residues were chosen for replacement by means of site-directed mutagenesis.Comparison of the mass spectrmn between the F35Y mutant and the wild type shows that the relative abundance of holoprotein ion of F35Y is lower than that of the wild type in gas phase. It is concluded that mutation from Phe35 residue to tyrosine decreases the hydrophobic character of cytochrome Tbs heme pocket, which decreases the stability of heme-binding pocket. ESI-MS spectra of the mutants V61E, V61K, V61H and V61Y show various contribution of amino acid to the stability of heme-binding pocket. The small and non-polar residue Vat61 was replaced with large or polar residues, resulting in enhancing the trend of heme leaving from the pocket. In addition, comparison of the mass relative abundance of bolo-proteins among all the Va161-mutants, shows that their stability in gas phase appropriately submit the following order: wild type > V61H > V61E > V61K ≈ V61Y. The extra great stability of quadruple sites mutant E44/48/56A/D60A shows that reduction of electrostatic or hydrogen bond interactions among the residues locating in the outside region of the heme edge remarkably affect the stability of heme. The results of analyzing the oxidation states of heme iron in Tbs and its mutants by insource-CAD experiment suggest that the charge states of heme iron maintain inflexible in mutation process.

  20. IL-8 dictates glycosaminoglycan binding and stability of IL-18 in cystic fibrosis.

    LENUS (Irish Health Repository)

    Reeves, Emer P

    2010-02-01

    Dysregulation of airway inflammation contributes to lung disease in cystic fibrosis (CF). Inflammation is mediated by inflammatory cytokines, including IL-8, which illustrates an increase in biological half-life and proinflammatory activity when bound to glycosaminoglycans (GAGs). The aim of this project was to compare IL-8 and IL-18 for their relative stability, activity, and interaction with GAGs, including chondroitin sulfate, hyaluronic acid, and heparan sulfate, present in high quantities in the lungs of patients with CF. Bronchoalveolar lavage fluid was collected from patients with CF (n = 28), non-CF controls (n = 14), and patients with chronic obstructive pulmonary disease (n = 12). Increased levels of IL-8 and reduced concentrations of IL-18 were detected in bronchial samples obtained from CF individuals. The low level of IL-18 was not a defect in IL-18 production, as the pro- and mature forms of the molecule were expressed and produced by CF epithelial cells and monocytes. There was, however, a marked competition between IL-8 and IL-18 for binding to GAGs. A pronounced loss of IL-18 binding capacity occurred in the presence of IL-8, which displaced IL-18 from these anionic-matrices, rendering the cytokine susceptible to proteolytic degradation by neutrophil elastase. As a biological consequence of IL-18 degradation, reduced levels of IL-2 were secreted by Jurkat T lymphocytes. In conclusion, a novel mechanism has been identified highlighting the potential of IL-8 to determine the fate of other inflammatory molecules, such as IL-18, within the inflammatory milieu of the CF lung.

  1. Increases thermal stability and cellulose-binding capacity of Cryptococcus sp. S-2 lipase by fusion of cellulose binding domain derived from Trichoderma reesei

    Energy Technology Data Exchange (ETDEWEB)

    Thongekkaew, Jantaporn, E-mail: jantaporn_25@yahoo.com [Department of Biological Science, Faculty of Science, Ubon-Ratchathani University, Warinchumrab, Ubon-Ratchathani 34190 (Thailand); Ikeda, Hiroko; Iefuji, Haruyuki [Application Research Division, National Research Institute of Brewing, 3-7-1 Kagamiyama, Higashi-Hiroshima 739-0046 (Japan)

    2012-03-30

    Highlights: Black-Right-Pointing-Pointer The CSLP and fusion enzyme were successfully expressed in the Pichia pastoris. Black-Right-Pointing-Pointer The fusion enzyme was stable at 80 Degree-Sign C for 120-min. Black-Right-Pointing-Pointer The fusion enzyme was responsible for cellulose-binding capacity. Black-Right-Pointing-Pointer The fusion enzyme has an attractive applicant for enzyme immobilization. -- Abstract: To improve the thermal stability and cellulose-binding capacity of Cryptococcus sp. S-2 lipase (CSLP), the cellulose-binding domain originates from Trichoderma reesei cellobiohydrolase I was engineered into C-terminal region of the CSLP (CSLP-CBD). The CSLP and CSLP-CBD were successfully expressed in the Pichia pastoris using the strong methanol inducible alcohol oxidase 1 (AOX1) promoter and the secretion signal sequence from Saccharomyces cerevisiae ({alpha} factor). The recombinant CSLP and CSLP-CBD were secreted into culture medium and estimated by SDS-PAGE to be 22 and 27 kDa, respectively. The fusion enzyme was stable at 80 Degree-Sign C and retained more than 80% of its activity after 120-min incubation at this temperature. Our results also found that the fusion of fungal exoglucanase cellulose-binding domain to CSLP is responsible for cellulose-binding capacity. This attribute should make it an attractive applicant for enzyme immobilization.

  2. Nanog RNA-binding proteins YBX1 and ILF3 affect pluripotency of embryonic stem cells.

    Science.gov (United States)

    Guo, Chuanliang; Xue, Yan; Yang, Guanheng; Yin, Shang; Shi, Wansheng; Cheng, Yan; Yan, Xiaoshuang; Fan, Shuyue; Zhang, Huijun; Zeng, Fanyi

    2016-08-01

    Nanog is a well-known transcription factor that plays a fundamental role in stem cell self-renewal and the maintenance of their pluripotent cell identity. There remains a large data gap with respect to the spectrum of the key pluripotency transcription factors' interaction partners. Limited information is available concerning Nanog-associated RNA-binding proteins (RBPs), and the intrinsic protein-RNA interactions characteristic of the regulatory activities of Nanog. Herein, we used an improved affinity protocol to purify Nanog-interacting RBPs from mouse embryonic stem cells (ESCs), and 49 RBPs of Nanog were identified. Among them, the interaction of YBX1 and ILF3 with Nanog mRNA was further confirmed by in vitro assays, such as Western blot, RNA immunoprecipitation (RIP), and ex vivo methods, such as immunofluorescence staining and fluorescent in situ hybridization (FISH), MS2 in vivo biotin-tagged RNA affinity purification (MS2-BioTRAP). Interestingly, RNAi studies revealed that YBX1 and ILF3 positively affected the expression of Nanog and other pluripotency-related genes. Particularly, downregulation of YBX1 or ILF3 resulted in high expression of mesoderm markers. Thus, a reduction in the expression of YBX1 and ILF3 controls the expression of pluripotency-related genes in ESCs, suggesting their roles in further regulation of the pluripotent state of ESCs. PMID:26289635

  3. The chromatin-binding protein HMGN1 regulates the expression of methyl CpG-binding protein 2 (MECP2) and affects the behavior of mice.

    Science.gov (United States)

    Abuhatzira, Liron; Shamir, Alon; Schones, Dustin E; Schäffer, Alejandro A; Bustin, Michael

    2011-12-01

    High mobility group N1 protein (HMGN1), a nucleosomal-binding protein that affects the structure and function of chromatin, is encoded by a gene located on chromosome 21 and is overexpressed in Down syndrome, one of the most prevalent genomic disorders. Misexpression of HMGN1 affects the cellular transcription profile; however, the biological function of this protein is still not fully understood. We report that HMGN1 modulates the expression of methyl CpG-binding protein 2 (MeCP2), a DNA-binding protein known to affect neurological functions including autism spectrum disorders, and whose alterations in HMGN1 levels affect the behavior of mice. Quantitative PCR and Western analyses of cell lines and brain tissues from mice that either overexpress or lack HMGN1 indicate that HMGN1 is a negative regulator of MeCP2 expression. Alterations in HMGN1 levels lead to changes in chromatin structure and histone modifications in the MeCP2 promoter. Behavior analyses by open field test, elevated plus maze, Reciprocal Social Interaction, and automated sociability test link changes in HMGN1 levels to abnormalities in activity and anxiety and to social deficits in mice. Targeted analysis of the Autism Genetic Resource Exchange genotype collection reveals a non-random distribution of genotypes within 500 kbp of HMGN1 in a region affecting its expression in families predisposed to autism spectrum disorders. Our results reveal that HMGN1 affects the behavior of mice and suggest that epigenetic changes resulting from altered HMGN1 levels could play a role in the etiology of neurodevelopmental disorders.

  4. Involvement of the heterodimeric interface region of the nucleotide binding domain-2 (NBD2) in the CFTR quaternary structure and membrane stability.

    Science.gov (United States)

    Micoud, Julien; Chauvet, Sylvain; Scheckenbach, Klaus Ernst Ludwig; Alfaidy, Nadia; Chanson, Marc; Benharouga, Mohamed

    2015-10-01

    The cystic fibrosis transmembrane conductance regulator (CFTR) is the only member of the ATP-binding cassette (ABC) superfamily that functions as a chloride channel. The predicted structure of CFTR protein contains two membrane-spanning domains (MSDs), each followed by a nucleotide binding domain (NBD1 and NBD2). The opening of the Cl- channel is directly linked to ATP-driven tight dimerization of CFTR's NBD1 and NBD2 domains. The presence of a heterodimeric interfaces (HI) region in NBD1 and NBD2 generated a head to tail orientation necessary for channel activity. This process was also suggested to promote important conformational changes in the associated transmembrane domains of CFTR, which may impact the CFTR plasma membrane stability. To better understand the role of the individual HI region in this process, we generated recombinant CFTR protein with suppressed HI-NBD1 and HI-NBD2. Our results indicate that HI-NBD2 deletion leads to the loss of the dimerization profile of CFTR that affect its plasma membrane stability. We conclude that, in addition to its role in Cl- transport, HI-NBD2 domain confers membrane stability of CFTR by consolidating its quaternary structure through interactions with HI-NBD1 region.

  5. Nucleobases bind to and stabilize aggregates of a prebiotic amphiphile, providing a viable mechanism for the emergence of protocells.

    Science.gov (United States)

    Black, Roy A; Blosser, Matthew C; Stottrup, Benjamin L; Tavakley, Ravi; Deamer, David W; Keller, Sarah L

    2013-08-13

    Primordial cells presumably combined RNAs, which functioned as catalysts and carriers of genetic information, with an encapsulating membrane of aggregated amphiphilic molecules. Major questions regarding this hypothesis include how the four bases and the sugar in RNA were selected from a mixture of prebiotic compounds and colocalized with such membranes, and how the membranes were stabilized against flocculation in salt water. To address these questions, we explored the possibility that aggregates of decanoic acid, a prebiotic amphiphile, interact with the bases and sugar found in RNA. We found that these bases, as well as some but not all related bases, bind to decanoic acid aggregates. Moreover, both the bases and ribose inhibit flocculation of decanoic acid by salt. The extent of inhibition by the bases correlates with the extent of their binding, and ribose inhibits to a greater extent than three similar sugars. Finally, the stabilizing effects of a base and ribose are additive. Thus, aggregates of a prebiotic amphiphile bind certain heterocyclic bases and sugars, including those found in RNA, and this binding stabilizes the aggregates against salt. These mutually reinforcing mechanisms might have driven the emergence of protocells. PMID:23901105

  6. Stability, protein binding and clearance studies of [99mTc]DTPA. Evaluation of a commercially available dry-kit

    DEFF Research Database (Denmark)

    Rehling, M

    1988-01-01

    the quality of a commercial [99mTc]DTPA preparation (C.I.S., France) with reference to stability, protein binding and accuracy of the determined plasma clearance values as a measure of GFR. The stability of the preparations was studied by thin-layer chromatography, the in vitro protein binding by Sephadex...... filtration after incubation with human serum albumin and in vivo protein binding by filtration of human plasma. The accuracy of the plasma clearance values was investigated by comparison with the simultaneously measured plasma clearance of [51Cr]EDTA. There was no detectable free pertechnetate or hydrolysed...... reduced technetium in eight vials five and six hours after the preparation. The in vitro protein binding 10 (20), 120 and 300 min after the preparation of eight vials was 2.3% (0.8%), 0.2% and 0.1%, respectively. The in vivo protein binding in 12 patients 5, 90 and 180 min after the injection was 0.3%, 0...

  7. Sequential dimerization of human zipcode-binding protein IMP1 on RNA: a cooperative mechanism providing RNP stability

    DEFF Research Database (Denmark)

    Nielsen, J.; Kristensen, M. A.; Willemoes, Martin;

    2004-01-01

    zipcode-binding protein IMP1 on targets in the 3'-UTR from Igf-II mRNA and in H19 RNA. In both cases, two molecules of IMP1 bound to RNA by a sequential, cooperative mechanism, characterized by an initial fast step, followed by a slow second step. The first step created an obligatory assembly intermediate...... of low stability, whereas the second step was the discriminatory event that converted a putative RNA target into a ‘locked' stable RNP. The ability to dimerize was also observed between members of the IMP family of zipcode-binding proteins, providing a multitude of further interaction possibilities...

  8. Habitat stability affects dispersal and the ability to track climate change

    DEFF Research Database (Denmark)

    Hof, Christian; Brändle, Martin; Dehling, D. Matthias;

    2012-01-01

    than lotic species. Assuming that climate is an important determinant of species distributions, we hypothesize that lentic species should have distributions that are closer to equilibrium with current climate, and should more rapidly track climatic changes. We tested these hypotheses using datasets......Habitat persistence should influence dispersal ability, selecting for stronger dispersal in habitats of lower temporal stability. As standing (lentic) freshwater habitats are on average less persistent over time than running (lotic) habitats, lentic species should show higher dispersal abilities...... that lentic species track climatic changes more rapidly than lotic species. These results are consistent with the proposed hypothesis that habitat persistence affects the evolution of dispersal....

  9. Creating Prebiotic Sanctuary: Self-Assembling Supramolecular Peptide Structures Bind and Stabilize RNA

    Science.gov (United States)

    Carny, Ohad; Gazit, Ehud

    2011-04-01

    Any attempt to uncover the origins of life must tackle the known `blind watchmaker problem'. That is to demonstrate the likelihood of the emergence of a prebiotic system simple enough to be formed spontaneously and yet complex enough to allow natural selection that will lead to Darwinistic evolution. Studies of short aromatic peptides revealed their ability to self-assemble into ordered and stable structures. The unique physical and chemical characteristics of these peptide assemblies point out to their possible role in the origins of life. We have explored mechanisms by which self-assembling short peptides and RNA fragments could interact together and go through a molecular co-evolution, using diphenylalanine supramolecular assemblies as a model system. The spontaneous formation of these self-assembling peptides under prebiotic conditions, through the salt-induced peptide formation (SIPF) pathway was demonstrated. These peptide assemblies possess the ability to bind and stabilize ribonucleotides in a sequence-depended manner, thus increase their relative fitness. The formation of these peptide assemblies is dependent on the homochirality of the peptide monomers: while homochiral peptides (L-Phe-L-Phe and D-Phe-D-Phe) self-assemble rapidly in aqueous environment, heterochiral diastereoisomers (L-Phe-D-Phe and D-Phe-L-Phe) do not tend to self-assemble. This characteristic consists with the homochirality of all living matter. Finally, based on these findings, we propose a model for the role of short self-assembling peptides in the prebiotic molecular evolution and the origin of life.

  10. Milk protein composition and stability changes affected by iron in water sources.

    Science.gov (United States)

    Wang, Aili; Duncan, Susan E; Knowlton, Katharine F; Ray, William K; Dietrich, Andrea M

    2016-06-01

    Water makes up more than 80% of the total weight of milk. However, the influence of water chemistry on the milk proteome has not been extensively studied. The objective was to evaluate interaction of water-sourced iron (low, medium, and high levels) on milk proteome and implications on milk oxidative state and mineral content. Protein composition, oxidative stability, and mineral composition of milk were investigated under conditions of iron ingestion through bovine drinking water (infused) as well as direct iron addition to commercial milk in 2 studies. Four ruminally cannulated cows each received aqueous infusions (based on water consumption of 100L) of 0, 2, 5, and 12.5mg/L Fe(2+) as ferrous lactate, resulting in doses of 0, 200, 500 or 1,250mg of Fe/d, in a 4×4Latin square design for a 14-d period. For comparison, ferrous sulfate solution was directly added into commercial retail milk at the same concentrations: control (0mg of Fe/L), low (2mg of Fe/L), medium (5mg of Fe/L), and high (12.5mg of Fe/L). Two-dimensional electrophoresis coupled with matrix-assisted laser desorption/ionization-tandem time-of-flight (MALDI-TOF/TOF) high-resolution tandem mass spectrometry analysis was applied to characterize milk protein composition. Oxidative stability of milk was evaluated by the thiobarbituric acid reactive substances (TBARS) assay for malondialdehyde, and mineral content was measured by inductively coupled plasma mass spectrometry. For milk from both abomasal infusion of ferrous lactate and direct addition of ferrous sulfate, an iron concentration as low as 2mg of Fe/L was able to cause oxidative stress in dairy cattle and infused milk, respectively. Abomasal infusion affected both caseins and whey proteins in the milk, whereas direct addition mainly influenced caseins. Although abomasal iron infusion did not significantly affect oxidation state and mineral balance (except iron), it induced oxidized off-flavor and partial degradation of whey proteins. Direct

  11. Milk protein composition and stability changes affected by iron in water sources.

    Science.gov (United States)

    Wang, Aili; Duncan, Susan E; Knowlton, Katharine F; Ray, William K; Dietrich, Andrea M

    2016-06-01

    Water makes up more than 80% of the total weight of milk. However, the influence of water chemistry on the milk proteome has not been extensively studied. The objective was to evaluate interaction of water-sourced iron (low, medium, and high levels) on milk proteome and implications on milk oxidative state and mineral content. Protein composition, oxidative stability, and mineral composition of milk were investigated under conditions of iron ingestion through bovine drinking water (infused) as well as direct iron addition to commercial milk in 2 studies. Four ruminally cannulated cows each received aqueous infusions (based on water consumption of 100L) of 0, 2, 5, and 12.5mg/L Fe(2+) as ferrous lactate, resulting in doses of 0, 200, 500 or 1,250mg of Fe/d, in a 4×4Latin square design for a 14-d period. For comparison, ferrous sulfate solution was directly added into commercial retail milk at the same concentrations: control (0mg of Fe/L), low (2mg of Fe/L), medium (5mg of Fe/L), and high (12.5mg of Fe/L). Two-dimensional electrophoresis coupled with matrix-assisted laser desorption/ionization-tandem time-of-flight (MALDI-TOF/TOF) high-resolution tandem mass spectrometry analysis was applied to characterize milk protein composition. Oxidative stability of milk was evaluated by the thiobarbituric acid reactive substances (TBARS) assay for malondialdehyde, and mineral content was measured by inductively coupled plasma mass spectrometry. For milk from both abomasal infusion of ferrous lactate and direct addition of ferrous sulfate, an iron concentration as low as 2mg of Fe/L was able to cause oxidative stress in dairy cattle and infused milk, respectively. Abomasal infusion affected both caseins and whey proteins in the milk, whereas direct addition mainly influenced caseins. Although abomasal iron infusion did not significantly affect oxidation state and mineral balance (except iron), it induced oxidized off-flavor and partial degradation of whey proteins. Direct

  12. Cloning and mutational analysis of the gamma gene from Azotobacter vinelandii defines a new family of proteins capable of metallocluster binding and protein stabilization.

    Science.gov (United States)

    Rubio, Luis M; Rangaraj, Priya; Homer, Mary J; Roberts, Gary P; Ludden, Paul W

    2002-04-19

    Dinitrogenase is a heterotetrameric (alpha(2)beta(2)) enzyme that catalyzes the reduction of dinitrogen to ammonium and contains the iron-molybdenum cofactor (FeMo-co) at its active site. Certain Azotobacter vinelandii mutant strains unable to synthesize FeMo-co accumulate an apo form of dinitrogenase (lacking FeMo-co), with a subunit composition alpha(2)beta(2)gamma(2), which can be activated in vitro by the addition of FeMo-co. The gamma protein is able to bind FeMo-co or apodinitrogenase independently, leading to the suggestion that it facilitates FeMo-co insertion into the apoenzyme. In this work, the non-nif gene encoding the gamma subunit (nafY) has been cloned, sequenced, and found to encode a NifY-like protein. This finding, together with a wealth of knowledge on the biochemistry of proteins involved in FeMo-co and FeV-co biosyntheses, allows us to define a new family of iron and molybdenum (or vanadium) cluster-binding proteins that includes NifY, NifX, VnfX, and now gamma. In vitro FeMo-co insertion experiments presented in this work demonstrate that gamma stabilizes apodinitrogenase in the conformation required to be fully activable by the cofactor. Supporting this conclusion, we show that strains containing mutations in both nafY and nifX are severely affected in diazotrophic growth and extractable dinitrogenase activity when cultured under conditions that are likely to occur in natural environments. This finding reveals the physiological importance of the apodinitrogenase-stabilizing role of which both proteins are capable. The relationship between the metal cluster binding capabilities of this new family of proteins and the ability of some of them to stabilize an apoenzyme is still an open matter. PMID:11823455

  13. The Study of Stability of Compression-Loaded Multispan Composite Panel Upon Failure of Elements Binding it to Panel Supports

    Science.gov (United States)

    Zamula, G. N.; Ierusalimsky, K. M.; Fomin, V. P.; Grishin, V. I.; Kalmykova, G. S.

    1999-01-01

    The present document is a final technical report carried out within co-operation between United States'NASA Langley RC and Russia's Goskomoboronprom in aeronautics, and continues similar programs, accomplished in 1996, 1997, and 1998, respectively). The report provides results of "The study of stability of compression-loaded multispan composite panels upon failure of elements binding it to panel supports"; these comply with requirements established at TsAGI on 24 March 1998 and at NASA on 15 September 1998.

  14. Direct Measurement of the Nanomechanical Stability of a Redox Protein Active Site and Its Dependence upon Metal Binding.

    Science.gov (United States)

    Giannotti, Marina I; Cabeza de Vaca, Israel; Artés, Juan M; Sanz, Fausto; Guallar, Victor; Gorostiza, Pau

    2015-09-10

    The structural basis of the low reorganization energy of cupredoxins has long been debated. These proteins reconcile a conformationally heterogeneous and exposed metal-chelating site with the highly rigid copper center required for efficient electron transfer. Here we combine single-molecule mechanical unfolding experiments with statistical analysis and computer simulations to show that the metal-binding region of apo-azurin is mechanically flexible and that high mechanical stability is imparted by copper binding. The unfolding pathway of the metal site depends on the pulling residue and suggests that partial unfolding of the metal-binding site could be facilitated by the physical interaction with certain regions of the redox protein. PMID:26305718

  15. Membrane binding of Escherichia coli RNase E catalytic domain stabilizes protein structure and increases RNA substrate affinity.

    Science.gov (United States)

    Murashko, Oleg N; Kaberdin, Vladimir R; Lin-Chao, Sue

    2012-05-01

    RNase E plays an essential role in RNA processing and decay and tethers to the cytoplasmic membrane in Escherichia coli; however, the function of this membrane-protein interaction has remained unclear. Here, we establish a mechanistic role for the RNase E-membrane interaction. The reconstituted highly conserved N-terminal fragment of RNase E (NRne, residues 1-499) binds specifically to anionic phospholipids through electrostatic interactions. The membrane-binding specificity of NRne was confirmed using circular dichroism difference spectroscopy; the dissociation constant (K(d)) for NRne binding to anionic liposomes was 298 nM. E. coli RNase G and RNase E/G homologs from phylogenetically distant Aquifex aeolicus, Haemophilus influenzae Rd, and Synechocystis sp. were found to be membrane-binding proteins. Electrostatic potentials of NRne and its homologs were found to be conserved, highly positive, and spread over a large surface area encompassing four putative membrane-binding regions identified in the "large" domain (amino acids 1-400, consisting of the RNase H, S1, 5'-sensor, and DNase I subdomains) of E. coli NRne. In vitro cleavage assay using liposome-free and liposome-bound NRne and RNA substrates BR13 and GGG-RNAI showed that NRne membrane binding altered its enzymatic activity. Circular dichroism spectroscopy showed no obvious thermotropic structural changes in membrane-bound NRne between 10 and 60 °C, and membrane-bound NRne retained its normal cleavage activity after cooling. Thus, NRne membrane binding induced changes in secondary protein structure and enzymatic activation by stabilizing the protein-folding state and increasing its binding affinity for its substrate. Our results demonstrate that RNase E-membrane interaction enhances the rate of RNA processing and decay. PMID:22509045

  16. ZipA binds to FtsZ with high affinity and enhances the stability of FtsZ protofilaments.

    Directory of Open Access Journals (Sweden)

    Anuradha Kuchibhatla

    Full Text Available A bacterial membrane protein ZipA that tethers FtsZ to the membrane is known to promote FtsZ assembly. In this study, the binding of ZipA to FtsZ was monitored using fluorescence spectroscopy. ZipA was found to bind to FtsZ with high affinities at three different (6.0, 6.8 and 8.0 pHs, albeit the binding affinity decreased with increasing pH. Further, thick bundles of FtsZ protofilaments were observed in the presence of ZipA under the pH conditions used in this study indicating that ZipA can promote FtsZ assembly and stabilize FtsZ polymers under unfavorable conditions. Bis-ANS, a hydrophobic probe, decreased the interaction of FtsZ and ZipA indicating that the interaction between FtsZ and ZipA is hydrophobic in nature. ZipA prevented the dilution induced disassembly of FtsZ polymers suggesting that it stabilizes FtsZ protofilaments. Fluorescein isothiocyanate-labeled ZipA was found to be uniformly distributed along the length of the FtsZ protofilaments indicating that ZipA stabilizes FtsZ protofilaments by cross-linking them.

  17. The First Residue of the PWWP Motif Modulates HATH Domain Binding, Stability, and Protein-Protein Interaction.

    Science.gov (United States)

    Hung, Yi-Lin; Lee, Hsia-Ju; Jiang, Ingjye; Lin, Shang-Chi; Lo, Wei-Cheng; Lin, Yi-Jan; Sue, Shih-Che

    2015-07-01

    Hepatoma-derived growth factor (hHDGF) and HDGF-related proteins (HRPs) contain conserved N-terminal HATH domains with a characteristic structural motif, namely the PWWP motif. The HATH domain has attracted attention because of its ability to bind with heparin/heparan sulfate, DNA, and methylated histone peptide. Depending on the sequence of the PWWP motif, HRP HATHs are classified into P-type (Pro-His-Trp-Pro) and A-type (Ala-His-Trp-Pro) forms. A-type HATH is highly unstable and tends to precipitate in solution. We replaced the Pro residue in P-type HATHHDGF with Ala and evaluated the influence on structure, dynamics, and ligand binding. Nuclear magnetic resonance (NMR) hydrogen/deuterium exchange and circular dichroism (CD) measurements revealed reduced stability. Analysis of NMR backbone (15)N relaxations (R1, R2, and nuclear Overhauser effect) revealed additional backbone dynamics in the interface between the β-barrel and the C-terminal helix bundle. The β1-β2 loop, where the AHWP sequence is located, has great structural flexibility, which aids HATH-HATH interaction through the loop. A-type HATH, therefore, shows a stronger tendency to aggregate when binding with heparin and DNA oligomers. This study defines the role of the first residue of the PWWP motif in modulating HATH domain stability and oligomer formation in binding.

  18. Hydrophobicity of reactive site loop of SCCA1 affects its binding to hepatitis B virus

    Institute of Scientific and Technical Information of China (English)

    Min Chen; Tong Cheng; Chen-Yu Xu; Ting Wu; Shan-Hai Ou; Tao Zhang; Jun Zhang; Ning-Shao Xia

    2005-01-01

    AIM: To investigate the role of SCCA2 and other SCCA1 molecules in the process of hepatitis B virus (HBV) binding to mammalian cells.METHODS: SCCA1 and SCCA2 were isolated from HepG2. Binding protein (BP) genes were obtained through PCR. Recombinant baculoviruses expressing SCCA1, SCCA2, BP, and different mutants were constructed and utilized to infect mammalian cells to investigate the binding ability of infected cells to HBV.RESULTS: A SCCA1 gene (A1) was isolated from HepG2, but it appeared to lack the binding ability of infected cells to HBV. Two mutants, A1-BP and BP-A1, were constructed by interchanging the carboxyl terminal of A1 and BP. Cells expressing A1-BP showed an increased virus bindingcapacity, but not BP-A1. Comparison of A1 sequence with the sequence of BP indicated the presence of only three amino acid changes in the carboxyl terminal, two of them were found in the reactive site loop (RSL) of SCCA1. Primary structure assay revealed that the hydrophobicity of BP and AJ515706 in this domain was strong, but A1 was relatively weak. Changing the aa349 of A1 from low hydrophobic glutamic acid to high hydrophobic valine enhanced HBV binding. In contrast, HBV binding was reduced by changing the aa349 of BP from valine to glutamic acid. CONCLUSION: The reslts suggest that the hydrophobicity of RSL of SCCA1 may play an important role in HBV binding to cells.

  19. Degenerate in vitro genetic selection reveals mutations that diminish alfalfa mosaic virus RNA replication without affecting coat protein binding.

    Science.gov (United States)

    Rocheleau, Gail; Petrillo, Jessica; Guogas, Laura; Gehrke, Lee

    2004-08-01

    The alfalfa mosaic virus (AMV) RNAs are infectious only in the presence of the viral coat protein; however, the mechanisms describing coat protein's role during replication are disputed. We reasoned that mechanistic details might be revealed by identifying RNA mutations in the 3'-terminal coat protein binding domain that increased or decreased RNA replication without affecting coat protein binding. Degenerate (doped) in vitro genetic selection, based on a pool of randomized 39-mers, was used to select 30 variant RNAs that bound coat protein with high affinity. AUGC sequences that are conserved among AMV and ilarvirus RNAs were among the invariant nucleotides in the selected RNAs. Five representative clones were analyzed in functional assays, revealing diminished viral RNA expression resulting from apparent defects in replication and/or translation. These data identify a set of mutations, including G-U wobble pairs and nucleotide mismatches in the 5' hairpin, which affect viral RNA functions without significant impact on coat protein binding. Because the mutations associated with diminished function were scattered over the 3'-terminal nucleotides, we considered the possibility that RNA conformational changes rather than disruption of a precise motif might limit activity. Native polyacrylamide gel electrophoresis experiments showed that the 3' RNA conformation was indeed altered by nucleotide substitutions. One interpretation of the data is that coat protein binding to the AUGC sequences determines the orientation of the 3' hairpins relative to one another, while local structural features within these hairpins are also critical determinants of functional activity. PMID:15254175

  20. Frontolimbic serotonin 2A receptor binding in healthy subjects is associated with personality risk factors for affective disorder

    DEFF Research Database (Denmark)

    Frokjaer, Vibe G.; Mortensen, Erik L.; Nielsen, Finn Årup;

    2008-01-01

    Background: Serotonergic dysfunction has been associated with affective disorders. High trait neuroticism, as measured on personality inventories, is a risk factor for major depression. In this study we investigated whether neuroticism is associated with serotonin 2A receptor binding in brain...... regions of relevance for affective disorders. Methods: Eighty-three healthy volunteers completed the standardized personality questionnaire NEO-PI-R (Revised NEO Personality Inventory) and underwent [F-18]altanserin positron emission tomography imaging for assessment of serotonin 2A receptor binding...... analysis of the contributions from the six constituent traits of neuroticism showed that the correlation was primarily driven by two of them: vulnerability and anxiety. Indeed, vulnerability, defined as a person's difficulties in coping with stress, displayed the strongest positive correlation, which...

  1. Disruption of NAD~+ binding site in glyceraldehyde 3-phosphate dehydrogenase affects its intranuclear interactions

    Institute of Scientific and Technical Information of China (English)

    Manali; Phadke; Natalia; Krynetskaia; Anurag; Mishra; Carlos; Barrero; Salim; Merali; Scott; A; Gothe; Evgeny; Krynetskiy

    2015-01-01

    AIM:To characterize phosphorylation of human glyceraldehyde 3-phosphate dehydrogenase(GAPDH),and mobility of GAPDH in cancer cells treated with chemotherapeutic agents. METHODS:We used proteomics analysis to detect and characterize phosphorylation sites within human GAPDH. Site-specific mutagenesis and alanine scanning was then performed to evaluate functional significance of phosphorylation sites in the GAPDH polypeptide chain. Enzymatic properties of mutated GAPDH variants were assessed using kinetic studies. Intranuclear dynamics parameters(diffusion coefficient and the immobile fraction) were estimated using fluorescence recovery after photobleaching(FRAP) experiments and confocal microscopy. Molecular modeling experiments were performed to estimate the effects of mutations on NAD+ cofactor binding.RESULTS:Using MALDI-TOF analysis,we identified novel phosphorylation sites within the NAD+ binding center of GAPDH at Y94,S98,and T99. Using polyclonal antibody specific to phospho-T99-containing peptide within GAPDH,we demonstrated accumulation of phospho-T99-GAPDH inthe nuclear fractions of A549,HCT116,and SW48 cancer cel s after cytotoxic stress. We performed site-mutagenesis,and estimated enzymatic properties,intranuclear distribution,and intranuclear mobility of GAPDH mutated variants. Site-mutagenesis at positions S98 and T99 in the NAD+ binding center reduced enzymatic activity of GAPDH due to decreased affinity to NAD+(Km = 741 ± 257 μmol/L in T99 I vs 57 ± 11.1 μmol/L in wild type GAPDH. Molecular modeling experiments revealed the effect of mutations on NAD+ binding with GAPDH. FRAP(fluorescence recovery after photo bleaching) analysis showed that mutations in NAD+ binding center of GAPDH abrogated its intranuclear interactions. CONCLUSION:Our results suggest an important functional role of phosphorylated amino acids in the NAD+ binding center in GAPDH interactions with its intranuclear partners.

  2. Influenza A viruses suppress cyclooxygenase-2 expression by affecting its mRNA stability

    Science.gov (United States)

    Dudek, Sabine Eva; Nitzsche, Katja; Ludwig, Stephan; Ehrhardt, Christina

    2016-01-01

    Infection with influenza A viruses (IAV) provokes activation of cellular defence mechanisms contributing to the innate immune and inflammatory response. In this process the cyclooxygenase-2 (COX-2) plays an important role in the induction of prostaglandin-dependent inflammation. While it has been reported that COX-2 is induced upon IAV infection, in the present study we observed a down-regulation at later stages of infection suggesting a tight regulation of COX-2 by IAV. Our data indicate the pattern-recognition receptor RIG-I as mediator of the initial IAV-induced COX-2 synthesis. Nonetheless, during on-going IAV replication substantial suppression of COX-2 mRNA and protein synthesis could be detected, accompanied by a decrease in mRNA half-life. Interestingly, COX-2 mRNA stability was not only imbalanced by IAV replication but also by stimulation of cells with viral RNA. Our results reveal tristetraprolin (TTP), which is known to bind COX-2 mRNA and promote its rapid degradation, as regulator of COX-2 expression in IAV infection. During IAV replication and viral RNA accumulation TTP mRNA synthesis was induced, resulting in reduced COX-2 levels. Accordingly, the down-regulation of TTP resulted in increased COX-2 protein expression after IAV infection. These findings indicate a novel IAV-regulated cellular mechanism, contributing to the repression of host defence and therefore facilitating viral replication. PMID:27265729

  3. Harvest date affects aronia juice polyphenols, sugars, and antioxidant activity, but not anthocyanin stability.

    Science.gov (United States)

    Bolling, Bradley W; Taheri, Rod; Pei, Ruisong; Kranz, Sarah; Yu, Mo; Durocher, Shelley N; Brand, Mark H

    2015-11-15

    The goal of this work was to characterize how the date of harvest of 'Viking' aronia berry impacts juice pigmentation, sugars, and antioxidant activity. Aronia juice anthocyanins doubled at the fifth week of the harvest, and then decreased. Juice hydroxycinnamic acids decreased 33% from the first week, while proanthocyanidins increased 64%. Juice fructose and glucose plateaued at the fourth week, but sorbitol increased 40% to the seventh harvest week. Aronia juice pigment density increased due to anthocyanin concentration, and polyphenol copigmentation did not significantly affect juice pigmentation. Anthocyanin stability at pH 4.5 was similar between weeks. However, addition of quercetin, sorbitol, and chlorogenic acid to aronia anthocyanins inhibited pH-induced loss of color. Sorbitol and citric acid may be partially responsible for weekly variation in antioxidant activity, as addition of these agents inhibited DPPH scavenging 13-30%. Thus, aronia polyphenol and non-polyphenol components contribute to its colorant and antioxidant functionality.

  4. Factors that Affect Social Stability of Rural Areas in Ganzi District

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    Through the sample investigation of Kangding County, Daofu County, Luhuo County and Xiangcheng County in Sichuan Province in 2010 and by combining the quantitative and qualitative methods, various kinds of indexes from the aspects of society, politics, economy and values in Ganzi District are analyzed, as well as the factors that affect the rural social stability of current Ganzi District area. The results show that rural areas of Ganzi District are stable on the whole, but the economic development level is backward; the social security measures are imperfect; disputes among rural residents still exist and most of them are economic disputes; the disputes among ethnics are mainly caused by religious belief; the autonomous situation of partial rural residents are bad and rural residents’ evaluation on social justice is low. Therefore, it should establish and perfect relevant prevention and control mechanism.

  5. Harvest date affects aronia juice polyphenols, sugars, and antioxidant activity, but not anthocyanin stability.

    Science.gov (United States)

    Bolling, Bradley W; Taheri, Rod; Pei, Ruisong; Kranz, Sarah; Yu, Mo; Durocher, Shelley N; Brand, Mark H

    2015-11-15

    The goal of this work was to characterize how the date of harvest of 'Viking' aronia berry impacts juice pigmentation, sugars, and antioxidant activity. Aronia juice anthocyanins doubled at the fifth week of the harvest, and then decreased. Juice hydroxycinnamic acids decreased 33% from the first week, while proanthocyanidins increased 64%. Juice fructose and glucose plateaued at the fourth week, but sorbitol increased 40% to the seventh harvest week. Aronia juice pigment density increased due to anthocyanin concentration, and polyphenol copigmentation did not significantly affect juice pigmentation. Anthocyanin stability at pH 4.5 was similar between weeks. However, addition of quercetin, sorbitol, and chlorogenic acid to aronia anthocyanins inhibited pH-induced loss of color. Sorbitol and citric acid may be partially responsible for weekly variation in antioxidant activity, as addition of these agents inhibited DPPH scavenging 13-30%. Thus, aronia polyphenol and non-polyphenol components contribute to its colorant and antioxidant functionality. PMID:25977015

  6. Plant species richness and functional traits affect community stability after a flood event.

    Science.gov (United States)

    Fischer, Felícia M; Wright, Alexandra J; Eisenhauer, Nico; Ebeling, Anne; Roscher, Christiane; Wagg, Cameron; Weigelt, Alexandra; Weisser, Wolfgang W; Pillar, Valério D

    2016-05-19

    Climate change is expected to increase the frequency and magnitude of extreme weather events. It is therefore of major importance to identify the community attributes that confer stability in ecological communities during such events. In June 2013, a flood event affected a plant diversity experiment in Central Europe (Jena, Germany). We assessed the effects of plant species richness, functional diversity, flooding intensity and community means of functional traits on different measures of stability (resistance, resilience and raw biomass changes from pre-flood conditions). Surprisingly, plant species richness reduced community resistance in response to the flood. This was mostly because more diverse communities grew more immediately following the flood. Raw biomass increased over the previous year; this resulted in decreased absolute value measures of resistance. There was no clear response pattern for resilience. We found that functional traits drove these changes in raw biomass: communities with a high proportion of late-season, short-statured plants with dense, shallow roots and small leaves grew more following the flood. Late-growing species probably avoided the flood, whereas greater root length density might have allowed species to better access soil resources brought from the flood, thus growing more in the aftermath. We conclude that resource inputs following mild floods may favour the importance of traits related to resource acquisition and be less associated with flooding tolerance.

  7. Plant species richness and functional traits affect community stability after a flood event.

    Science.gov (United States)

    Fischer, Felícia M; Wright, Alexandra J; Eisenhauer, Nico; Ebeling, Anne; Roscher, Christiane; Wagg, Cameron; Weigelt, Alexandra; Weisser, Wolfgang W; Pillar, Valério D

    2016-05-19

    Climate change is expected to increase the frequency and magnitude of extreme weather events. It is therefore of major importance to identify the community attributes that confer stability in ecological communities during such events. In June 2013, a flood event affected a plant diversity experiment in Central Europe (Jena, Germany). We assessed the effects of plant species richness, functional diversity, flooding intensity and community means of functional traits on different measures of stability (resistance, resilience and raw biomass changes from pre-flood conditions). Surprisingly, plant species richness reduced community resistance in response to the flood. This was mostly because more diverse communities grew more immediately following the flood. Raw biomass increased over the previous year; this resulted in decreased absolute value measures of resistance. There was no clear response pattern for resilience. We found that functional traits drove these changes in raw biomass: communities with a high proportion of late-season, short-statured plants with dense, shallow roots and small leaves grew more following the flood. Late-growing species probably avoided the flood, whereas greater root length density might have allowed species to better access soil resources brought from the flood, thus growing more in the aftermath. We conclude that resource inputs following mild floods may favour the importance of traits related to resource acquisition and be less associated with flooding tolerance. PMID:27114578

  8. Periodic Tail Motion Linked to Wing Motion Affects the Longitudinal Stability of Ornithopter Flight

    Institute of Scientific and Technical Information of China (English)

    Jun-seong Lee; Joong-kwan Kim; Jae-hung Han; Charles P. Ellington

    2012-01-01

    During slow level flight of a pigeon,a caudal muscle involved in tail movement,the levator caudae pars vertebralis,is activated at a particular phase with the pectoralis wing muscle.Inspired by mechanisms for the control of stability in flying animals,especially the role of the tail in avian flight,we investigated how periodic tail motion linked to motion of the wings affects the longitudinal stability of omithopter flight.This was achieved by using an integrative ornithopter flight simulator that included aeroelastic behaviour of the flexible wings and tail.Trim flight trajectories of the simulated ornithopter model were calculated by time integration of the nonlinear equations of a flexible multi-body dynamics coupled with a semi-empirical flapping-wing and tail aerodynamic models.The unique trim flight characteristics of ornithopter,Limit-Cycle Oscillation,were found under the sets of wingbeat frequency and tail elevation angle,and the appropriate phase angle of tail motion was determined by parameter studies minimizing the amplitude of the oscillations.The numerical simulation results show that tail actuation synchronized with wing motion suppresses the oscillation of body pitch angle over a wide range of wingbeat frequencies.

  9. How Chain Length and Charge Affect Surfactant Denaturation of Acyl Coenzyme A Binding Protein (ACBP)

    DEFF Research Database (Denmark)

    Andersen, Kell Kleiner; Otzen, Daniel

    2009-01-01

    . This behavior contrasts with the simplicity of unfolding in chemical denaturants and highlights the changing properties of surfactant micelles. We suggest that the transition from spherical to more elongated micelles leads to inhibition of unfolding kinetics, while weaker binding sites may cause a subsequent...

  10. Nectar vs. pollen loading affects the tradeoff between flight stability and maneuverability in bumblebees.

    Science.gov (United States)

    Mountcastle, Andrew M; Ravi, Sridhar; Combes, Stacey A

    2015-08-18

    Bumblebee foragers spend a significant portion of their lives transporting nectar and pollen, often carrying loads equivalent to more than half their body mass. Whereas nectar is stored in the abdomen near the bee's center of mass, pollen is carried on the hind legs, farther from the center of mass. We examine how load position changes the rotational moment of inertia in bumblebees and whether this affects their flight maneuverability and/or stability. We applied simulated pollen or nectar loads of equal mass to Bombus impatiens bumblebees and examined flight performance in a wind tunnel under three conditions: flight in unsteady flow, tracking an oscillating flower in smooth flow, and flower tracking in unsteady flow. Using an inertial model, we estimated that carrying a load on the legs rather than in the abdomen increases a bee's moment of inertia about the roll and yaw axes but not the pitch axis. Consistent with these predictions, we found that bees carrying a load on their legs displayed slower rotations about their roll and yaw axes, regardless of whether these rotations were driven by external perturbations or self-initiated steering maneuvers. This allowed pollen-loaded bees to maintain a more stable body orientation and higher median flight speed in unsteady flow but reduced their performance when tracking a moving flower, supporting the concept of a tradeoff between stability and maneuverability. These results demonstrate that the types of resources collected by bees affect their flight performance and energetics and suggest that wind conditions may influence resource selection. PMID:26240364

  11. Experimental and molecular dynamics studies showed that CBP KIX mutation affects the stability of CBP:c-Myb complex.

    Science.gov (United States)

    Odoux, Anne; Jindal, Darren; Tamas, Tamara C; Lim, Benjamin W H; Pollard, Drake; Xu, Wu

    2016-06-01

    The coactivators CBP (CREBBP) and its paralog p300 (EP300), two conserved multi-domain proteins in eukaryotic organisms, regulate gene expression in part by binding DNA-binding transcription factors. It was previously reported that the CBP/p300 KIX domain mutant (Y650A, A654Q, and Y658A) altered both c-Myb-dependent gene activation and repression, and that mice with these three point mutations had reduced numbers of platelets, B cells, T cells, and red blood cells. Here, our transient transfection assays demonstrated that mouse embryonic fibroblast cells containing the same mutations in the KIX domain and without a wild-type allele of either CBP or p300, showed decreased c-Myb-mediated transcription. Dr. Wright's group solved a 3-D structure of the mouse CBP:c-Myb complex using NMR. To take advantage of the experimental structure and function data and improved theoretical calculation methods, we performed MD simulations of CBP KIX, CBP KIX with the mutations, and c-Myb, as well as binding energy analysis for both the wild-type and mutant complexes. The binding between CBP and c-Myb is mainly mediated by a shallow hydrophobic groove in the center where the side-chain of Leu302 of c-Myb plays an essential role and two salt bridges at the two ends. We found that the KIX mutations slightly decreased stability of the CBP:c-Myb complex as demonstrated by higher binding energy calculated using either MM/PBSA or MM/GBSA methods. More specifically, the KIX mutations affected the two salt bridges between CBP and c-Myb (CBP-R646 and c-Myb-E306; CBP-E665 and c-Myb-R294). Our studies also revealed differing dynamics of the hydrogen bonds between CBP-R646 and c-Myb-E306 and between CBP-E665 and c-Myb-R294 caused by the CBP KIX mutations. In the wild-type CBP:c-Myb complex, both of the hydrogen bonds stayed relatively stable. In contrast, in the mutant CBP:c-Myb complex, hydrogen bonds between R646 and E306 showed an increasing trend followed by a decreasing trend, and hydrogen

  12. Preparation of 125I-labeled human growth hormone of high quality binding properties endowed with long-term stability

    International Nuclear Information System (INIS)

    125I-labeled human growth hormone (125I-labeled.hGH) was prepared by using two variants of the chloramine T labelling procedure and purified by polyacrylamide gel electrophoresis (PAGE) of the reaction mixture. Variant A produced a tracer with high specific activity (100 +/- 10 microCi/microgram), high maximal binding capacity to antibodies (93%) and long-term stability (at least 150 days at -20/degree/C). No diiodinated tyrosil residues could be detected in this tracer. Variant B was devised to obtain higher yields of labeled hormone. The electrophoresis of the iodination mixture revealed two radioactive components with Rm values of 0.49 and 0.55 which result from the iodination of hGH variants preexisting in the starting material. Both tracers had similar specific activities (70 +/- 10 microCi/microgram), high maximal binding capacity to antibodies or receptors (80-100%, after 80 days of their obtention) and high stability (at least 100 days at -20/degree/C). It is concluded that the iododerivatives of hGH obtained by either method are adequate to perform radioimmunoassay and receptor studies and have long-term stability

  13. Stabilizing a flexible interdomain hinge region harboring the SMB binding site drives uPAR into its closed conformation.

    Science.gov (United States)

    Zhao, Baoyu; Gandhi, Sonu; Yuan, Cai; Luo, Zhipu; Li, Rui; Gårdsvoll, Henrik; de Lorenzi, Valentina; Sidenius, Nicolai; Huang, Mingdong; Ploug, Michael

    2015-03-27

    The urokinase-type plasminogen activator receptor (uPAR) is a multidomain glycolipid-anchored membrane protein, which facilitates extracellular matrix remodeling by focalizing plasminogen activation to cell surfaces via its high-affinity interaction with uPA. The modular assembly of its three LU (Ly6/uPAR-like) domains is inherently flexible and binding of uPA drives uPAR into its closed conformation, which presents the higher-affinity state for vitronectin thus providing an allosteric regulatory mechanism. Using a new class of epitope-mapped anti-uPAR monoclonal antibodies (mAbs), we now demonstrate that the reciprocal stabilization is indeed also possible. By surface plasmon resonance studies, we show that these mAbs and vitronectin have overlapping binding sites on uPAR and that they share Arg91 as hotspot residue in their binding interfaces. The crystal structure solved for one of these uPAR·mAb complexes at 3.0Å clearly shows that this mAb preselects the closed uPAR conformation with an empty but correctly assembled large hydrophobic binding cavity for uPA. Accordingly, these mAbs inhibit the uPAR-dependent lamellipodia formation and migration on vitronectin-coated matrices irrespective of the conformational status of uPAR and its occupancy with uPA. This is the first study to the best of our knowledge, showing that the dynamic assembly of the three LU domains in uPARwt can be driven toward the closed form by an external ligand, which is not engaging the hydrophobic uPA binding cavity. As this binding interface is also exploited by the somatomedin B domain of vitronectin, therefore, this relationship should be taken into consideration when exploring uPAR-dependent cell adhesion and migration in vitronectin-rich environments. PMID:25659907

  14. Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method

    Directory of Open Access Journals (Sweden)

    Lund Ole

    2007-07-01

    Full Text Available Abstract Background Antigen presenting cells (APCs sample the extra cellular space and present peptides from here to T helper cells, which can be activated if the peptides are of foreign origin. The peptides are presented on the surface of the cells in complex with major histocompatibility class II (MHC II molecules. Identification of peptides that bind MHC II molecules is thus a key step in rational vaccine design and developing methods for accurate prediction of the peptide:MHC interactions play a central role in epitope discovery. The MHC class II binding groove is open at both ends making the correct alignment of a peptide in the binding groove a crucial part of identifying the core of an MHC class II binding motif. Here, we present a novel stabilization matrix alignment method, SMM-align, that allows for direct prediction of peptide:MHC binding affinities. The predictive performance of the method is validated on a large MHC class II benchmark data set covering 14 HLA-DR (human MHC and three mouse H2-IA alleles. Results The predictive performance of the SMM-align method was demonstrated to be superior to that of the Gibbs sampler, TEPITOPE, SVRMHC, and MHCpred methods. Cross validation between peptide data set obtained from different sources demonstrated that direct incorporation of peptide length potentially results in over-fitting of the binding prediction method. Focusing on amino terminal peptide flanking residues (PFR, we demonstrate a consistent gain in predictive performance by favoring binding registers with a minimum PFR length of two amino acids. Visualizing the binding motif as obtained by the SMM-align and TEPITOPE methods highlights a series of fundamental discrepancies between the two predicted motifs. For the DRB1*1302 allele for instance, the TEPITOPE method favors basic amino acids at most anchor positions, whereas the SMM-align method identifies a preference for hydrophobic or neutral amino acids at the anchors. Conclusion

  15. Dynamic Factors Affecting Gaseous Ligand Binding in an Artificial Oxygen Transport Protein‡

    OpenAIRE

    Zhang, Lei; Andersen, Eskil M.E.; Khajo, Abdelahad; Magliozzo, Richard S.; Koder, Ronald L.

    2013-01-01

    We report the functional analysis of an artificial hexacoordinate oxygen transport protein, HP7, which operates via a mechanism similar to that of human neuroglobin and cytoglobin: the destabilization of one of two heme-ligating histidine residues. In the case of HP7 this is the result of the coupling of histidine side chain ligation with the burial of three charged glutamate residues on the same helix. Here we compare gaseous ligand binding, including rates, affinities and oxyferrous state l...

  16. The importance of sulphide binding for leaching of heavy metals from contaminated Norwegian marine sediments treated by stabilization/solidification.

    Science.gov (United States)

    Sparrevik, Magnus; Eek, Espen; Grini, Randi Skirstad

    2009-07-01

    Over time, Norwegian fjords and harbour areas have received contaminants from industrial activities and urban run-off, and measures to remediate contaminated marine sediments are therefore needed. Stabilization/solidification (S/S) technology, in which the contaminated marine sediments are mixed with cement and other binding agents, has been shown to be a promising remediation technology. This paper summarizes a study of the environmental effect of stabilization, highlighting the importance of sulphide binding governing the leaching of heavy metals from the S/S of contaminated marine sediments. The study is a part of a research project focusing on developing effective methods for S/S of contaminated seabed sediments for use in new construction areas. Four cementitious binders were tested on sediments from six different locations: Bergen, Gilhus, Grenland, Hammerfest, Sandvika and Trondheim. The sediments differed with respect to properties such as concentration of contaminants, water content, organic content and grain size distribution. Portland cement, Portland cement with fly ash, industry cement, and sulphate resistant cement, were tested as binders. The leaching from the S/S sediments after 28 days of curing was measured by using a standard leaching batch test (EN 12457-2: 2003), with seawater as leaching agent. The eluate was analysed for pH and redox, as well as content of heavy metals and organic contaminants. Available volatile sulphide (AVS) and simultaneously extractable metals (SEM) were also measured in the sediments. This paper focuses on the leaching of lead (Pb) and copper (Cu). A reduced leaching of Pb after stabilization was observed for the mixtures, whereas the leaching of Cu from Hammerfest sediments increased substantially after stabilization for all cementitious additions. Experiments show that Hammerfest samples had lower values of AVS than the other sediments. This was confirmed by the SEM/AVS analysis, highlighting the importance of

  17. ICAM-5 affects spine maturation by regulation of NMDA receptor binding to α-actinin

    Directory of Open Access Journals (Sweden)

    Lin Ning

    2015-01-01

    Full Text Available ICAM-5 is a negative regulator of dendritic spine maturation and facilitates the formation of filopodia. Its absence results in improved memory functions, but the mechanisms have remained poorly understood. Activation of NMDA receptors induces ICAM-5 ectodomain cleavage through a matrix metalloproteinase (MMP-dependent pathway, which promotes spine maturation and synapse formation. Here, we report a novel, ICAM-5-dependent mechanism underlying spine maturation by regulating the dynamics and synaptic distribution of α-actinin. We found that GluN1 and ICAM-5 partially compete for the binding to α-actinin; deletion of the cytoplasmic tail of ICAM-5 or ablation of the gene resulted in increased association of GluN1 with α-actinin, whereas internalization of ICAM-5 peptide perturbed the GluN1/α-actinin interaction. NMDA treatment decreased α-actinin binding to ICAM-5, and increased the binding to GluN1. Proper synaptic distribution of α-actinin requires the ICAM-5 cytoplasmic domain, without which α-actinin tended to accumulate in filopodia, leading to F-actin reorganization. The results indicate that ICAM-5 retards spine maturation by preventing reorganization of the actin cytoskeleton, but NMDA receptor activation is sufficient to relieve the brake and promote the maturation of spines.

  18. Cardiac myosin binding protein C phosphorylation affects cross-bridge cycle's elementary steps in a site-specific manner.

    Directory of Open Access Journals (Sweden)

    Li Wang

    Full Text Available Based on our recent finding that cardiac myosin binding protein C (cMyBP-C phosphorylation affects muscle contractility in a site-specific manner, we further studied the force per cross-bridge and the kinetic constants of the elementary steps in the six-state cross-bridge model in cMyBP-C mutated transgenic mice for better understanding of the influence of cMyBP-C phosphorylation on contractile functions. Papillary muscle fibres were dissected from cMyBP-C mutated mice of ADA (Ala273-Asp282-Ala302, DAD (Asp273-Ala282-Asp302, SAS (Ser273-Ala282-Ser302, and t/t (cMyBP-C null genotypes, and the results were compared to transgenic mice expressing wide-type (WT cMyBP-C. Sinusoidal analyses were performed with serial concentrations of ATP, phosphate (Pi, and ADP. Both t/t and DAD mutants significantly reduced active tension, force per cross-bridge, apparent rate constant (2πc, and the rate constant of cross-bridge detachment. In contrast to the weakened ATP binding and enhanced Pi and ADP release steps in t/t mice, DAD mice showed a decreased ADP release without affecting the ATP binding and the Pi release. ADA showed decreased ADP release, and slightly increased ATP binding and cross-bridge detachment steps, whereas SAS diminished the ATP binding step and accelerated the ADP release step. t/t has the broadest effects with changes in most elementary steps of the cross-bridge cycle, DAD mimics t/t to a large extent, and ADA and SAS predominantly affect the nucleotide binding steps. We conclude that the reduced tension production in DAD and t/t is the result of reduced force per cross-bridge, instead of the less number of strongly attached cross-bridges. We further conclude that cMyBP-C is an allosteric activator of myosin to increase cross-bridge force, and its phosphorylation status modulates the force, which is regulated by variety of protein kinases.

  19. Screening Effects on the Binding Energy and Stability of Quarkonia States

    CERN Document Server

    Bhatt, Palak; Patel, Smruti; Vinodkumar, P C

    2016-01-01

    We have studied the thermal stability of Quarkonia states by computing the effects of color-screening and vacuum screening based on a temperature dependent screened coulomb plus power potential for the quark-antiquark interaction. Medium effects on the properties of charmonia and bottomonia states are studied. The color screening and the vacuum screening effects on the stability of the quarkonia states are also separately calculated for comparison.

  20. A Phytophthora sojae effector suppresses endoplasmic reticulum stress-mediated immunity by stabilizing plant Binding immunoglobulin Proteins

    Science.gov (United States)

    Jing, Maofeng; Guo, Baodian; Li, Haiyang; Yang, Bo; Wang, Haonan; Kong, Guanghui; Zhao, Yao; Xu, Huawei; Wang, Yan; Ye, Wenwu; Dong, Suomeng; Qiao, Yongli; Tyler, Brett M.; Ma, Wenbo; Wang, Yuanchao

    2016-01-01

    Phytophthora pathogens secrete an array of specific effector proteins to manipulate host innate immunity to promote pathogen colonization. However, little is known about the host targets of effectors and the specific mechanisms by which effectors increase susceptibility. Here we report that the soybean pathogen Phytophthora sojae uses an essential effector PsAvh262 to stabilize endoplasmic reticulum (ER)-luminal binding immunoglobulin proteins (BiPs), which act as negative regulators of plant resistance to Phytophthora. By stabilizing BiPs, PsAvh262 suppresses ER stress-triggered cell death and facilitates Phytophthora infection. The direct targeting of ER stress regulators may represent a common mechanism of host manipulation by microbes. PMID:27256489

  1. Soil water retention and structure stability as affected by water quality

    Directory of Open Access Journals (Sweden)

    Amrakh I. Mamedov

    2014-04-01

    Full Text Available In arid and semi-arid zones with a short water resources studying the effects of water quality on soil water retention and structure is important for the development of effective soil and water conservation and management practices. Three water qualities (electrical conductivity, EC ~ 2, 100 and 500 μS cm-1 with a low SAR representing rain, canal-runoff and irrigation water respectively and semi-arid loam and clay soils were tested to evaluate an effect of soil texture and water quality on water retention, and aggregate and structure stability using the high energy moisture characteristic (HEMC method. The water retention curves obtained by the HEMC method were characterized by the modified van Genuchten (1980 model that provides (i model parameters α and n, which represent the location (of the inflection point and the steepness of the S-shaped water retention curve respectively, and (ii a volume of drainable pores (VDP, which is an indicator for the quantity of water released by the tested sample over the range of suction studied, and modal suction (MS, which corresponds to the most frequent pore sizes, and soil structure index, SI =VDP/MS. Generally (i treatments significantly affected the shape of the water retention curves (α and n and (ii contribution of soil type, water EC, and wetting rate and their interaction had considerable effect on the stability induces and model parameters. Most of changes due to the water quality and wetting condition were in the range of matric potential (ψ, 1.2-2.4; and 2.4-5.0 J kg-1 (pore size 125-250 μm and 60-125 μm. The VDP, SI and α increased, and MS and n decreased with the increase in clay content, water EC and the decrease in rate of aggregate wetting. The SI increased exponentially with the increase in VDP, and with the decrease in MS. Contribution of water EC on stability indices and model parameters was not linear and was soil dependent, and could be more valuable at medium water EC. Effect of

  2. Binding stability of peptides derived from 1ALA residue and 7GLY residues to sites near active center of fluctuating papain

    Science.gov (United States)

    Nishiyama, Katsuhiko

    2012-05-01

    We investigated the binding stability of peptides derived from 1ALA residue and 7GLY residues to sites near active center of fluctuating papain via molecular dynamics and docking simulations. Replacing GLY residue in 8GLY with ALA residue had a positive effect on binding stability to the sites in some cases although the replacing had a negative effect on it in other cases. Furthermore the replacing had a negative effect on the chance of binding to the sites. Residue in peptide should be replaced on the basis of systematic exploration of its position.

  3. Charged histidine affects alpha-helix stability at all positions in the helix by interacting with the backbone charges.

    OpenAIRE

    Armstrong, K M; Baldwin, R L

    1993-01-01

    To determine whether a charged histidine side chain affects alpha-helix stability only when histidine is close to one end of the helix or also when it is in the central region, we substitute a single histidine residue at many positions in two reference peptides and measure helix stability and histidine pKa. The position of a charged histidine residue has a major effect on helix stability in 0.01 M NaCl: the helix content of a 17-residue peptide is 24% when histidine is at position 3 compared ...

  4. Affectivity

    OpenAIRE

    Stenner, Paul; Greco, Monica

    2013-01-01

    The concept of affectivity has assumed central importance in much recent scholarship, and many in the social sciences and humanities now talk of an ‘affective turn’. The concept of affectivity at play in this ‘turn’ remains, however, somewhat vague and slippery. Starting with Silvan Tomkins’ influential theory of affect, this paper will explore the relevance of the general assumptions (or ‘utmost abstractions’) that inform thinking about affectivity. The technological and instrumentalist char...

  5. Structure-based stabilization of HIV-1 gp120 enhances humoral immune responses to the induced co-receptor binding site.

    Directory of Open Access Journals (Sweden)

    Barna Dey

    2009-05-01

    Full Text Available The human immunodeficiency virus type 1 (HIV-1 exterior envelope glycoprotein, gp120, possesses conserved binding sites for interaction with the primary virus receptor, CD4, and also for the co-receptor, generally CCR5. Although gp120 is a major target for virus-specific neutralizing antibodies, the gp120 variable elements and its malleable nature contribute to evasion of effective host-neutralizing antibodies. To understand the conformational character and immunogenicity of the gp120 receptor binding sites as potential vaccine targets, we introduced structure-based modifications to stabilize gp120 core proteins (deleted of the gp120 major variable regions into the conformation recognized by both receptors. Thermodynamic analysis of the re-engineered core with selected ligands revealed significant stabilization of the receptor-binding regions. Stabilization of the co-receptor-binding region was associated with a marked increase in on-rate of ligand binding to this site as determined by surface plasmon resonance. Rabbit immunization studies showed that the conformational stabilization of core proteins, along with increased ligand affinity, was associated with strikingly enhanced humoral immune responses against the co-receptor-binding site. These results demonstrate that structure-based approaches can be exploited to stabilize a conformational site in a large functional protein to enhance immunogenic responses specific for that region.

  6. Characterization of How DNA Modifications Affect DNA Binding by C2H2 Zinc Finger Proteins

    Science.gov (United States)

    Patel, A.; Hashimoto, H.; Zhang, X.; Cheng, X.

    2016-01-01

    Much is known about vertebrate DNA methylation and oxidation; however, much less is known about how modified cytosine residues within particular sequences are recognized. Among the known methylated DNA-binding domains, the Cys2-His2 zinc finger (ZnF) protein superfamily is the largest with hundreds of members, each containing tandem ZnFs ranging from 3 to >30 fingers. We have begun to biochemically and structurally characterize these ZnFs not only on their sequence specificity but also on their sensitivity to various DNA modifications. Rather than following published methods of refolding insoluble ZnF arrays, we have expressed and purified soluble forms of ZnFs, ranging in size from a tandem array of two to six ZnFs, from seven different proteins. We also describe a fluorescence polarization assay to measure ZnFs affinity with oligonucleotides containing various modifications and our approaches for cocrystallization of ZnFs with oligonucleotides. PMID:27372763

  7. A Varp-Binding Protein, RACK1, Regulates Dendrite Outgrowth through Stabilization of Varp Protein in Mouse Melanocytes.

    Science.gov (United States)

    Marubashi, Soujiro; Ohbayashi, Norihiko; Fukuda, Mitsunori

    2016-08-01

    Varp (VPS9-ankyrin repeat protein) in melanocytes is thought to function as a key player in the pigmentation of mammals. Varp regulates two different melanocyte functions: (i) transport of melanogenic enzymes to melanosomes by functioning as a Rab32/38 effector and (ii) promotion of dendrite outgrowth by functioning as a Rab21-guanine nucleotide exchange factor. The Varp protein level has recently been shown to be negatively regulated by proteasomal degradation through interaction of the ankyrin repeat 2 (ANKR2) domain of Varp with Rab40C. However, the molecular mechanisms by which Varp escapes from Rab40C and retains its own expression level remain completely unknown. Here, we identified RACK1 (receptor of activated protein kinase C 1) as a Varp-ANKR2 binding partner and investigated its involvement in Varp stabilization in mouse melanocytes. The results showed that knockdown of endogenous RACK1 in melanocytes caused dramatic reduction of the Varp protein level and inhibition of dendrite outgrowth, and intriguingly, overexpression of RACK1 inhibited the interaction between Varp and Rab40C and counteracted the negative effect of Rab40C on dendrite outgrowth. These findings indicated that RACK1 competes with Rab40C for binding to the ANKR2 domain of Varp and regulates dendrite outgrowth through stabilization of Varp in mouse melanocytes. PMID:27066885

  8. TANK-binding kinase-1 broadly affects oyster immune response to bacteria and viruses.

    Science.gov (United States)

    Tang, Xueying; Huang, Baoyu; Zhang, Linlin; Li, Li; Zhang, Guofan

    2016-09-01

    As a benthic filter feeder of estuaries, the immune system of oysters provides one of the best models for studying the genetic and molecular basis of the innate immune pathway in marine invertebrates and examining the influence of environmental factors on the immune system. Here, the molecular function of molluscan TANK-binding kinase-1 (TBK1) (which we named CgTBK1) was studied in the Pacific oyster, Crassostrea gigas. Compared with known TBK1 proteins in other model organisms, CgTBK1 contains a conserved S-TKc domain and a coiled coil domain at the N- and C-terminals but lacks an important ubiquitin domain. Quantitative real-time PCR analysis revealed that the expression level of CgTBK1 was ubiquitous in all selected tissues, with highest expression in the gills. CgTBK1 expression was significantly upregulated in response to infections with Vibrio alginolyticus, ostreid herpesvirus 1 (OsHV-1 reference strain and μvar), and polyinosinic:polycytidylic acid sodium salt, suggesting its broad function in immune response. Subcellular localization showed the presence of CgTBK1 in the cytoplasm of HeLa cells, suggesting its potential function as the signal transducer between the receptor and transcription factor. We further demonstrated that CgTBK1 interacted with CgSTING in HEK293T cells, providing evidence that CgTBK1 could be activated by direct binding to CgSTING. In summary, we characterized the TBK1 gene in C. gigas and demonstrated its role in the innate immune response to pathogen infections. PMID:27422757

  9. Whole genome sequencing identifies a deletion in protein phosphatase 2A that affects its stability and localization in Chlamydomonas reinhardtii.

    Directory of Open Access Journals (Sweden)

    Huawen Lin

    Full Text Available Whole genome sequencing is a powerful tool in the discovery of single nucleotide polymorphisms (SNPs and small insertions/deletions (indels among mutant strains, which simplifies forward genetics approaches. However, identification of the causative mutation among a large number of non-causative SNPs in a mutant strain remains a big challenge. In the unicellular biflagellate green alga Chlamydomonas reinhardtii, we generated a SNP/indel library that contains over 2 million polymorphisms from four wild-type strains, one highly polymorphic strain that is frequently used in meiotic mapping, ten mutant strains that have flagellar assembly or motility defects, and one mutant strain, imp3, which has a mating defect. A comparison of polymorphisms in the imp3 strain and the other 15 strains allowed us to identify a deletion of the last three amino acids, Y313F314L315, in a protein phosphatase 2A catalytic subunit (PP2A3 in the imp3 strain. Introduction of a wild-type HA-tagged PP2A3 rescues the mutant phenotype, but mutant HA-PP2A3 at Y313 or L315 fail to rescue. Our immunoprecipitation results indicate that the Y313, L315, or YFLΔ mutations do not affect the binding of PP2A3 to the scaffold subunit, PP2A-2r. In contrast, the Y313, L315, or YFLΔ mutations affect both the stability and the localization of PP2A3. The PP2A3 protein is less abundant in these mutants and fails to accumulate in the basal body area as observed in transformants with either wild-type HA-PP2A3 or a HA-PP2A3 with a V310T change. The accumulation of HA-PP2A3 in the basal body region disappears in mated dikaryons, which suggests that the localization of PP2A3 may be essential to the mating process. Overall, our results demonstrate that the terminal YFL tail of PP2A3 is important in the regulation on Chlamydomonas mating.

  10. Variation in Biofilm Stability with Decreasing pH Affects Porous Medium Hydraulic Properties

    Science.gov (United States)

    Kirk, M. F.; Santillan, E. F.; McGrath, L. K.; Altman, S. J.

    2010-12-01

    Changes to microbial communities caused by subsurface CO2 injection may have many consequences, including possible impacts to CO2 transport. We used column experiments to examine how decreasing pH, a geochemical change associated with CO2 injection, will affect biofilm stability and ultimately the hydraulic properties of porous media. Columns consisted of 1 mm2 square capillary tubes filled with 105-150 µm diameter glass beads. Artificial groundwater medium containing 1 mM glucose was pumped through the columns at a rate of 0.01 mL/min (q = 14.4 m/day; Re = 0.03). Columns were inoculated with 3 × 10^8 CFU (avg.) of Pseudomonas fluorescens, a model biofilm former, transformed with a green fluorescent protein. Biomass distribution and transport was examined using scanning laser confocal microscopy and effluent plating. Variation in the bulk hydraulic properties of the columns was measured using manometers. In an initial experiment, biofilm growth was allowed to occur for seven days in medium with pH 7.3. Within this period, cells uniformly coated bead surfaces, effluent cell numbers stabilized at 1 × 10^9 CFU/mL, and hydraulic conductivity (K) decreased 77%. Next, medium with pH 4 was introduced. As a result, biomass within the reactor redistributed from bead surfaces to pores, effluent cell numbers decreased to 3 × 10^5 CFU/mL, and K decreased even further (>94% reduction). This decreased K was maintained until the experiment was terminated, seven days after introducing low pH medium. These results suggest that changes in biomass distribution as a result of decreased pH may initially limit transport of solubility-trapped CO2 following CO2 injection. Experiments in progress and planned will test this result in more detail and over longer periods of time. This material is based upon work supported as part of the Center for Frontiers of Subsurface Energy Security, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office

  11. Exchanging murine and human immunoglobulin constant chains affects the kinetics and thermodynamics of antigen binding and chimeric antibody autoreactivity.

    Directory of Open Access Journals (Sweden)

    Marcela Torres

    Full Text Available Mouse-human chimeric antibodies composed of murine variable (V and human (C chains are useful therapeutic reagents. Consequently, we investigated whether heterologous C-regions from mice and humans affected specificity and affinity, and determined the contribution of C(H glycosylation to antigen binding. The interaction of a 12-mer peptide mimetic with monoclonal antibody (mAb 18B7 to Cryptococcus neoformans glucuronoxylomannan, and its chimeric (ch and deglycosylated forms were studied by surface plasmon resonance. The equilibrium and rate association constants for the chAb were higher than for mAb 18B7. V region affinity was not affected by C(H region glycosylation whereas heterologous C region of the same isotype altered the Ab binding affinity and the specificity for self-antigens. Structural models displayed local differences that implied changes on the connectivity of residues. These findings suggest that V region conformational changes can be dictated by the C(H domains through an allosteric effect involving networks of highly connected amino acids.

  12. Size-dependent stability toward dissociation and ligand binding energies of phosphine-ligated gold cluster ions

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Grant E.; Priest, Thomas A.; Laskin, Julia

    2014-01-01

    The stability of sub-nanometer size gold clusters ligated with organic molecules is of paramount importance to the scalable synthesis of monodisperse size-selected metal clusters with highly tunable chemical and physical properties. For the first time, a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR-MS) equipped with surface induced dissociation (SID) has been employed to investigate the time and collision energy resolved fragmentation behavior of cationic doubly charged gold clusters containing 7-9 gold atoms and 6-7 triphenylphosphine (TPP) ligands prepared by reduction synthesis in solution. The TPP ligated gold clusters are demonstrated to fragment through three primary dissociation pathways: (1) Loss of a neutral TPP ligand from the precursor gold cluster, (2) asymmetric fission and (3) symmetric fission and charge separation of the gold core resulting in formation of complementary pairs of singly charged fragment ions. Threshold energies and activation entropies of these fragmentation pathways have been determined employing Rice-Ramsperger-Kassel-Marcus (RRKM) modeling of the experimental SID data. It is demonstrated that the doubly charged cluster ion containing eight gold atoms and six TPP ligands, (8,6)2+, exhibits exceptional stability compared to the other cationic gold clusters examined in this study due to its large ligand binding energy of 1.76 eV. Our findings demonstrate the dramatic effect of the size and extent of ligation on the gas-phase stability and preferred fragmentation pathways of small TPP-ligated gold clusters.

  13. Effect of polyethylene glycol conjugation on conformational and colloidal stability of a monoclonal antibody antigen-binding fragment (Fab').

    Science.gov (United States)

    Roque, Cristopher; Sheung, Anthony; Rahman, Nausheen; Ausar, S Fernando

    2015-02-01

    We have investigated the effects of site specific "hinge" polyethylene glycol conjugation (PEGylation) on thermal, pH, and colloidal stability of a monoclonal antibody antigen-binding fragment (Fab') using a variety of biophysical techniques. The results obtained by circular dichroism (CD), ultraviolet (UV) absorbance, and fluorescence spectroscopy suggested that the physical stability of the Fab' is maximized at pH 6-7 with no apparent differences due to PEGylation. Temperature-induced aggregation experiments revealed that PEGylation was able to increase the transition temperature, as well as prevent the formation of visible and subvisible aggregates. Statistical comparison of the three-index empirical phase diagram (EPD) revealed significant differences in thermal and pH stability signatures between Fab' and PEG-Fab'. Upon mechanical stress, micro-flow imaging (MFI) and measurement of the optical density at 360 nm showed that the PEG-Fab' had significantly higher resistance to surface-induced aggregation compared to the Fab'. Analysis of the interaction parameter, kD, indicated repulsive intermolecular forces for PEG-Fab' and attractive forces for Fab'. In conclusion, PEGylation appears to protect Fab' against thermal and mechanical stress-induced aggregation, likely due to a steric hindrance mechanism.

  14. Characterization and small-molecule stabilization of the multisite tandem binding between 14-3-3 and the R domain of CFTR.

    Science.gov (United States)

    Stevers, Loes M; Lam, Chan V; Leysen, Seppe F R; Meijer, Femke A; van Scheppingen, Daphne S; de Vries, Rens M J M; Carlile, Graeme W; Milroy, Lech G; Thomas, David Y; Brunsveld, Luc; Ottmann, Christian

    2016-03-01

    Cystic fibrosis is a fatal genetic disease, most frequently caused by the retention of the CFTR (cystic fibrosis transmembrane conductance regulator) mutant protein in the endoplasmic reticulum (ER). The binding of the 14-3-3 protein to the CFTR regulatory (R) domain has been found to enhance CFTR trafficking to the plasma membrane. To define the mechanism of action of this protein-protein interaction, we have examined the interaction in vitro. The disordered multiphosphorylated R domain contains nine different 14-3-3 binding motifs. Furthermore, the 14-3-3 protein forms a dimer containing two amphipathic grooves that can potentially bind these phosphorylated motifs. This results in a number of possible binding mechanisms between these two proteins. Using multiple biochemical assays and crystal structures, we show that the interaction between them is governed by two binding sites: The key binding site of CFTR (pS768) occupies one groove of the 14-3-3 dimer, and a weaker, secondary binding site occupies the other binding groove. We show that fusicoccin-A, a natural-product tool compound used in studies of 14-3-3 biology, can stabilize the interaction between 14-3-3 and CFTR by selectively interacting with a secondary binding motif of CFTR (pS753). The stabilization of this interaction stimulates the trafficking of mutant CFTR to the plasma membrane. This definition of the druggability of the 14-3-3-CFTR interface might offer an approach for cystic fibrosis therapeutics.

  15. Regulation of mRNA stability via BRF1 and other AU-binding proteins

    OpenAIRE

    Schmidlin-Stalder, Martin

    2005-01-01

    Steady state levels of mRNAs are determined by the rate of synthesis and degradation. A well-known cis-element conferring instability to mRNA is the so-called AU-rich element (ARE), which is present in the 3’ untranslated region (3’UTR) of many cytokines, chemokines, growth factors or proto-oncogenes. The ARE is recognized by a variety of ARE-binding proteins (AUBPs), which decide about the fate of the RNA. Multiple signaling cascades regulate the activity of the AUBPs. Butyrate response fact...

  16. Heterozygous nucleotide-binding oligomerization domain-2 mutations affect monocyte maturation in Crohn's disease

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    AIM: To investigate the function of monocytes in Crohn's disease (CD) patients and to correlate this with diseaseassociated nucleotide-binding oligomerization domain-2 (NOD2) gene variants.METHODS: Monocytes from 47 consecutively referred CD patients and 9 healthy blood donors were cultured with interleukin (IL)-4 and granulocyte-macrophage colony-stimulating factor (GM-CSF), and stimulated with lipopolysaccharide (LPS) or muramyldipeptide (MDP), the putative ligand of NOD2.RESULTS: We found that monocytes from CD patients differentiated in vitro to mature dendritic cells (DCs), as determined by immunophenotype and morphology.NOD2 genotype was assessed in all subjects, and we observed high CD86 expression on immature and LPS-stimulated DCs in NOD2 mutated CD patients, as compared with wtNOD2 CD patients and controls. By contrast, CD86 expression levels of DCs induced to maturity with MDP derived from NOD2-mutated subjects were comparable to those of normal subjects. The amount of IL-12p70 in patient-cell cultures was larger than in controls after LPS treatment, but not after treatment with MDP.CONCLUSION: Our results suggest that DCs obtained from patients with mutations in the NOD2 gene display an activated phenotype characterized by high CD86 expression, but have a diminished response to MDP when compared to the terminal differentiation phase. We speculate that the altered differentiation of monocytes might lead to an imbalance between inflammation and the killing ability of monocytes, and may be relevant to the pathogenesis of CD.

  17. Effect of Lysine Modification on the Stability and Cellular Binding of Human Amyloidogenic Light Chains

    Energy Technology Data Exchange (ETDEWEB)

    O' Neill, Hugh Michael [ORNL; Davern, Sandra M. [University of Tennessee Graduate School of Medicine; Murphy, Charles L. [University of Tennessee Graduate School of Medicine; Wall, Jonathan [ORNL; Deborah, Weiss T. [University of Tennessee Graduate School of Medicine; Solomon, Alan [ORNL

    2011-01-01

    AL amyloidosis is characterized by the pathologic deposition as fibrils of monoclonal light chains (i.e., Bence Jones proteins [BJPs]) in particular organs and tissues. This phenomenon has been attributed to the presence in amyloidogenic proteins of particular amino acids that cause these molecules to become unstable, as well as post-translational modifications and, in regard to the latter, we have investigated the effect of biotinylation of lysyl residues on cell binding. We utilized an experimental system designed to test if BJPs obtained from patients with AL amyloidosis or, as a control, multiple myeloma (MM), bound human fibroblasts and renal epithelial cells. As documented by fluorescent microscopy and ELISA, the amyloidogenic BJPs, as compared with MM components, bound preferentially and this reactivity increased significantly after chemical modification of their lysyl residues with sulfo-NHS-biotin. Further, based on tryptophan fluorescence and circular dichorism data, it was apparent that their conformation was altered, which we hypothesize exposed a binding site not accessible on the native protein. The results of our studies indicate that post-translational structural modifications of pathologic light chains can enhance their capacity for cellular interaction and thus may contribute to the pathogenesis of AL amyloidosis and multiple myeloma.

  18. Tubulin assembly, taxoid site binding, and cellular effects of the microtubule-stabilizing agent dictyostatin.

    Science.gov (United States)

    Madiraju, Charitha; Edler, Michael C; Hamel, Ernest; Raccor, Brianne S; Balachandran, Raghavan; Zhu, Guangyu; Giuliano, Kenneth A; Vogt, Andreas; Shin, Youseung; Fournier, Jean-Hugues; Fukui, Yoshikazu; Brückner, Arndt M; Curran, Dennis P; Day, Billy W

    2005-11-15

    (-)-Dictyostatin is a sponge-derived, 22-member macrolactone natural product shown to cause cells to accumulate in the G2/M phase of the cell cycle, with changes in intracellular microtubules analogous to those observed with paclitaxel treatment. Dictyostatin also induces assembly of purified tubulin more rapidly than does paclitaxel, and nearly as vigorously as does dictyostatin's close structural congener, (+)-discodermolide (Isbrucker et al. (2003), Biochem. Pharmacol. 65, 75-82). We used synthetic (-)-dictyostatin to study its biochemical and cytological activities in greater detail. The antiproliferative activity of dictyostatin did not differ greatly from that of paclitaxel or discodermolide. Like discodermolide, dictyostatin retained antiproliferative activity against human ovarian carcinoma cells resistant to paclitaxel due to beta-tubulin mutations and caused conversion of cellular soluble tubulin pools to microtubules. Detailed comparison of the abilities of dictyostatin and discodermolide to induce tubulin assembly demonstrated that the compounds had similar potencies. Dictyostatin inhibited the binding of radiolabeled discodermolide to microtubules more potently than any other compound examined, and dictyostatin and discodermolide had equivalent activity as inhibitors of the binding of both radiolabeled epothilone B and paclitaxel to microtubules. These results are consistent with the idea that the macrocyclic structure of dictyostatin represents the template for the bioactive conformation of discodermolide.

  19. The Role of RNA Binding Proteins in Insulin Messenger Stability and Translation

    OpenAIRE

    Fred, Rikard G.

    2010-01-01

    Although the reason for insufficient release of insulin in diabetes mellitus may vary depending on the type and stage of the disease, it is of vital importance that an amplified insulin biosynthesis can meet the increased need during periods of hyperglycemia. The insulin mRNA is highly abundant in beta cells and changes in insulin mRNA levels are, at least in part, controlled by altered rates of mRNA degradation. Since the mechanisms behind the control of insulin messenger stability and trans...

  20. The ties that bind: perceived social support, stress, and IBS in severely affected patients

    Science.gov (United States)

    LACKNER, J. M.; BRASEL, A. M.; QUIGLEY, B M.; KEEFER, L.; KRASNER, S. S.; POWELL, C.; KATZ, L. A.; SITRIN, M. D.

    2016-01-01

    Background This study assessed the association between social support and the severity of irritable bowel syndrome (IBS) symptoms in a sample of severely affected IBS patients recruited to an NIH-funded clinical trial. In addition, we examined if the effects of social support on IBS pain are mediated through the effects on stress. Methods Subjects were 105 Rome II diagnosed IBS patients (F = 85%) who completed seven questionnaires which were collected as part of a pretreatment baseline assessment. Key Results Partial correlations were conducted to clarify the relationships between social support and clinically relevant variables with baseline levels of psychopathology, holding constant number of comorbid medical diseases, age, gender, marital status, ethnicity, and education. Analyses indicated that social support was inversely related to IBS symptom severity. Social support was positively related with less severe pain. A similar pattern of data was found for perceived stress but not quality of life impairment. Regression analyses examined if the effects of social support on pain are mediated by stress. The effects of social support on bodily pain were mediated by stress such that the greater the social support the less stress and the less pain. This effect did not hold for symptom severity, quality of life, or psychological distress. Conclusions & Inferences This study links the perceived adequacy of social support to the global severity of symptoms of IBS and its cardinal symptom (pain). It also suggests that the mechanism by which social support alleviates pain is through a reduction in stress levels. PMID:20465594

  1. Formulation factors affecting the binding properties of Chi-nese yam (Dioscorea oppositifolia)and corn starches

    Institute of Scientific and Technical Information of China (English)

    Adenike Okunlola; Oluwatoyin A.Odeku

    2009-01-01

    Objective:The quantitative effects of formulation and processing variables affecting the binding properties of Chinese yam starch (Dioscorea oppositifolia)in chloroquine phosphate tablet formulations have been investiga-ted in comparison with corn starch using a 23 factorial experimental design.Methods:Chinese yam starch,re-presenting the "low"level,and corn starch,representing the "high"level were used as binders at concentra-tions of 2.5 %w/w and 10 % w/w in chloroquine phosphate tablet formulations.The mechanical properties of the tablets,measured by the tensile strength (T)and brittle fracture index (BFI)as well as the release prop-erties measured by the disintegration time (DT)and dissolution time (t8 0-time for 80 % drug release),were used as assessment parameters.Results:The ranking of the individual coefficient values for the formulations on T was D >N C,on BFI was N >D C,on DT was D >N >C and on t8 0 was C >N >D while the ranking of the interaction coefficient on T was N-D >C-D  N-C,on BFI was N-D >N-C =C-D,on DT and t8 0 was N-C >N-D >C-D.Changing the binding agent from Chinese to corn starch,led to a decrease in T,DT and t8 0 but increase in BFI of the tablets.There were significant (P <0.001)interactions between the nature of binder,N and the other two variables,C and D.Conclusion:The result showed that Chinese yam possessed stronger binding capacity than corn starch and could be useful as an alternative binder when tablets with high mechanical strength with minimal problems of lamination,and slow release are required.

  2. Spectroscopic study of drug-binding characteristics of unmodified and pNPA-based acetylated human serum albumin: Does esterase activity affect microenvironment of drug binding sites on the protein?

    Energy Technology Data Exchange (ETDEWEB)

    Moradi, Nastaran [Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Faculty of Pharmaceutical Sciences, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Ashrafi-Kooshk, Mohammad Reza [Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Ghobadi, Sirous [Department of Biology, Faculty of Sciences, Razi University, Kermanshah (Iran, Islamic Republic of); Shahlaei, Mohsen [Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Faculty of Pharmaceutical Sciences, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Khodarahmi, Reza, E-mail: rkhodarahmi@mbrc.ac.ir [Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Faculty of Pharmaceutical Sciences, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of)

    2015-04-15

    Human serum albumin (HSA) is the most prominent extracellular protein in blood plasma. There are several binding sites on the protein which provide accommodation for structurally-unrelated endogenous and exogenous ligands and a wide variety of drugs. “Esterase-like” activity (hydrolysis of p-nitrophenyl esters) by the protein has been also reported. In the current study, we set out to investigate the interaction of indomethacin and ibuprofen with the unmodified and modified HSA (pNPA-modified HSA) using various spectroscopic techniques. Fluorescence data showed that 1:1 binding of drug to HSA is associated with quenching of the protein intrinsic fluorescence. Decrease of protein surface hydrophobicity (PSH), alteration in drug binding affinity and change of the protein stability, after esterase-like activity and permanent acetylation of HSA, were also documented. Analysis of the quenching and thermodynamic parameters indicated that forces involved in drug–HSA interactions change upon the protein modification. - Highlights: • Binding propensity of indomethacin extremely decreased upon the protein acetylation. • There is no ibuprofen binding after protein acetylation. • Protein stability changes upon drug binding as well as protein acetylation. • Drug pharmacokinetics may be influenced under co-administration of HSA-modifier drugs.

  3. Spectroscopic study of drug-binding characteristics of unmodified and pNPA-based acetylated human serum albumin: Does esterase activity affect microenvironment of drug binding sites on the protein?

    International Nuclear Information System (INIS)

    Human serum albumin (HSA) is the most prominent extracellular protein in blood plasma. There are several binding sites on the protein which provide accommodation for structurally-unrelated endogenous and exogenous ligands and a wide variety of drugs. “Esterase-like” activity (hydrolysis of p-nitrophenyl esters) by the protein has been also reported. In the current study, we set out to investigate the interaction of indomethacin and ibuprofen with the unmodified and modified HSA (pNPA-modified HSA) using various spectroscopic techniques. Fluorescence data showed that 1:1 binding of drug to HSA is associated with quenching of the protein intrinsic fluorescence. Decrease of protein surface hydrophobicity (PSH), alteration in drug binding affinity and change of the protein stability, after esterase-like activity and permanent acetylation of HSA, were also documented. Analysis of the quenching and thermodynamic parameters indicated that forces involved in drug–HSA interactions change upon the protein modification. - Highlights: • Binding propensity of indomethacin extremely decreased upon the protein acetylation. • There is no ibuprofen binding after protein acetylation. • Protein stability changes upon drug binding as well as protein acetylation. • Drug pharmacokinetics may be influenced under co-administration of HSA-modifier drugs

  4. Covalent binding of sulfamethazine to natural and synthetic humic acids: assessing laccase catalysis and covalent bond stability.

    Science.gov (United States)

    Gulkowska, Anna; Sander, Michael; Hollender, Juliane; Krauss, Martin

    2013-07-01

    Sulfonamide antibiotics form stable covalent bonds with quinone moieties in organic matter via nucleophilic addition reactions. In this work, we combined analytical electrochemistry with trace analytics to assess the catalytic role of the oxidoreductase laccase in the binding of sulfamethazine (SMZ) to Leonardite humic acid (LHA) and to four synthetic humic acids (SHAs) polymerized from low molecular weight precursors and to determine the stability of the formed bonds. In the absence of laccase, a significant portion of the added SMZ formed covalent bonds with LHA, but only a very small fraction (<0.4%) of the total quinone moieties in LHA reacted. Increasing absolute, but decreasing relative concentrations of SMZ-LHA covalent bonds with increasing initial SMZ concentration suggested that the quinone moieties in LHA covered a wide distribution in reactivity for the nucleophilic addition of SMZ. Laccase catalyzed the formation of covalent bonds by oxidizing unreactive hydroquinone moieties in LHA to reactive, electrophilic quinone moieties, of which a large fraction (5%) reacted with SMZ. Compared to LHA, the SHA showed enhanced covalent bond formation in the absence of laccase, suggesting a higher reactivity of their quinone moieties toward nucleophilic addition. This work supports that binding to soil organic matter (SOM) is an important process governing the fate, bioactivity, and extractability of sulfonamides in soils. PMID:23384282

  5. TRAIP is a PCNA-binding ubiquitin ligase that protects genome stability after replication stress

    DEFF Research Database (Denmark)

    Hoffmann, Saskia; Smedegaard, Stine; Nakamura, Kyosuke;

    2016-01-01

    , allowing cells to mitigate the threats to genome stability posed by replication stress. We identify the E3 ubiquitin ligase TRAIP as a new factor at active and stressed replication forks that directly interacts with PCNA via a conserved PCNA-interacting peptide (PIP) box motif. We show that TRAIP promotes......Cellular genomes are highly vulnerable to perturbations to chromosomal DNA replication. Proliferating cell nuclear antigen (PCNA), the processivity factor for DNA replication, plays a central role as a platform for recruitment of genome surveillance and DNA repair factors to replication forks...... ATR-dependent checkpoint signaling in human cells by facilitating the generation of RPA-bound single-stranded DNA regions upon replication stress in a manner that critically requires its E3 ligase activity and is potentiated by the PIP box. Consequently, loss of TRAIP function leads to enhanced...

  6. Trp RNA-binding attenuation protein: modifying symmetry and stability of a circular oligomer.

    Directory of Open Access Journals (Sweden)

    Oliver W Bayfield

    Full Text Available BACKGROUND: Subunit number is amongst the most important structural parameters that determine size, symmetry and geometry of a circular protein oligomer. The L-tryptophan biosynthesis regulator, TRAP, present in several Bacilli, is a good model system for investigating determinants of the oligomeric state. A short segment of C-terminal residues defines whether TRAP forms an 11-mer or 12-mer assembly. To understand which oligomeric state is more stable, we examine the stability of several wild type and mutant TRAP proteins. METHODOLOGY/PRINCIPAL FINDINGS: Among the wild type B. stearothermophilus, B. halodurans and B. subtilis TRAP, we find that the former is the most stable whilst the latter is the least. Thermal stability of all TRAP is shown to increase with L-tryptophan concentration. We also find that mutant TRAP molecules that are truncated at the C-terminus - and hence induced to form 12-mers, distinct from their 11-mer wild type counterparts--have increased melting temperatures. We show that the same effect can be achieved by a point mutation S72N at a subunit interface, which leads to exclusion of C-terminal residues from the interface. Our findings are supported by dye-based scanning fluorimetry, CD spectroscopy, and by crystal structure and mass spectrometry analysis of the B. subtilis S72N TRAP. CONCLUSIONS/SIGNIFICANCE: We conclude that the oligomeric state of a circular protein can be changed by introducing a point mutation at a subunit interface. Exclusion (or deletion of the C-terminus from the subunit interface has a major impact on properties of TRAP oligomers, making them more stable, and we argue that the cause of these changes is the altered oligomeric state. The more stable TRAP oligomers could be used in potential applications of TRAP in bionanotechnology.

  7. Quality of casein based Mozzarella cheese analogue as affected by stabilizer blends

    OpenAIRE

    Jana, A. H.; Patel, H. G.; Suneeta, Pinto; Prajapati, J. P.

    2010-01-01

    Suitability of xanthan gum (XG)-locust bean gum (LBG), carrageenan (CAR)-LBG, and XG-CAR in 1:1 proportion at 0.42% in the formulation was assessed in the manufacture of Mozzarella cheese analogue. The stabilizer blends did not significantly influence the composition, texture profile, organoleptic, baking qualities and pizza-related characteristics of cheese analogues. Considering the influence of stabilizer blend on the sensory quality of analogue and sensory rating of pizza pie, XG-LBG blen...

  8. Affects of N-terminal variation in the SeM protein of Streptococcus equi on antibody and fibrinogen binding.

    Science.gov (United States)

    Timoney, John F; DeNegri, Rafaela; Sheoran, Abhineet; Forster, Nathalie

    2010-02-10

    The clonal Streptococcus equi causes equine strangles, a highly contagious suppurative lymphadenopathy and rhinopharyngitis. An important virulence factor and vaccine component, the antiphagocytic fibrinogen binding SeM of S. equi is a surface anchored fibrillar protein. Two recent studies of N. American, Japanese and European isolates have revealed a high frequency of N-terminal amino acid variation in SeM of S. equi CF32 that suggests this region of the protein is subject to immunologic selection pressure. The aims of the present study were firstly to map regions of SeM reactive with convalescent equine IgG and IgA and stimulatory for lymph node cells and secondly to determine effects of N-terminal variation on the functionality of SeM. Variation did not significantly affect fibrinogen binding or susceptibility of S. equi to an opsonic equine serum. Linear epitopes reactive with convalescent IgG and mucosal IgA were concentrated toward the conserved center of SeM. However, IgA but not IgG from every horse reacted with at least one peptide that contained variable sequence. Lymph node cells (CD4+) from horses immunized with SeM were strongly responsive to a peptide (alphaalpha36-138) encoding the entire variable region. SeM (CF32) specific mouse Mab 04D11 which reacted strongly with this larger peptide but not with shorter peptides within that sequence reacted strongly with whole cells of S. equi CF32 but only weakly with cells of any of 14 isolates of S. equi expressing different variants of SeM. These results in combination suggest that N-terminal variation alters a conformational epitope of significance in mucosal IgA and systemic T cell responses but does not affect antibody mediated phagocytosis and killing.

  9. Functionalized gold nanoparticles for the binding, stabilization, and delivery of therapeutic DNA, RNA, and other biological macromolecules

    Directory of Open Access Journals (Sweden)

    Robert K DeLong

    2010-09-01

    Full Text Available Robert K DeLong1, Christopher M Reynolds1, Yaneika Malcolm1, Ashley Schaeffer1, Tiffany Severs2, Adam Wanekaya21Department of Biomedical Science (Cell and Molecular Biology Program, 2Department of Chemistry, Missouri State University, Springfield, MO, USAAbstract: Nanotechnology has virtually exploded in the last few years with seemingly limitless opportunity across all segments of our society. If gene and RNA therapy are to ever realize their full potential, there is a great need for nanomaterials that can bind, stabilize, and deliver these macromolecular nucleic acids into human cells and tissues. Many researchers have turned to gold nanomaterials, as gold is thought to be relatively well tolerated in humans and provides an inert material upon which nucleic acids can attach. Here, we review the various strategies for associating macromolecular nucleic acids to the surface of gold nanoparticles (GNPs, the characterization chemistries involved, and the potential advantages of GNPs in terms of stabilization and delivery.Keywords: gold, nanoparticles, nanomaterials, RNA, nucleic acid

  10. C11orf83, a Mitochondrial Cardiolipin-Binding Protein Involved in bc1 Complex Assembly and Supercomplex Stabilization

    Science.gov (United States)

    Foti, Michelangelo; Raemy, Etienne; Vaz, Frédéric Maxime; Martinou, Jean-Claude; Bairoch, Amos

    2015-01-01

    Mammalian mitochondria may contain up to 1,500 different proteins, and many of them have neither been confidently identified nor characterized. In this study, we demonstrated that C11orf83, which was lacking experimental characterization, is a mitochondrial inner membrane protein facing the intermembrane space. This protein is specifically associated with the bc1 complex of the electron transport chain and involved in the early stages of its assembly by stabilizing the bc1 core complex. C11orf83 displays some overlapping functions with Cbp4p, a yeast bc1 complex assembly factor. Therefore, we suggest that C11orf83, now called UQCC3, is the functional human equivalent of Cbp4p. In addition, C11orf83 depletion in HeLa cells caused abnormal crista morphology, higher sensitivity to apoptosis, a decreased ATP level due to impaired respiration and subtle, but significant, changes in cardiolipin composition. We showed that C11orf83 binds to cardiolipin by its α-helices 2 and 3 and is involved in the stabilization of bc1 complex-containing supercomplexes, especially the III2/IV supercomplex. We also demonstrated that the OMA1 metalloprotease cleaves C11orf83 in response to mitochondrial depolarization, suggesting a role in the selection of cells with damaged mitochondria for their subsequent elimination by apoptosis, as previously described for OPA1. PMID:25605331

  11. Emotional modulation of control dilemmas: the role of positive affect, reward, and dopamine in cognitive stability and flexibility.

    Science.gov (United States)

    Goschke, Thomas; Bolte, Annette

    2014-09-01

    Goal-directed action in changing environments requires a dynamic balance between complementary control modes, which serve antagonistic adaptive functions (e.g., to shield goals from competing responses and distracting information vs. to flexibly switch between goals and behavioral dispositions in response to significant changes). Too rigid goal shielding promotes stability but incurs a cost in terms of perseveration and reduced flexibility, whereas too weak goal shielding promotes flexibility but incurs a cost in terms of increased distractibility. While research on cognitive control has long been conducted relatively independently from the study of emotion and motivation, it is becoming increasingly clear that positive affect and reward play a central role in modulating cognitive control. In particular, evidence from the past decade suggests that positive affect not only influences the contents of cognitive processes, but also modulates the balance between complementary modes of cognitive control. In this article we review studies from the past decade that examined effects of induced positive affect on the balance between cognitive stability and flexibility with a focus on set switching and working memory maintenance and updating. Moreover, we review recent evidence indicating that task-irrelevant positive affect and performance-contingent rewards exert different and sometimes opposite effects on cognitive control modes, suggesting dissociations between emotional and motivational effects of positive affect. Finally, we critically review evidence for the popular hypothesis that effects of positive affect may be mediated by dopaminergic modulations of neural processing in prefrontal and striatal brain circuits, and we refine this "dopamine hypothesis of positive affect" by specifying distinct mechanisms by which dopamine may mediate effects of positive affect and reward on cognitive control. We conclude with a discussion of limitations of current research, point to

  12. CYCLIC CHOLECYSTOKININ ANALOGUES EXHIBIT HIGH BLOOD STABILITY AND BINDING AFFINITY WITH CHOLECYSTOKININ RECEPTOR

    Directory of Open Access Journals (Sweden)

    Eun-Ha Joh

    2014-01-01

    Full Text Available Recently, incidence of Cholecystokinin (CCK receptor is recognized as a factor that determines the aggressive phenotype of pancreatic cancer. In this study, a novel Cholecystokinin (CCK analogues; DOTA-Nle-cyclo (Glu-Trp-Met-Asp-Phe-Lys-NH2 (DOTA-cCCK and DOTA-Nle-cyclo (Glu-Trp-Nle-Asp-Phe-Lys-NH2 (DOTA-[Nle]-cCCK were synthesized and radiolabeled and the targeting abilities on the CCK receptor were evaluated for new CCK receptor targeting agents searching. Peptides were prepared through a solid phase synthesis method and their purity was over 98%. DOTA is the chelating agent for 68Ga-labelling, which the peptides were radiolabeled with 68Ga by a high radiolabeling yield (>98%. Peptides were stable over 98% by incubation in mouse blood at 37°C for 2 h. A competitive displacement of 125I-CCK8 on the AR42J human pancreatic carcinoma cells revealed that 50% inhibitory concentration value (IC50 were 12.31 nM of DOTA-cCCK and 1.69 nM of DOTA-[Nle]-cCCK. Stable in the blood of both DOTA-cCCK and DOTA-[Nle]-cCCK, but the binding rate with the CCK receptor on AR42J cells, DOTA-[Nle]-cCCK confirmed better than DOTA-cCCK. Therefore, it is concluded that 68Ga-DOTA-[Nle]-cCCK can be potential candidate as a targeting modality for the CCK receptor over-expressing tumors and further studies to evaluate their biological characteristics are needed.

  13. Denaturation and Oxidative Stability of Hemp Seed (Cannabis sativa L.) Protein Isolate as Affected by Heat Treatment.

    Science.gov (United States)

    Raikos, Vassilios; Duthie, Garry; Ranawana, Viren

    2015-09-01

    The present study investigated the impact of heat treatments on the denaturation and oxidative stability of hemp seed protein during simulated gastrointestinal digestion (GID). Heat-denatured hemp protein isolate (HPI) solutions were prepared by heating HPI (2 mg/ml, pH 6.8) to 40, 60, 80 and 100 °C for 10 min. Heat-induced denaturation of the protein isolates was monitored by polyacrylamide gel electrophoresis. Heating HPI at temperatures above 80 °C significantly reduced solubility and led to the formation of large protein aggregates. The isolates were then subjected to in vitro GID and the oxidative stability of the generated peptides was investigated. Heating did not significantly affect the formation of oxidation products during GID. The results suggest that heat treatments should ideally remain below 80 °C if heat stability and solubility of HPI are to be preserved.

  14. Ligand induced stabilization of the melting temperature of the HSV-1 single-strand DNA binding protein using the thermal shift assay

    Science.gov (United States)

    Rupesh, Kanchi Ravi; Smith, Aaron; Boehmer, Paul E.

    2014-01-01

    We have adapted the thermal shift assay to measure the ligand binding properties of the herpes simplex virus-1 single-strand DNA binding protein, ICP8. By measuring SYPRO Orange fluorescence in microtiter plates using a fluorescence-enabled thermal cycler, we have quantified the effects of oligonucleotide ligands on the melting temperature of ICP8. We found that single-stranded oligomers raise the melting temperature of ICP8 in a length- and concentration-dependent manner, ranging from 1 °C for (dT)5 to a maximum of 9 °C with oligomers ≥10 nucleotides, with an apparent Kd of <1 µM for (dT)20. Specifically, the results indicate that ICP8 is capable of interacting with oligomers as short as 5 nucleotides. Moreover, the observed increases in melting temperature of up to 9 °C, indicates that single-strand DNA binding significantly stabilizes the structure of ICP8. This assay may be applied to investigate the ligand binding proteins of other single-strand DNA binding proteins and used as a high-throughput screen to identify compounds with therapeutic potential that inhibit single-strand DNA binding. As proof of concept, the single-strand DNA binding agent ciprofloxacin reduces the ligand induced stabilization of the melting temperature of ICP8 in a dose-dependent manner. PMID:25449284

  15. PENGIKATAN GARAM EMPEDU OLEH SUSU KEDELAI TERFERMENTASI DAN STABILITASNYA TERHADAP PEPSIN DAN PANKREATIN [Binding of Bile Salts by Fermented Soymilk and Its Stability Against Pepsin and Pancreatin

    Directory of Open Access Journals (Sweden)

    Yusmarini1*

    2013-06-01

    Full Text Available Processed soybean products especially the fermented ones have beneficial health effects since they are capable of reducing the level of plasmacholesterol (hypocholesterolemic effect. One of the mechanisms is by increasing the binding of bile salt. This research was aimed to assess the ability of soymilk, fermented soymilk products and fermented soymilk products combined with enzymatic hydrolysis to bind bile salts. The stability of the binding against hydrolysis by digestive enzymes (pepsin and pancreatin was also evaluated. Fermented soybean products inoculated with isolates of L. plantarum 1 R.11.1.2 was be able to bind 1.40 μmol/100 mg protein (62.26% of natrium taurocholate. This binding ability is slightly higher than that of soymilk to natrium taurocholate, i.e.1.33 μmol/100 mg protein (59.04%. Addition of a protease enzyme specific to hydrophobic amino acid (thermolysin on fermented soymilk products was able to enhance the ability of bind natrium taurocholate. Enzymatic hydrolysis products having a molecular weight of <7 kDa could bind 1.51 μmol/100 mg protein natrium taurocholate (67.4%. There was a significant increase in the binding, i.e. 7.9% by the fermented products or an increase of 13.5% from soymilk. Meanwhile peptides measuring ≥7 kDa showed no binding ability against natrium taurocholate.

  16. Formation and Water Stability of Aggregates in Red Soils as Affected by Organic Matter

    Institute of Scientific and Technical Information of China (English)

    ZHANGMINGKUI等; M.J.WILSON; 等

    1996-01-01

    The water stability of aggregates in various size classes separated from 18 samples of red soils under different managements,and the mechanisms responsible for the formation of waer-stable soil aggregates were studied.The results showed that the water stbility of soil aggregates declined with increasing size,especially for the low organic matter soils.Organic matter plays a key role in the formation of water-stable soil aggregates.The larger the soil aggregate size.the greater the impact of organic matter on the water stability of soil aggregates.Removal of organic matter markedly disintegrated the large water-stable aggregates(>2.0mm)and increased the small ones(2.0mm)were mainly glued up by organic mater,Both free oxides and organic matter contribute to the formation and water stability of aggregates in red soils.

  17. Type of packaging affects the colour stability of vitamin E enriched beef.

    Science.gov (United States)

    Nassu, Renata T; Uttaro, Bethany; Aalhus, Jennifer L; Zawadski, Sophie; Juárez, Manuel; Dugan, Michael E R

    2012-12-01

    Colour stability is a very important parameter for meat retail display, as appearance of the product is the deciding factor for consumers at time of purchase. This study investigated the possibility of extending appearance shelf-life through the combined use of packaging method (overwrapping - OVER, modified atmosphere - MAP, vacuum skin packaging - VSP and a combination of modified atmosphere and vacuum skin packaging - MAPVSP) and antioxidants (vitamin E enriched beef). Retail attributes (appearance, lean colour, % surface discolouration), as well as colour space analysis of images for red, green and blue parameters were measured over 18days. MAPVSP provided the most desirable retail appearance during the first 4days of retail display, while VSP-HB had the best colour stability. Overall, packaging type was more influential than α-tocopherol levels on meat colour stability, although α-tocopherol levels (>4μgg(-1) meat) had a protective effect when using high oxygen packaging methods. PMID:22953936

  18. Stability of Intercellular Exchange of Biochemical Substances Affected by Variability of Environmental Parameters

    Science.gov (United States)

    Mihailović, Dragutin T.; Budinčević, Mirko; Balaž, Igor; Mihailović, Anja

    Communication between cells is realized by exchange of biochemical substances. Due to internal organization of living systems and variability of external parameters, the exchange is heavily influenced by perturbations of various parameters at almost all stages of the process. Since communication is one of essential processes for functioning of living systems it is of interest to investigate conditions for its stability. Using previously developed simplified model of bacterial communication in a form of coupled difference logistic equations we investigate stability of exchange of signaling molecules under variability of internal and external parameters.

  19. Quality of casein based Mozzarella cheese analogue as affected by stabilizer blends.

    Science.gov (United States)

    Jana, A H; Patel, H G; Suneeta, Pinto; Prajapati, J P

    2010-03-01

    Suitability of xanthan gum (XG)-locust bean gum (LBG), carrageenan (CAR)-LBG, and XG-CAR in 1:1 proportion at 0.42% in the formulation was assessed in the manufacture of Mozzarella cheese analogue. The stabilizer blends did not significantly influence the composition, texture profile, organoleptic, baking qualities and pizza-related characteristics of cheese analogues. Considering the influence of stabilizer blend on the sensory quality of analogue and sensory rating of pizza pie, XG-LBG blend (1:1) was preferred over XG-CAR and CAR-LBG. PMID:23572632

  20. Homogenization Pressure and Temperature Affect Protein Partitioning and Oxidative Stability of Emulsions

    DEFF Research Database (Denmark)

    Horn, Anna Frisenfeldt; Barouh, Nathalie; Nielsen, Nina Skall;

    2013-01-01

    The oxidative stability of 10 % fish oil-in-water emulsions was investigated for emulsions prepared under different homogenization conditions. Homogenization was conducted at two different pressures (5 or 22.5 MPa), and at two different temperatures (22 and 72 °C). Milk proteins were used as the ...

  1. Sulfur bacteria in wastewater stabilization ponds periodically affected by the 'red-water' phenomenon

    NARCIS (Netherlands)

    A. Belila; B. Abbas; I. Fazaa; N. Saidi; M. Snoussi; A. Hassen; G. Muyzer

    2013-01-01

    Several wastewater stabilization ponds (WSP) in Tunisia suffer periodically from the ‘red-water’ phenomenon due to blooming of purple sulfur bacteria, indicating that sulfur cycle is one of the main element cycles in these ponds. In this study, we investigated the microbial diversity of the El Menze

  2. Sulfur bacteria in wastewater stabilization ponds periodically affected by the ‘red-water’ phenomenon

    NARCIS (Netherlands)

    Belila, A.; Abbas, B.; Fazaa, I.; Saidi, N.; Snoussi, M.; Hassen, A.; Muyzer, G.

    2012-01-01

    Several wastewater stabilization ponds (WSP) in Tunisia suffer periodically from the ‘red-water’ phenomenon due to blooming of purple sulfur bacteria, indicating that sulfur cycle is one of the main element cycles in these ponds. In this study, we investigated the microbial diversity of the El Menze

  3. Comparison of Temperature and Additives Affecting the Stability of the Probiotic Weissella cibaria

    OpenAIRE

    Kang, Mi-Sun; Kim, Youn-Shin; Lee, Hyun-chul; Lim, Hoi-Soon; Oh, Jong-Suk

    2012-01-01

    Daily use of probiotic chewing gum might have a beneficial effect on oral health, and it is important that the viability of the probiotics be maintained in this food product. In this study, we examined the stability of probiotic chewing gum containing Weissella cibaria. We evaluated the effects of various factors, including temperature and additives, on the survival of freeze-dried probiotic W. cibaria powder. No changes in viability were detected during storage at 4℃ for 5 months, whereas th...

  4. Binding properties of ruthenium(II) complexes [Ru(bpy)2(ppn)](2+) and [Ru(phen)2(ppn)](2+) with triplex RNA: As molecular "light switches" and stabilizers for poly(U)·poly(A)*poly(U) triplex.

    Science.gov (United States)

    Li, Jia; Sun, Yanmei; Zhu, Zhiyuan; Zhao, Hong; Tan, Lifeng

    2016-08-01

    Stable RNA triplexes play key roles in many biological processes, while triplexes are thermodynamically less stable than the corresponding duplexes due to the Hoogsteen base pairing. To understand the factors affecting the stabilization of RNA triplexes by octahedral ruthenium(II) complexes, the binding of [Ru(bpy)2(ppn)](2+) (1, bpy=2,2'-bipyridine, ppn=2,4-diaminopyrimido[5,6-b]dipyrido[2,3-f:2',3'-h]quinoxaline) and [Ru(phen)2(ppn)](2+) (2, phen=1,10-phenanthroline) to poly(U)·poly(A)*poly(U) (· denotes the Watson-Crick base pairing and * denotes the Hoogsteen base pairing) has been investigated. The main results obtained here suggest that complexes 1 and 2 can serve as molecular "light switches" and stabilizers for poly(U)·poly(A)*poly(U), while the effectiveness of complex 2 are more marked, suggesting that the hydrophobicity of ancillary ligands has a significant effect on the two Ru(II) complexes binding to poly(U)·poly(A)*poly(U). This study further advances our knowledge on the binding of RNA triplexes with metal complexes, particularly with octahedral ruthenium polypyridyl complexes. PMID:27287059

  5. Polymorphism rs11085226 in the gene encoding polypyrimidine tract-binding protein 1 negatively affects glucose-stimulated insulin secretion.

    Directory of Open Access Journals (Sweden)

    Martin Heni

    Full Text Available OBJECTIVE: Polypyrimidine tract-binding protein 1 (PTBP1 promotes stability and translation of mRNAs coding for insulin secretion granule proteins and thereby plays a role in β-cells function. We studied whether common genetic variations within the PTBP1 locus influence insulin secretion, and/or proinsulin conversion. METHODS: We genotyped 1,502 healthy German subjects for four tagging single nucleotide polymorphisms (SNPs within the PTBP1 locus (rs351974, rs11085226, rs736926, and rs123698 covering 100% of genetic variation with an r(2≥0.8. The subjects were metabolically characterized by an oral glucose tolerance test with insulin, proinsulin, and C-peptide measurements. A subgroup of 320 subjects also underwent an IVGTT. RESULTS: PTBP1 SNP rs11085226 was nominally associated with lower insulinogenic index and lower cleared insulin response in the OGTT (p≤0.04. The other tested SNPs did not show any association with the analyzed OGTT-derived secretion parameters. In the IVGTT subgroup, SNP rs11085226 was accordingly associated with lower insulin levels within the first ten minutes following glucose injection (p = 0.0103. Furthermore, SNP rs351974 was associated with insulin levels in the IVGTT (p = 0.0108. Upon interrogation of MAGIC HOMA-B data, our rs11085226 result was replicated (MAGIC p = 0.018, but the rs351974 was not. CONCLUSIONS: We conclude that common genetic variation in PTBP1 influences glucose-stimulated insulin secretion. This underlines the importance of PTBP1 for beta cell function in vivo.

  6. Combined Chemical and Mineralogical Evidence for Heavy Metal Binding in Mining- and Smelting-Affected Alluvial Soils

    Institute of Scientific and Technical Information of China (English)

    A. VAN(E)K; V. ETTLER; T. GRYGAR; L. BOR(U)VKA; O. (S)EBEK; O. DR(A)BEK

    2008-01-01

    The binding of metallic contaminants (Pb, Cd, and Zn) and As on soil constituents was studied on four highly con-taminated alluvial soil profiles from the mining/smelting district of Pribram (Czech Republic) using a combination of mineralogical and chemical methods. Sequential extraction analysis (SEA) was supplemented by mineralogical investi-gation of both bulk samples and hcavy mineral fractions using X-ray diffraction analysis (XRD) and scanning electron microscopy with an energy dispersive X-ray spectrometer (SEM/EDS). The mineralogy of Fe and Mn oxides was studied by voltammetry of microparticles (VMP) and diffuse reflectance spectrometry (DRS). Zinc and Pb were predominantly were detected in soils by XRD and SEM/EDS. In contrast, Cd was the most mobile contaminant and was predominantly present in the exchangeable fraction. Arsenic was bound to the residual and reducible fractions (corresponding to Fe oxides or to unidentified Fe-Pb arsenates). SEM/EDS observations indicate the predominant affinity of Pb for Mn oxides,and to a lesser extent, for Fe oxidcs. Thus, a more suitable SEA procedure should be used for these mining-affected soils to distinguish between the contaminant fraction bound to Mn oxides and Fe oxides.

  7. The calcium binding protein ALG-2 binds and stabilizes Scotin, a p53-inducible gene product localized at the endoplasmic reticulum membrane

    DEFF Research Database (Denmark)

    Draeby, Ingrid; Woods, Yvonne L; la Cour, Jonas Marstrand;

    2007-01-01

    ALG-2 (apoptosis linked gene 2 product) is a calcium binding protein for which no clear cellular function has been established. In this study we identified Scotin as a novel ALG-2 target protein containing 6 PXY and 4 PYP repeats, earlier identified in the ALG-2 binding regions of AIP1/ALIX and T...... cells. Overexpression of ALG-2 led to accumulation of Scotin in MCF7 and H1299 cells. In vitro and in vivo binding of ALG-2 to Scotin was demonstrated to be strictly calcium dependent indicating a role of this interaction in calcium signaling pathways....

  8. Aluminium fluoride and magnesium, activators of heterotrimeric GTP-binding proteins, affect high-affinity binding of the fungal toxin fusicoccin to the fusicoccin-binding protein in oat root plasma membranes.

    NARCIS (Netherlands)

    de Boer, A.H.; Van der Molen, G.W.; Prins, H.B.A.; Korthout, H.A.A.J.; van der Hoeven, P.C.J.

    1994-01-01

    The fusicoccin-binding protein was solubilised from purified oat root plasma membranes. The solubilised protein retained full binding activity, provided that protease inhibitors were included. Sodium fluoride reduced the high-affinity [H-3]fusicoccin binding to almost zero in a concentration-depende

  9. Factors affecting the stability and performance of ionic liquid-based planar transient photodetectors.

    Science.gov (United States)

    Dalgleish, Simon; Reissig, Louisa; Hu, Laigui; Matsushita, Michio M; Sudo, Yuki; Awaga, Kunio

    2015-05-12

    A novel planar architecture has been developed for the study of photodetectors utilizing the transient photocurrent response induced by a metal/insulator/semiconductor/metal (MISM) structured device, where the insulator is an ionic liquid (IL-MISM). Using vanadyl 2,3-naphthalocyanine, which absorbs in the communications-relevant near-infrared wavelength region (λ(max,film) ≈ 850 nm), in conjunction with C60 as a bulk heterojunction, the high capacitance of the formed electric double layers at the ionic liquid interfaces yields high charge separation efficiency within the semiconductor layer, and the minimal potential drop in the bulk ionic liquid allows the electrodes to be offset by distances of over 7 mm. Furthermore, the decrease in operational speed with increased electrode separation is beneficial for a clear modeling of the waveform of the photocurrent signal, free from the influence of measurement circuitry. Despite the use of a molecular semiconductor as the active layer in conjunction with a liquid insulating layer, devices with a stability of several days could be achieved, and the operational stability of such devices was shown to be dependent solely on the solubility of the active layer in the ionic liquid, even under atmospheric conditions. Furthermore, the greatly simplified device construction process, which does not rely on transparent electrode materials or direct electrode deposition, provides a highly reproducible platform for the study of the electronic processes within IL-MISM detectors that is largely free from architectural constraints. PMID:25895167

  10. Oxidative stability of soybean oil in oleosomes as affected by pH and iron.

    Science.gov (United States)

    Kapchie, Virginie N; Yao, Linxing; Hauck, Catherine C; Wang, Tong; Murphy, Patricia A

    2013-12-01

    The oxidative stability of oil in soybean oleosomes, isolated using the Enzyme-Assisted Aqueous Extraction Process (EAEP), was evaluated. The effects of ferric chloride, at two concentration levels (100 and 500 μM), on lipid oxidation, was examined under pH 2 and 7. The peroxide value (PV) and thiobarbituric acid-reactive substance (TBARS) value of oil, in oleosome suspensions stored at 60 °C, were measured over a 12 day period. The presence of ferric chloride significantly (Poil in the isolated oleosome, as measured by the PV and TBARS. Greater lipid oxidation occurred under an acidic pH. In the pH 7 samples, the positively charged transition metals were strongly attracted to the negatively charged droplets. However, the low ζ-potential and the high creaming rate at this pH, may have limited the oxidation. Freezing, freeze-drying or heating of oleosomes have an insignificant impact on the oxidative stability of oil in isolated soybean oleosomes. Manufacturers should be cautious when adding oleosomes as ingredients in food systems containing transition metal ions.

  11. The temporal stability and predictive validity of affect-based and cognition-based intentions

    NARCIS (Netherlands)

    Keer, M.; Conner, M.; Putte, B. van den; Neijens, P.

    2014-01-01

    Recent research has revealed individual differences in the extent to which people base their intentions on affect and cognition. Two studies are presented that assess whether such differences predict the strength of individuals' intention-behaviour relationships. Participants completed measures of a

  12. Stabilization of Oncostatin-M mRNA by Binding of Nucleolin to a GC-Rich Element in Its 3'UTR.

    Science.gov (United States)

    Saha, Sucharita; Chakraborty, Alina; Bandyopadhyay, Sumita Sengupta

    2016-04-01

    Oncostatin-M (OSM) is a patho-physiologically important pleiotropic, multifunctional cytokine. OSM mRNA sequence analysis revealed that its 3'UTR contains three highly conserved GC-rich cis-elements (GCREs) whose role in mRNA stability is unidentified. In the present study, the functional role of the proximal GC-rich region of osm 3'-UTR (GCRE-1) in post-transcriptional regulation of osm expression in U937 cells was assessed by transfecting construct containing GCRE-1 at 3'-end of a fairly stable reporter gene followed by analysis of the expression of the reporter. GCRE-1 showed mRNA destabilizing activity; however, upon PMA treatment the reporter message containing GCRE-1 was stabilized. This stabilization is owing to a time-dependent progressive binding of trans-factors (at least five proteins) to GCRE-1 post-PMA treatment. Nucleolin was identified as one of the proteins in the RNP complex of GCRE-1 with PMA-treated U937 cytosolic extracts by oligo-dT affinity chromatography of poly-adenylated GCRE-1. Immuno-blot revealed time-dependent enhancement of nucleolin in the cytoplasm which in turn directly binds GCRE-1. RNA co-immunoprecipitation confirmed the GCRE-1-nucleolin interaction in vivo. To elucidate the functional role of nucleolin in stabilization of osm mRNA, nucleolin was overexpressed in U937 cells and found to stabilize the intrinsic osm mRNA, where co-transfection with the reporter containing GCRE-1 confirms the role of GCRE-1 in stabilization of the reporter mRNA. Thus, in conclusion, the results asserted that PMA treatment in U937 cells leads to cytoplasmic translocation of nucleolin that directly binds GCRE-1, one of the major GC-rich instability elements, thereby stabilizing the osm mRNA. PMID:26399567

  13. Unique structure and stability of HmuY, a novel heme-binding protein of Porphyromonas gingivalis.

    Directory of Open Access Journals (Sweden)

    Halina Wójtowicz

    2009-05-01

    Full Text Available Infection, survival, and proliferation of pathogenic bacteria in humans depend on their capacity to impair host responses and acquire nutrients in a hostile environment. Among such nutrients is heme, a co-factor for oxygen storage, electron transport, photosynthesis, and redox biochemistry, which is indispensable for life. Porphyromonas gingivalis is the major human bacterial pathogen responsible for severe periodontitis. It recruits heme through HmuY, which sequesters heme from host carriers and delivers it to its cognate outer-membrane transporter, the TonB-dependent receptor HmuR. Here we report that heme binding does not significantly affect the secondary structure of HmuY. The crystal structure of heme-bound HmuY reveals a new all-beta fold mimicking a right hand. The thumb and fingers pinch heme iron through two apical histidine residues, giving rise to highly symmetric octahedral iron co-ordination. The tetrameric quaternary arrangement of the protein found in the crystal structure is consistent with experiments in solution. It shows that thumbs and fingertips, and, by extension, the bound heme groups, are shielded from competing heme-binding proteins from the host. This may also facilitate heme transport to HmuR for internalization. HmuY, both in its apo- and in its heme-bound forms, is resistant to proteolytic digestion by trypsin and the major secreted proteases of P. gingivalis, gingipains K and R. It is also stable against thermal and chemical denaturation. In conclusion, these studies reveal novel molecular properties of HmuY that are consistent with its role as a putative virulence factor during bacterial infection.

  14. A mutation in the ligand binding domain of the androgen receptor of human LNCaP cells affects steroid binding characteristics and response to anti-androgens

    NARCIS (Netherlands)

    J. Veldscholte (Jos); C. Ris-Stalpers (Carolyn); G.G.J.M. Kuiper (George); G.W. Jenster (Guido); C.A. Berrevoets (Cor); H.J.H.M. Claassen (Eric); H.C.J. van Rooij (Henri); J. Trapman (Jan); A.O. Brinkmann (Albert); E. Mulder (Eppo)

    1990-01-01

    markdownabstractAbstract INCaP prostate tumor cells contain an abnormal androgen receptor system. Progestagens, estradiol and anti-androgens can compete with androgens for binding to the androgen receptor and can stimulate both cell growth and excretion of prostate specific acid phosphatase. We ha

  15. Polymer incorporation method affects the physical stability of amorphous indomethacin in aqueous suspension

    DEFF Research Database (Denmark)

    Surwase, S A; Itkonen, L; Aaltonen, J;

    2015-01-01

    This study reports the potential of different polymers and polymer incorporation methods to inhibit crystallisation and maintain supersaturation of amorphous indomethacin (IND) in aqueous suspensions during storage. Three different polymers (poly(vinyl pyrrolidone) (PVP), hydroxypropyl methylcell...... and polymer incorporation method strongly impact amorphous form stability and drug supersaturation in aqueous suspensions....... of polymer incorporation. All the polymers (with both incorporation methods) inhibited crystallisation of the amorphous IND. The SDs were better than the predissolved polymer solutions at inhibiting crystallisation. The SDs were also better at maintaining drug supersaturation. SP showed a higher IND...... crystallisation inhibition and supersaturation potential than the other polymers. However, this depended on the method of addition. IND in SD with SP did not crystallise, nor did the SD generate any drug supersaturation, whereas IND in the corresponding predissolved SP solution crystallised (into the recently...

  16. Stability of micronutrients and phytochemicals of grapefruit jam as affected by the obtention process.

    Science.gov (United States)

    Igual, M; García-Martínez, E; Camacho, M M; Martínez-Navarrete, N

    2016-04-01

    Fruits are widely revered for their micronutrient properties. They serve as a primary source of vitamins and minerals as well as of natural phytonutrients with antioxidant properties. Jam constitutes an interesting way to preserve fruit. Traditionally, this product is obtained by intense heat treatment that may cause irreversible loss of these bioactive compounds responsible for the health-related properties of fruits. In this work, different grapefruit jams obtained by conventional, osmotic dehydration (OD) without thermal treatment and/or microwave (MW) techniques were compared in terms of their vitamin, organic acid and phytochemical content and their stability through three months of storage. If compared with heating, osmotic treatments lead to a greater loss of organic acids and vitamin C during both processing and storage. MW treatments permit jam to be obtained which has a similar nutritional and functional value than that obtained when using a conventional heating method, but in a much shorter time. PMID:25956906

  17. A CSTR-hollow-fiber system for continuous hydrolysis of proteins. Factors affecting long-term stability of the reactor.

    Science.gov (United States)

    Deeslie, W D; Cheryan, M

    1982-01-01

    Factors affecting the long-term operational stability of a CSTR-hollow-fiber reactor for continuous hydrolysis of proteins were studied. The activity declined in a stepwise manner during a run. Declining from 92% conversion to 60% conversion in about ten hours at a space time of four minutes. Initial decay appears to be due to leakage of small active fragments of the enzyme mixture (Pronase) through the membrane, and later decay due to thermal degradation and loss of activators such as calcium through the membrane. The rate of buildup of unconverted substrate in the reaction vessel was controlled by operational variables, but did not appear to affect the reactor output or the operation of the reactor. The decay of the reactor could be partially compensated for by appropriate manipulation of the space-time variables.

  18. To what extent clay mineralogy affects soil aggregation? Consequences for soil organic matter stabilization

    Science.gov (United States)

    Fernandez-Ugalde, O.; Barré, P.; Hubert, F.; Virto, I.; Chenu, C.; Ferrage, E.; Caner, L.

    2012-12-01

    Aggregation is a key process for soil functioning as it influences C storage, vulnerability to erosion and water holding capacity. While the influence of soil organic C on aggregation has been documented, much less is known about the role of soil mineralogy. Soils usually contain a mixture of clay minerals with contrasted surface properties, which should result on different abilities of clay minerals to aggregation. We took advantage of the intrinsic mineral heterogeneity of a temperate Luvisol to compare the role of clay minerals (illite, smectite, kaolinite, and mixed-layer illite-smectite) in aggregation. In a first step, grassland and tilled soil samples were fractionated in water in aggregate-size classes according to the hierarchical model of aggregation (Tisdall and Oades, 1982). Clay mineralogy and organic C in the aggregate-size classes were analyzed. The results showed that interstratified minerals containing swelling phases accumulated in aggregated fractions (>2 μm) compared to free clay fractions (500 μm) to micro-aggregates (50-250 μm). C concentration and C/N ratio followed the opposite trend. These results constitute a clay mineral-based evidence for the hierarchical model of aggregation, which postulates an increasing importance of the reactivity of clay minerals in the formation of micro-aggregates compared to larger aggregates. In the latter aggregates, formation relies on the physical enmeshment of particles by fungal hyphae, and root and microbial exudates. In a second step, micro-aggregates from the tilled soil samples were submitted to increasingly disaggregating treatments by sonication to evaluate the link between their water stability and clay mineralogy. Micro-aggregates with increasing stability showed an increase of interstratified minerals containing swelling phases and C concentration for low intensities of disaggregation (from 0 to 5 J mL-1). This suggests that swelling phases promote their stability. Swelling phases and organic C

  19. Stabilization

    Directory of Open Access Journals (Sweden)

    Muhammad H. Al-Malack

    2016-07-01

    Full Text Available Fuel oil flyash (FFA produced in power and water desalination plants firing crude oils in the Kingdom of Saudi Arabia is being disposed in landfills, which increases the burden on the environment, therefore, FFA utilization must be encouraged. In the current research, the effect of adding FFA on the engineering properties of two indigenous soils, namely sand and marl, was investigated. FFA was added at concentrations of 5%, 10% and 15% to both soils with and without the addition of Portland cement. Mixtures of the stabilized soils were thoroughly evaluated using compaction, California Bearing Ratio (CBR, unconfined compressive strength (USC and durability tests. Results of these tests indicated that stabilized sand mixtures could not attain the ACI strength requirements. However, marl was found to satisfy the ACI strength requirement when only 5% of FFA was added together with 5% of cement. When the FFA was increased to 10% and 15%, the mixture’s strength was found to decrease to values below the ACI requirements. Results of the Toxicity Characteristics Leaching Procedure (TCLP, which was performed on samples that passed the ACI requirements, indicated that FFA must be cautiously used in soil stabilization.

  20. Physico-chemical factors affecting the in vitro stability of phycobiliproteins from Phormidium rubidum A09DM.

    Science.gov (United States)

    Rastogi, Rajesh Prasad; Sonani, Ravi Raghav; Madamwar, Datta

    2015-08-01

    The functionality and stability of phycobiliproteins (PBPs) phycoerythrin (PE), phycocyanin (PC) and allophycocyanin (APC) were investigated under various temperatures, pHs and oxidative stressors. All PBPs were thermostable up to 4-40°C; however, their concentration decreased rapidly at 60-80°C. The maximum stability of all PBPs was in the pH range 6.0-7.0. Decrease in PBPs content was found under high acidic (pH 2-4) and alkaline conditions (pH 8-12). The oxidizing agent (0.1-0.6%) showed the least effect on the stability of PBPs; however, 0.8-1.0% H2O2 caused significant loss of PBPs. Contrary to PE, PC and APC was more susceptible to an oxidizing agent. The chromophore associated with α- and β-subunit of PBPs and thus, their functionality (fluorescence) was severely affected under high temperature (60-80°C), and oxidizing agent, as well as low (2-4) and high (8-12) pH. Contrary to PC and APC, functionality of PE was surprisingly maintained even at pHs 6-12 and under oxidative stress. PMID:25958145

  1. Screening of mutations affecting protein stability and dynamics of FGFR1—A simulation analysis

    Directory of Open Access Journals (Sweden)

    C. George Priya Doss

    2012-12-01

    Full Text Available Single amino acid substitutions in Fibroblast Growth Factor Receptor 1 (FGFR1 destabilize protein and have been implicated in several genetic disorders like various forms of cancer, Kallamann syndrome, Pfeiffer syndrome, Jackson Weiss syndrome, etc. In order to gain functional insight into mutation caused by amino acid substitution to protein function and expression, special emphasis was laid on molecular dynamics simulation techniques in combination with in silico tools such as SIFT, PolyPhen 2.0, I-Mutant 3.0 and SNAP. It has been estimated that 68% nsSNPs were predicted to be deleterious by I-Mutant, slightly higher than SIFT (37%, PolyPhen 2.0 (61% and SNAP (58%. From the observed results, P722S mutation was found to be most deleterious by comparing results of all in silico tools. By molecular dynamics approach, we have shown that P722S mutation leads to increase in flexibility, and deviated more from the native structure which was supported by the decrease in the number of hydrogen bonds. In addition, biophysical analysis revealed a clear insight of stability loss due to P722S mutation in FGFR1 protein. Majority of mutations predicted by these in silico tools were in good concordance with the experimental results.

  2. Static Magnetic Field Attenuates Lipopolysaccharide-Induced Inflammation in Pulp Cells by Affecting Cell Membrane Stability

    Directory of Open Access Journals (Sweden)

    Sung-Chih Hsieh

    2015-01-01

    Full Text Available One of the causes of dental pulpitis is lipopolysaccharide- (LPS- induced inflammatory response. Following pulp tissue inflammation, odontoblasts, dental pulp cells (DPCs, and dental pulp stem cells (DPSCs will activate and repair damaged tissue to maintain homeostasis. However, when LPS infection is too serious, dental repair is impossible and disease may progress to irreversible pulpitis. Therefore, the aim of this study was to examine whether static magnetic field (SMF can attenuate inflammatory response of dental pulp cells challenged with LPS. In methodology, dental pulp cells were isolated from extracted teeth. The population of DPSCs in the cultured DPCs was identified by phenotypes and multilineage differentiation. The effects of 0.4 T SMF on DPCs were observed through MTT assay and fluorescent anisotropy assay. Our results showed that the SMF exposure had no effect on surface markers or multilineage differentiation capability. However, SMF exposure increases cell viability by 15%. In addition, SMF increased cell membrane rigidity which is directly related to higher fluorescent anisotropy. In the LPS-challenged condition, DPCs treated with SMF demonstrated a higher tolerance to LPS-induced inflammatory response when compared to untreated controls. According to these results, we suggest that 0.4 T SMF attenuates LPS-induced inflammatory response to DPCs by changing cell membrane stability.

  3. Enzyme bread improvers affect the stability of deoxynivalenol and deoxynivalenol-3-glucoside during breadmaking.

    Science.gov (United States)

    Vidal, Arnau; Ambrosio, Asier; Sanchis, Vicente; Ramos, Antonio J; Marín, Sonia

    2016-10-01

    The stability of deoxynivalenol (DON) and deoxynivalenol-3-glucoside (DON-3-glucoside) during the breadmaking process was studied. Some enzymes used in the bakery industry were examined to evaluate their effects on DON and DON-3-glucoside. The level of DON in breads without added enzymes was reduced (17-21%). Similarly, the addition of cellulase, protease, lipase and glucose-oxidase did not modify this decreasing trend. The effect of xylanase and α-amylase on DON content depended on the fermentation temperature. These enzymes reduced the DON content by 10-14% at 45°C. In contrast, at 30°C, these enzymes increased the DON content by 13-23%. DON-3-glucoside levels decreased at the end of fermentation, with a final reduction of 19-48% when no enzymes were used. However, the presence of xylanase, α-amylase, cellulase and lipase resulted in bread with greater quantities of DON-3-glucoside when fermentation occurred at 30°C. The results showed that wheat bran and flour may contain hidden DON that may be enzymatically released during the breadmaking process when the fermentation temperature is close to 30°C. PMID:27132852

  4. Polymer incorporation method affects the physical stability of amorphous indomethacin in aqueous suspension.

    Science.gov (United States)

    Surwase, S A; Itkonen, L; Aaltonen, J; Saville, D; Rades, T; Peltonen, L; Strachan, C J

    2015-10-01

    This study reports the potential of different polymers and polymer incorporation methods to inhibit crystallisation and maintain supersaturation of amorphous indomethacin (IND) in aqueous suspensions during storage. Three different polymers (poly(vinyl pyrrolidone) (PVP), hydroxypropyl methylcellulose (HPMC) and Soluplus® (SP)) were used and included in the suspensions either as a solid dispersion (SD) with IND or dissolved in the suspension medium prior to the addition of amorphous IND. The total concentrations of both IND and the polymer in the suspensions were kept the same for both methods of polymer incorporation. All the polymers (with both incorporation methods) inhibited crystallisation of the amorphous IND. The SDs were better than the predissolved polymer solutions at inhibiting crystallisation. The SDs were also better at maintaining drug supersaturation. SP showed a higher IND crystallisation inhibition and supersaturation potential than the other polymers. However, this depended on the method of addition. IND in SD with SP did not crystallise, nor did the SD generate any drug supersaturation, whereas IND in the corresponding predissolved SP solution crystallised (into the recently characterised η polymorphic form of the drug) but also led to a more than 20-fold higher IND solution concentration than that observed for crystalline IND. The ranking of the polymers with respect to crystallisation inhibition potential in SDs was SP≫PVP>HPMC. Overall, this study showed that both polymer type and polymer incorporation method strongly impact amorphous form stability and drug supersaturation in aqueous suspensions. PMID:26092472

  5. Biochar affects carbon composition and stability in soil: a combined spectroscopy-microscopy study

    Science.gov (United States)

    Hernandez-Soriano, Maria C.; Kerré, Bart; Kopittke, Peter M.; Horemans, Benjamin; Smolders, Erik

    2016-04-01

    The use of biochar can contribute to carbon (C) storage in soil. Upon addition of biochar, there is a spatial reorganization of C within soil particles, but the mechanisms remain unclear. Here, we used Fourier transformed infrared-microscopy and confocal laser scanning microscopy to examine this reorganization. A silty-loam soil was amended with three different organic residues and with the biochar produced from these residues and incubated for 237 d. Soil respiration was lower in biochar-amended soils than in residue-amended soils. Fluorescence analysis of the dissolved organic matter revealed that biochar application increased a humic-like fluorescent component, likely associated with biochar-C in solution. The combined spectroscopy-microscopy approach revealed the accumulation of aromatic-C in discrete spots in the solid-phase of microaggregates and its co-localization with clay minerals for soil amended with raw residue or biochar.The co-localization of aromatic-C:polysaccharides-C was consistently reduced upon biochar application. We conclude that reduced C metabolism is an important mechanism for C stabilization in biochar-amended soils.

  6. CaMKII binding to GluN2B is differentially affected by macromolecular crowding reagents.

    Directory of Open Access Journals (Sweden)

    Dayton J Goodell

    Full Text Available Binding of the Ca2+/calmodulin(CaM-dependent protein kinase II (CaMKII to the NMDA-type glutamate receptor (NMDAR subunit GluN2B controls long-term potentiation (LTP, a form of synaptic plasticity thought to underlie learning and memory. Regulation of this interaction is well-studied biochemically, but not under conditions that mimic the macromolecular crowding found within cells. Notably, previous molecular crowding experiments with lysozyme indicated an effect on the CaMKII holoenzyme conformation. Here, we found that the effect of molecular crowding on Ca2+/CaM-induced CaMKII binding to immobilized GluN2B in vitro depended on the specific crowding reagent. While binding was reduced by lysozyme, it was enhanced by BSA. The ATP content in the BSA preparation caused CaMKII autophosphorylation at T286 during the binding reaction; however, enhanced binding was also observed when autophosphorylation was blocked. Importantly, the positive regulation by nucleotide and BSA (as well as other macromolecular crowding reagents did not alleviate the requirement for CaMKII stimulation to induce GluN2B binding. The differential effect of lysozyme (14 kDa and BSA (66 kDa was not due to size difference, as both dextran-10 and dextran-70 enhanced binding. By contrast, crowding with immunoglobulin G (IgG reduced binding. Notably, lysozyme and IgG but not BSA directly bound to Ca2+/CaM in an overlay assay, suggesting a competition of lysozyme and IgG with the Ca2+/CaM-stimulus that induces CaMKII/GluN2B binding. However, lysozyme negatively regulated binding even when it was instead induced by CaMKII T286 phosphorylation. Alternative modes of competition would be with CaMKII or GluN2B, and the negative effects of lysozyme and IgG indeed also correlated with specific or non-specific binding to the immobilized GluN2B. Thus, the effect of any specific crowding reagent can differ, depending on its additional direct effects on CaMKII/GluN2B binding. However, the

  7. Dispersal, environmental forcing, and parasites combine to affect metapopulation synehrony and stability.

    Science.gov (United States)

    Duncan, Alison B; Gonzalez, Andrew; Kaltz, Oliver

    2015-01-01

    Dispersal can have positive and negative effects on metapopulation stability and persistence. One prediction is that high levels of dispersal synchronize density fluctuations between subpopulations. However, little is still known about how biotic and abiotic factors combine to modify the effects of dispersal rate on synchrony and metapopulation dynamics. In a fully factorial experimental design, we investigated the combined effects of (1) dispersal, (2) parasite infection, and (3) synchrony in temperature fluctuations on subpopulation synchrony, metapopulation instability, and minimum population size, in laboratory metapopulations of the ciliate Paramecium caudatum. Metapopulations, comprising two subpopulations linked by high or low levels of dispersal, were exposed to daily fluctuations in temperature between permissive (23 degrees C) and restrictive (5 degrees C) conditions. Infected metapopulations started the experiment with one subpopulation uninfected, while the other was infected at a prevalence of 5% with the bacterial parasite Holospora undulata. The temperature synchrony treatment involved subpopulations within a metapopulation following the same (synchronous temperatures) or different (asynchronous temperatures) temporal sequences. Population size was tracked over the 56-day experiment. We found that subpopulation density fluctuations were synchronized by high dispersal in infected metapopulations, and by synchronous temperatures in all metapopulations. Subpopulation synchrony was positively correlated with metapopulation instability and minimum metapopulation size, highlighting the multiple consequences of our treatments for metapopulation dynamics. Our results illustrate how parasites can generate dispersal-driven synchrony in non-cycling, declining populations. This "biotic forcing" via a natural enemy added to the temperature-dependent environmental forcing. We therefore conclude that predictions of metapopulation persistence in natural populations

  8. Factors affecting emulsion stability and quality of oil recovered from enzyme-assisted aqueous extraction of soybeans.

    Science.gov (United States)

    Jung, S; Maurer, D; Johnson, L A

    2009-11-01

    The objectives of the present study were to assess how the stability of the emulsion recovered from aqueous extraction processing of soybeans was affected by characteristics of the starting material and extraction and demulsification conditions. Adding endopeptidase Protex 6L during enzyme-assisted aqueous extraction processing (EAEP) of extruded soybean flakes was vital to obtaining emulsions that were easily demulsified with enzymes. Adding salt (up to 1.5 mM NaCl or MgCl(2)) during extraction and storing extruded flakes before extraction at 4 and 30 degrees C for up to 3 months did not affect the stabilities of emulsions recovered from EAEP of soy flour, flakes and extruded flakes. After demulsification, highest free oil yield was obtained with EAEP of extruded flakes, followed by flour and then flakes. The same protease used for the extraction step was used to demulsify the EAEP cream emulsion from extruded full-fat soy flakes at concentrations ranging from 0.03% to 2.50% w/w, incubation times ranging from 2 to 90 min, and temperatures of 25, 50 or 65 degrees C. Highest free oil recoveries were achieved at high enzyme concentrations, mild temperatures, and short incubation times. Both the nature of enzyme (i.e., protease and phospholipase), added alone or as a cocktail, concentration of enzymes (0.5% vs. 2.5%) and incubation time (1 vs. 3 h), use during the extraction step, and nature of enzyme added for demulsifying affected free oil yield. The free oil recovered from EAEP of extruded flakes contained less phosphorus compared with conventional hexane-extracted oil. The present study identified conditions rendering the emulsion less stable, which is critical to increasing free oil yield recovered during EAEP of soybeans, an environmentally friendly alternative processing method to hexane extraction. PMID:19570674

  9. Chemolithoautotrophy supports macroinvertebrate food webs and affects diversity and stability in groundwater communities.

    Science.gov (United States)

    Hutchins, Benjamin T; Engel, Annette Summers; Nowlin, Weston H; Schwartz, Benjamin F

    2016-06-01

    compared to the other two sites. Our results suggest that diverse OM sources and in situ, chemolithoautotrophic OM production can support complex groundwater food webs and increase species richness. Chemolithoautotrophy has been fundamental for the long-term maintenance of species diversity, trophic complexity, and community stability in this subterranean ecosystem, especially during periods of decreased photosynthetic production and groundwater recharge that have occurred over geologic time scales.

  10. Chemolithoautotrophy supports macroinvertebrate food webs and affects diversity and stability in groundwater communities.

    Science.gov (United States)

    Hutchins, Benjamin T; Engel, Annette Summers; Nowlin, Weston H; Schwartz, Benjamin F

    2016-06-01

    compared to the other two sites. Our results suggest that diverse OM sources and in situ, chemolithoautotrophic OM production can support complex groundwater food webs and increase species richness. Chemolithoautotrophy has been fundamental for the long-term maintenance of species diversity, trophic complexity, and community stability in this subterranean ecosystem, especially during periods of decreased photosynthetic production and groundwater recharge that have occurred over geologic time scales. PMID:27459783

  11. The Conditions of the Environment as Factors Affecting the Social and Political Stability of Populations

    Directory of Open Access Journals (Sweden)

    Fausto Pedrazzini

    2010-10-01

    Full Text Available In this review article, the different conditions of the environment which could affect the well-being of the populations living on it are taken into consideration and analysed. A specific attention is paid to the phenomenon of water reduction, land degradation and consequent desertification. Such a phenomenon is particularly worrying in selected regions of the world (the Mediterranean Region and Central Asia in which a combination of several factors including climate variations, pressure of populations and increased competition for the available resources have a direct consequence on the economical, social and political conditions of the population. In addition, migrations could also take place, increasing the instability of entire regions. A proper management of water resources and the preservation of land and soil resources are essential requisites to counteract the mentioned adverse effects. Such a management is frequently a transboundary concern since it might involve different regions and countries; this is an additional reason for debating the environment degradation issues at the international level and for increasing the awareness of the civil society, the policy makers and governments.

  12. Dynamics of aggregate stability and soil organic C distribution as affected by climatic aggressiveness: a mesocosm approach

    Science.gov (United States)

    Pellegrini, Sergio; Elio Agnelli, Alessandro; Costanza Andrenelli, Maria; Barbetti, Roberto; Castelli, Fabio; Costantini, Edoardo A. C.; Lagomarsino, Alessandra; Pasqui, Massimiliano; Tomozeiu, Rodica; Razzaghi, Somayyeh; Vignozzi, Nadia

    2014-05-01

    In the framework of a research project aimed at evaluating the adaptation scenarios of the Italian agriculture to the current climate change, a mesocosm experiment under controlled conditions was set up for studying the dynamics of soil aggregate stability and organic C in different size fractions. Three alluvial loamy soils (BOV - Typic Haplustalfs coarse-loamy; CAS - Typic Haplustalfs fine-loamy; MED - Typic Hapludalfs fine-loamy) along a climatic gradient (from dryer to moister pedoclimatic conditions) in the river Po valley (northern Italy), under crop rotation for animal husbandry from more than 40 years, were selected. The Ap horizons (0-30cm) were taken and placed in 9 climatic chambers under controlled temperature and rainfall. Each soil was subjected to three different climate scenarios in terms of erosivity index obtained by combining Modified Fournier and Bagnouls-Gaussen indexes: i) typical (TYP), the median year of each site related to the 1961-1990 reference period; ii) maximum aggressive year (MAX) observed in the same period, and iii) the simulated climate (SIM), obtained by projections of climate change precipitation and temperature for the period 2021-2050 as provided by the IPCC-A1B emission scenario. In the climatic chambers the year climate was reduced to six months. The soils were analyzed for particle size distribution, aggregate stability by wet and dry sieving, and organic C content at the beginning and at the end of the trial. The soils showed different behaviour in terms of aggregate stability and dynamics of organic C in the diverse size fractions. The soils significantly differed in terms of initial mean weight diameter (MWD) (CAS>MED>BOV). A general reduction of MWD in all sites was observed at the end of the experiment, with the increase of the smallest aggregate fractions (0.250-0.05 mm). In particular, BOV showed the maximum decrease of the aggregate stability and MED the lowest. C distribution in aggregate fractions significantly

  13. How can climate, soil, and monitoring schedule affect temporal stability of soil water contents?

    Science.gov (United States)

    Martinez, G.; Pachepsky, Y. A.; Vereecken, H.

    2012-12-01

    Temporal stability (TS) of soil water content (SWC) reflects the spatio-temporal organization of soil water. The TS SWC was originally recognized as a phenomenon that can be used to provide temporal average SWC of an area of interest from observations at a representative location(s). Currently application fields of TS SWC are numerous, e.g. up- and downscaling SWC, SWC monitoring and data assimilation, precision farming, and sensor network design and optimization. However, the factors that control the SWC organization and TS SWC are not completely understood. Among these factors are soil hydraulic properties that are considered as local controls, weather patterns, and the monitoring schedule. The objective of this work was to use modeling to assess the effect of these factors on the spatio-temporal patterns of SWC. We ran the HYDRUS6 code to simulate four years of SWC in 4-m long soil columns. The columns were assumed homogeneous, soil hydraulic conductivity was drawn from lognormal distributions. Sets of columns were generated separately for sandy loam and loamy soils, soil water retention was set to typical values for those soil textures. Simulations were carried out for four climates present at the continental US. The climate-specific weather patterns were obtained with the CLIGEN code using climate-specific weather observation locations that were humid subtropical from College Station (TX), humid continental from Indianapolis (IN), cold semiarid from Moscow (ID) and hot semiarid from Tucson (AZ). We evaluated the TS and representative location (RL) selections by comparing i) different climates; ii) for the same climates different years; iii) different time intervals between samplings; iv) one year duration surveys vs. one month summer campaigns; and v) different seasons of the same year. Spatial variability of the mean relative differences (MRD) differed among climates for both soils, as the probability of observing the same variance in the MRD was lower than

  14. Detection of DNA damage by Escherichia coli UvrB-binding competition assay is limited by the stability of the UvrB-DNA complex.

    Science.gov (United States)

    Routledge, M N; Allan, J M; Garner, R C

    1997-07-01

    To investigate the use of UvrB-binding to detect DNA damage, mobility shift gel electrophoresis was used to detect binding of UvrB protein to a 136 bp DNA fragment that was randomly adducted with aflatoxin B1 8,9-epoxide and end-labelled with 32P. After polyacrylamide gel electrophoresis, the shifted band that contained DNA bound by UvrB was quantified as a percentage of total radioactive substrate DNA. This method was applied to analyse plasmid DNA that was adducted with various DNA modifying agents in vitro. These adducts competed for UvrB-binding to the labelled substrate. By competing for UvrB-binding with 10 ng of plasmid DNA that was adducted with known levels of aflatoxin B1, 2-amino-3-methylimidazo[4,5-f]quinoline, or benzo[a]pyrene diol epoxide, UvrB competition could be quantified for DNA adducted with between one adduct in 10(2) and one adduct in 10(5) normal nucleotides. However, plasmid DNA exposed to N-methyl-N-nitrosourea or methylene blue + visible light, did not compete for UvrB-binding, even though the presence of UvrABC sensitive sites were confirmed on this DNA by a UvrABC incision assay. Mono-adducted 96-bp DNA substrates, which contained an internal 32P-label and either a single apurinic site, aflatoxin B1-guanine adduct, O6-methylguanine, 8-oxo-deoxyguanosine or non-adducted guanine, were also used as substrates for UvrA- and UvrB-binding to examine the stability of UvrB-DNA complexes with specific adducts. Under similar conditions used for the competition assay, significant UvrB-binding was seen only for the aflatoxin adducted substrate. These results suggest that stability of UvrB-binding varies greatly between bulky and non-bulky adducts. It was also found that rat liver DNA from untreated rats inhibited UvrB-binding to the substrate DNA in the competition assay, to a degree that was equivalent to competition with plasmid adducted at one adduct in 10(3) normal nucleotides.

  15. Binding of calcium in the EF-hand of Escherichia coli lytic transglycosylase Slt35 is important for stability

    NARCIS (Netherlands)

    Asselt, Erik J. van; Dijkstra, Bauke W.

    1999-01-01

    The Escherichia coli lytic transglycosylase Slt35 contains a single metal ion-binding site that resembles EF-hand calcium-binding sites. The Slt35 EF-hand is only the second observation of such a domain in a prokaryotic protein. Two crystal structures at 2.1 Å resolution show that both Ca2+ ions and

  16. Increased Stability and DNA Site Discrimination of Single Chain Variants of the Dimeric beta-Barrel DNA Binding Domain of the Human Papillomavirus E2 Transcriptional Regulator

    Energy Technology Data Exchange (ETDEWEB)

    Dellarole,M.; Sanchez, I.; Freire, E.; de Prat-Gay, G.

    2007-01-01

    Human papillomavirus infects millions of people worldwide and is a causal agent of cervical cancer in women. The HPV E2 protein controls the expression of all viral genes through binding of its dimeric C-terminal domain (E2C) to its target DNA site. We engineered monomeric versions of the HPV16 E2C, in order to probe the link of the dimeric {beta}-barrel fold to stability, dimerization, and DNA binding. Two single-chain variants, with 6 and 12 residue linkers (scE2C-6 and scE2C-12), were purified and characterized. Spectroscopy and crystallography show that the native structure is unperturbed in scE2C-12. The single chain variants are stabilized with respect to E2C, with effective concentrations of 0.6 to 6 mM. The early folding events of the E2C dimer and scE2C-12 are very similar and include formation of a compact species in the submillisecond time scale and a non-native monomeric intermediate with a half-life of 25 ms. However, monomerization changes the unfolding mechanism of the linked species from two-state to three-state, with a high-energy intermediate. Binding to the specific target site is up to 5-fold tighter in the single chain variants. Nonspecific DNA binding is up to 7-fold weaker in the single chain variants, leading to an overall 10-fold increased site discrimination capacity, the largest described so far for linked DNA binding domains. Titration calorimetric binding analysis, however, shows almost identical behavior for dimer and single-chain species, suggesting very subtle changes behind the increased specificity. Global analysis of the mechanisms probed suggests that the dynamics of the E2C domain, rather than the structure, are responsible for the differential properties. Thus, the plastic and dimeric nature of the domain did not evolve for a maximum affinity, specificity, and stability of the quaternary structure, likely because of regulatory reasons and for roles other than DNA binding played by partly folded dimeric or monomeric conformers.

  17. Insights into the interaction of discodermolide and docetaxel with tubulin. Mapping the binding sites of microtubule-stabilizing agents by using an integrated NMR and computational approach.

    Science.gov (United States)

    Canales, Angeles; Rodríguez-Salarichs, Javier; Trigili, Chiara; Nieto, Lidia; Coderch, Claire; Andreu, José Manuel; Paterson, Ian; Jiménez-Barbero, Jesús; Díaz, J Fernando

    2011-08-19

    The binding interactions of two antitumor agents that target the paclitaxel site, docetaxel and discodermolide, to unassembled α/β-tubulin heterodimers and microtubules have been studied using biochemical and NMR techniques. The use of discodermolide as a water-soluble paclitaxel biomimetic and extensive NMR experiments allowed the detection of binding of microtubule-stabilizing agents to unassembled tubulin α/β-heterodimers. The bioactive 3D structures of docetaxel and discodermolide bound to α/β-heterodimers were elucidated and compared to those bound to microtubules, where subtle changes in the conformations of docetaxel in its different bound states were evident. Moreover, the combination of experimental TR-NOE and STD NMR data with CORCEMA-ST calculations indicate that docetaxel and discodermolide target an additional binding site at the pore of the microtubules, which is different from the internal binding site at the lumen previously determined by electron crystallography. Binding to this pore site can then be considered as the first ligand-protein recognition event that takes place in advance of the drug internalization process and interaction with the lumen of the microtubules.

  18. Two glycosylation sites in H5N1 influenza virus hemagglutinin that affect binding preference by computer-based analysis.

    Directory of Open Access Journals (Sweden)

    Wentian Chen

    Full Text Available Increasing numbers of H5N1 influenza viruses (IVs are responsible for human deaths, especially in North Africa and Southeast Asian. The binding of hemagglutinin (HA on the viral surface to host sialic acid (SA receptors is a requisite step in the infection process. Phylogenetic analysis reveals that H5N1 viruses can be divided into 10 clades based on their HA sequences, with most human IVs centered from clade 1 and clade 2.1 to clade 2.3. Protein sequence alignment in various clades indicates the high conservation in the receptor-binding domains (RBDs is essential for binding with the SA receptor. Two glycosylation sites, 158N and 169N, also participate in receptor recognition. In the present work, we attempted to construct a serial H5N1 HA models including diverse glycosylated HAs to simulate the binding process with various SA receptors in silico. As the SA-α-2,3-Gal and SA-α-2,6-Gal receptor adopted two distinctive topologies, straight and fishhook-like, respectively, the presence of N-glycans at 158N would decrease the affinity of HA for all of the receptors, particularly SA-α-2,6-Gal analogs. The steric clashes of the huge glycans shown at another glycosylation site, 169N, located on an adjacent HA monomer, would be more effective in preventing the binding of SA-α-2,3-Gal analogs.

  19. RNA-binding protein Hermes/RBPMS inversely affects synapse density and axon arbor formation in retinal ganglion cells in vivo.

    Science.gov (United States)

    Hörnberg, Hanna; Wollerton-van Horck, Francis; Maurus, Daniel; Zwart, Maarten; Svoboda, Hanno; Harris, William A; Holt, Christine E

    2013-06-19

    The RNA-binding protein Hermes [RNA-binding protein with multiple splicing (RBPMS)] is expressed exclusively in retinal ganglion cells (RGCs) in the CNS, but its function in these cells is not known. Here we show that Hermes protein translocates in granules from RGC bodies down the growing axons. Hermes loss of function in both Xenopus laevis and zebrafish embryos leads to a significant reduction in retinal axon arbor complexity in the optic tectum, and expression of a dominant acting mutant Hermes protein, defective in RNA-granule localization, causes similar defects in arborization. Time-lapse analysis of branch dynamics reveals that the decrease in arbor complexity is caused by a reduction in new branches rather than a decrease in branch stability. Surprisingly, Hermes depletion also leads to enhanced early visual behavior and an increase in the density of presynaptic puncta, suggesting that reduced arborization is accompanied by increased synaptogenesis to maintain synapse number. PMID:23785151

  20. A3 domain region 1803-1818 contributes to the stability of activated factor VIII and includes a binding site for activated factor IX.

    Science.gov (United States)

    Bloem, Esther; Meems, Henriet; van den Biggelaar, Maartje; Mertens, Koen; Meijer, Alexander B

    2013-09-01

    A recent chemical footprinting study in our laboratory suggested that region 1803-1818 might contribute to A2 domain retention in activated factor VIII (FVIIIa). This site has also been implicated to interact with activated factor IX (FIXa). Asn-1810 further comprises an N-linked glycan, which seems incompatible with a role of the amino acids 1803-1818 for FIXa or A2 domain binding. In the present study, FVIIIa stability and FIXa binding were evaluated in a FVIII-N1810C variant, and two FVIII variants in which residues 1803-1810 and 1811-1818 are replaced by the corresponding residues of factor V (FV). Enzyme kinetic studies showed that only FVIII/FV 1811-1818 has a decreased apparent binding affinity for FIXa. Flow cytometry analysis indicated that fluorescent FIXa exhibits impaired complex formation with only FVIII/FV 1811-1818 on lipospheres. Site-directed mutagenesis revealed that Phe-1816 contributes to the interaction with FIXa. To evaluate FVIIIa stability, the FVIII/FV chimeras were activated by thrombin, and the decline in cofactor function was followed over time. FVIII/FV 1803-1810 and FVIII/FV 1811-1818 but not FVIII-N1810C showed a decreased FVIIIa half-life. However, when the FVIII variants were activated in presence of FIXa, only FVIII/FV 1811-1818 demonstrated an enhanced decline in cofactor function. Surface plasmon resonance analysis revealed that the FVIII variants K1813A/K1818A, E1811A, and F1816A exhibit enhanced dissociation after activation. The results together demonstrate that the glycan at 1810 is not involved in FVIII cofactor function, and that Phe-1816 of region 1811-1818 contributes to FIXa binding. Both regions 1803-1810 and 1811-1818 contribute to FVIIIa stability. PMID:23884417

  1. A3 Domain Region 1803–1818 Contributes to the Stability of Activated Factor VIII and Includes a Binding Site for Activated Factor IX

    Science.gov (United States)

    Bloem, Esther; Meems, Henriet; van den Biggelaar, Maartje; Mertens, Koen; Meijer, Alexander B.

    2013-01-01

    A recent chemical footprinting study in our laboratory suggested that region 1803–1818 might contribute to A2 domain retention in activated factor VIII (FVIIIa). This site has also been implicated to interact with activated factor IX (FIXa). Asn-1810 further comprises an N-linked glycan, which seems incompatible with a role of the amino acids 1803–1818 for FIXa or A2 domain binding. In the present study, FVIIIa stability and FIXa binding were evaluated in a FVIII-N1810C variant, and two FVIII variants in which residues 1803–1810 and 1811–1818 are replaced by the corresponding residues of factor V (FV). Enzyme kinetic studies showed that only FVIII/FV 1811–1818 has a decreased apparent binding affinity for FIXa. Flow cytometry analysis indicated that fluorescent FIXa exhibits impaired complex formation with only FVIII/FV 1811–1818 on lipospheres. Site-directed mutagenesis revealed that Phe-1816 contributes to the interaction with FIXa. To evaluate FVIIIa stability, the FVIII/FV chimeras were activated by thrombin, and the decline in cofactor function was followed over time. FVIII/FV 1803–1810 and FVIII/FV 1811–1818 but not FVIII-N1810C showed a decreased FVIIIa half-life. However, when the FVIII variants were activated in presence of FIXa, only FVIII/FV 1811–1818 demonstrated an enhanced decline in cofactor function. Surface plasmon resonance analysis revealed that the FVIII variants K1813A/K1818A, E1811A, and F1816A exhibit enhanced dissociation after activation. The results together demonstrate that the glycan at 1810 is not involved in FVIII cofactor function, and that Phe-1816 of region 1811–1818 contributes to FIXa binding. Both regions 1803–1810 and 1811–1818 contribute to FVIIIa stability. PMID:23884417

  2. Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method

    DEFF Research Database (Denmark)

    Nielsen, Morten; Lundegaard, Claus; Lund, Ole

    2007-01-01

    by favoring binding registers with a minimum PFR length of two amino acids. Visualizing the binding motif as obtained by the SMM-align and TEPITOPE methods highlights a series of fundamental discrepancies between the two predicted motifs. For the DRB1*1302 allele for instance, the TEPITOPE method favors basic...... benchmark data set, and SMM-align prediction method (NetMHCII) are made publicly available....

  3. Role of hydrophobic mutations on the binding affinity and stability of blood coagulation factor VIIIa: a computational molecular dynamics and free-energy analysis.

    Science.gov (United States)

    Venkateswarlu, Divi

    2014-07-18

    Factor VIIIa is a non-covalently bound hetero-trimer among A1, A2 and A3-C1-C2 domains and an essential co-factor for factor IXa enzyme during proteolytic activation of factor X zymogen. The relatively weak interactions between A2 and the interface A1/A3 domains dampen the functional stability of FVIIIa in plasma and results in rapid degradation. We studied the mutational effect of three charged residues (Asp519, Glu665 and Asp666) to several hydrophobic residues by molecular dynamics simulations. Analysis of the binding free energy by MM-PBSA and MM-GBSA methods shows that the mutation of Asp519 and Glu665 residues to either Val or Ala enhance the A2 domain binding affinity in agreement with the experimental site-specific mutagenesis data. Mutation of Asp666 to Val, Tyr, Met and Phe showed largest improvement in the A2-domain binding among the eight hydrophobic mutants studied. Our studies suggest that the enrichment of hydrophobic interactions in the buried surface regions of A2 domain plays crucial role in improving the overall stability of FVIIIa. PMID:24952158

  4. Thermal Treatment of Iron Oxide Stabilized APC Residues from Waste Incineration and the Effect on Heavy Metal Binding

    DEFF Research Database (Denmark)

    Sørensen, Mette Abildgaard; Stackpoole, M.; Bender-Koch, C.;

    2000-01-01

    Iron oxide stabilized APC residues from MSWI were heat treated at 600°C and 900°C. The thermal treatments resulted in a change in product stability by forcing a transformation in the mineralogical structures of the products. The treatments, moreover, simulated somewhat the natural aging processes...

  5. The stability and the hydrological behavior of biological soil crusts is significantly affected by the complex nature of their polysaccharidic matrix

    Science.gov (United States)

    De Philippis, Roberto

    2015-04-01

    Biological crusts (BSCs) are complex microbial associations constituted by cells and microbial filaments embedded in a polysaccharidic matrix (EPS) that binds them together and with soil particles. EPSs of BSCs play a key role in structuring the soil and in affecting the hydrological processes taking place at the topsoil in desert environments. Recently, the amphiphilic nature of the EPSs, due to the contemporaneous presence in the macromolecules of hydrophilic and hydrophobic constituents, was put in relation with their capability to contribute to the structuring of the soil particles in BSCs and to hydrological behavior of the crusts. Indeed, in the EPSs the hydrophobicity due to the non-polar constituents (i.e. deoxysugars, ester-linked fatty acids, non polar aminoacids) was associated with the adhesion of the microbial cells to solid surfaces and to the clogging of micropores in the crusts. On the other hand, the hydrophilic constituents of the EPSs (i.e. acidic sugars, ketal-linked pyruvic acid, sulphate groups etc) were suggested to determine the final water content and distribution in the soil. The presence of BSCs facilitates the uptake of moisture from the atmosphere and at the same time contributes to enriching the soils with organic matter. In this lecture, the role of the EPSs in affecting the hydrological behavior of BSCs will be discussed by comparing the results obtained with natural and artificially induced BSCs also in relation with the texture of the soils. Furthermore, the contribution to the structuring of the soils of the polysaccharidic matrix of the crusts will be discussed moving from the different characteristics of two operationally-defined EPS fractions, the colloidal (C-EPS) and the EDTA extractable (tightly bound, TB-EPS) fractions. In BSCs, C-EPSs are loosely bound to cells and sediments while TB-EPSs are tightly bound to the crustal biotic and abiotic constituents of the crusts. The results obtained in a recent study suggest that the

  6. Alteration of tropomyosin-binding properties of tropomodulin-1 affects its capping ability and localization in skeletal myocytes.

    Science.gov (United States)

    Moroz, Natalia A; Novak, Stefanie M; Azevedo, Ricardo; Colpan, Mert; Uversky, Vladimir N; Gregorio, Carol C; Kostyukova, Alla S

    2013-02-15

    Tropomodulin (Tmod) is an actin-capping protein that binds to the two tropomyosins (TM) at the pointed end of the actin filament to prevent further actin polymerization and depolymerization. Therefore, understanding the role of Tmod is very important when studying actin filament dependent processes such as muscle contraction and intracellular transport. The capping ability of Tmod is highly influenced by TM and is 1000-fold greater in the presence of TM. There are four Tmod isoforms (Tmod1-4), three of which, Tmod1, Tmod3, and Tmod4, are expressed in skeletal muscles. The affinity of Tmod1 to skeletal striated TM (stTM) is higher than that of Tmod3 and Tmod4 to stTM. In this study, we tested mutations in the TM-binding sites of Tmod1, using circular dichroism (CD) and prediction analysis (PONDR). The mutations R11K, D12N, and Q144K were chosen because they decreased the affinity of Tmod1 to stTM, making it similar to that of affinity of Tmod3 and Tmod4 to stTM. Significant reduction of inhibition of actin pointed-end polymerization in the presence of stTM was shown for Tmod1 (R11K/D12N/Q144K) as compared with WT Tmod1. When GFP-Tmod1 and mutants were expressed in primary chicken skeletal myocytes, decreased assembly of Tmod1 mutants was revealed. This indicates a direct correlation between TM-binding and the actin-capping abilities of Tmod. Our data confirmed the hypothesis that assembly of Tmod at the pointed-end of the actin filament depends on its TM-binding affinity.

  7. The N-terminal cellulose-binding domain of EGXA increases thermal stability of xylanase and changes its specific activities on different substrates

    Institute of Scientific and Technical Information of China (English)

    Ming Ding; Yigang Teng; Qiuyu Yin; Jie Zhao; Fukun Zhao

    2008-01-01

    A full-length EGXA enzyme from a mollusk, Ampullaria crossean, was cloned into pFastBac vector and then heterogeneously expressed in insect Tn5 cells. Its natural N-terminal signal peptide worked well in the insect Tn5 cells.The recombinant EGXA was a 63 kDa protein and had active endo-β-1,4-glucanase (EC 3.2.1.4) and endo-β-1,4-xylanase (EC 3.2.1.8). The specific activity of endo-β-1,4-xylanase was higher than in the EGX, which was purified from the stomach tissues of Ampullaria crossen. The N-terminal cellulosebinding domain of EGXA made it bind to cellulose and xylan more efficiently. This cellulose-binding domain also increased the thermal stability of this recombinant enzyme and decreased the recombinant EGXA's specific activities on p-nitrophenyi-β-D-cellobioside and sodium carboxymethyl cellulose.

  8. The kinesin-13 KLP10A motor regulates oocyte spindle length and affects EB1 binding without altering microtubule growth rates

    Directory of Open Access Journals (Sweden)

    Kevin K. Do

    2014-06-01

    Full Text Available Kinesin-13 motors are unusual in that they do not walk along microtubules, but instead diffuse to the ends, where they remove tubulin dimers, regulating microtubule dynamics. Here we show that Drosophila kinesin-13 klp10A regulates oocyte meiosis I spindle length and is haplo-insufficient – KLP10A, reduced by RNAi or a loss-of-function P element insertion mutant, results in elongated and mispositioned oocyte spindles, and abnormal cortical microtubule asters and aggregates. KLP10A knockdown by RNAi does not significantly affect microtubule growth rates in oocyte spindles, but, unexpectedly, EB1 binding and unbinding are slowed, suggesting a previously unobserved role for kinesin-13 in mediating EB1 binding interactions with microtubules. Kinesin-13 may regulate spindle length both by disassembling subunits from microtubule ends and facilitating EB1 binding to plus ends. We also observe an increased number of paused microtubules in klp10A RNAi knockdown spindles, consistent with a reduced frequency of microtubule catastrophes. Overall, our findings indicate that reduced kinesin-13 decreases microtubule disassembly rates and affects EB1 interactions with microtubules, rather than altering microtubule growth rates, causing spindles to elongate and abnormal cortical microtubule asters and aggregates to form.

  9. A loose domain swapping organization confers a remarkable stability to the dimeric structure of the arginine binding protein from Thermotoga maritima.

    Directory of Open Access Journals (Sweden)

    Alessia Ruggiero

    Full Text Available The arginine binding protein from Thermatoga maritima (TmArgBP, a substrate binding protein (SBP involved in the ABC system of solute transport, presents a number of remarkable properties. These include an extraordinary stability to temperature and chemical denaturants and the tendency to form multimeric structures, an uncommon feature among SBPs involved in solute transport. Here we report a biophysical and structural characterization of the TmArgBP dimer. Our data indicate that the dimer of the protein is endowed with a remarkable stability since its full dissociation requires high temperature as well as SDS and urea at high concentrations. In order to elucidate the atomic level structural properties of this intriguing protein, we determined the crystallographic structures of the apo and the arginine-bound forms of TmArgBP using MAD and SAD methods, respectively. The comparison of the liganded and unliganded models demonstrates that TmArgBP tertiary structure undergoes a very large structural re-organization upon arginine binding. This transition follows the Venus Fly-trap mechanism, although the entity of the re-organization observed in TmArgBP is larger than that observed in homologous proteins. Intriguingly, TmArgBP dimerizes through the swapping of the C-terminal helix. This dimer is stabilized exclusively by the interactions established by the swapping helix. Therefore, the TmArgBP dimer combines a high level of stability and conformational freedom. The structure of the TmArgBP dimer represents an uncommon example of large tertiary structure variations amplified at quaternary structure level by domain swapping. Although the biological relevance of the dimer needs further assessments, molecular modelling suggests that the two TmArgBP subunits may simultaneously interact with two distinct ABC transporters. Moreover, the present protein structures provide some clues about the determinants of the extraordinary stability of the biomolecule

  10. A binding-site barrier affects imaging efficiency of high affinity amyloid-reactive peptide radiotracers in vivo.

    Directory of Open Access Journals (Sweden)

    Jonathan S Wall

    Full Text Available Amyloid is a complex pathology associated with a growing number of diseases including Alzheimer's disease, type 2 diabetes, rheumatoid arthritis, and myeloma. The distribution and extent of amyloid deposition in body organs establishes the prognosis and can define treatment options; therefore, determining the amyloid load by using non-invasive molecular imaging is clinically important. We have identified a heparin-binding peptide designated p5 that, when radioiodinated, was capable of selectively imaging systemic visceral AA amyloidosis in a murine model of the disease. The p5 peptide was posited to bind effectively to amyloid deposits, relative to similarly charged polybasic heparin-reactive peptides, because it adopted a polar α helix secondary structure. We have now synthesized a variant, p5R, in which the 8 lysine amino acids of p5 have been replaced with arginine residues predisposing the peptide toward the α helical conformation in an effort to enhance the reactivity of the peptide with the amyloid substrate. The p5R peptide had higher affinity for amyloid and visualized AA amyloid in mice by using SPECT/CT imaging; however, the microdistribution, as evidenced in micro-autoradiographs, was dramatically altered relative to the p5 peptide due to its increased affinity and a resultant "binding site barrier" effect. These data suggest that radioiodinated peptide p5R may be optimal for the in vivo detection of discreet, perivascular amyloid, as found in the brain and pancreatic vasculature, by using molecular imaging techniques; however, peptide p5, due to its increased penetration, may yield more quantitative imaging of expansive tissue amyloid deposits.

  11. Genetic stability of murine pluripotent and somatic hybrid cells may be affected by conditions of their cultivation.

    Science.gov (United States)

    Ivanovna, Shramova Elena; Alekseevich, Larionov Oleg; Mikhailovich, Khodarovich Yurii; Vladimirovna, Zatsepina Olga

    2011-01-01

    Using mouse pluripotent teratocarcinoma PCC4azal cells and proliferating spleen lymphocytes we obtained a new type of hybrids, in which marker lymphocyte genes were suppressed, but expression the Oct-4 gene was not effected; the hybrid cells were able to differentiate to cardiomyocytes. In order to specify the environmental factors which may affect the genetic stability and other hybrid properties, we analyzed the total chromosome number and differentiation potencies of hybrids respectively to conditions of their cultivation. Particular attention was paid to the number and transcription activity of chromosomal nucleolus organizing regions (NORs), which harbor the most actively transcribed - ribosomal - genes. The results showed that the hybrids obtained are characterized by a relatively stable chromosome number which diminished less than in 5% during 27 passages. However, a long-term cultivation of hybrid cells in non-selective conditions resulted in preferential elimination of some NO- chromosomes, whereas the number of active NORs per cell was increased due to activation of latent NORs. On the contrary, in selective conditions, i.e. in the presence of hypoxantine, aminopterin and thymidine, the total number of NOR-bearing chromosomes was not changed, but a partial inactivation of remaining NORs was observed. The higher number of active NORs directly correlated with the capability of hybrid cells for differentiation to cardiomyocytes.

  12. An inverted repeat motif stabilizes binding of E2F and enhances transcription of the dihydrofolate reductase gene

    DEFF Research Database (Denmark)

    Wade, M; Blake, M C; Jambou, R C;

    1995-01-01

    An overlapping inverted repeat sequence that binds the eukaryotic transcription factor E2F is 100% conserved near the major transcription start sites in the promoters of three mammalian genes encoding dihydrofolate reductase, and is also found in the promoters of several other important cellular ...

  13. Role of cysteines in the stability and DNA-binding activity of the hypochlorite-specific transcription factor HypT.

    Directory of Open Access Journals (Sweden)

    Adrian Drazic

    Full Text Available Reactive oxygen species are important components of the immune response. Hypochlorite (HOCl is produced by neutrophils to kill invading microorganisms. The bactericidal activity of HOCl is due to proteome-wide unfolding and oxidation of proteins at cysteine and methionine residues. Escherichia coli cells are protected from HOCl-killing by the previously identified dodecameric transcription factor HypT (YjiE. Here, we aimed to unravel whether HOCl activates HypT directly or via a reaction product of HOCl with a cellular component. Bacterial viability assays and analysis of target gene regulation indicate that HypT is highly specific to activation by HOCl and that no reaction products of HOCl such as monochloramine, hydroxyl radicals, or methionine sulfoxide activate HypT in vivo. Surprisingly, purified HypT lost its DNA-binding activity upon incubation with HOCl or reaction products that oxidize HypT to form a disulfide-linked dimer, and regained DNA-binding activity upon reduction. Thus, we postulate that the cysteines in HypT contribute to control the DNA-binding activity of HypT in vitro. HypT contains five cysteine residues; a HypT mutant with all cysteines substituted by serine is aggregation-prone and forms tetramers in addition to the typical dodecamers. Using single and multiple cysteine-to-serine mutants, we identified Cys150 to be required for stability and Cys4 being important for oligomerization of HypT to dodecamers. Further, oxidation of Cys4 is responsible for the loss of DNA-binding of HypT upon oxidation in vitro. It appears that Cys4 oxidation upon conditions that are insufficient to stimulate the DNA-binding activity of HypT prevents unproductive interactions of HypT with DNA. Thus, Cys4 oxidation may be a check point in the activation process of HypT.

  14. Steroid hormones affect binding of the sigma ligand 11C-SA4503 in tumour cells and tumour-bearing rats

    International Nuclear Information System (INIS)

    Sigma receptors are implicated in memory and cognitive functions, drug addiction, depression and schizophrenia. In addition, sigma receptors are strongly overexpressed in many tumours. Although the natural ligands are still unknown, steroid hormones are potential candidates. Here, we examined changes in binding of the sigma-1 agonist 11C-SA4503 in C6 glioma cells and in living rats after modification of endogenous steroid levels. 11C-SA4503 binding was assessed in C6 monolayers by gamma counting and in anaesthetized rats by microPET scanning. C6 cells were either repeatedly washed and incubated in steroid-free medium or exposed to five kinds of exogenous steroids (1 h or 5 min before tracer addition, respectively). Tumour-bearing male rats were repeatedly treated with pentobarbital (a condition known to result in reduction of endogenous steroid levels) or injected with progesterone. Binding of 11C-SA4503 to C6 cells was increased (∝50%) upon removal and decreased (∝60%) upon addition of steroid hormones (rank order of potency: progesterone > allopregnanolone = testosterone = androstanolone > dehydroepiandrosterone-3-sulphate, IC50 progesterone 33 nM). Intraperitoneally administered progesterone reduced tumour uptake and tumour-to-muscle contrast (36%). Repeated treatment of animals with pentobarbital increased the PET standardized uptake value of 11C-SA4503 in tumour (16%) and brain (27%), whereas the kinetics of blood pool radioactivity was unaffected. The binding of 11C-SA4503 is sensitive to steroid competition. Since not only increases but also decreases of steroid levels affect ligand binding, a considerable fraction of the sigma-1 receptor population in cultured tumour cells or tumour-bearing animals is normally occupied by endogenous steroids. (orig.)

  15. Steroid hormones affect binding of the sigma ligand {sup 11}C-SA4503 in tumour cells and tumour-bearing rats

    Energy Technology Data Exchange (ETDEWEB)

    Rybczynska, Anna A.; Elsinga, Philip H.; Sijbesma, Jurgen W.; Jong, Johan R. de; Vries, Erik F. de; Dierckx, Rudi A.; Waarde, Aren van [University of Groningen, Nuclear Medicine and Molecular Imaging, University of Groningen Medical Center, Groningen (Netherlands); Ishiwata, Kiichi [Tokyo Metropolitan Institute of Gerontology, Positron Medical Center, Tokyo (Japan)

    2009-07-15

    Sigma receptors are implicated in memory and cognitive functions, drug addiction, depression and schizophrenia. In addition, sigma receptors are strongly overexpressed in many tumours. Although the natural ligands are still unknown, steroid hormones are potential candidates. Here, we examined changes in binding of the sigma-1 agonist {sup 11}C-SA4503 in C6 glioma cells and in living rats after modification of endogenous steroid levels. {sup 11}C-SA4503 binding was assessed in C6 monolayers by gamma counting and in anaesthetized rats by microPET scanning. C6 cells were either repeatedly washed and incubated in steroid-free medium or exposed to five kinds of exogenous steroids (1 h or 5 min before tracer addition, respectively). Tumour-bearing male rats were repeatedly treated with pentobarbital (a condition known to result in reduction of endogenous steroid levels) or injected with progesterone. Binding of {sup 11}C-SA4503 to C6 cells was increased ({proportional_to}50%) upon removal and decreased ({proportional_to}60%) upon addition of steroid hormones (rank order of potency: progesterone > allopregnanolone = testosterone = androstanolone > dehydroepiandrosterone-3-sulphate, IC{sub 50} progesterone 33 nM). Intraperitoneally administered progesterone reduced tumour uptake and tumour-to-muscle contrast (36%). Repeated treatment of animals with pentobarbital increased the PET standardized uptake value of {sup 11}C-SA4503 in tumour (16%) and brain (27%), whereas the kinetics of blood pool radioactivity was unaffected. The binding of {sup 11}C-SA4503 is sensitive to steroid competition. Since not only increases but also decreases of steroid levels affect ligand binding, a considerable fraction of the sigma-1 receptor population in cultured tumour cells or tumour-bearing animals is normally occupied by endogenous steroids. (orig.)

  16. MAP1B binds to the NMDA receptor subunit NR3A and affects NR3A protein concentrations

    DEFF Research Database (Denmark)

    Eriksson, Maria; Samuelsson, Helena; Björklund, Stefan;

    2010-01-01

    protein interaction between NR3A and microtubule associated-protein (MAP) 1B, which both are localized to dendritic shafts and filopodia. NR3A protein levels were increased in MAP1B deficient (-/-) mice, with a corresponding decrease in NR1 levels, but the fraction of filopodia immunoreactive for NR3A was...... equal in cells from -/- and wild type (WT) mice. NR3A has previously been shown to interact with another member of the MAP1 family, MAP1S. We showed that MAP1S binds to microtubules in a similar manner as MAP1B, and suggest that MAP1S and MAP1B both are involved in regulating trafficking of NR3A...

  17. Novel C3 mutation p.Lys65Gln in aHUS affects complement factor H binding.

    NARCIS (Netherlands)

    Volokhina, E.; Westra, D.; Xue, X.; Gros, P.; Kar, N.C. van de; Heuvel, L.P. van den

    2012-01-01

    BACKGROUND: Atypical hemolytic uremic syndrome (aHUS) is associated with mutations affecting complement proteins and regulators and with autoantibodies against complement factor H (CFH). Approximately half of the aHUS patients progress to end-stage renal disease. DNA analysis of the risk factor gene

  18. Novel C3 mutation p.Lys65Gln in aHUS affects complement factor H binding

    NARCIS (Netherlands)

    Volokhina, E.B.; Westra, D.; Xue, X; Gros, P.; van der Kar, N.C.A.J.; van den Heuvel, L.

    2012-01-01

    Background Atypical hemolytic uremic syndrome (aHUS) is associated with mutations affecting complement proteins and regulators and with autoantibodies against complement factor H (CFH). Approximately half of the aHUS patients progress to end-stage renal disease. DNA analysis of the risk factor genes

  19. Microwave-Assisted Synthesis of Arene Ru(II Complexes Induce Tumor Cell Apoptosis Through Selectively Binding and Stabilizing bcl-2 G-Quadruplex DNA

    Directory of Open Access Journals (Sweden)

    Yanhua Chen

    2016-05-01

    Full Text Available A series of arene Ru(II complexes coordinated with phenanthroimidazole derivatives, [(η6-C6H6Ru(lCl]Cl(1b L = p-ClPIP = 2-(4-Chlorophenylimidazole[4,5f] 1,10-phenanthroline; 2b L = m-ClPIP = 2-(3-Chlorophenylimidazole[4,5f] 1,10-phenanthroline; 3b L = p-NPIP = 2-(4-Nitrophenylimidazole[4,5f] 1,10-phenanthroline; 4b L = m-NPIP = 2-(3-Nitrophenyl imidazole [4,5f] 1,10-phenanthroline were synthesized in yields of 89.9%–92.7% under conditions of microwave irradiation heating for 30 min to liberate four arene Ru(II complexes (1b, 2b, 3b, 4b. The anti-tumor activity of 1b against various tumor cells was evaluated by MTT assay. The results indicated that this complex blocked the growth of human lung adenocarcinoma A549 cells with an IC50 of 16.59 μM. Flow cytometric analysis showed that apoptosis of A549 cells was observed following treatment with 1b. Furthermore, the in vitro DNA-binding behaviors that were confirmed by spectroscopy indicated that 1b could selectively bind and stabilize bcl-2 G-quadruplex DNA to induce apoptosis of A549 cells. Therefore, the synthesized 1b has impressive bcl-2 G-quadruplex DNA-binding and stabilizing activities with potential applications in cancer chemotherapy.

  20. How Hinge Positioning in Cross-Country Ski Bindings Affect Exercise Efficiency, Cycle Characteristics and Muscle Coordination during Submaximal Roller Skiing.

    Directory of Open Access Journals (Sweden)

    Conor M Bolger

    Full Text Available The purposes of the current study were to 1 test if the hinge position in the binding of skating skis has an effect on gross efficiency or cycle characteristics and 2 investigate whether hinge positioning affects synergistic components of the muscle activation in six lower leg muscles. Eleven male skiers performed three 4-min sessions at moderate intensity while cross-country ski-skating and using a klapskate binding. Three different positions were tested for the binding's hinge, ranging from the front of the first distal phalange to the metatarsal-phalangeal joint. Gross efficiency and cycle characteristics were determined, and the electromyographic (EMG signals of six lower limb muscles were collected. EMG signals were wavelet transformed, normalized, joined into a multi-dimensional vector, and submitted to a principle component analysis (PCA. Our results did not reveal any changes to gross efficiency or cycle characteristics when altering the hinge position. However, our EMG analysis found small but significant effects of hinge positioning on muscle coordinative patterns (P < 0.05. The changed patterns in muscle activation are in alignment with previously described mechanisms that explain the effects of hinge positioning in speed-skating klapskates. Finally, the within-subject results of the EMG analysis suggested that in addition to the between-subject effects, further forms of muscle coordination patterns appear to be employed by some, but not all participants.

  1. How Hinge Positioning in Cross-Country Ski Bindings Affect Exercise Efficiency, Cycle Characteristics and Muscle Coordination during Submaximal Roller Skiing.

    Science.gov (United States)

    Bolger, Conor M; Sandbakk, Øyvind; Ettema, Gertjan; Federolf, Peter

    2016-01-01

    The purposes of the current study were to 1) test if the hinge position in the binding of skating skis has an effect on gross efficiency or cycle characteristics and 2) investigate whether hinge positioning affects synergistic components of the muscle activation in six lower leg muscles. Eleven male skiers performed three 4-min sessions at moderate intensity while cross-country ski-skating and using a klapskate binding. Three different positions were tested for the binding's hinge, ranging from the front of the first distal phalange to the metatarsal-phalangeal joint. Gross efficiency and cycle characteristics were determined, and the electromyographic (EMG) signals of six lower limb muscles were collected. EMG signals were wavelet transformed, normalized, joined into a multi-dimensional vector, and submitted to a principle component analysis (PCA). Our results did not reveal any changes to gross efficiency or cycle characteristics when altering the hinge position. However, our EMG analysis found small but significant effects of hinge positioning on muscle coordinative patterns (P < 0.05). The changed patterns in muscle activation are in alignment with previously described mechanisms that explain the effects of hinge positioning in speed-skating klapskates. Finally, the within-subject results of the EMG analysis suggested that in addition to the between-subject effects, further forms of muscle coordination patterns appear to be employed by some, but not all participants.

  2. Insight into factors affecting the presence, degree, and temporal stability of fluorescence intensification on ZnO nanorod ends

    Science.gov (United States)

    Singh, Manpreet; Jiang, Ruibin; Coia, Heidi; Choi, Daniel S.; Alabanza, Anginelle; Chang, Jae Young; Wang, Jianfang; Hahm, Jong-In

    2015-01-01

    We have carried out a combined experimental and simulation study identifying the key physical and optical parameters affecting the presence and degree of fluorescence intensification measured on zinc oxide nanorod (ZnO NR) ends. Previously, we reported on the highly localized, intensified, and prolonged fluorescence signal measured on the NR ends, termed fluorescence intensification on NR ends (FINE). As a step towards understanding the mechanism of FINE, the present study aims to provide insight into the unique optical phenomenon of FINE through experimental and simulation approaches and to elucidate the key factors affecting the occurrence, degree, and temporal stability of FINE. Specifically, we examined the effect of the length, width, and growth orientation of single ZnO NRs on the NR-enhanced biomolecular emission profile after decorating the NR surfaces with different amounts and types of fluorophore-coupled protein molecules. We quantitatively and qualitatively profiled the biomolecular fluorescence signal from individual ZnO NRs as a function of both position along the NR long axis and time. Regardless of the physical dimensions and growth orientations of the NRs, we confirmed the presence of FINE in all ZnO NRs tested by using a range of protein concentrations. We also showed that the manifestation of FINE is not dependent on the spectroscopic signatures of the fluorophores employed. We further observed that the degree of FINE is dependent on the length of the NR with longer NRs showing increased levels of FINE. We also demonstrated that vertically oriented NRs exhibit much stronger fluorescence intensity at the NR ends and a higher level of FINE than the laterally oriented NRs. Additionally, we employed finite-difference time-domain (FDTD) methods to understand the experimental outcomes and to promote our understanding of the mechanism of FINE. Particularly, we utilized the electrodynamic simulations to examine both near-field and far-field emission

  3. Expression, protein stability and transcriptional activity of retinoic acid receptors are affected by microtubules interfering agents and all-trans retinoic acid in primary rat hepatocytes

    OpenAIRE

    2007-01-01

    Expression, protein stability and transcriptional activity of retinoic acid receptors are affected by microtubules interfering agents and all-trans retinoic acid in primary rat hepatocytes CZECH REPUBLIC (Dvorak, Zdenek) CZECH REPUBLIC Received: 2006-08-22 Revised: 2006-11-16 Accepted: 2007-01-02

  4. Pin1-mediated Sp1 phosphorylation by CDK1 increases Sp1 stability and decreases its DNA-binding activity during mitosis.

    Science.gov (United States)

    Yang, Hang-Che; Chuang, Jian-Ying; Jeng, Wen-Yih; Liu, Chia-I; Wang, Andrew H-J; Lu, Pei-Jung; Chang, Wen-Chang; Hung, Jan-Jong

    2014-12-16

    We have shown that Sp1 phosphorylation at Thr739 decreases its DNA-binding activity. In this study, we found that phosphorylation of Sp1 at Thr739 alone is necessary, but not sufficient for the inhibition of its DNA-binding activity during mitosis. We demonstrated that Pin1 could be recruited to the Thr739(p)-Pro motif of Sp1 to modulate the interaction between phospho-Sp1 and CDK1, thereby facilitating CDK1-mediated phosphorylation of Sp1 at Ser720, Thr723 and Thr737 during mitosis. Loss of the C-terminal end of Sp1 (amino acids 741-785) significantly increased Sp1 phosphorylation, implying that the C-terminus inhibits CDK1-mediated Sp1 phosphorylation. Binding analysis of Sp1 peptides to Pin1 by isothermal titration calorimetry indicated that Pin1 interacts with Thr739(p)-Sp1 peptide but not with Thr739-Sp1 peptide. X-ray crystallography data showed that the Thr739(p)-Sp1 peptide occupies the active site of Pin1. Increased Sp1 phosphorylation by CDK1 during mitosis not only stabilized Sp1 levels by decreasing interaction with ubiquitin E3-ligase RNF4 but also caused Sp1 to move out of the chromosomes completely by decreasing its DNA-binding activity, thereby facilitating cell cycle progression. Thus, Pin1-mediated conformational changes in the C-terminal region of Sp1 are critical for increased CDK1-mediated Sp1 phosphorylation to facilitate cell cycle progression during mitosis.

  5. Nucleobases bind to and stabilize aggregates of a prebiotic amphiphile, providing a viable mechanism for the emergence of protocells

    OpenAIRE

    Black, RA; Blosser, MC; Stottrup, BL; Tavakley, R; Deamer, DW; Keller, SL

    2013-01-01

    Primordial cells presumably combined RNAs, which functioned as catalysts and carriers of genetic information, with an encapsulating membrane of aggregated amphiphilic molecules. Major questions regarding this hypothesis include how the four bases and the sugar in RNA were selected from a mixture of prebiotic compounds and colocalized with such membranes, and how the membranes were stabilized against flocculation in salt water. To address these questions, we explored the possibility that aggre...

  6. Aromatic Amino Acid Mutagenesis at the Substrate Binding Pocket of Yarrowia lipolytica Lipase Lip2 Affects Its Activity and Thermostability

    Directory of Open Access Journals (Sweden)

    Guilong Wang

    2014-01-01

    Full Text Available The lipase2 from Yarrowia lipolytica (YLLip2 is a yeast lipase exhibiting high homologous to filamentous fungal lipase family. Though its crystal structure has been resolved, its structure-function relationship has rarely been reported. By contrast, there are two amino acid residues (V94 and I100 with significant difference in the substrate binding pocket of YLLip2; they were subjected to site-directed mutagenesis (SDM to introduce aromatic amino acid mutations. Two mutants (V94W and I100F were created. The enzymatic properties of the mutant lipases were detected and compared with the wild-type. The activities of mutant enzymes dropped to some extent towards p-nitrophenyl palmitate (pNPC16 and their optimum temperature was 35°C, which was 5°C lower than that of the wild-type. However, the thermostability of I100F increased 22.44% after incubation for 1 h at 40°C and its optimum substrate shifted from p-nitrophenyl laurate (pNPC12 to p-nitrophenyl caprate (pNPC10. The above results demonstrated that the two substituted amino acid residuals have close relationship with such enzymatic properties as thermostability and substrate selectivity.

  7. Midbrain serotonin transporter binding potential measured with [11C]DASB is affected by serotonin transporter genotype

    International Nuclear Information System (INIS)

    Homozygote carriers of two long (L) alleles of the serotonin transporter (5-HTT) regulatory region displayed in vitro a twofold increase in 5-HTT expression compared with carriers of one or two short (S) alleles. However, in vivo imaging studies yielded contradictory results. Recently, an A > G exchange leading to differential transcriptional activation of 5-HTT mRNA in lymphobalstoid cell lines was discovered in the 5-HTT regulatory region. In vitro and in vivo evidence suggests that [11C]DASB, a new 5-HTT ligand offers some advantages over the ligands used in previous studies in measuring 5-HTT density independent of synaptic levels of serotonin. We assessed 5-HTT binding potential (BP 2) in the midbrain of 19 healthy subjects with positron emission tomography and [11C]DASB. Accounting for the hypothesized functional similarity of LG and S in driving 5-HTT transcription, we assessed whether LALA homozygotes display increased midbrain BP2 compared with carriers of at least one S allele. BP2 in the midbrain was significantly increased in LALA homozygotes compared with carriers of at least one S allele. Interestingly, the genotype effect on the midbrain was significantly different from that on the thalamus and the amygdala where no group differences were detected. This in vivo study provides further evidence that subjects homozygous for the LA allele display increased expression of 5-HTT in the midbrain, the origin of central serotonergic projections. (author)

  8. HUMAN LIVER FATTY ACID BINDING PROTEIN (L-FABP) T94A VARIANT ALTERS STRUCTURE, STABILITY, AND INTERACTION WITH FIBRATES

    OpenAIRE

    Martin, Gregory G.; McIntosh, Avery L.; Huang, Huan; Gupta, Shipra; Atshaves, Barbara P.; Landrock, Kerstin K.; Landrock, Danilo; Kier, Ann B.; Schroeder, Friedhelm

    2013-01-01

    Although the human L-FABP T94A variant arises from the most commonly occurring SNP in the entire FABP family, there is a complete lack of understanding regarding the role of this polymorphism in human disease. It has been hypothesized that the T94A substitution results in complete loss of ligand binding ability and function analogous to L-FABP gene ablation. This possibility was addressed using recombinant human WT T94T and T94A variant L-FABP and cultured primary human hepatocytes. Non-conse...

  9. How do how internal and external processes affect the behaviors of coupled marsh mudflat systems; infill, stabilize, retreat, or drown?

    Science.gov (United States)

    Carr, J. A.; Mariotti, G.; Wiberg, P.; Fagherazzi, S.; McGlathery, K.

    2013-12-01

    an eventual lateral equilibrium are possible only with large allochthonous sediment supply. Once marshes expanded, marsh retreat can be prevented by a sediment supply smaller than the one that filled the basin. At the GCE, the Altamaha River allows for enhanced allochthonous supply directly to the salt marsh platform, reducing the importance of waves on the tidal flat. As a result, infilling or retreat become the prevalent behaviors. For the VCR, the presence of seagrass decreases near bed shear stresses and sediment flux to the salt marsh platform, however, seagrass also reduces the wave energy acting on the boundary of the marsh reducing boundary erosion. Results indicate that the reduction in wave power allows for seagrass to provide a strong stabilizing affect on the coupled salt marsh tidal flat system, but as external sediment supply increases and light conditions decline the system reverts to that of a bare tidal flat. Across all systems and with current rates of sea level rise, retreat is a more likely marsh loss modality than drowning.

  10. Insulin-like growth factor binding protein-3 affects osteogenic efficacy on dental implants in rat mandible

    International Nuclear Information System (INIS)

    Insulin like growth factor binding protein-3 (IGFBP-3) in bone cells and its utilization in dental implants have not been well studied. The aim of this study was to determine the osteogenic efficacy of chitosan gold nanoparticles (Ch-GNPs) conjugated with IGFBP-3 coated titanium (Ti) implants. Ch-GNPs were conjugated with IGFBP-3 plasmid DNA through a coacervation process. Conjugation was cast over Ti surfaces, and cells were seeded on coated surfaces. For in vitro analysis the expression of different proteins was analyzed by immunoblotting. For in vivo analysis, Ch-GNP/IGFBP-3 coated implants were installed in rat mandibles. Four weeks post-implantation, mandibles were examined by microcomputed tomography (μCT), immunohistochemistry, hematoxylin & eosin and tartrate resistance acid phosphatase staining. In vitro overexpressed Ch-GNP/IGFBP-3 coated Ti surfaces was associated with activation of extracellular signal related kinase (ERK), inhibition of the stress activated protein c-Jun N-terminal kinase (JNK) and enhanced bone morphogenetic protein (BMP)-2 and 7 compared to control. Further, in vivo, Ch-GNP/IGFBP-3 coated implants were associated with inhibition of implant induced osteoclastogenesis molecules, receptor activator of nuclear factor kappa-B ligand (RANKL) and enhanced expression of osteogenic molecules including BMP2/7 and osteopontin (OPN). The μCT analysis demonstrated that IGFBP-3 increased the volume of newly formed bone surrounding the implants compared to control (n = 5; p < 0.05). These results support the view that IGFBP-3 overexpression diminishes osteoclastogenesis and enhances osteogenesis of Ti implants, and can serve as a potent molecule for the development of good implantation. - Highlights: • Chitosan gold nanoparticles were conjugated with IGFBP-3 and coated onto surface of the titanium implants for gene delivery to bone. • Implants were inserted in rat mandible for 4 weeks. • Parameters studied: histopathology and radiology.

  11. Insulin-like growth factor binding protein-3 affects osteogenic efficacy on dental implants in rat mandible

    Energy Technology Data Exchange (ETDEWEB)

    Bhattarai, Govinda; Lee, Young-Hee [Department of Oral Biochemistry, Institute of Oral Bioscience, School of Dentistry, Chonbuk National University, Jeonju (Korea, Republic of); Lee, Min-Ho [Department of Dental Materials, Institute of Oral Bioscience, School of Dentistry, Chonbuk National University, Jeonju (Korea, Republic of); Park, Il-Song [Division of Advanced Materials Engineering, Research Center for Advanced Materials, Development and Institute of Biodegradable Materials, Chonbuk National University, Jeonju 561-756 (Korea, Republic of); Yi, Ho-Keun, E-mail: yihokn@chonbuk.ac.kr [Department of Oral Biochemistry, Institute of Oral Bioscience, School of Dentistry, Chonbuk National University, Jeonju (Korea, Republic of)

    2015-10-01

    Insulin like growth factor binding protein-3 (IGFBP-3) in bone cells and its utilization in dental implants have not been well studied. The aim of this study was to determine the osteogenic efficacy of chitosan gold nanoparticles (Ch-GNPs) conjugated with IGFBP-3 coated titanium (Ti) implants. Ch-GNPs were conjugated with IGFBP-3 plasmid DNA through a coacervation process. Conjugation was cast over Ti surfaces, and cells were seeded on coated surfaces. For in vitro analysis the expression of different proteins was analyzed by immunoblotting. For in vivo analysis, Ch-GNP/IGFBP-3 coated implants were installed in rat mandibles. Four weeks post-implantation, mandibles were examined by microcomputed tomography (μCT), immunohistochemistry, hematoxylin & eosin and tartrate resistance acid phosphatase staining. In vitro overexpressed Ch-GNP/IGFBP-3 coated Ti surfaces was associated with activation of extracellular signal related kinase (ERK), inhibition of the stress activated protein c-Jun N-terminal kinase (JNK) and enhanced bone morphogenetic protein (BMP)-2 and 7 compared to control. Further, in vivo, Ch-GNP/IGFBP-3 coated implants were associated with inhibition of implant induced osteoclastogenesis molecules, receptor activator of nuclear factor kappa-B ligand (RANKL) and enhanced expression of osteogenic molecules including BMP2/7 and osteopontin (OPN). The μCT analysis demonstrated that IGFBP-3 increased the volume of newly formed bone surrounding the implants compared to control (n = 5; p < 0.05). These results support the view that IGFBP-3 overexpression diminishes osteoclastogenesis and enhances osteogenesis of Ti implants, and can serve as a potent molecule for the development of good implantation. - Highlights: • Chitosan gold nanoparticles were conjugated with IGFBP-3 and coated onto surface of the titanium implants for gene delivery to bone. • Implants were inserted in rat mandible for 4 weeks. • Parameters studied: histopathology and radiology.

  12. Mutations in the DNA-binding domain of NR2E3 affect in vivo dimerization and interaction with CRX.

    Directory of Open Access Journals (Sweden)

    Raphael Roduit

    Full Text Available BACKGROUND: NR2E3 (PNR is an orphan nuclear receptor essential for proper photoreceptor determination and differentiation. In humans, mutations in NR2E3 have been associated with the recessively inherited enhanced short wavelength sensitive (S- cone syndrome (ESCS and, more recently, with autosomal dominant retinitis pigmentosa (adRP. NR2E3 acts as a suppressor of the cone generation program in late mitotic retinal progenitor cells. In adult rod photoreceptors, NR2E3 represses cone-specific gene expression and acts in concert with the transcription factors CRX and NRL to activate rod-specific genes. NR2E3 and CRX have been shown to physically interact in vitro through their respective DNA-binding domains (DBD. The DBD also contributes to homo- and heterodimerization of nuclear receptors. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed NR2E3 homodimerization and NR2E3/CRX complex formation in an in vivo situation by Bioluminescence Resonance Energy Transfer (BRET(2. NR2E3 wild-type protein formed homodimers in transiently transfected HEK293T cells. NR2E3 homodimerization was impaired in presence of disease-causing mutations in the DBD, except for the p.R76Q and p.R104W mutant proteins. Strikingly, the adRP-linked p.G56R mutant protein interacted with CRX with a similar efficiency to that of NR2E3 wild-type and p.R311Q proteins. In contrast, all other NR2E3 DBD-mutant proteins did not interact with CRX. The p.G56R mutant protein was also more effective in abolishing the potentiation of rhodospin gene transactivation by the NR2E3 wild-type protein. In addition, the p.G56R mutant enhanced the transrepression of the M- and S-opsin promoter, while all other NR2E3 DBD-mutants did not. CONCLUSIONS/SIGNIFICANCE: These results suggest different disease mechanisms in adRP- and ESCS-patients carrying NR2E3 mutations. Titration of CRX by the p.G56R mutant protein acting as a repressor in trans may account for the severe clinical phenotype in adRP patients.

  13. Role of the distal phenylalanine 54 on the structure, stability, and ligand binding of Coprinus cinereus peroxidase.

    Science.gov (United States)

    Neri, F; Indiani, C; Baldi, B; Vind, J; Welinder, K G; Smulevich, G

    1999-06-15

    Resonance Raman and electronic absorption spectra obtained at various pH values for the Fe3+ form of distal F54 mutants of Coprinus cinereus peroxidase are reported, together with the Fe2+ form and fluoride and imidazole adducts at pH 6.0, 5.0, and 10.5, respectively. The distal phenylalanine residue has been replaced by the small aliphatic residues glycine and valine and the hydrogen-bonding aromatic residues tyrosine and tryptophan (F54G, -V, -Y, and -W, respectively). These mutations resulted in transitions between ferric high-spin five-coordinate and six-coordinate forms, and caused a decrease of the pKa of the alkaline transition together with a higher tendency for unfolding. The mutations also alter the ability of the proteins to bind fluoride in such a way that those that are six-coordinate at pH 5.0 bind more strongly than both wild-type CIP and F54Y which are five-coordinate at this pH value. The data provide evidence that the architecture of the distal pocket of CIP is altered by the mutations. Direct evidence is provided that the distal phenylalanine plays an important role in controlling the conjugation between the vinyl double bonds and the porphyrin macrocycle, as indicated by the reorientation of the vinyl groups upon mutation of phenylalanine with the small aliphatic side chains of glycine and valine residues. Furthermore, it appears that the presence of the hydrogen-bonding tyrosine or tryptophan in the cavity increases the pKa of the distal histidine for protonation compared with that of wild-type CIP.

  14. Some Numerical Investigations of the Stability of Electrochemical Digital Simulation, Particularly as affected by First-Order Homogeneous Reactions

    DEFF Research Database (Denmark)

    Britz, Dieter; Østerby, Ole

    1994-01-01

    A reported analysis of the stability of some digital simulation methods is investigated by numerical experiments and the results are consistent with the analysis. Traditional stability conditions need to be modified slightly in the presence of homogeneous reactions, though not to a degree that has...... practical significance. The oscillatory response of the Crank-Nicolson method compared with the Laasonen method can be reduced or eliminated by a preliminary expansion of the time steps, as suggested by Feldberg....

  15. Constrained H-Phe-Phe-NH2 analogues with high affinity to the substance P 1-7 binding site and with improved metabolic stability and cell permeability.

    Science.gov (United States)

    Fransson, Rebecca; Sköld, Christian; Kratz, Jadel M; Svensson, Richard; Artursson, Per; Nyberg, Fred; Hallberg, Mathias; Sandström, Anja

    2013-06-27

    We recently reported the discovery of H-Phe-Phe-NH2 as a small and high affinity ligand for the substance P 1-7 (SP(1-7), H-Arg-Pro-Lys-Pro-Gln-Gln-Phe-OH) specific binding site and its intriguing ability to reduce neuropathic pain. With the overall aim to develop stable and orally bioavailable SP(1-7) mimetics, the dipeptide was chosen as a lead compound. Herein the structure-activity relationship (SAR) of a set of modified H-Phe-Phe-NH2 analogues is presented together with their potential active uptake by PEPT1 transporter, intestinal permeability, and metabolic stability. Local constraints via peptide backbone methylation or preparation of cyclized analogues based on pyrrolidine were evaluated and were shown to significantly improve the in vitro pharmacokinetic properties. The SAR was rationalized by deriving a plausible binding pose for the high affinity ligands. Rigidification using a 3-phenylpyrrolidine moiety in the C-terminal of H-Phe-Phe-NH2 resulted in high affinity and improved intrinsic clearance and intestinal epithelial permeability. PMID:23735006

  16. Cysteine-10 on 17 β -Hydroxysteroid Dehydrogenase 1 Has Stabilizing Interactions in the Cofactor Binding Region and Renders Sensitivity to Sulfhydryl Modifying Chemicals.

    Science.gov (United States)

    Nashev, Lyubomir G; Atanasov, Atanas G; Baker, Michael E; Odermatt, Alex

    2013-01-01

    17 β -Hydroxysteroid dehydrogenase type 1 (17 β -HSD1) catalyzes the conversion of estrone to the potent estrogen estradiol. 17 β -HSD1 is highly expressed in breast and ovary tissues and represents a prognostic marker for the tumor progression and survival of patients with breast cancer and other estrogen-dependent tumors. Therefore, the enzyme is considered a promising drug target against estrogen-dependent cancers. For the development of novel inhibitors, an improved understanding of the structure-function relationships is essential. In the present study, we examined the role of a cysteine residue, Cys(10), in the Rossmann-fold NADPH binding region, for 17 β -HSD1 function and tested the sensitivity towards sulfhydryl modifying chemicals. 3D structure modeling revealed important interactions of Cys(10) with residues involved in the stabilization of amino acids of the NADPH binding pocket. Analysis of enzyme activity revealed that 17 β -HSD1 was irreversibly inhibited by the sulfhydryl modifying agents N-ethylmaleimide (NEM) and dithiocarbamates. Preincubation with increasing concentrations of NADPH protected 17 β -HSD1 from inhibition by these chemicals. Cys(10)Ser mutant 17 β -HSD1 was partially protected from inhibition by NEM and dithiocarbamates, emphasizing the importance of Cys(10) in the cofactor binding region. Substitution of Cys(10) with serine resulted in a decreased protein half-life, without significantly altering kinetic properties. Despite the fact that Cys(10) on 17 β -HSD1 seems to have limited potential as a target for new enzyme inhibitors, the present study provides new insight into the structure-function relationships of this enzyme. PMID:24348564

  17. Cysteine-10 on 17β-Hydroxysteroid Dehydrogenase 1 Has Stabilizing Interactions in the Cofactor Binding Region and Renders Sensitivity to Sulfhydryl Modifying Chemicals

    Directory of Open Access Journals (Sweden)

    Lyubomir G. Nashev

    2013-01-01

    Full Text Available 17β-Hydroxysteroid dehydrogenase type 1 (17β-HSD1 catalyzes the conversion of estrone to the potent estrogen estradiol. 17β-HSD1 is highly expressed in breast and ovary tissues and represents a prognostic marker for the tumor progression and survival of patients with breast cancer and other estrogen-dependent tumors. Therefore, the enzyme is considered a promising drug target against estrogen-dependent cancers. For the development of novel inhibitors, an improved understanding of the structure-function relationships is essential. In the present study, we examined the role of a cysteine residue, Cys10, in the Rossmann-fold NADPH binding region, for 17β-HSD1 function and tested the sensitivity towards sulfhydryl modifying chemicals. 3D structure modeling revealed important interactions of Cys10 with residues involved in the stabilization of amino acids of the NADPH binding pocket. Analysis of enzyme activity revealed that 17β-HSD1 was irreversibly inhibited by the sulfhydryl modifying agents N-ethylmaleimide (NEM and dithiocarbamates. Preincubation with increasing concentrations of NADPH protected 17β-HSD1 from inhibition by these chemicals. Cys10Ser mutant 17β-HSD1 was partially protected from inhibition by NEM and dithiocarbamates, emphasizing the importance of Cys10 in the cofactor binding region. Substitution of Cys10 with serine resulted in a decreased protein half-life, without significantly altering kinetic properties. Despite the fact that Cys10 on 17β-HSD1 seems to have limited potential as a target for new enzyme inhibitors, the present study provides new insight into the structure-function relationships of this enzyme.

  18. Polymorphisms of the T cell receptor CD3delta and CD3varepsilon chains affect anti-CD3 antibody binding and T cell activation

    DEFF Research Database (Denmark)

    Boding, Lasse; Nielsen, Martin Weiss; Bonefeld, Charlotte Menné;

    2010-01-01

    suitable embryonic stem (ES) cell lines. Traditionally, ES cell lines from the 129 mouse strains have been used followed by backcrossing to the C57BL/6 strain. In the present study, we demonstrate the existence of polymorphisms in the CD3 genes from mice of the 129 and C57BL/6 strains. These polymorphisms...... CD3delta and varepsilon ectodomains exist in mice, and that some of these polymorphisms lead to amino acid substitutions which cause structural changes and affect anti-CD3 antibody binding. Thus, functional T cell studies should be interpreted with caution when anti-CD3 antibodies are used for......T cell receptor (TCR) structure and function have been thoroughly studied for decades. Production and analyses of knock-out and knock-in mice with mutations in the CD3 chains have contributed significantly to these studies. The generation of such gene-modified mice relies on the availability of...

  19. Does the Implant Surgical Technique Affect the Primary and/or Secondary Stability of Dental Implants? A Systematic Review

    Directory of Open Access Journals (Sweden)

    Rola Muhammed Shadid

    2014-01-01

    Full Text Available Background. A number of surgical techniques for implant site preparation have been advocated to enhance the implant of primary and secondary stability. However, there is insufficient scientific evidence to support the association between the surgical technique and implant stability. Purpose. This review aimed to investigate the influence of different surgical techniques including the undersized drilling, the osteotome, the piezosurgery, the flapless procedure, and the bone stimulation by low-level laser therapy on the primary and/or secondary stability of dental implants. Materials and methods. A search of PubMed, Cochrane Library, and grey literature was performed. The inclusion criteria comprised observational clinical studies and randomized controlled trials (RCTs conducted in patients who received dental implants for rehabilitation, studies that evaluated the association between the surgical technique and the implant primary and/or secondary stability. The articles selected were carefully read and classified as low, moderate, and high methodological quality and data of interest were tabulated. Results. Eight clinical studies were included then they were classified as moderate or high methodological quality and control of bias. Conclusions. There is a weak evidence suggesting that any of previously mentioned surgical techniques could influence the primary and/or secondary implant stability.

  20. How hydrophobicity and the glycosylation site of glycans affect protein folding and stability: a molecular dynamics simulation.

    Science.gov (United States)

    Lu, Diannan; Yang, Cheng; Liu, Zheng

    2012-01-12

    Glycosylation is one of the most common post-translational modifications in the biosynthesis of protein, but its effect on the protein conformational transitions underpinning folding and stabilization is poorly understood. In this study, we present a coarse-grained off-lattice 46-β barrel model protein glycosylated by glycans with different hydrophobicity and glycosylation sites to examine the effect of glycans on protein folding and stabilization using a Langevin dynamics simulation, in which an H term was proposed as the index of the hydrophobicity of glycan. Compared with its native counterpart, introducing glycans of suitable hydrophobicity (0.1 enthalpy effect. The simulations have shown both the stabilization and the destabilization effects of glycosylation, as experimentally reported in the literature, and provided molecular insight into glycosylated proteins. The understanding of the effects of glycans with different hydrophobicities on the folding and stability of protein, as attempted by the present work, is helpful not only to explain the stabilization and destabilization effect of real glycoproteins but also to design protein-polymer conjugates for biotechnological purposes.

  1. FK506 binding protein 8 peptidylprolyl isomerase activity manages a late stage of cystic fibrosis transmembrane conductance regulator (CFTR) folding and stability.

    Science.gov (United States)

    Hutt, Darren M; Roth, Daniela Martino; Chalfant, Monica A; Youker, Robert T; Matteson, Jeanne; Brodsky, Jeffrey L; Balch, William E

    2012-06-22

    Cystic fibrosis (CF) is caused by mutations in the apical chloride channel cystic fibrosis transmembrane conductance regulator (CFTR) with 90% of patients carrying at least one deletion of the F508 (ΔF508) allele. This mutant form of CFTR is characterized by a folding and trafficking defect that prevents exit from the endoplasmic reticulum. We previously reported that ΔF508 CFTR can be recovered in a complex with Hsp90 and its co-chaperones as an on-pathway folding intermediate, suggesting that Δ508 CF disease arises due to a failure of the proteostasis network (PN), which manages protein folding and degradation in the cell. We have now examined the role of FK506-binding protein 8 (FKBP8), a component of the CFTR interactome, during the biogenesis of wild-type and ΔF508 CFTR. FKBP8 is a member of the peptidylprolyl isomerase family that mediates the cis/trans interconversion of peptidyl prolyl bonds. Our results suggest that FKBP8 is a key PN factor required at a post-Hsp90 step in CFTR biogenesis. In addition, changes in its expression level or alteration of its activity by a peptidylprolyl isomerase inhibitor alter CFTR stability and transport. We propose that CF is caused by the sequential failure of the prevailing PN pathway to stabilize ΔF508-CFTR for endoplasmic reticulum export, a pathway that can be therapeutically managed.

  2. Anaerobic and aerobic transformations affecting stability of dewatered sludge during long-term storage in a lagoon.

    Science.gov (United States)

    Lukicheva, Irina; Tian, Guanglong; Cox, Albert; Granato, Thomas; Pagilla, Krishna

    2012-01-01

    The goal of this work was to study long-term behavior of anaerobically digested and dewatered sludge (biosolids) in a lagoon under anaerobic and aerobic conditions to determine the stability of the final product as an indicator of its odor potential. Field lagoons were sampled to estimate spatial and temporal variations in the physical-chemical properties and biological stability characteristics such as volatile solids content, accumulated oxygen uptake, and soluble protein content and odorous compound assessment. The analyses of collected data suggest that the surface layer of the lagoon (depth of above 0.15 m) undergoes long-term aerobic oxidation resulting in a higher degree of stabilization in the final product. The subsurface layers (depth 0.15 m below the surface and deeper) are subjected to an anaerobic environment where the conditions favor the initial rapid organic matter degradation within approximately the first year, followed by slow degradation. PMID:22368823

  3. Restricted Arm Swing Affects Gait Stability and Increased Walking Speed Alters Trunk Movements in Children with Cerebral Palsy

    Science.gov (United States)

    Delabastita, Tijs; Desloovere, Kaat; Meyns, Pieter

    2016-01-01

    Observational research suggests that in children with cerebral palsy, the altered arm swing is linked to instability during walking. Therefore, the current study investigates whether children with cerebral palsy use their arms more than typically developing children, to enhance gait stability. Evidence also suggests an influence of walking speed on gait stability. Moreover, previous research highlighted a link between walking speed and arm swing. Hence, the experiment aimed to explore differences between typically developing children and children with cerebral palsy taking into account the combined influence of restricting arm swing and increasing walking speed on gait stability. Spatiotemporal gait characteristics, trunk movement parameters and margins of stability were obtained using three dimensional gait analysis to assess gait stability of 26 children with cerebral palsy and 24 typically developing children. Four walking conditions were evaluated: (i) free arm swing and preferred walking speed; (ii) restricted arm swing and preferred walking speed; (iii) free arm swing and high walking speed; and (iv) restricted arm swing and high walking speed. Double support time and trunk acceleration variability increased more when arm swing was restricted in children with bilateral cerebral palsy compared to typically developing children and children with unilateral cerebral palsy. Trunk sway velocity increased more when walking speed was increased in children with unilateral cerebral palsy compared to children with bilateral cerebral palsy and typically developing children and in children with bilateral cerebral palsy compared to typically developing children. Trunk sway velocity increased more when both arm swing was restricted and walking speed was increased in children with bilateral cerebral palsy compared to typically developing children. It is proposed that facilitating arm swing during gait rehabilitation can improve gait stability and decrease trunk movements in

  4. Comprehensive Analysis of Contributions from Protein Conformational Stability and Major Histocompatibility Complex Class II-Peptide Binding Affinity to CD4+ Epitope Immunogenicity in HIV-1 Envelope Glycoprotein

    Science.gov (United States)

    Li, Tingfeng; Steede, N. Kalaya; Nguyen, Hong-Nam P.; Freytag, Lucy C.; McLachlan, James B.; Mettu, Ramgopal R.; Robinson, James E.

    2014-01-01

    ABSTRACT Helper T-cell epitope dominance in human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein gp120 is not adequately explained by peptide binding to major histocompatibility complex (MHC) proteins. Antigen processing potentially influences epitope dominance, but few, if any, studies have attempted to reconcile the influences of antigen processing and MHC protein binding for all helper T-cell epitopes of an antigen. Epitopes of gp120 identified in both humans and mice occur on the C-terminal flanks of flexible segments that are likely to be proteolytic cleavage sites. In this study, the influence of gp120 conformation on the dominance pattern in gp120 from HIV strain 89.6 was examined in CBA mice, whose MHC class II protein has one of the most well defined peptide-binding preferences. Only one of six dominant epitopes contained the most conserved element of the I-Ak binding motif, an aspartic acid. Destabilization of the gp120 conformation by deletion of single disulfide bonds preferentially enhanced responses to the cryptic I-Ak motif-containing sequences, as reported by T-cell proliferation or cytokine secretion. Conversely, inclusion of CpG in the adjuvant with gp120 enhanced responses to the dominant CD4+ T-cell epitopes. The gp120 destabilization affected secretion of some cytokines more than others, suggesting that antigen conformation could modulate T-cell functions through mechanisms of antigen processing. IMPORTANCE CD4+ helper T cells play an essential role in protection against HIV and other pathogens. Thus, the sites of helper T-cell recognition, the dominant epitopes, are targets for vaccine design; and the corresponding T cells may provide markers for monitoring infection and immunity. However, T-cell epitopes are difficult to identify and predict. It is also unclear whether CD4+ T cells specific for one epitope are more protective than T cells specific for other epitopes. This work shows that the three-dimensional (3D) structure of an

  5. A sequence that affects the copy number and stability of pSW200 and ColE1.

    Science.gov (United States)

    Wu, Ying-Chung; Liu, Shih-Tung

    2010-07-01

    Pantoea stewartii SW2 contains 13 plasmids. One of these plasmids, pSW200, has a replicon that resembles that of ColE1. This study demonstrates that pSW200 contains a 9-bp UP element, 5'-AAGATCTTC, which is located immediately upstream of the -35 box in the RNAII promoter. A transcriptional fusion study reveals that substituting this 9-bp sequence reduces the activity of the RNAII promoter by 78%. The same mutation also reduced the number of plasmid copies from 13 to 5, as well as the plasmid stability. When a similar sequence in a ColE1 derivative, pYCW301, is mutated, the copy number of the plasmid also declines from 34 to 16 per cell. Additionally, inserting this 9-bp sequence stabilizes an unstable pSW100 derivative, pSW142K, which also contains a replicon resembling that of ColE1, indicating the importance of this sequence in maintaining the stability of the plasmid. In conclusion, the 9-bp sequence upstream of the -35 box in the RNAII promoter is required for the efficient synthesis of RNAII and maintenance of the stability of the plasmids in the ColE1 family. PMID:20494993

  6. Stability of Chloropyromorphite in Ryegrass Rhizosphere as Affected by Root-Secreted Low Molecular Weight Organic Acids

    Science.gov (United States)

    Wei, Wei; Wang, Yu; Wang, Zheng; Han, Ruiming; Li, Shiyin; Wei, Zhenggui; Zhang, Yong

    2016-01-01

    Understanding the stability of chloropyromorphite (CPY) is of considerable benefit for improving risk assessment and remediation strategies in contaminated water and soil. The stability of CPY in the rhizosphere of phosphorus-deficient ryegrass was evaluated to elucidate the role of root-secreted low molecular weight organic acids (LMWOAs) on the dissolution of CPY. Results showed that CPY treatments significantly reduced the ryegrass biomass and rhizosphere pH. The presence of calcium nitrate extractable lead (Pb) and phosphorus (P) suggested that CPY in the rhizosphere could be bioavailable, because P and Pb uptake by ryegrass potentially provided a significant concentration gradient that would promote CPY dissolution. Pb accumulation and translocation in ryegrass was found to be significantly higher in P-sufficient conditions than in P-deficient conditions. CPY treatments significantly enhanced root exudation of LMWOAs irrigated with P-nutrient solution or P-free nutrient solution. Oxalic acid was the dominant species in root-secreted LMWOAs of ryegrass under P-free nutrient solution treatments, suggesting that root-secreted oxalic acid may be the driving force of root-induced dissolution of CPY. Hence, our work, provides clarifying hints on the role of LMWOAs in controlling the stability of CPY in the rhizosphere. PMID:27494023

  7. Stability of Chloropyromorphite in Ryegrass Rhizosphere as Affected by Root-Secreted Low Molecular Weight Organic Acids.

    Science.gov (United States)

    Wei, Wei; Wang, Yu; Wang, Zheng; Han, Ruiming; Li, Shiyin; Wei, Zhenggui; Zhang, Yong

    2016-01-01

    Understanding the stability of chloropyromorphite (CPY) is of considerable benefit for improving risk assessment and remediation strategies in contaminated water and soil. The stability of CPY in the rhizosphere of phosphorus-deficient ryegrass was evaluated to elucidate the role of root-secreted low molecular weight organic acids (LMWOAs) on the dissolution of CPY. Results showed that CPY treatments significantly reduced the ryegrass biomass and rhizosphere pH. The presence of calcium nitrate extractable lead (Pb) and phosphorus (P) suggested that CPY in the rhizosphere could be bioavailable, because P and Pb uptake by ryegrass potentially provided a significant concentration gradient that would promote CPY dissolution. Pb accumulation and translocation in ryegrass was found to be significantly higher in P-sufficient conditions than in P-deficient conditions. CPY treatments significantly enhanced root exudation of LMWOAs irrigated with P-nutrient solution or P-free nutrient solution. Oxalic acid was the dominant species in root-secreted LMWOAs of ryegrass under P-free nutrient solution treatments, suggesting that root-secreted oxalic acid may be the driving force of root-induced dissolution of CPY. Hence, our work, provides clarifying hints on the role of LMWOAs in controlling the stability of CPY in the rhizosphere. PMID:27494023

  8. Structures, stabilization energies, and binding energies of quinoxaline···(H2O)(n), quinoxaline dimer, and quinoxaline···Cu complexes: a theoretical study.

    Science.gov (United States)

    Kabanda, Mwadham M; Ebenso, Eno E

    2013-02-21

    Quinoxaline is a parent structure for a broad class of N-heteroaromatic compounds, many of which exhibit various biological activities. The interaction of quinoxaline with explicit water molecules or metal ions and the formation of quinoxaline dimer play an important role in many of the biological activities of quinoxaline. This study investigates the structures, stabilization, and binding energies of quinoxaline complexes with water, transition metal ions, and quinoxaline dimer to provide information on the preferred geometries, interaction energies, and type of noncovalent interactions accounting for the stability of the complexes. The investigations are performed in vacuo and in water solution using MP2 and DFT methods. The results of the study on the quinoxaline···(H(2)O)(n) show that the preferred adducts in vacuo involve one, two, or three water molecules hydrogen bonded to the N atom and the neighboring H atom of the C(sp2)-H group. The results in water solution show a preference for water-water clustering. The dimers of quinoxaline are stabilized by either π-π stacking or weak C-H···N intermolecular hydrogen bonds. The relative stability of the quinoxaline···Cu complexes depends on the site on which the Cu ion binds and the binding strength depends on both the nature of the cation and the binding site.

  9. LHON/MELAS overlap mutation in ND1 subunit of mitochondrial complex I affects ubiquinone binding as revealed by modeling in Escherichia coli NDH-1.

    Science.gov (United States)

    Pätsi, Jukka; Maliniemi, Pilvi; Pakanen, Salla; Hinttala, Reetta; Uusimaa, Johanna; Majamaa, Kari; Nyström, Thomas; Kervinen, Marko; Hassinen, Ilmo E

    2012-02-01

    Defects in complex I due to mutations in mitochondrial DNA are associated with clinical features ranging from single organ manifestation like Leber hereditary optic neuropathy (LHON) to multiorgan disorders like mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like episodes (MELAS) syndrome. Specific mutations cause overlap syndromes combining several phenotypes, but the mechanisms of their biochemical effects are largely unknown. The m.3376G>A transition leading to p.E24K substitution in ND1 with LHON/MELAS phenotype was modeled here in a homologous position (NuoH-E36K) in the Escherichia coli enzyme and it almost totally abolished complex I activity. The more conservative mutation NuoH-E36Q resulted in higher apparent K(m) for ubiquinone and diminished inhibitor sensitivity. A NuoH homolog of the m.3865A>G transition, which has been found concomitantly in the overlap syndrome patient with the m.3376G>A, had only a minor effect. Consequences of a primary LHON-mutation m.3460G>A affecting the same extramembrane loop as the m.3376G>A substitution were also studied in the E. coli model and were found to be mild. The results indicate that the overlap syndrome-associated m.3376G>A transition in MTND1 is the pathogenic mutation and m.3865A>G transition has minor, if any, effect on presentation of the disease. The kinetic effects of the NuoH-E36Q mutation suggest its proximity to the putative ubiquinone binding domain in 49kD/PSST subunits. In all, m.3376G>A perturbs ubiquinone binding, a phenomenon found in LHON, and decreases the activity of fully assembled complex I as in MELAS.

  10. The Central Polybasic Region of the Soluble SNARE (Soluble N-Ethylmaleimide-sensitive Factor Attachment Protein Receptor) Vam7 Affects Binding to Phosphatidylinositol 3-Phosphate by the PX (Phox Homology) Domain.

    Science.gov (United States)

    Miner, Gregory E; Starr, Matthew L; Hurst, Logan R; Sparks, Robert P; Padolina, Mark; Fratti, Rutilio A

    2016-08-19

    The yeast vacuole requires four SNAREs to trigger membrane fusion including the soluble Qc-SNARE Vam7. The N-terminal PX domain of Vam7 binds to the lipid phosphatidylinositol 3-phosphate (PI3P) and the tethering complex HOPS (homotypic fusion and vacuole protein sorting complex), whereas the C-terminal SNARE motif forms SNARE complexes. Vam7 also contains an uncharacterized middle domain that is predicted to be a coiled-coil domain with multiple helices. One helix contains a polybasic region (PBR) composed of Arg-164, Arg-168, Lys-172, Lys-175, Arg-179, and Lys-186. Polybasic regions are often associated with nonspecific binding to acidic phospholipids including phosphoinositides. Although the PX (phox homology) domain alone binds PI3P, we theorized that the Vam7 PBR could bind to additional acidic phospholipids enriched at fusion sites. Mutating each of the basic residues in the PBR to an alanine (Vam7-6A) led to attenuated vacuole fusion. The defective fusion of Vam7-6A was due in part to inefficient association with its cognate SNAREs and HOPS, yet the overall vacuole association of Vam7-6A was similar to wild type. Experiments testing the binding of Vam7 to specific signaling lipids showed that mutating the PBR to alanines augmented binding to PI3P. The increased binding to PI3P by Vam7-6A likely contributed to the observed wild type levels of vacuole association, whereas protein-protein interactions were diminished. PI3P binding was inhibited when the PX domain mutant Y42A was introduced into Vam7-6A to make Vam7-7A. Thus the Vam7 PBR affects PI3P binding by the PX domain and in turn affects binding to SNAREs and HOPS to support efficient fusion. PMID:27365394

  11. The smallest capsid protein mediates binding of the essential tegument protein pp150 to stabilize DNA-containing capsids in human cytomegalovirus.

    Directory of Open Access Journals (Sweden)

    Xinghong Dai

    2013-08-01

    Full Text Available Human cytomegalovirus (HCMV is a ubiquitous herpesvirus that causes birth defects in newborns and life-threatening complications in immunocompromised individuals. Among all human herpesviruses, HCMV contains a much larger dsDNA genome within a similarly-sized capsid compared to the others, and it was proposed to require pp150, a tegument protein only found in cytomegaloviruses, to stabilize its genome-containing capsid. However, little is known about how pp150 interacts with the underlying capsid. Moreover, the smallest capsid protein (SCP, while dispensable in herpes simplex virus type 1, was shown to play essential, yet undefined, role in HCMV infection. Here, by cryo electron microscopy (cryoEM, we determine three-dimensional structures of HCMV capsid (no pp150 and virion (with pp150 at sub-nanometer resolution. Comparison of these two structures reveals that each pp150 tegument density is composed of two helix bundles connected by a long central helix. Correlation between the resolved helices and sequence-based secondary structure prediction maps the tegument density to the N-terminal half of pp150. The structures also show that SCP mediates interactions between the capsid and pp150 at the upper helix bundle of pp150. Consistent with this structural observation, ribozyme inhibition of SCP expression in HCMV-infected cells impairs the formation of DNA-containing viral particles and reduces viral yield by 10,000 fold. By cryoEM reconstruction of the resulting "SCP-deficient" viral particles, we further demonstrate that SCP is required for pp150 functionally binding to the capsid. Together, our structural and biochemical results point to a mechanism whereby SCP recruits pp150 to stabilize genome-containing capsid for the production of infectious HCMV virion.

  12. The influence of somatosensory and muscular deficits on postural stabilization: Insights from an instrumented analysis of subjects affected by different types of Charcot-Marie-Tooth disease.

    Science.gov (United States)

    Lencioni, Tiziana; Piscosquito, Giuseppe; Rabuffetti, Marco; Bovi, Gabriele; Calabrese, Daniela; Aiello, Alessia; Di Sipio, Enrica; Padua, Luca; Diverio, Manuela; Pareyson, Davide; Ferrarin, Maurizio

    2015-08-01

    Charcot-Marie-Tooth (CMT) disease is the most common hereditary neuromuscular disorder. CMT1 is primarily demyelinating, CMT2 is primarily axonal, and CMTX1 is characterized by both axonal and demyelinating abnormalities. We investigated the role of somatosensory and muscular deficits on quiet standing and postural stabilization in patients affected by different forms of CMT, comparing their performances with those of healthy subjects. Seventy-six CMT subjects (CMT1A, CMT2 and CMTX1) and 41 healthy controls were evaluated during a sit-to-stand transition and the subsequent quiet upright posture by means of a dynamometric platform. All CMT patients showed altered balance and postural stabilization compared to controls. Multivariate analysis showed that in CMT patients worsening of postural stabilization was related to vibration sense deficit and to dorsi-flexor's weakness, while quiet standing instability was related to the reduction of pinprick sensibility and to plantar-flexor's weakness. Our results show that specific sensory and muscular deficits play different roles in balance impairment of CMT patients, both during postural stabilization and in static posture. An accurate evaluation of residual sensory and muscular functions is therefore necessary to plan for the appropriate balance rehabilitation treatment for each patient, besides the CMT type.

  13. Cooperative binding modes of Cu(II) in prion protein

    Science.gov (United States)

    Hodak, Miroslav; Chisnell, Robin; Lu, Wenchang; Bernholc, Jerry

    2007-03-01

    The misfolding of the prion protein, PrP, is responsible for a group of neurodegenerative diseases including mad cow disease and Creutzfeldt-Jakob disease. It is known that the PrP can efficiently bind copper ions; four high-affinity binding sites located in the octarepeat region of PrP are now well known. Recent experiments suggest that at low copper concentrations new binding modes, in which one copper ion is shared between two or more binding sites, are possible. Using our hybrid Thomas-Fermi/DFT computational scheme, which is well suited for simulations of biomolecules in solution, we investigate the geometries and energetics of two, three and four binding sites cooperatively binding one copper ion. These geometries are then used as inputs for classical molecular dynamics simulations. We find that copper binding affects the secondary structure of the PrP and that it stabilizes the unstructured (unfolded) part of the protein.

  14. Longevity and developmental stability in the dung fly Sepsis cynipsea, as affected by the ectoparasitic mite, Pediculoides mesembrinae

    Directory of Open Access Journals (Sweden)

    Oliver Y. Martin

    2009-12-01

    Full Text Available Fluctuating asymmetry (FA is a widely employed measure of developmental stability. It has been found to increase with many stressors including parasite infection. Associations between parasites and FA may exist for several reasons in addition to parasites being the direct cause of increased FA. Developmentally stable individuals may have superior immune systems, and be less susceptible to parasite infection, and/or may be less exposed to parasites than developmentally unstable ones. Mites negatively impact host fitness in a number of insects, and if FA is a reflection of general genetic quality, as has been proposed, associations between mite number and FA are predicted. Potential relationships were investigated between an ectoparasitic mite, Pediculoides mesembrinae (Canestrini (Phthiraptera: Menoponidae and FA in the common dung fly Sepsis cynipsea (L. (Diptera: Sepsidae. While it was found that mite infested flies died much faster than flies without mites, indicating that mites indeed stress their hosts, counter to expectations, no associations between mites and FA were found in any analyses. Additionally, FA in mite-infected flies generally did not differ from previously published FA data from uninfected S. cynipsea. Nevertheless, parasitized males tended to be somewhat less asymmetrical than non-parasitized males, but based on our data, it does not appear that mite infestation is generally associated with developmental stability in S. cynipsea.

  15. The Scribble polarity protein stabilizes E-cadherin/p120-catenin binding and blocks retrieval of E-cadherin to the Golgi.

    Directory of Open Access Journals (Sweden)

    Madhura Lohia

    Full Text Available Several polarity proteins, including Scribble (Scrb have been implicated in control of vesicle traffic, and in particular the endocytosis of E-cadherin, but through unknown mechanisms. We now show that depletion of Scrb enhances endocytosis of E-cadherin by weakening the E-cadherin-p120catenin interaction. Unexpectedly, however, the internalized E-cadherin is not degraded but accumulates in the Golgi apparatus. Silencing p120-catenin causes degradation of E-cadherin in lysosomes, but degradation is blocked by the co-depletion of Scrb, which diverts the internalized E-cadherin to the Golgi. Loss of Scrb also enhances E-cadherin binding to retromer components, and retromer is required for Golgi accumulation of Scrb, and E-cadherin stability. These data identify a novel and unanticipated function for Scrb in blocking retromer-mediated diversion of E-cadherin to the Golgi. They provide evidence that polarity proteins can modify the intracellular itinerary for endocytosed membrane proteins.

  16. Cloning and molecular analysis of genes affecting expression of binding substance, the recipient-encoded receptor(s) mediating mating aggregate formation in Enterococcus faecalis.

    Science.gov (United States)

    Bensing, B A; Dunny, G M

    1993-11-01

    Transfer of the conjugative plasmid pCF10 in Enterococcus faecalis strains involves production of a plasmid-encoded aggregation substance on the surface of donor cells in response to stimulation by a pheromone secreted by recipient cells. Aggregation substance then facilitates attachment to recipient cells via a chromosomally encoded receptor, termed binding substance (BS). A BS mutant, strain INY3000, generated by random Tn916 insertions, was previously found to carry copies of the transposon at four unique sites (K. M. Trotter and G. M. Dunny, Plasmid 24:57-67, 1990). In the present study, DNA flanking the Tn916 insertions was used to complement the BS mutation of INY3000 following Tn916 excision from cloned chromosomal fragments. Complementation results showed that three of the four regions mutated in INY3000 play some role in BS expression. Tn5 mutagenesis and DNA sequence analysis of the complementing fragment from one of these regions indicated the presence of three genes (ebsA, ebsB, and ebsC) that affect BS expression. The ebsA and ebsB genes encode peptides likely to function in cell wall metabolism, whereas ebsC may encode a product that suppresses the function or expression of EbsB.

  17. Can air pollution affect tear film stability? a cross-sectional study in the aftermath of an explosion accident

    Directory of Open Access Journals (Sweden)

    Granslo JT

    2011-04-01

    Full Text Available Abstract Background After an explosion and fire in two tanks containing contaminated oil and sulphur products in a Norwegian industrial harbour in 2007, the surrounding area was polluted. This caused an intense smell, lasting until the waste was removed two years later. The present study reports examinations of tear film break up time among the population. The examinations were carried out because many of the people in the area complained of sore eyes. The purpose of the study was to assess the relationship between living or working close to the polluted area and tear film stability one and a half years after the explosion. Methods All persons working or living in an area less than six kilometres from the explosion site were invited to take part in the study together with a similar number of persons matched for age and gender living more than 20 kilometres away. Three groups were established: workers in the explosion area and inhabitants near the explosion area (but not working there were considered to have been exposed, and inhabitants far away (who did not work in the explosion area were considered to be unexposed. A total of 734 people were examined, and the response rate was 76 percent. Tear film stability was studied by assessing non-invasive break-up time (NIBUT using ocular microscopy. In addition Self-reported Break Up Time (SBUT was assessed by recording the time the subject could keep his or hers eyes open without blinking when watching a fixed point on a wall. Background information was obtained using a questionnaire. Non-parametric Wilcoxon-Mann-Whitney-tests with exact p-values and multiple logistic regression analyses were performed. Results Both NIBUT and SBUT were shorter among the male exposed workers than among the inhabitants both near and far away from the explosion area. This was also found for SBUT among males in a multiple logistic regression analysis, adjusting for age and smoking. Conclusions Reduced tear film stability

  18. Deciphering the Dynamics of Non-Covalent Interactions Affecting Thermal Stability of a Protein: Molecular Dynamics Study on Point Mutant of Thermus thermophilus Isopropylmalate Dehydrogenase.

    Science.gov (United States)

    Sharma, Reetu; Sastry, G Narahari

    2015-01-01

    Thermus thermophilius isopropylmalate dehydrogenase catalyzes oxidative decarboxylation and dehydrogenation of isopropylmalate. Substitution of leucine to alanine at position 172 enhances the thermal stability among the known point mutants. Exploring the dynamic properties of non-covalent interactions such as saltbridges, hydrogen bonds and hydrophobic interactions to explain thermal stability of a protein is interesting in its own right. In this study dynamic changes in the non-covalent interactions are studied to decipher the deterministic features of thermal stability of a protein considering a case study of a point mutant in Thermus thermophilus isopropylmalate dehydrogenase. A total of four molecular dynamic simulations of 0.2 μs were carried out on wild type and mutant's functional dimers at 300 K and 337 K. Higher thermal stability of the mutant as compared to wild type is revealed by root mean square deviation, root mean square fluctuations and Cα-Cα distance with an increase in temperature from 300 K to 337 K. Most of the regions of wild type fluctuate higher than the corresponding regions of mutant with an increase in temperature. Cα-Cα distance analysis suggests that long distance networks are significantly affected in wild type as compared to the mutant. Short lived contacts are higher in wild type, while long lived contacts are lost at 337 K. The mutant forms less hydrogen bonds with water as compared to wild type at 337 K. In contrast to wild type, the mutant shows significant increase in unique saltbridges, hydrogen bonds and hydrophobic contacts at 337 K. The current study indicates that there is a strong inter-dependence of thermal stability on the way in which non-covalent interactions reorganize, and it is rewarding to explore this connection in single mutant studies.

  19. Deciphering the Dynamics of Non-Covalent Interactions Affecting Thermal Stability of a Protein: Molecular Dynamics Study on Point Mutant of Thermus thermophilus Isopropylmalate Dehydrogenase.

    Directory of Open Access Journals (Sweden)

    Reetu Sharma

    Full Text Available Thermus thermophilius isopropylmalate dehydrogenase catalyzes oxidative decarboxylation and dehydrogenation of isopropylmalate. Substitution of leucine to alanine at position 172 enhances the thermal stability among the known point mutants. Exploring the dynamic properties of non-covalent interactions such as saltbridges, hydrogen bonds and hydrophobic interactions to explain thermal stability of a protein is interesting in its own right. In this study dynamic changes in the non-covalent interactions are studied to decipher the deterministic features of thermal stability of a protein considering a case study of a point mutant in Thermus thermophilus isopropylmalate dehydrogenase. A total of four molecular dynamic simulations of 0.2 μs were carried out on wild type and mutant's functional dimers at 300 K and 337 K. Higher thermal stability of the mutant as compared to wild type is revealed by root mean square deviation, root mean square fluctuations and Cα-Cα distance with an increase in temperature from 300 K to 337 K. Most of the regions of wild type fluctuate higher than the corresponding regions of mutant with an increase in temperature. Cα-Cα distance analysis suggests that long distance networks are significantly affected in wild type as compared to the mutant. Short lived contacts are higher in wild type, while long lived contacts are lost at 337 K. The mutant forms less hydrogen bonds with water as compared to wild type at 337 K. In contrast to wild type, the mutant shows significant increase in unique saltbridges, hydrogen bonds and hydrophobic contacts at 337 K. The current study indicates that there is a strong inter-dependence of thermal stability on the way in which non-covalent interactions reorganize, and it is rewarding to explore this connection in single mutant studies.

  20. MAIZE YIELD AND ITS STABILITY AS AFFECTED BY TILLAGE AND CROP RESIDUE MANAGEMENT IN THE EASTERN ROMANIAN DANUBE PLAIN

    Directory of Open Access Journals (Sweden)

    Alexandru COCIU

    2015-10-01

    Full Text Available Rainfed crop management systems need to be optimized to provide more resilient options in order to cope with projected climatic scenarios which are forecasting a decrease in mean precipitation and more frequent extreme drought periods in the Eastern Romanian Danube Plain. This research, carried out in the period of 2011-2014, had as main purpose the determination of influence of tillage practices and residue management on rainfall use efficiency, maize yield and its stability, in order to evaluate the advantages of conservation agriculture (CA in the time of stabilization of direct seeding effects, in comparison with traditional chisel tillage. The maize grain yields are presented for each crop management practices, as follows: (1 chisel tillage, retained crop residues being chopped and incorporated (ciz; (2 zero tillage, retained crop residue chopped and kept on the field in short flat condition (rvt; (3 zero tillage, crop residues kept on the field in short root-anchored condition (1/2rva, and (4 zero tillage, crop residues kept on the field in tall root-anchored condition (1/1rva. In 2012, a year with prolonged drought during vegetative growth, yield differences between zero tillage with short root-anchored residue retention (1/2rva and chisel tillage with residue incorporation (ciz were positive, up to 840 kg ha-1. In average over 2011-2014, conservation agriculture (CA practices had a yield advantage over traditional chisel tillage practice. Zero tillage with residue retention used rainfall more efficiently so suggesting that it is a more resilient agronomic system than traditional (conventional practices involving chisel tillage with residue incorporation.

  1. Aggregate stability and associated C and N in a silty loam soil as affected by organic material inputs

    Institute of Scientific and Technical Information of China (English)

    LONG Pan; SUI Peng; GAO Wang-sheng; WANG Bin-bin; HUANG Jian-xiong; YAN Peng; ZOU Juan-xiu; YAN Ling-ling; CHEN Yuan-quan

    2015-01-01

    To make recycling utilization of organic materials produced in various agricultural systems, ifve kinds of organic materials were applied in a ifeld test, including crop straw (CS), biogas residue (BR), mushroom residue (MR), wine residue (WR), pig manure (PM), with a mineral fertilizer (CF) and a no-fertilizer (CK) treatment as a control. Our objectives were:i) to quantify the effects of organic materials on soil C and N accumulation;i ) to evaluate the effects of organic materials on soil aggregate stability, along with the total organic carbon (TOC), and N in different aggregate fractions;and i i) to assess the relationships among the organic material components, soil C and N, and C, N in aggregate fractions. The trial was conducted in Wuqiao County, Hebei Province, China. The organic materials were incorporated at an equal rate of C, and combined with a mineral fertilizer in amounts of 150 kg N ha-1, 26 kg P ha-1 and 124 kg K ha-1 respectively during each crop season of a wheat-maize rotation system. The inputted C quantity of each organic material treatment was equivalent to the total amount of C contained in the crop straw harvested in CS treatement in the previous season. TOC, N, water-stable aggregates, and aggregate-associated TOC and N were investigated. The results showed that organic material incorpora-tion increased soil aggregation and stabilization. On average, the soil macroaggregate proportion increased by 14%, the microaggregate proportion increased by 3%, and mean-weight diameter (MWD) increased by 20%. TOC content fol owed the order of PM>WR>MR>BR>CS>CK>CF;N content fol owed the order WR>PM>MR>BR>CS>CF>CK. No signiifcant correlation was found between TOC, N, and the quality of organic material. Soil silt and clay particles contained the largest part of TOC, whereas the smal macroaggregate fraction was the most sensitive to organic materials. Our results indicate that PM and WR exerted better effects on soil C and N accumulation, fol owed by MR

  2. Storage Stability of Kinnow Fruit (Citrus reticulata as Affected by CMC and Guar Gum-Based Silver Nanoparticle Coatings

    Directory of Open Access Journals (Sweden)

    Syed Wasim Ahmad Shah

    2015-12-01

    Full Text Available The influence of carboxy methyl cellulose (CMC and guargum-based coatings containing silver nanoparticles was studied on the postharvest storage stability of the kinnow mandarin (Citrus reticulata cv. Blanco for a period of 120 days (85%–90% relative humidity at 4 °C and 10 °C. Physicochemical and microbiological qualities were monitored after every 15 days of storage. Overall results revealed an increase in total soluble solid (TSS, total sugars, reducing sugars and weight loss but this increase was comparatively less significant in coated fruits stored at 4 °C. Ascorbic acid, total phenolics, and antioxidant activity was significantly enhanced in coated fruits stored at 4 °C. Titratable acidity significantly decreased during storage except for coated kinnow stored at 4 °C. In control samples stored at 10 °C, high intensity of fruit rotting and no chilling injury was observed. Total aerobic psychrotrophic bacteria and yeast and molds were noticed in all treatments during storage but the growth was not significant in coated fruits at 4 °C. Kinnow fruit can be kept in good quality after coating for four months at 4 °C and for 2 months at 10 °C.

  3. Storage Stability of Kinnow Fruit (Citrus reticulata) as Affected by CMC and Guar Gum-Based Silver Nanoparticle Coatings.

    Science.gov (United States)

    Shah, Syed Wasim Ahmad; Jahangir, Muhammad; Qaisar, Muhammad; Khan, Sher Aslam; Mahmood, Talat; Saeed, Muhammad; Farid, Abid; Liaquat, Muhammad

    2015-01-01

    The influence of carboxy methyl cellulose (CMC) and guargum-based coatings containing silver nanoparticles was studied on the postharvest storage stability of the kinnow mandarin (Citrus reticulata cv. Blanco) for a period of 120 days (85%-90% relative humidity) at 4 °C and 10 °C. Physicochemical and microbiological qualities were monitored after every 15 days of storage. Overall results revealed an increase in total soluble solid (TSS), total sugars, reducing sugars and weight loss but this increase was comparatively less significant in coated fruits stored at 4 °C. Ascorbic acid, total phenolics, and antioxidant activity was significantly enhanced in coated fruits stored at 4 °C. Titratable acidity significantly decreased during storage except for coated kinnow stored at 4 °C. In control samples stored at 10 °C, high intensity of fruit rotting and no chilling injury was observed. Total aerobic psychrotrophic bacteria and yeast and molds were noticed in all treatments during storage but the growth was not significant in coated fruits at 4 °C. Kinnow fruit can be kept in good quality after coating for four months at 4 °C and for 2 months at 10 °C. PMID:26694344

  4. Hepatitis B Virus Core Protein Phosphorylation Sites Affect Capsid Stability and Transient Exposure of the C-terminal Domain.

    Science.gov (United States)

    Selzer, Lisa; Kant, Ravi; Wang, Joseph C-Y; Bothner, Brian; Zlotnick, Adam

    2015-11-20

    Hepatitis B virus core protein has 183 amino acids divided into an assembly domain and an arginine-rich C-terminal domain (CTD) that regulates essential functions including genome packaging, reverse transcription, and intracellular trafficking. Here, we investigated the CTD in empty hepatitis B virus (HBV) T=4 capsids. We examined wild-type core protein (Cp183-WT) and a mutant core protein (Cp183-EEE), in which three CTD serines are replaced with glutamate to mimic phosphorylated protein. We found that Cp183-WT capsids were less stable than Cp183-EEE capsids. When we tested CTD sensitivity to trypsin, we detected two different populations of CTDs differentiated by their rate of trypsin cleavage. Interestingly, CTDs from Cp183-EEE capsids exhibited a much slower rate of proteolytic cleavage when compared with CTDs of Cp183-WT capsids. Cryo-electron microscopy studies of trypsin-digested capsids show that CTDs at five-fold symmetry vertices are most protected. We hypothesize that electrostatic interactions between glutamates and arginines in Cp183-EEE, particularly at five-fold, increase capsid stability and reduce CTD exposure. Our studies show that quasi-equivalent CTDs exhibit different rates of exposure and thus might perform distinct functions during the hepatitis B virus lifecycle. Our results demonstrate a structural role for CTD phosphorylation and indicate crosstalk between CTDs within a capsid particle. PMID:26405031

  5. Artificial climate warming positively affects arbuscular mycorrhizae but decreases soil aggregate water stability in an annual grassland

    Energy Technology Data Exchange (ETDEWEB)

    Rillig, M.C.; Wright, S.F.; Shaw, M.R.; Field, C.B.

    2002-04-01

    Despite the importance of arbuscular mycorrhizae to the functioning of terrestrial ecosystems (e.g. nutrient uptake, soil aggregation), and the increasing evidence of global warming, responses of arbuscular mycorrhizal fungi (AMF) to climate warming are poorly understood. In a field experiment using infrared heaters, we found effects of warming on AMF after one growing season in an annual grassland, in the absence of any effects on measured root parameters (weight, length, average diameter). AMF soil hyphal length was increased by over 40% in the warmed plots, accompanied by a strong trend for AMF root colonization increase. In the following year, root weight was again not significantly changed, and AMF root colonization increased significantly in the warmed plots. Concentration of the soil protein glomalin, a glycoprotein produced by AMF hyphae with importance in soil aggregation, was decreased in the warmed plots. Soil aggregate water stability, measured for five diameter size classes, was also decreased significantly. In the following year, soil aggregate weight in two size classes was decreased significantly, but the effect size was very small. These results indicate that ecosystem warming may have stimulated carbon allocation to AMF. Other factors either influenced glomalin decomposition or production, hence influencing the role of these symbionts in soil aggregation. The observed small changes in soil aggregation, if widespread among terrestrial ecosystems, could have important consequences for soil carbon storage and erosion in a warmed climate, especially if there are cumulative effects of warming. (au)

  6. Characterization of a clock based on coherent population trapping in a thermal cesium vapor. Main effects that may affect its mid- and long-term frequency stability

    International Nuclear Information System (INIS)

    This thesis describes a Cs - buffer gas vapor cell atomic clock based on coherent population trapping (CPT), and the main frequency shifts affecting its mid- and long-term stability. The developed atomic clock based on CPT uses two original techniques: a so-called double-Λ scheme for the CPT-resonance excitation and a temporal Ramsey interrogation technique, which produce a high contrast and narrow resonances with reduced light shift dependence. Generally, the mid and long term stability of the vapor cell atomic clock is limited by the collisional shift induced by alkali-buffer gas collisions and the light shift (or the effects depending on the laser intensity). We report on the study of the collisional shift of Cs clock frequency in the presence of Ne, N2 or Ar buffer gas, and its temperature dependence. The coefficient values of this dependence for these three buffer gases were revealed (some of them for the first time), allowing us to realise a cell with optimal combination of buffer gases to cancel the temperature dependence around the working temperature. Following the study of the signal amplitude and the coherence relaxation rate the optimal values for such parameters as interrogation cycle, magnetic field, cell temperature, pressure of the buffer gas mixture, etc. were found for the chosen cell. The investigation on the light shift and the effects depending on the laser intensity allowed us to determine the most sensitive parameters (laser intensity ratio, temperature) and to implement the required stabilizations in order to better control them. Finally, the mid- and long-term clock frequency stability was improved by a factor 40, reaching 2.5 10-14 at 1 hour. (author)

  7. Revised stability constant, spectroscopic properties and binding mode of Zn(II) to FluoZin-3, the most common zinc probe in life sciences.

    Science.gov (United States)

    Marszałek, I; Krężel, A; Goch, W; Zhukov, I; Paczkowska, I; Bal, W

    2016-08-01

    2-[2-[2-[2-[bis(carboxylatomethyl)amino]-5-methoxyphenoxy]ethoxy]-4-(2,7-difluoro-3-oxido-6-oxo-4a,9a-dihydroxanthen-9-yl)anilino]acetate (FluoZin-3) is used very broadly in life sciences as intra- and extracellular Zn(II) sensor selective for Zn(II) over Co(II), Ca(II) and Mg(II) ions at their physiological concentrations. It has been used for determination of relative and absolute levels of exchangeable Zn(II) in cells and extracellular fluids. Despite its popularity, the knowledge of its acid/base and Zn(II) coordination abilities and of its spectroscopic properties remained very limited. Also the published conditional dissociation constant ((C)Kd) values at pH7.4 are slightly discrepant, (15nM or 8.9nM). In this work we determined the (C)Kd for Zn(II) complexation by FluoZin-3 at pH7.4 with nitrilotriacetic acid (NTA) as competitor using two independent methods: fluorimetry and UV-Vis spectroscopy. For the first time, we investigated FluoZin-3 alone and complexed with Zn(II) in the wide range of pH, determining the total of eight pKa values from fluorescence spectra and from various regions of UV-Vis spectra. The validated values of (C)Kd (9.1±0.4nM; -log (C)Kd=8.04) and of the absolute (pH-independent) stability constant log βZnL (8.16±0.05) were provided by fluorescence spectroscopy experiments performed at 1μM concentrations. Our experiments demonstrated that both of aminocarboxylate moieties of FluoZin-3 bind the Zn(II) ion synergistically. PMID:27216451

  8. Cerebral 5-HT2A receptor and serotonin transporter binding in humans are not affected by the val66met BDNF polymorphism status or blood BDNF levels

    DEFF Research Database (Denmark)

    Klein, Anders Bue; Trajkovska, Viktorija; Erritzoe, David;

    2010-01-01

    Recent studies have proposed an interrelation between the brain-derived neurotrophic factor (BDNF) val66met polymorphism and the serotonin system. In this study, we investigated whether the BDNF val66met polymorphism or blood BDNF levels are associated with cerebral 5-hydroxytryptamine 2A (5-HT(2A......)) receptor or serotonin transporter (SERT) binding in healthy subjects. No statistically significant differences in 5-HT(2A) receptor or SERT binding were found between the val/val and met carriers, nor were blood BDNF values associated with SERT binding or 5-HT(2A) receptor binding. In conclusion, val66met...... BDNF polymorphism status is not associated with changes in the serotonergic system. Moreover, BDNF levels in blood do not correlate with either 5-HT(2A) or SERT binding....

  9. Structural stability of Burkholderia cenocepacia biofilms is reliant on eDNA structure and presence of a bacterial nucleic acid binding protein.

    Directory of Open Access Journals (Sweden)

    Laura A Novotny

    Full Text Available Cystic fibrosis (CF is the most common lethal inherited genetic disorder affection Caucasians. Even with medical advances, CF is life-shortening with patients typically surviving only to age 38. Infection of the CF lung by Burkholderia cenocepacia presents exceptional challenges to medical management of these patients as clinically this microbe is resistant to virtually all antibiotics, is highly transmissible and infection of CF patients with this microbe renders them ineligible for lung transplant, often the last lifesaving option. Here we have targeted two abundant components of the B. cenocepacia biofilm for immune intervention: extracellular DNA and DNABII proteins, the latter of which are bacterial nucleic acid binding proteins. Treatment of B. cenocepacia biofilms with antiserum directed at one of these DNABII proteins (integration host factor or IHF resulted in significant disruption of the biofilm. Moreover, when anti-IHF mediated destabilization of a B. cenocepacia biofilm was combined with exposure to traditional antibiotics, B. cenocepacia resident within the biofilm and thereby typically highly resistant to the action of antibiotics, were now rendered susceptible to killing. Pre-incubation of B. cenocepacia with anti-IHF serum prior to exposure to murine CF macrophages, which are normally unable to effectively degrade ingested B. cenocepacia, resulted in a statistically significant increase in killing of phagocytized B. cenocepacia. Collectively, these findings support further development of strategies that target DNABII proteins as a novel approach for treatment of CF patients, particularly those whose lungs are infected with B. cenocepacia.

  10. Pot1通过泛素化修饰影响自身的稳定性%The Stability of Pot1 Affected by the Ubiquitinytion

    Institute of Scientific and Technical Information of China (English)

    杨丹丹; 金蕊; 张金丁; 王亚楠; 黄君健; 魏道智

    2015-01-01

    目的:研究Pot1蛋白的稳定性。方法:利用慢病毒表达载体构建表达外源Flag-Pot1的HeLa细胞稳定克隆,在该克隆中加入CHX抑制新蛋白的合成,检测外源Pot1的半衰期,确定Pot1的稳定性;将Pot1质粒与Ub质粒共转293T细胞后,加入MG132阻止蛋白酶体途径,确定Pot1的稳定性是否受泛素化修饰的影响;构建点突变和截短突变的Pot1质粒,与Ub质粒共转293T细胞后,加入MG132阻止蛋白酶体途径,确定影响Pot1稳定性的区域。结果与结论:Pot1通过泛素化修饰影响自身稳定性;点突变和截断突变实验证实Pot1存在多个泛素化位点,且主要发生在C端400~634位氨基酸残基。%Objective: To study the stability of Pot1. Methods: The stability of Pot1 expression, the half life pe⁃riod of Pot1 expression, in HeLa cells infected retroviruses express Flag-Pot1, was detected after CHX was added to inhibite new proteins expression. In order to validate the relationship between the ubiquitinylation and the stabil⁃ity of Pot1, MG132 was used to prohibit proteasomes after the cotransfection of Pot1 plasmid and Ub plasmid in 293T cells, and then the expression of Pot1 was detected by Western blot. Point mutation and deletion plasmids of Pot1 were constructed, and then were cotransfected in 293T cells with Ub plasmid before MG132 was used to prohibit proteasomes to study definitely the region which affected the stability of Pot1. Results & Conclusion:The stability of Pot1 is affected by ubiquitinytion, and the key region is in 400~634 of Pot1 protein sequence.

  11. Expression, Purification, and Biochemical Characterization of the Antiinflammatory Tristetraprolin: A Zinc-Dependent mRNA Binding Protein Affected by Posttranslational Modifications†,‡

    OpenAIRE

    Cao, Heping

    2004-01-01

    Tristetraprolin (TTP) is a hyperphosphorylated protein that destabilizes mRNA by binding to an AU-rich element (ARE). Mice deficient in TTP develop a severe inflammatory syndrome. The biochemical properties of TTP have not been adequately characterized, due to the difficulties in protein purification and lack of a high-titer antiserum. Full-length human TTP was expressed in human HEK293 cells and purified to at least 70% homogeneity. The purified protein was free of endogenous ARE binding act...

  12. The Factors Affecting the Counting Stability of the Spark Counter%影响火花计数器计数稳定性的因素

    Institute of Scientific and Technical Information of China (English)

    郝启辰; 过惠平; 王洪超

    2013-01-01

    设计不同的实验,对影响火花计数器计数稳定性的因素进行了研究.主要包括稳压块重量、CR-39的蚀刻情况、清扫电压以及电极表面的光滑程度.通过实验找到了适合CR-39在火花计数器上进行稳定径迹判读的工作条件.%The factors what affect the counting stability of the spark counter including the heft, the CR-39 etched, cleaning voltage and the electrode surface smoothness have been studied by the different experiments.And the best methods for the spark counter are found to interpret well.

  13. C4b-binding protein is present in affected areas of myocardial infarction during the acute inflammatory phase and covers a larger area than C3.

    Directory of Open Access Journals (Sweden)

    Leendert A Trouw

    Full Text Available BACKGROUND: During myocardial infarction reduced blood flow in the heart muscle results in cell death. These dying/dead cells have been reported to bind several plasma proteins such as IgM and C-reactive protein (CRP. In the present study we investigated whether fluid-phase complement inhibitor C4b-binding protein (C4BP would also bind to the infarcted heart tissue. METHODS AND FINDINGS: Initial studies using immunohistochemistry on tissue arrays for several cardiovascular disorders indicated that C4BP can be found in heart tissue in several cardiac diseases but that it is most abundantly found in acute myocardial infarction (AMI. This condition was studied in more detail by analyzing the time window and extent of C4BP positivity. The binding of C4BP correlates to the same locations as C3b, a marker known to correlate to the patterns of IgM and CRP staining. Based on criteria that describe the time after infarction we were able to pinpoint that C4BP binding is a relatively early marker of tissue damage in myocardial infarction with a peak of binding between 12 hours and 5 days subsequent to AMI, the phase in which infiltration of neutrophilic granulocytes in the heart is the most extensive. CONCLUSIONS: C4BP, an important fluid-phase inhibitor of the classical and lectin pathway of complement activation binds to jeopardized cardiomyocytes early after AMI and co-localizes to other well known markers such as C3b.

  14. Mutation of light-dependent phosphorylation sites of the Drosophila transient receptor potential-like (TRPL) ion channel affects its subcellular localization and stability.

    Science.gov (United States)

    Cerny, Alexander C; Oberacker, Tina; Pfannstiel, Jens; Weigold, Sebastian; Will, Carina; Huber, Armin

    2013-05-31

    The Drosophila phototransduction cascade terminates in the opening of the ion channel transient receptor potential (TRP) and TRP-like (TRPL). Contrary to TRP, TRPL undergoes light-dependent subcellular trafficking between rhabdomeric photoreceptor membranes and an intracellular storage compartment, resulting in long term light adaptation. Here, we identified in vivo phosphorylation sites of TRPL that affect TRPL stability and localization. Quantitative mass spectrometry revealed a light-dependent change in the TRPL phosphorylation pattern. Mutation of eight C-terminal phosphorylation sites neither affected multimerization of the channels nor the electrophysiological response of flies expressing the mutated channels. However, these mutations resulted in mislocalization and enhanced degradation of TRPL after prolonged dark-adaptation. Mutation of subsets of the eight C-terminal phosphorylation sites also led to a reduction of TRPL content and partial mislocalization in the dark. This suggests that a light-dependent switch in the phosphorylation pattern of the TRPL channel mediates stable expression of TRPL in the rhabdomeres upon prolonged dark-adaptation. PMID:23592784

  15. Mutation of Light-dependent Phosphorylation Sites of the Drosophila Transient Receptor Potential-like (TRPL) Ion Channel Affects Its Subcellular Localization and Stability*

    Science.gov (United States)

    Cerny, Alexander C.; Oberacker, Tina; Pfannstiel, Jens; Weigold, Sebastian; Will, Carina; Huber, Armin

    2013-01-01

    The Drosophila phototransduction cascade terminates in the opening of the ion channel transient receptor potential (TRP) and TRP-like (TRPL). Contrary to TRP, TRPL undergoes light-dependent subcellular trafficking between rhabdomeric photoreceptor membranes and an intracellular storage compartment, resulting in long term light adaptation. Here, we identified in vivo phosphorylation sites of TRPL that affect TRPL stability and localization. Quantitative mass spectrometry revealed a light-dependent change in the TRPL phosphorylation pattern. Mutation of eight C-terminal phosphorylation sites neither affected multimerization of the channels nor the electrophysiological response of flies expressing the mutated channels. However, these mutations resulted in mislocalization and enhanced degradation of TRPL after prolonged dark-adaptation. Mutation of subsets of the eight C-terminal phosphorylation sites also led to a reduction of TRPL content and partial mislocalization in the dark. This suggests that a light-dependent switch in the phosphorylation pattern of the TRPL channel mediates stable expression of TRPL in the rhabdomeres upon prolonged dark-adaptation. PMID:23592784

  16. The thermodynamic stability of insulin disulfides is not affected by the C-domain of insulin-like growth factor 1

    Institute of Scientific and Technical Information of China (English)

    GUO; Zhanyun(郭占云); FENG; Youmin(冯佑民)

    2002-01-01

    Both Insulin and insulin-like growth factor 1 are members of insulin superfamily. They share homologous primary and tertiary structure as well as weakly overlapping biological activity. However, their folding behavior is different: insulin and its recombinant precursor (PIP) fold into one unique tertiary structure, while IGF-1 folds into two disulfides isomers with similar thermodynamic stability. To elucidate the molecular mechanism of their different folding behavior, we prepared a single-chain hybrid of insulin and IGF-1, [B10Glu]Ins/IGF-1(C), and studied its folding behavior compared with that of PIP and IGF-1. We also separated a major non-native disulfides isomer of the hybrid and studied its refolding. The data showed that the C-domain of IGF-1 did not affect the folding thermodynamics of insulin, that is, the primary structure of the hybrid encoded only one thermodynamically stable disulfides linkage. However, the folding kinetics of insulin was affected by the C-domain of IGF-1.

  17. N-Glycosylation of Human R-Spondin 1 Is Required for Efficient Secretion and Stability but Not for Its Heparin Binding Ability

    Directory of Open Access Journals (Sweden)

    Chiung-Fang Chang

    2016-06-01

    Full Text Available R-spondin 1 (Rspo1 plays an essential role in stem cell biology by potentiating Wnt signaling activity. Despite the fact that Rspo1 holds therapeutic potential for a number of diseases, its biogenesis is not fully elucidated. All Rspo proteins feature two amino-terminal furin-like repeats, which are responsible for Wnt signal potentiation, and a thrombospondin type 1 (TSR1 domain that can provide affinity towards heparan sulfate proteoglycans. Using chemical inhibitors, deglycosylase and site-directed mutagenesis, we found that human Rspo1 and Rspo3 are both N-glycosylated at N137, a site near the C-terminus of the furin repeat 2 domain, and Rspo2 is N-glycosylated at N160, a position near the N-terminus of TSR1 domain. Elimination of N-glycosylation at these sites affects their accumulation in media but have no effect on the ability towards heparin. Introduction of the N-glycosylation site to Rspo2 mutant at the position homologous to N137 in Rspo1 restored full glycosylation and rescued the accumulation defect of nonglycosylated Rspo2 mutant in media. Similar effect can be observed in the N137 Rspo1 or Rspo3 mutant engineered with Rspo2 N-glycosylation site. The results highlight the importance of N-glycosylation at these two positions in efficient folding and secretion of Rspo family. Finally, we further showed that human Rspo1 is subjected to endoplasmic reticulum (ER quality control in N-glycan-dependent manner. While N-glycan of Rspo1 plays a role in its intracellular stability, it had little effect on secreted Rspo1. Our findings provide evidence for the critical role of N-glycosylation in the biogenesis of Rspo1.

  18. N-Glycosylation of Human R-Spondin 1 Is Required for Efficient Secretion and Stability but Not for Its Heparin Binding Ability.

    Science.gov (United States)

    Chang, Chiung-Fang; Hsu, Li-Sung; Weng, Chieh-Yu; Chen, Chih-Kai; Wang, Shu-Ying; Chou, Yi-Hwa; Liu, Yan-Yu; Yuan, Zi-Xiu; Huang, Wen-Ying; Lin, Ho; Chen, Yau-Hung; Tsai, Jen-Ning

    2016-01-01

    R-spondin 1 (Rspo1) plays an essential role in stem cell biology by potentiating Wnt signaling activity. Despite the fact that Rspo1 holds therapeutic potential for a number of diseases, its biogenesis is not fully elucidated. All Rspo proteins feature two amino-terminal furin-like repeats, which are responsible for Wnt signal potentiation, and a thrombospondin type 1 (TSR1) domain that can provide affinity towards heparan sulfate proteoglycans. Using chemical inhibitors, deglycosylase and site-directed mutagenesis, we found that human Rspo1 and Rspo3 are both N-glycosylated at N137, a site near the C-terminus of the furin repeat 2 domain, and Rspo2 is N-glycosylated at N160, a position near the N-terminus of TSR1 domain. Elimination of N-glycosylation at these sites affects their accumulation in media but have no effect on the ability towards heparin. Introduction of the N-glycosylation site to Rspo2 mutant at the position homologous to N137 in Rspo1 restored full glycosylation and rescued the accumulation defect of nonglycosylated Rspo2 mutant in media. Similar effect can be observed in the N137 Rspo1 or Rspo3 mutant engineered with Rspo2 N-glycosylation site. The results highlight the importance of N-glycosylation at these two positions in efficient folding and secretion of Rspo family. Finally, we further showed that human Rspo1 is subjected to endoplasmic reticulum (ER) quality control in N-glycan-dependent manner. While N-glycan of Rspo1 plays a role in its intracellular stability, it had little effect on secreted Rspo1. Our findings provide evidence for the critical role of N-glycosylation in the biogenesis of Rspo1. PMID:27314333

  19. Conserved retinoblastoma protein-binding motif in human cytomegalovirus UL97 kinase minimally impacts viral replication but affects susceptibility to maribavir

    Directory of Open Access Journals (Sweden)

    Chou Sunwen

    2009-01-01

    Full Text Available Abstract The UL97 kinase has been shown to phosphorylate and inactivate the retinoblastoma protein (Rb and has three consensus Rb-binding motifs that might contribute to this activity. Recombinant viruses containing mutations in the Rb-binding motifs generally replicated well in human foreskin fibroblasts with only a slight delay in replication kinetics. Their susceptibility to the specific UL97 kinase inhibitor, maribavir, was also examined. Mutation of the amino terminal motif, which is involved in the inactivation of Rb, also renders the virus hypersensitive to the drug and suggests that the motif may play a role in its mechanism of action.

  20. Comprehensive Analysis of Contributions from Protein Conformational Stability and Major Histocompatibility Complex Class II-Peptide Binding Affinity to CD4+ Epitope Immunogenicity in HIV-1 Envelope Glycoprotein

    OpenAIRE

    Li, Tingfeng; Steede, N. Kalaya; Nguyen, Hong-Nam P.; Freytag, Lucy C.; McLachlan, James B.; Mettu, Ramgopal R.; Robinson, James E.; Landry, Samuel J.

    2014-01-01

    Helper T-cell epitope dominance in human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein gp120 is not adequately explained by peptide binding to major histocompatibility complex (MHC) proteins. Antigen processing potentially influences epitope dominance, but few, if any, studies have attempted to reconcile the influences of antigen processing and MHC protein binding for all helper T-cell epitopes of an antigen. Epitopes of gp120 identified in both humans and mice occur on the C-te...

  1. COX7A2L is a mitochondrial complex III-binding protein that stabilizes the III2+IV supercomplex without affecting respirasome formation

    OpenAIRE

    Pérez-Pérez, Rafael; Lobo-Jarne, Teresa; Milenkovic, Dusanka; Mourier, Arnaud; Bratic, Ana; García-Bartolomé, Alberto; Fernández-Vizarra, Erika; Cadenas, Susana; Delmiro, Aitor; García-Consuegra, Inés; Arenas, Joaquín; Martín, Miguel A.; Larsson, Nils-Göran; Ugalde, Cristina

    2016-01-01

    Mitochondrial respiratory chain (MRC) complexes I, III and IV associate into a variety of supramolecular structures known as supercomplexes and respirasomes. While COX7A2L was originally described as a supercomplex-specific factor responsible for the dynamic association of complex IV into these structures to adapt MRC function to metabolic variations, this role has been disputed. Here we further examine the functional significance of COX7A2L in the structural organization of the mammalian res...

  2. COX7A2L Is a Mitochondrial Complex III Binding Protein that Stabilizes the III2+IV Supercomplex without Affecting Respirasome Formation

    OpenAIRE

    Rafael Pérez-Pérez; Teresa Lobo-Jarne; Dusanka Milenkovic; Arnaud Mourier; Ana Bratic; Alberto García-Bartolomé; Erika Fernández-Vizarra; Susana Cadenas; Aitor Delmiro; Inés García-Consuegra; Joaquín Arenas; Miguel A. Martín; Nils-Göran Larsson; Cristina Ugalde

    2016-01-01

    Mitochondrial respiratory chain (MRC) complexes I, III, and IV associate into a variety of supramolecular structures known as supercomplexes and respirasomes. While COX7A2L was originally described as a supercomplex-specific factor responsible for the dynamic association of complex IV into these structures to adapt MRC function to metabolic variations, this role has been disputed. Here, we further examine the functional significance of COX7A2L in the structural organization of the mammalian r...

  3. How Do Structure and Charge Affect Metal-Complex Binding to DNA? An Upper-Division Integrated Laboratory Project Using Cyclic Voltammetry

    Science.gov (United States)

    Kulczynska, Agnieszka; Johnson, Reed; Frost, Tony; Margerum, Lawrence D.

    2011-01-01

    An advanced undergraduate laboratory project is described that integrates inorganic, analytical, physical, and biochemical techniques to reveal differences in binding between cationic metal complexes and anionic DNA (herring testes). Students were guided to formulate testable hypotheses based on the title question and a list of different metal…

  4. The Binding Ring Illusion: assimilation affects the perceived size of a circular array [v1; ref status: indexed, http://f1000r.es/nv

    Directory of Open Access Journals (Sweden)

    J Daniel McCarthy

    2013-02-01

    Full Text Available Our perception of an object’s size arises from the integration of multiple sources of visual information including retinal size, perceived distance and its size relative to other objects in the visual field. This constructive process is revealed through a number of classic size illusions such as the Delboeuf Illusion, the Ebbinghaus Illusion and others illustrating size constancy. Here we present a novel variant of the Delbouef and Ebbinghaus size illusions that we have named the Binding Ring Illusion. The illusion is such that the perceived size of a circular array of elements is underestimated when superimposed by a circular contour – a binding ring – and overestimated when the binding ring slightly exceeds the overall size of the array. Here we characterize the stimulus conditions that lead to the illusion, and the perceptual principles that underlie it. Our findings indicate that the perceived size of an array is susceptible to the assimilation of an explicitly defined superimposed contour. Our results also indicate that the assimilation process takes place at a relatively high level in the visual processing stream, after different spatial frequencies have been integrated and global shape has been constructed. We hypothesize that the Binding Ring Illusion arises due to the fact that the size of an array of elements is not explicitly defined and therefore can be influenced (through a process of assimilation by the presence of a superimposed object that does have an explicit size.

  5. The Binding Ring Illusion: assimilation affects the perceived size of a circular array [v2; ref status: indexed, http://f1000r.es/12q

    Directory of Open Access Journals (Sweden)

    J Daniel McCarthy

    2013-04-01

    Full Text Available Our perception of an object’s size arises from the integration of multiple sources of visual information including retinal size, perceived distance and its size relative to other objects in the visual field. This constructive process is revealed through a number of classic size illusions such as the Delboeuf Illusion, the Ebbinghaus Illusion and others illustrating size constancy. Here we present a novel variant of the Delbouef and Ebbinghaus size illusions that we have named the Binding Ring Illusion. The illusion is such that the perceived size of a circular array of elements is underestimated when superimposed by a circular contour – a binding ring – and overestimated when the binding ring slightly exceeds the overall size of the array. Here we characterize the stimulus conditions that lead to the illusion, and the perceptual principles that underlie it. Our findings indicate that the perceived size of an array is susceptible to the assimilation of an explicitly defined superimposed contour. Our results also indicate that the assimilation process takes place at a relatively high level in the visual processing stream, after different spatial frequencies have been integrated and global shape has been constructed. We hypothesize that the Binding Ring Illusion arises due to the fact that the size of an array of elements is not explicitly defined and therefore can be influenced (through a process of assimilation by the presence of a superimposed object that does have an explicit size.

  6. Effect of phosphorothioate modifications on the ability of GTn oligodeoxynucleotides to specifically recognize single-stranded DNA-binding proteins and to affect human cancer cellular growth.

    Science.gov (United States)

    Morassutti, C; Scaggiante, B; Dapas, B; Xodo, L; Tell, G; Quadrifoglio, F

    1999-12-01

    We have previously identified phosphodiester oligonucleotides exclusively made of G and T bases, named GTn, that significantly inhibit human cancer cell growth and recognize specific nuclear single-stranded DNA binding proteins. We wished to examine the ability of the modified GTn oligonucleotides with different degrees of phosphorothioate modifications to bind specifically to the same nuclear proteins recognized by the GTn phosphodiester analogues and their cytotoxic effect on the human T-lymphoblastic CCRF-CEM cell line. We showed that the full phosphorothioate GTn oligonucleotide was neither able to specifically recognize those nuclear proteins, nor cytotoxic. In contrast, the 3'-phosphorothioate-protected GTn oligonucleotides can maintain the specific protein-binding activity. The end-modified phosphorothioate oligonucleotides were also able to elicit the dose-dependent cell growth inhibition effect, but a loss in the cytotoxic ability was observed increasing the extent of sulphur modification of the sequences. Our results indicate that phosphorothioate oligonucleotides directed at specific single-stranded DNA-binding proteins should contain a number of phosphorothioate end-linkages which should be related to the length of the sequence, in order to maintain the same biological activities exerted by their phosphodiester analogues.

  7. Climate, soil texture, and soil types affect the contributions of fine-fraction-stabilized carbon to total soil organic carbon in different land uses across China.

    Science.gov (United States)

    Cai, Andong; Feng, Wenting; Zhang, Wenju; Xu, Minggang

    2016-05-01

    Mineral-associated organic carbon (MOC), that is stabilized by fine soil particles (i.e., silt plus clay, organic carbon (SOC) persistence and sequestration, due to its large contribution to total SOC (TSOC) and long turnover time. Our objectives were to investigate how climate, soil type, soil texture, and agricultural managements affect MOC contributions to TSOC in China. We created a dataset from 103 published papers, including 1106 data points pairing MOC and TSOC across three major land use types: cropland, grassland, and forest. Overall, the MOC/TSOC ratio ranged from 0.27 to 0.80 and varied significantly among soil groups in cropland, grassland, and forest. Croplands and forest exhibited significantly higher median MOC/TSOC ratios than in grassland. Moreover, forest and grassland soils in temperate regions had higher MOC/TSOC ratios than in subtropical regions. Furthermore, the MOC/TSOC ratio was much higher in ultisol, compared with the other soil types. Both the MOC content and MOC/TSOC ratio were positively correlated with the amount of fine fraction (silt plus clay) in soil, highlighting the importance of soil texture in stabilizing organic carbon across various climate zones. In cropland, different fertilization practices and land uses (e.g., upland, paddy, and upland-paddy rotation) significantly altered MOC/TSOC ratios, but not in cropping systems (e.g., mono- and double-cropping) characterized by climatic differences. This study demonstrates that the MOC/TSOC ratio is mainly driven by soil texture, soil types, and related climate and land uses, and thus the variations in MOC/TSOC ratios should be taken into account when quantitatively estimating soil C sequestration potential of silt plus clay particles on a large scale. PMID:26905446

  8. Climate, soil texture, and soil types affect the contributions of fine-fraction-stabilized carbon to total soil organic carbon in different land uses across China.

    Science.gov (United States)

    Cai, Andong; Feng, Wenting; Zhang, Wenju; Xu, Minggang

    2016-05-01

    Mineral-associated organic carbon (MOC), that is stabilized by fine soil particles (i.e., silt plus clay, organic carbon (SOC) persistence and sequestration, due to its large contribution to total SOC (TSOC) and long turnover time. Our objectives were to investigate how climate, soil type, soil texture, and agricultural managements affect MOC contributions to TSOC in China. We created a dataset from 103 published papers, including 1106 data points pairing MOC and TSOC across three major land use types: cropland, grassland, and forest. Overall, the MOC/TSOC ratio ranged from 0.27 to 0.80 and varied significantly among soil groups in cropland, grassland, and forest. Croplands and forest exhibited significantly higher median MOC/TSOC ratios than in grassland. Moreover, forest and grassland soils in temperate regions had higher MOC/TSOC ratios than in subtropical regions. Furthermore, the MOC/TSOC ratio was much higher in ultisol, compared with the other soil types. Both the MOC content and MOC/TSOC ratio were positively correlated with the amount of fine fraction (silt plus clay) in soil, highlighting the importance of soil texture in stabilizing organic carbon across various climate zones. In cropland, different fertilization practices and land uses (e.g., upland, paddy, and upland-paddy rotation) significantly altered MOC/TSOC ratios, but not in cropping systems (e.g., mono- and double-cropping) characterized by climatic differences. This study demonstrates that the MOC/TSOC ratio is mainly driven by soil texture, soil types, and related climate and land uses, and thus the variations in MOC/TSOC ratios should be taken into account when quantitatively estimating soil C sequestration potential of silt plus clay particles on a large scale.

  9. Major Bio-Factors Affecting Beef Color Stability%影响牛肉肉色稳定性的主要生化因子

    Institute of Scientific and Technical Information of China (English)

    陈景宜; 牛力; 黄明; 周光宏

    2012-01-01

    [Objective] The experiment was designed to investigate the major bio-factors affecting color stability from different bovine muscles, [Method] Three representative bovine muscles- M. longissimus lumborum (LL), M. semimembranosus (SM), and M. psoas major (PM) were obtained from 8 beef carcasses. Instrumental color, pigment content, pH value, MDA content, NADH concentration, LDH and metmyoglobin reductase activity were measured every two days over a period of 7d retail display at 0-4℃. [Result] The order of color stability of the three muscles was: LL>SM>PM. The a* value, NADH concentration, LDH and metmyoglobin reductase activity was the highest in LL and the MDA content was the least. While the a* value, NADH concentration, LDH and metmyoglobin reductase activity of PM was the lowest and MDA content was the highest. I Conclusion] NADH concentration, LDH and metmyoglobin reductase activity in beef muscle have a significant correlation with color stability (P<0.05) .%[目的]探讨影响不同部位的牛肉肉色稳定性差异的主要生化因素.[方法]从8头牛胴体上分别取背最长肌、半膜肌和腰大肌,在0-4℃冷藏7d,每隔1d分别测定肉色、色素含量、pH、MDA含量、NADH浓度、乳酸脱氢酶和高铁肌红蛋白还原酶活性等指标.[结果]背最长肌在整个冷藏期间的a*值最高且变化最小,MDA含量最少,NADH浓度、乳酸脱氢酶和高铁肌红蛋白还原酶活性最高,肉色最稳定;半膜肌居中,而腰大肌的a*值最小,变化最显著,MDA含量最高,NADH浓度、乳酸脱氢酶和高铁肌红蛋白还原酶活性最低,肉色最不稳定.[结论]牛肉肉色稳定性与其NADH浓度、乳酸脱氢酶和高铁肌红蛋白还原酶活性显著相关(P<0.05).

  10. RNA-binding proteins in plants: the tip of an iceberg?

    Science.gov (United States)

    Fedoroff, Nina V.; Federoff, N. V. (Principal Investigator)

    2002-01-01

    RNA-binding proteins, which are involved in the synthesis, processing, transport, translation, and degradation of RNA, are emerging as important, often multifunctional, cellular regulatory proteins. Although relatively few RNA-binding proteins have been studied in plants, they are being identified with increasing frequency, both genetically and biochemically. RNA-binding proteins that regulate chloroplast mRNA stability and translation in response to light and that have been elegantly analyzed in Clamydomonas reinhardtii have counterparts with similar functions in higher plants. Several recent reports describe mutations in genes encoding RNA-binding proteins that affect plant development and hormone signaling.

  11. Bioreversible Derivatives of Phenol. 1. The Role of Human Serum Albumin as Related to the Stability and Binding Properties of Carbonate Esters with Fatty Acid-like Structures in Aqueous Solution and Biological Media

    Directory of Open Access Journals (Sweden)

    Claus Larsen

    2007-10-01

    Full Text Available With the overall objective of assessing the potential of utilizing plasma protein binding interactions in combination with the prodrug approach for improving the pharmacokinetics of drug substances, a series of model carbonate ester prodrugs of phenol, encompassing derivatives with fatty acid-like structures, were characterized in vitro. Stability of the derivatives was studied in aqueous solution, human serum albumin solution, human plasma, and rat liver homogenate at 37°C. Stability of the derivatives in aqueous solution varied widely, with half-lives ranging from 31 to 1.7 × 104 min at pH 7.4 and 37°C. The carbonate esters were subject to catalysis by plasma esterases except for the t-butyl and acetic acid derivatives, which were stabilized in both human plasma and human serum albumin solutions relative to buffer. In most cases, however, hydrolysis was accelerated in the presence of human serum albumin indicating that the derivatives interacted with the protein, a finding which was confirmed using the p-nitrophenyl acetate kinetic assay. Different human serum albumin binding properties of the phenol model prodrugs with fatty acid-like structure and neutral carbonate esters were observed. In the context of utilizing plasma protein binding in combination with the prodrug approach for optimizing drug pharmacokinetics, the esterase-like properties of human serum albumin towards the carbonate esters potentially allowing the protein to act as a catalyst of parent compound regenerations is interesting.

  12. Insight Into Folding,Binding and Stability of Insulin by NMR%胰岛素折叠、结合与稳定性的核磁共振研究

    Institute of Scientific and Technical Information of China (English)

    华庆新

    2004-01-01

    Insulin is one of the most important hormonal regulators of metabolism. Since the diabetes patients increase dramatically, the chemical properties, biological and physiological effects of insulin had been extensively studied. In last decade the development of NMR technique allowed us to determine the solution structures of insulin and its variety mutants in various conditions, so that the knowledge of folding, binding and stability of insulin in solution have been largely increased. The solution structure of insulin monomers is essentially identical to those of insulin monomers within the dimer and hexamer as determined by X-ray diffraction. The studies of insulin mutants at the putative residues for receptor binding explored the possible conformational change and fitting between insulin and its receptor. The systematical studies of disulfide paring coupled insulin folding intermediates revealed that in spite of the conformational variety of the intermediates, one structural feature is always remained: a "native-like B chain super-secondary structure", which consists of B9-B19 helix with adjoining B23-B26 segment folded back against the central segment of B chain, an internal cystine A20-B19 disulfide bridge and a short α-helix at C-terminal of A chain linked. The "super-secondary structure" might be the "folding nucleus" in insulin folding mechanism. Cystine A20-B19 is the most important one among three disulfides to stabilize the nascent polypeptide in early stage of the folding. The NMR structure of C.elegans insulin-like peptide resembles that of human insulin and the peptide interacts with human insulin receptor. Other members of insulin super-family adopt the "insulin fold" mostly. The structural study of insulin-insulin receptor complex, that of C.elegans and other invertebrate insulin-like peptide, insulin fibril study and protein disulfide isomerase (PDI) assistant proinsulin folding study will be new topics in future to get insight into folding, binding

  13. Phosphorylation of thymidylate synthase affects slow-binding inhibition by 5-fluoro-dUMP and N(4)-hydroxy-dCMP.

    Science.gov (United States)

    Ludwiczak, Jan; Maj, Piotr; Wilk, Piotr; Frączyk, Tomasz; Ruman, Tomasz; Kierdaszuk, Borys; Jarmuła, Adam; Rode, Wojciech

    2016-04-01

    Endogenous thymidylate synthases, isolated from tissues or cultured cells of the same specific origin, have been reported to show differing slow-binding inhibition patterns. These were reflected by biphasic or linear dependence of the inactivation rate on time and accompanied by differing inhibition parameters. Considering its importance for chemotherapeutic drug resistance, the possible effect of thymidylate synthase inhibition by post-translational modification was tested, e.g. phosphorylation, by comparing sensitivities to inhibition by two slow-binding inhibitors, 5-fluoro-dUMP and N(4)-hydroxy-dCMP, of two fractions of purified recombinant mouse enzyme preparations, phosphorylated and non-phosphorylated, separated by metal oxide/hydroxide affinity chromatography on Al(OH)3 beads. The modification, found to concern histidine residues and influence kinetic properties by lowering Vmax, altered both the pattern of dependence of the inactivation rate on time from linear to biphasic, as well as slow-binding inhibition parameters, with each inhibitor studied. Being present on only one subunit of at least a great majority of phosphorylated enzyme molecules, it probably introduced dimer asymmetry, causing the altered time dependence of the inactivation rate pattern (biphasic with the phosphorylated enzyme) and resulting in asymmetric binding of each inhibitor studied. The latter is reflected by the ternary complexes, stable under denaturing conditions, formed by only the non-phosphorylated subunit of the phosphorylated enzyme with each of the two inhibitors and N(5,10)-methylenetetrahydrofolate. Inhibition of the phosphorylated enzyme by N(4)-hydroxy-dCMP was found to be strongly dependent on [Mg(2+)], cations demonstrated previously to also influence the activity of endogenous mouse TS isolated from tumour cells.

  14. The RNA-binding protein quaking maintains endothelial barrier function and affects VE-cadherin and β-catenin protein expression.

    Science.gov (United States)

    de Bruin, Ruben G; van der Veer, Eric P; Prins, Jurriën; Lee, Dae Hyun; Dane, Martijn J C; Zhang, Huayu; Roeten, Marko K; Bijkerk, Roel; de Boer, Hetty C; Rabelink, Ton J; van Zonneveld, Anton Jan; van Gils, Janine M

    2016-02-24

    Proper regulation of endothelial cell-cell contacts is essential for physiological functioning of the endothelium. Interendothelial junctions are actively involved in the control of vascular leakage, leukocyte diapedesis, and the initiation and progression of angiogenesis. We found that the RNA-binding protein quaking is highly expressed by endothelial cells, and that its expression was augmented by prolonged culture under laminar flow and the transcription factor KLF2 binding to the promoter. Moreover, we demonstrated that quaking directly binds to the mRNA of VE-cadherin and β-catenin and can induce mRNA translation mediated by the 3'UTR of these genes. Reduced quaking levels attenuated VE-cadherin and β-catenin expression and endothelial barrier function in vitro and resulted in increased bradykinin-induced vascular leakage in vivo. Taken together, we report that quaking is essential in maintaining endothelial barrier function. Our results provide novel insight into the importance of post-transcriptional regulation in controlling vascular integrity.

  15. The size, shape and specificity of the sugar-binding site of the jacalin-related lectins is profoundly affected by the proteolytic cleavage of the subunits.

    Science.gov (United States)

    Houlès Astoul, Corinne; Peumans, Willy J; van Damme, Els J M; Barre, Annick; Bourne, Yves; Rougé, Pierre

    2002-11-01

    Mannose-specific lectins with high sequence similarity to jacalin and the Maclura pomifera agglutinin have been isolated from species belonging to the families Moraceae, Convolvulaceae, Brassicaceae, Asteraceae, Poaceae and Musaceae. Although these novel mannose-specific lectins are undoubtedly related to the galactose-specific Moraceae lectins there are several important differences. Apart from the obvious differences in specificity, the mannose- and galactose-specific jacalin-related lectins differ in what concerns their biosynthesis and processing, intracellular location and degree of oligomerization of the protomers. Taking into consideration that the mannose-specific lectins are widely distributed in higher plants, whereas their galactose-specific counterparts are confined to a subgroup of the Moraceae sp. one can reasonably assume that the galactose-specific Moraceae lectins are a small-side group of the main family. The major change that took place in the structure of the binding site of the diverging Moraceae lectins concerns a proteolytic cleavage close to the N-terminus of the protomer. To corroborate the impact of this change, the specificity of jacalin was re-investigated using surface plasmon resonance analysis. This approach revealed that in addition to galactose and N -acetylgalactosamine, the carbohydrate-binding specificity of jacalin extends to mannose, glucose, N -acetylmuramic acid and N -acetylneuraminic acid. Owing to this broad carbohydrate-binding specificity, jacalin is capable of recognizing complex glycans from plant pathogens or predators.

  16. The genetic background affects composition, oxidative stability and quality traits of Iberian dry-cured hams: purebred Iberian versus reciprocal Iberian × Duroc crossbred pigs.

    Science.gov (United States)

    Fuentes, Verónica; Ventanas, Sonia; Ventanas, Jesús; Estévez, Mario

    2014-02-01

    This study examined the physico-chemical characteristics, oxidative stability and sensory properties of Iberian cry-cured hams as affected by the genetic background of the pigs: purebred Iberian (PBI) pigs vs reciprocal cross-bred Iberian × Duroc pigs (IB × D pigs: Iberian dams × Duroc sires; D × IB pigs: Duroc dams × Iberian sires). Samples from PBI pigs contained significantly higher amounts of IMF, monounsaturated fatty acids, heme pigments and iron than those from crossbred pigs. The extent of lipid and protein oxidation was significantly larger in dry-cured hams of crossbred pigs than in those from PBI pigs. Dry-cured hams from PBI pigs were defined by positive sensory properties (i.e. redness, brightness and juiciness) while hams from crossbred pigs were ascribed to negative ones (i.e. hardness, bitterness and sourness). Hams from PBI pigs displayed a superior quality than those from crossbred pigs. The position of the dam or the sire in reciprocal Iberian × Duroc crosses had no effect on the quality of Iberian hams.

  17. Parameters affecting the stability of the digestate from a two-stage anaerobic process treating the organic fraction of municipal solid waste

    International Nuclear Information System (INIS)

    This paper focused on the factors affecting the respiration rate of the digestate taken from a continuous anaerobic two-stage process treating the organic fraction of municipal solid waste (OFMSW). The process involved a hydrolytic reactor (HR) that produced a leachate fed to a submerged anaerobic membrane bioreactor (SAMBR). It was found that a volatile solids (VS) removal in the range 40-75% and an operating temperature in the HR between 21 and 35 oC resulted in digestates with similar respiration rates, with all digestates requiring 17 days of aeration before satisfying the British Standard Institution stability threshold of 16 mg CO2 g VS-1 day-1. Sanitization of the digestate at 65 oC for 7 days allowed a mature digestate to be obtained. At 4 g VS L-1 d-1 and Solid Retention Times (SRT) greater than 70 days, all the digestates emitted CO2 at a rate lower than 25 mg CO2 g VS-1 d-1 after 3 days of aeration, while at SRT lower than 20 days all the digestates displayed a respiration rate greater than 25 mg CO2 g VS-1 d-1. The compliance criteria for Class I digestate set by the European Commission (EC) and British Standard Institution (BSI) could not be met because of nickel and chromium contamination, which was probably due to attrition of the stainless steel stirrer in the HR.

  18. Mechanism of formation of the C-terminal β-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. Part I. Importance of hydrophobic interactions in stabilization of β-hairpin structure

    OpenAIRE

    Skwierawska, Agnieszka; Makowska, Joanna; Ołdziej, Stanisław; Liwo, Adam; Scheraga, Harold A.

    2009-01-01

    We previously studied a 16-amino acid-residue fragment of the C-terminal β-hairpin (residues 46–61), [IG(46–61)], of the B3 domain of the immunoglobulin binding protein G from Streptoccocus, and found that hydrophobic interactions and the turn region play an important role in stabilizing the structure. Based on these results, we carried out systematic structural studies of peptides derived from the sequence of IG(46–61) by systematically shortening the peptide by one residue at a time from bo...

  19. Ligand induced stabilization of the melting temperature of the HSV-1 single-strand DNA binding protein using the thermal shift assay

    OpenAIRE

    Rupesh, Kanchi Ravi; Smith, Aaron; Boehmer, Paul E.

    2014-01-01

    We have adapted the thermal shift assay to measure the ligand binding properties of the herpes simplex virus-1 single-strand DNA binding protein, ICP8. By measuring SYPRO Orange fluorescence in microtiter plates using a fluorescence-enabled thermal cycler, we have quantified the effects of oligonucleotide ligands on the melting temperature of ICP8. We found that single-stranded oligomers raise the melting temperature of ICP8 in a length- and concentration-dependent manner, ranging from 1 °C f...

  20. Salicylic acid binding of mitochondrial alpha-ketoglutarate dehydrogenase E2 affects mitochondrial oxidative phosphorylation and electron transport chain components and plays a role in basal defense against tobacco mosaic virus in tomato.

    Science.gov (United States)

    Liao, Yangwenke; Tian, Miaoying; Zhang, Huan; Li, Xin; Wang, Yu; Xia, Xiaojian; Zhou, Jie; Zhou, Yanhong; Yu, Jingquan; Shi, Kai; Klessig, Daniel F

    2015-02-01

    Salicylic acid (SA) plays a critical role in plant defense against pathogen invasion. SA-induced viral defense in plants is distinct from the pathways mediating bacterial and fungal defense and involves a specific pathway mediated by mitochondria; however, the underlying mechanisms remain largely unknown. The SA-binding activity of the recombinant tomato (Solanum lycopersicum) alpha-ketoglutarate dehydrogenase (Slα-kGDH) E2 subunit of the tricarboxylic acid (TCA) cycle was characterized. The biological role of this binding in plant defenses against tobacco mosaic virus (TMV) was further investigated via Slα-kGDH E2 silencing and transient overexpression in plants. Slα-kGDH E2 was found to bind SA in two independent assays. SA treatment, as well as Slα-kGDH E2 silencing, increased resistance to TMV. SA did not further enhance TMV defense in Slα-kGDH E2-silenced tomato plants but did reduce TMV susceptibility in Nicotiana benthamiana plants transiently overexpressing Slα-kGDH E2. Furthermore, Slα-kGDH E2-silencing-induced TMV resistance was fully blocked by bongkrekic acid application and alternative oxidase 1a silencing. These results indicated that binding by Slα-kGDH E2 of SA acts upstream of and affects the mitochondrial electron transport chain, which plays an important role in basal defense against TMV. The findings of this study help to elucidate the mechanisms of SA-induced viral defense.

  1. Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. I. Importance of hydrophobic interactions in stabilization of beta-hairpin structure.

    Science.gov (United States)

    Skwierawska, Agnieszka; Makowska, Joanna; Ołdziej, Stanisław; Liwo, Adam; Scheraga, Harold A

    2009-06-01

    We previously studied a 16-amino acid-residue fragment of the C-terminal beta-hairpin of the B3 domain (residues 46-61), [IG(46-61)] of the immunoglobulin binding protein G from Streptoccocus, and found that hydrophobic interactions and the turn region play an important role in stabilizing the structure. Based on these results, we carried out systematic structural studies of peptides derived from the sequence of IG (46-61) by systematically shortening the peptide by one residue at a time from both the C- and the N-terminus. To determine the structure and stability of two resulting 12- and 14-amino acid-residue peptides, IG(48-59) and IG(47-60), respectively, we carried out circular dichroism, NMR, and calorimetric studies of these peptides in pure water. Our results show that IG(48-59) possesses organized three-dimensional structure stabilized by hydrophobic interactions (Tyr50-Phe57 and Trp48-Val59) at T = 283 and 305 K. At T = 313 K, the structure breaks down because of increased chain entropy, but the turn region is preserved in the same position observed for the structure of the whole protein. The breakdown of structure occurs near the melting temperature of this peptide (T(m) = 310 K) measured by differential scanning calorimetry (DSC). The melting temperature of IG(47-60) determined by DSC is T(m) = 330 K and its structure is similar to that of the native beta-hairpin at all (lower) temperatures examined (283-313 K). Both of these truncated sequences are conserved in all known amino acid sequences of the B domains of the immunoglobulin binding protein G from bacteria. Thus, this study contributes to an understanding of the mechanism of folding of this whole family of proteins, and provides information about the mechanism of formation and stabilization of a beta-hairpin structural element. PMID:19089955

  2. Deciphering ligand specificity of a Clostridium thermocellum family 35 carbohydrate binding module (CtCBM35 for gluco- and galacto- substituted mannans and its calcium induced stability.

    Directory of Open Access Journals (Sweden)

    Arabinda Ghosh

    Full Text Available This study investigated the role of CBM35 from Clostridium thermocellum (CtCBM35 in polysaccharide recognition. CtCBM35 was cloned into pET28a (+ vector with an engineered His6 tag and expressed in Escherichia coli BL21 (DE3 cells. A homogenous 15 kDa protein was purified by immobilized metal ion chromatography (IMAC. Ligand binding analysis of CtCBM35 was carried out by affinity electrophoresis using various soluble ligands. CtCBM35 showed a manno-configured ligand specific binding displaying significant association with konjac glucomannan (Ka = 14.3×10(4 M(-1, carob galactomannan (Ka = 12.4×10(4 M(-1 and negligible association (Ka = 12 µM(-1 with insoluble mannan. Binding of CtCBM35 with polysaccharides which was calcium dependent exhibited two fold higher association in presence of 10 mM Ca(2+ ion with konjac glucomannan (Ka = 41×10(4 M(-1 and carob galactomannan (Ka = 30×10(4 M(-1. The polysaccharide binding was further investigated by fluorescence spectrophotometric studies. On binding with carob galactomannan and konjac glucomannan the conformation of CtCBM35 changed significantly with regular 21 nm peak shifts towards lower quantum yield. The degree of association (K a with konjac glucomannan and carob galactomannan, 14.3×10(4 M(-1 and 11.4×10(4 M(-1, respectively, corroborated the findings from affinity electrophoresis. The association of CtCBM35with konjac glucomannan led to higher free energy of binding (ΔG -25 kJ mole(-1 as compared to carob galactomannan (ΔG -22 kJ mole(-1. On binding CtCBM35 with konjac glucomannan and carob galactomannan the hydrodynamic radius (RH as analysed by dynamic light scattering (DLS study, increased to 8 nm and 6 nm, respectively, from 4.25 nm in absence of ligand. The presence of 10 mM Ca(2+ ions imparted stiffer orientation of CtCBM35 particles with increased RH of 4.52 nm. Due to such stiffer orientation CtCBM35 became more thermostable and its melting temperature was

  3. Cleavage of the sarcin–ricin loop of 23S rRNA differentially affects EF-G and EF-Tu binding

    OpenAIRE

    García-Ortega, Lucía; Álvarez-García, Elisa; Gavilanes, José G.; Martínez-del-Pozo, Álvaro; Joseph, Simpson

    2010-01-01

    Ribotoxins are potent inhibitors of protein biosynthesis and inactivate ribosomes from a variety of organisms. The ribotoxin α-sarcin cleaves the large 23S ribosomal RNA (rRNA) at the universally conserved sarcin–ricin loop (SRL) leading to complete inactivation of the ribosome and cellular death. The SRL interacts with translation factors that hydrolyze GTP, and it is important for their binding to the ribosome, but its precise role is not yet understood. We studied the effect of α-sarcin on...

  4. Loss of the Otx2-Binding Site in the Nanog Promoter Affects the Integrity of Embryonic Stem Cell Subtypes and Specification of Inner Cell Mass-Derived Epiblast

    Directory of Open Access Journals (Sweden)

    Dario Acampora

    2016-06-01

    Full Text Available Mouse embryonic stem cells (ESCs and the inner cell mass (ICM-derived epiblast exhibit naive pluripotency. ESC-derived epiblast stem cells (EpiSCs and the postimplantation epiblast exhibit primed pluripotency. Although core pluripotency factors are well-characterized, additional regulators, including Otx2, recently have been shown to function during the transition from naive to primed pluripotency. Here we uncover a role for Otx2 in the control of the naive pluripotent state. We analyzed Otx2-binding activity in ESCs and EpiSCs and identified Nanog, Oct4, and Sox2 as direct targets. To unravel the Otx2 transcriptional network, we targeted the strongest Otx2-binding site in the Nanog promoter, finding that this site modulates the size of specific ESC-subtype compartments in cultured cells and promotes Nanog expression in vivo, predisposing ICM differentiation to epiblast. Otx2-mediated Nanog regulation thus contributes to the integrity of the ESC state and cell lineage specification in preimplantation development.

  5. Effect of four-alpha-helix bundle cavity size on volatile anesthetic binding energetics.

    Science.gov (United States)

    Manderson, Gavin A; Michalsky, Stuart J; Johansson, Jonas S

    2003-09-30

    Currently, it is thought that inhalational anesthetics cause anesthesia by binding to ligand-gated ion channels. This is being investigated using four-alpha-helix bundles, small water-soluble analogues of the transmembrane domains of the "natural" receptor proteins. The study presented here specifically investigates how multiple alanine-to-valine substitutions (which each decrease the volume of the internal binding cavity by 38 A(3)) affect structure, stability, and anesthetic binding affinity of the four-alpha-helix bundles. Structure remains essentially unchanged when up to four alanine residues are changed to valine. However, stability increases as the number of these substitutions is increased. Anesthetic binding affinities are also affected. Halothane binds to the four-alpha-helix bundle variants with 0, 1, and 2 substitutions with equivalent affinities but binds to the variants with 3 and 4 more tightly. The same order of binding affinities was observed for chloroform, although for a particular variant, chloroform was bound less tightly. The observed differences in binding affinities may be explained in terms of a modulation of van der Waals and hydrophobic interactions between ligand and receptor. These, in turn, could result from increased four-alpha-helix bundle binding cavity hydrophobicity, a decrease in cavity size, or improved ligand/receptor shape complementarity.

  6. Nutritional Control of mRNA Stability Is Mediated by a Conserved AU-rich Element That Binds the Cytoplasmic Shuttling Protein HuR*

    OpenAIRE

    Yaman, Ibrahim; Fernandez, James; Sarkar, Bedabrata; Schneider, Robert J.; Snider, Martin D.; Nagy, Laura E.; Hatzoglou, Maria

    2002-01-01

    The cationic amino acid transporter, Cat-1, is a high affinity transporter of the essential amino acids, arginine and lysine. Expression of the cat-1 gene increases during nutritional stress as part of the adaptive response to starvation. Amino acid limitation induces coordinate increases in stability and translation of the cat-1 mRNA, at a time when global protein synthesis decreases. It is shown here that increased cat-1 mRNA stability requires an 11 nucleotide AU-rich element within the di...

  7. Control of mRNA stability contributes to low levels of nuclear poly(A) binding protein 1 (PABPN1) in skeletal muscle

    OpenAIRE

    Apponi, Luciano H.; Corbett, Anita H.; Pavlath, Grace K.

    2013-01-01

    Background The nuclear poly(A) binding protein 1 (PABPN1) is a ubiquitously expressed protein that plays critical roles at multiple steps in post-transcriptional regulation of gene expression. Short expansions of the polyalanine tract in the N-terminus of PABPN1 lead to oculopharyngeal muscular dystrophy (OPMD), which is an adult onset disease characterized by eyelid drooping, difficulty in swallowing, and weakness in the proximal limb muscles. Why alanine-expanded PABPN1 leads to muscle-spec...

  8. Temperature and pressure dependence of protein stability: The engineered fluorescein-binding lipocalin FluA shows an elliptic phase diagram

    OpenAIRE

    Wiedersich, Johannes; Köhler, Simone; Skerra, Arne; Friedrich, Josef

    2008-01-01

    We have measured the equilibrium constant for the denaturation transition of the engineered fluorescein-binding lipocalin FluA as a function of pressure and temperature, taking advantage of the fact that the ligand's fluorescence is almost fully quenched when complexed with the folded protein, but reversibly reappears on denaturation. From the equilibrium constant as a function of pressure and temperature all of the involved thermodynamic parameters of protein folding, in particular the chang...

  9. Site-specific binding of a PPR protein defines and stabilizes 5′ and 3′ mRNA termini in chloroplasts

    OpenAIRE

    Pfalz, Jeannette; Bayraktar, Omer Ali; Prikryl, Jana; Barkan, Alice

    2009-01-01

    Chloroplast mRNA populations are characterized by overlapping transcripts derived by processing from polycistronic precursors. The mechanisms and functional significance of these processing events are poorly understood. We describe a pentatricopeptide repeat (PPR) protein, PPR10, whose binding defines mRNA segments derived from two transcription units in maize chloroplasts. PPR10 interacts in vivo and in vitro with two intergenic RNA regions of similar sequence. The processed 5′ and 3′ RNA te...

  10. Host factor I, Hfq, binds to Escherichia coli ompA mRNA in a growth rate-dependent fashion and regulates its stability

    DEFF Research Database (Denmark)

    Vytvytska, O; Jakobsen, J S; Balcunaite, G;

    1998-01-01

    ompA was purified and identified as Hfq, a host factor initially recognized for its function in phage Qbeta replication. The ompA RNA-binding activity parallels the amount of Hfq, which is elevated in bacteria cultured at slow growth rate, a condition leading to facilitated degradation of the ompA m...... suggest a regulatory role for Hfq that specifically facilitates the ompA mRNA degradation in a growth rate-dependent manner....

  11. Ribosomal protein S7 as a novel modulator of p53-MDM2 interaction: binding to MDM2, stabilization of p53 protein, and activation of p53 function.

    Science.gov (United States)

    Chen, D; Zhang, Z; Li, M; Wang, W; Li, Y; Rayburn, E R; Hill, D L; Wang, H; Zhang, R

    2007-08-01

    As a major negative regulator of p53, the MDM2 oncogene plays an important role in carcinogenesis and tumor progression. MDM2 promotes p53 proteasomal degradation and negatively regulates p53 function. The mechanisms by which the MDM2-p53 interaction is regulated are not fully understood, although several MDM2-interacting molecules have recently been identified. To search for novel MDM2-binding partners, we screened a human prostate cDNA library by the yeast two-hybrid assay using full-length MDM2 protein as the bait. Among the candidate proteins, ribosomal protein S7 was identified and confirmed as a novel MDM2-interacting protein. Herein, we demonstrate that S7 binds to MDM2, in vitro and in vivo, and that the interaction between MDM2 and S7 leads to modulation of MDM2-p53 binding by forming a ternary complex among MDM2, p53 and S7. This results in the stabilization of p53 protein through abrogation of MDM2-mediated p53 ubiquitination. Consequently, S7 overexpression increases p53 transactivational activities, induces apoptosis, and inhibits cell proliferation. The identification of S7 as a novel MDM2-interacting partner contributes to elucidation of the complex regulation of the MDM2-p53 interaction and has implications in cancer prevention and therapy.

  12. The influence of the binding of low molecular weight surfactants on the thermal stability and secondary structure of IgG

    NARCIS (Netherlands)

    Vermeer, AWP; Norde, W

    2000-01-01

    The effect of low molecular weight surfactants on the thermal stability of immunoglobulin G is studied by differential scanning calorimetry. The corresponding change in the secondary structure is investigated using circular dichroism spectroscopy and the rate of aggregate formation, both in the pres

  13. The protein binding substance Ibuprofen does not affect the T1 time or partition coefficient in contrast-enhanced cardiovascular magnetic resonance

    Directory of Open Access Journals (Sweden)

    Kawel Nadine

    2012-10-01

    Full Text Available Abstract Background Contrast enhanced cardiovascular magnetic resonance (CMR with T1 mapping enables quantification of diffuse myocardial fibrosis. Various factors, however, can interfere with T1 measurements. The purpose of the current study was to assess the effect of co-medication with a typical protein binding drug (Ibuprofen on T1 values in vitro and in vivo. Methods 50 vials were prepared with different concentrations of gadobenate dimeglumine, Ibuprofen and human serum albumin in physiologic NaCl solution and imaged at 1.5T with a spin echo sequence at multiple TRs to measure T1 values and calculate relaxivities. 10 volunteers (5 men; 31±6.3 years were imaged at 1.5T. T1 values for myocardium and blood pool were determined for various time points after administration of 0.15mmol/kg gadobenate dimeglumine using a modified look-locker inversion-recovery sequence before and after administration of Ibuprofen over 24 hours. The partition coefficient was calculated as ΔR1myocardium/ΔR1blood, where R1=1/T1. Results In vitro no significant correlation was found between relaxivity and Ibuprofen concentration, neither in absence (r=−0.15, p=0.40 nor in presence of albumin (r=−0.32, p=0.30. In vivo there was no significant difference in post contrast T1 times of myocardium and blood, respectively and also in the partition coefficient between exam 1 and 2 (p>0.05. There was good agreement of the T1 times of myocardium and blood and the partition coefficient, respectively between exam 1 and 2. Conclusions Contrast enhanced T1 mapping is unaffected by co-medication with the protein binding substance Ibuprofen and has an excellent reproducibility.

  14. The stability region of the Streptomyces lividans plasmid pIJ101 encodes a DNA-binding protein recognizing a highly conserved short palindromic sequence motif

    OpenAIRE

    Thoma, Lina; Sepulveda, Edgardo; Latus, Annette; Muth, Günther

    2014-01-01

    Conjugation is a driving force in the evolution and shaping of bacterial genomes. In antibiotic producing streptomycetes even small plasmids replicating via the rolling-circle mechanism are conjugative. Although they encode only genes involved in replication and transfer, the molecular function of most plasmid encoded proteins is unknown. In this work we show that the conjugative plasmid pIJ101 encodes an overlooked protein, SpdA2. We show that SpdA2 is a DNA binding protein which specificall...

  15. Odorant-binding proteins OBP57d and OBP57e affect taste perception and host-plant preference in Drosophila sechellia.

    Directory of Open Access Journals (Sweden)

    Takashi Matsuo

    2007-05-01

    Full Text Available Despite its morphological similarity to the other species in the Drosophila melanogaster species complex, D. sechellia has evolved distinct physiological and behavioral adaptations to its host plant Morinda citrifolia, commonly known as Tahitian Noni. The odor of the ripe fruit of M. citrifolia originates from hexanoic and octanoic acid. D. sechellia is attracted to these two fatty acids, whereas the other species in the complex are repelled. Here, using interspecies hybrids between D. melanogaster deficiency mutants and D. sechellia, we showed that the Odorant-binding protein 57e (Obp57e gene is involved in the behavioral difference between the species. D. melanogaster knock-out flies for Obp57e and Obp57d showed altered behavioral responses to hexanoic acid and octanoic acid. Furthermore, the introduction of Obp57d and Obp57e from D. simulans and D. sechellia shifted the oviposition site preference of D. melanogaster Obp57d/e(KO flies to that of the original species, confirming the contribution of these genes to D. sechellia's specialization to M. citrifolia. Our finding of the genes involved in host-plant determination may lead to further understanding of mechanisms underlying taste perception, evolution of plant-herbivore interactions, and speciation.

  16. The two-component system CpxR/A represses the expression of Salmonella virulence genes by affecting the stability of the transcriptional regulator HilD

    Science.gov (United States)

    De la Cruz, Miguel A.; Pérez-Morales, Deyanira; Palacios, Irene J.; Fernández-Mora, Marcos; Calva, Edmundo; Bustamante, Víctor H.

    2015-01-01

    Salmonella enterica can cause intestinal or systemic infections in humans and animals mainly by the presence of pathogenicity islands SPI-1 and SPI-2, containing 39 and 44 genes, respectively. The AraC-like regulator HilD positively controls the expression of the SPI-1 genes, as well as many other Salmonella virulence genes including those located in SPI-2. A previous report indicates that the two-component system CpxR/A regulates the SPI-1 genes: the absence of the sensor kinase CpxA, but not the absence of its cognate response regulator CpxR, reduces their expression. The presence and absence of cell envelope stress activates kinase and phosphatase activities of CpxA, respectively, which in turn controls the level of phosphorylated CpxR (CpxR-P). In this work, we further define the mechanism for the CpxR/A-mediated regulation of SPI-1 genes. The negative effect exerted by the absence of CpxA on the expression of SPI-1 genes was counteracted by the absence of CpxR or by the absence of the two enzymes, AckA and Pta, which render acetyl-phosphate that phosphorylates CpxR. Furthermore, overexpression of the lipoprotein NlpE, which activates CpxA kinase activity on CpxR, or overexpression of CpxR, repressed the expression of SPI-1 genes. Thus, our results provide several lines of evidence strongly supporting that the absence of CpxA leads to the phosphorylation of CpxR via the AckA/Pta enzymes, which represses both the SPI-1 and SPI-2 genes. Additionally, we show that in the absence of the Lon protease, which degrades HilD, the CpxR-P-mediated repression of the SPI-1 genes is mostly lost; moreover, we demonstrate that CpxR-P negatively affects the stability of HilD and thus decreases the expression of HilD-target genes, such as hilD itself and hilA, located in SPI-1. Our data further expand the insight on the different regulatory pathways for gene expression involving CpxR/A and on the complex regulatory network governing virulence in Salmonella. PMID:26300871

  17. Factors Affecting the Oxidative Stability of Foods-Interesterified Soybean Oil with High Intensity Ultrasound Treatment and Trona Mineral in Packaged Fresh Meats

    OpenAIRE

    Lee, Jiwon

    2013-01-01

    Oxidation in oils and muscle foods has been studied for many years to understand its mechanism and furthermore to control and manage it. A series of different processing steps or different packaging techniques can alter oxidative stability. The objective of the current study was to examine oxidative stability of processed oil and to evaluate the effect of carbon dioxide generating mineral on quality of beef and chicken under different storage conditions. In Study 1 (Chapter 3), the effect of ...

  18. Role of Hydrophobic Mutations on the Binding Affinity and Stability of Blood Coagulation Factor VIIIa: A Computational Molecular Dynamics and Free-Energy Analysis

    OpenAIRE

    Venkateswarlu, Divi

    2014-01-01

    Factor VIIIa is a non-covalently bound hetero-trimer among A1, A2 and A3-C1-C2 domains and an essential co-factor for factor IXa enzyme during proteolytic activation of factor X zymogen. The relatively weak interactions between A2 and the interface A1/A3 domains dampen the functional stability of FVIIIa in plasma and results in rapid degradation. We studied the mutational effect of three charged residues (Asp519, Glu665 and Asp666) to several hydrophobic residues by molecular dynamics simulat...

  19. Extended N-terminal region of the essential phosphorelay signaling protein Ypd1 from Cryptococcus neoformans contributes to structural stability, phosphostability and binding of calcium ions.

    Science.gov (United States)

    Kennedy, Emily N; Menon, Smita K; West, Ann H

    2016-09-01

    Rapid response to external stimuli is crucial for survival and proliferation of microorganisms. Pathogenic fungi employ histidine-to-aspartate multistep phosphorelay systems to respond to environmental stress, progress through developmental stages and to produce virulence factors. Because these His-to-Asp phosphorelay systems are not found in humans, they are potential targets for the development of new antifungal therapies. Here we report the characterization of the histidine phosphotransfer (HPt) protein Ypd1 from the human fungal pathogen Cryptococcus neoformans Results from this study demonstrate that CnYpd1 indeed functions as a phosphorelay protein in vitro, and that H138 is confirmed as the site of phosphorylation. We found that CnYpd1 exhibits unique characteristics in comparison to other histidine phosphotransfer proteins, such as an extended N-terminal amino acid sequence, which we find contributes to structural integrity, a longer phosphorylated life time and the ability to bind calcium ions. PMID:27549628

  20. A transient α-helical molecular recognition element in the disordered N-terminus of the Sgs1 helicase is critical for chromosome stability and binding of Top3/Rmi1.

    Science.gov (United States)

    Kennedy, Jessica A; Daughdrill, Gary W; Schmidt, Kristina H

    2013-12-01

    The RecQ-like DNA helicase family is essential for the maintenance of genome stability in all organisms. Sgs1, a member of this family in Saccharomyces cerevisiae, regulates early and late steps of double-strand break repair by homologous recombination. Using nuclear magnetic resonance spectroscopy, we show that the N-terminal 125 residues of Sgs1 are disordered and contain a transient α-helix that extends from residue 25 to 38. Based on the residue-specific knowledge of transient secondary structure, we designed proline mutations to disrupt this α-helix and observed hypersensitivity to DNA damaging agents and increased frequency of genome rearrangements. In vitro binding assays show that the defects of the proline mutants are the result of impaired binding of Top3 and Rmi1 to Sgs1. Extending mutagenesis N-terminally revealed a second functionally critical region that spans residues 9-17. Depending on the position of the proline substitution in the helix functional impairment of Sgs1 function varied, gradually increasing from the C- to the N-terminus. The multiscale approach we used to interrogate structure/function relationships in the long disordered N-terminal segment of Sgs1 allowed us to precisely define a functionally critical region and should be generally applicable to other disordered proteins. PMID:24038467

  1. The role of N1 domain on the activity, stability, substrate specificity and raw starch binding of amylopullulanase of the extreme thermophile Geobacillus thermoleovorans.

    Science.gov (United States)

    Nisha, M; Satyanarayana, T

    2015-07-01

    In order to understand the role of N1 domain (1-257 aa) in the amylopullulanase (gt-apu) of the extremely thermophilic bacterium Geobacillus thermoleovorans NP33, N1 deletion construct (gt-apuΔN) has been generated and expressed in Escherichia coli. The truncated amylopullulanase (gt-apuΔN) exhibits similar pH and temperature optima like gt-apu, but enhanced thermostability. The gt-apuΔN has greater hydrolytic action and specific activity on pullulan than gt-apu. The k cat (starch and pullulan) and K m (starch) values of gt-apuΔN increased, while K m (pullulan) decreased. The enzyme upon N1 deletion hydrolyzed maltotetraose as the smallest substrate in contrast to maltopentaose of gt-apu. The role of N1 domain of gt-apu in raw starch binding has been confirmed, for the first time, based on deletion and Langmuir-Hinshelwood kinetics. Furthermore, N1 domain appears to exert a negative influence on the thermostability of gt-apu because N1 truncation significantly improves thermostability.

  2. The role of N1 domain on the activity, stability, substrate specificity and raw starch binding of amylopullulanase of the extreme thermophile Geobacillus thermoleovorans.

    Science.gov (United States)

    Nisha, M; Satyanarayana, T

    2015-07-01

    In order to understand the role of N1 domain (1-257 aa) in the amylopullulanase (gt-apu) of the extremely thermophilic bacterium Geobacillus thermoleovorans NP33, N1 deletion construct (gt-apuΔN) has been generated and expressed in Escherichia coli. The truncated amylopullulanase (gt-apuΔN) exhibits similar pH and temperature optima like gt-apu, but enhanced thermostability. The gt-apuΔN has greater hydrolytic action and specific activity on pullulan than gt-apu. The k cat (starch and pullulan) and K m (starch) values of gt-apuΔN increased, while K m (pullulan) decreased. The enzyme upon N1 deletion hydrolyzed maltotetraose as the smallest substrate in contrast to maltopentaose of gt-apu. The role of N1 domain of gt-apu in raw starch binding has been confirmed, for the first time, based on deletion and Langmuir-Hinshelwood kinetics. Furthermore, N1 domain appears to exert a negative influence on the thermostability of gt-apu because N1 truncation significantly improves thermostability. PMID:25573470

  3. Spectroscopic capture and reactivity of a low-spin cobalt(IV)-oxo complex stabilized by binding redox-inactive metal ions.

    Science.gov (United States)

    Hong, Seungwoo; Pfaff, Florian F; Kwon, Eunji; Wang, Yong; Seo, Mi-Sook; Bill, Eckhard; Ray, Kallol; Nam, Wonwoo

    2014-09-22

    High-valent cobalt-oxo intermediates are proposed as reactive intermediates in a number of cobalt-complex-mediated oxidation reactions. Herein we report the spectroscopic capture of low-spin (S=1/2) Co(IV)-oxo species in the presence of redox-inactive metal ions, such as Sc(3+), Ce(3+), Y(3+), and Zn(2+), and the investigation of their reactivity in C-H bond activation and sulfoxidation reactions. Theoretical calculations predict that the binding of Lewis acidic metal ions to the cobalt-oxo core increases the electrophilicity of the oxygen atom, resulting in the redox tautomerism of a highly unstable [(TAML)Co(III)(O˙)](2-) species to a more stable [(TAML)Co(IV)(O)(M(n+))] core. The present report supports the proposed role of the redox-inactive metal ions in facilitating the formation of high-valent metal-oxo cores as a necessary step for oxygen evolution in chemistry and biology.

  4. Temperature and pressure dependence of protein stability: The engineered fluorescein-binding lipocalin FluA shows an elliptic phase diagram

    Science.gov (United States)

    Wiedersich, Johannes; Köhler, Simone; Skerra, Arne; Friedrich, Josef

    2008-01-01

    We have measured the equilibrium constant for the denaturation transition of the engineered fluorescein-binding lipocalin FluA as a function of pressure and temperature, taking advantage of the fact that the ligand's fluorescence is almost fully quenched when complexed with the folded protein, but reversibly reappears on denaturation. From the equilibrium constant as a function of pressure and temperature all of the involved thermodynamic parameters of protein folding, in particular the changes in entropy and volume, compressibility, thermal expansion, and specific heat, were deduced in a global fitting procedure. Assuming that these parameters are independent of temperature and pressure, we can demonstrate from the ratio of Δβ, Δα2, ΔCp that the phase diagram of protein folding assumes an elliptic shape. Furthermore, we can show that the thermodynamic condition for such an elliptic phase diagram is related to the degree of correlation between the fluctuations of the changes in volume and enthalpy at the phase boundary. For the protein investigated this correlation is low, as generally expected for highly degenerate systems. Our study suggests that the elliptic phase diagram is a consequence of the inherent conformational disorder of proteins and that it may be viewed as the thermodynamic manifestation of the high degeneracy of conformational energies that is characteristic for this class of macromolecules. PMID:18391216

  5. Conserved arginine residues in the carboxyl terminus of the equine arteritis virus E protein may play a role in heparin binding but may not affect viral infectivity in equine endothelial cells.

    Science.gov (United States)

    Lu, Zhengchun; Sarkar, Sanjay; Zhang, Jianqiang; Balasuriya, Udeni B R

    2016-04-01

    Equine arteritis virus (EAV), the causative agent of equine viral arteritis, has relatively broad cell tropism in vitro. In horses, EAV primarily replicates in macrophages and endothelial cells of small blood vessels. Until now, neither the cellular receptor(s) nor the mechanism(s) of virus attachment and entry have been determined for this virus. In this study, we investigated the effect of heparin on EAV infection in equine endothelial cells (EECs). Heparin, but not other glycosaminoglycans, could reduce EAV infection up to 93 %. Sequence analysis of the EAV E minor envelope protein revealed a conserved amino acid sequence (52 RSLVARCSRGARYR 65) at the carboxy terminus of the E protein, which was predicted to be the heparin-binding domain. The basic arginine (R) amino acid residues were subsequently mutated to glycine by site-directed mutagenesis of ORF2a in an E protein expression vector and an infectious cDNA clone of EAV. Two single mutations in E (R52G and R57G) did not affect the heparin-binding capability, whereas the E double mutation (R52,60G) completely eliminated the interaction between the E protein and heparin. Although the mutant R52,60G EAV did not bind heparin, the mutations did not completely abolish infectivity, indicating that heparin is not the only critical factor for EAV infection. This also suggested that other viral envelope protein(s) might be involved in attachment through heparin or other cell-surface molecules, and this warrants further investigation.

  6. One motif to bind them: A small-XXX-small motif affects transmembrane domain 1 oligomerization, function, localization, and cross-talk between two yeast GPCRs.

    Science.gov (United States)

    Lock, Antonia; Forfar, Rachel; Weston, Cathryn; Bowsher, Leo; Upton, Graham J G; Reynolds, Christopher A; Ladds, Graham; Dixon, Ann M

    2014-12-01

    G protein-coupled receptors (GPCRs) are the largest family of cell-surface receptors in mammals and facilitate a range of physiological responses triggered by a variety of ligands. GPCRs were thought to function as monomers, however it is now accepted that GPCR homo- and hetero-oligomers also exist and influence receptor properties. The Schizosaccharomyces pombe GPCR Mam2 is a pheromone-sensing receptor involved in mating and has previously been shown to form oligomers in vivo. The first transmembrane domain (TMD) of Mam2 contains a small-XXX-small motif, overrepresented in membrane proteins and well-known for promoting helix-helix interactions. An ortholog of Mam2 in Saccharomyces cerevisiae, Ste2, contains an analogous small-XXX-small motif which has been shown to contribute to receptor homo-oligomerization, localization and function. Here we have used experimental and computational techniques to characterize the role of the small-XXX-small motif in function and assembly of Mam2 for the first time. We find that disruption of the motif via mutagenesis leads to reduction of Mam2 TMD1 homo-oligomerization and pheromone-responsive cellular signaling of the full-length protein. It also impairs correct targeting to the plasma membrane. Mutation of the analogous motif in Ste2 yielded similar results, suggesting a conserved mechanism for assembly. Using co-expression of the two fungal receptors in conjunction with computational models, we demonstrate a functional change in G protein specificity and propose that this is brought about through hetero-dimeric interactions of Mam2 with Ste2 via the complementary small-XXX-small motifs. This highlights the potential of these motifs to affect a range of properties that can be investigated in other GPCRs.

  7. Homogenization conditions affect the oxidative stability of fish oil enriched milk emulsions: oxidation linked to changes in protein composition at the oil-water interface

    DEFF Research Database (Denmark)

    Sørensen, Ann-Dorit M.; Baron, Caroline P.; Let, Mette B.;

    2007-01-01

    Fish oil was incorporated into milk under different homogenization temperatures (50 and 72 °C) and pressures (5, 15, and 22.5 MPa). Subsequently, the oxidative stability of the milk and changes in the protein composition of the milk fat globule membrane (MFGM) were examined. Results showed that h...

  8. A flexible system of remediation to stabilize a road affected by landslide in the area of Val di Maso (North-Eastern Italian Apls)

    Science.gov (United States)

    Tessari, G.; Cioli, C.; Floris, M.; Stevan, G.; Genevois, R.

    2012-04-01

    Slope stabilization follows different design procedures and approaches finalized to reduce the driving forces or increase resisting forces or avoid the problem at all by completely or partially remove unstable materials. But often the cost of stabilization works is very high. Therefore it is necessary to find new effective solutions with low or moderate costs. In this frame, this work reports the case study of a road in the area of Val di Maso, located in the North-Eastern Italian Alps. The road is threatened by the evolution of a mass movement occurred on November 2010 due to an extreme rainfall event that hit the entire North-Eastern sector of Italy. The complex landslide consists of a debris flow involving eluvial/colluvial deposits and past landslide debris. In the upper part, clear morphological evidences indicate that the instability is rapidly retrogressing by multiple rotational slides involving volcanic deposits that can be referred to a paleo-landslide. In the crown area, unstable materials have a thickness of around 20 m. For this reason, a stabilization system using rigid structures anchored to the stable bedrock for an appropriate length would be burdensome and costly. Starting from the geological model of the unstable slope, an innovative stabilization solution is proposed, a numerical simulation to analyze the effects of the stabilization is performed and an integrated monitoring system to control and verify the slope behaviour is planned. The proposed remediation works consist of a "floating belt", placed close to the edge of the road, and some "floating anchors" some meters further down behind the main scarp of the landslide. The system allows small displacements to induce a stress re-distribution favourable to the stability of the slope. The main advantages of the proposed solution are the adaptability to different geo-environmental situations and the low cost compared to other alternatives. On the basis of field data collected, a geological

  9. TGF-β activates APC through Cdh1 binding for Cks1 and Skp2 proteasomal destruction stabilizing p27kip1 for normal endometrial growth.

    Science.gov (United States)

    Pavlides, Savvas C; Lecanda, Jon; Daubriac, Julien; Pandya, Unnati M; Gama, Patricia; Blank, Stephanie; Mittal, Khushbakhat; Shukla, Pratibha; Gold, Leslie I

    2016-01-01

    We previously reported that aberrant TGF-β/Smad2/3 signaling in endometrial cancer (ECA) leads to continuous ubiquitylation of p27(kip1)(p27) by the E3 ligase SCF-Skp2/Cks1 causing its degradation, as a putative mechanism involved in the pathogenesis of this cancer. In contrast, normal intact TGF-β signaling prevents degradation of nuclear p27 by SCF-Skp2/Cks1 thereby accumulating p27 to block Cdk2 for growth arrest. Here we show that in ECA cell lines and normal primary endometrial epithelial cells, TGF-β increases Cdh1 and its binding to APC/C to form the E3 ligase complex that ubiquitylates Cks1 and Skp2 prompting their proteasomal degradation and thus, leaving p27 intact. Knocking-down Cdh1 in ECA cell lines increased Skp2/Cks1 E3 ligase activity, completely diminished nuclear and cytoplasmic p27, and obviated TGF-β-mediated inhibition of proliferation. Protein synthesis was not required for TGF-β-induced increase in nuclear p27 and decrease in Cks1 and Skp2. Moreover, half-lives of Cks1 and Skp2 were extended in the Cdh1-depleted cells. These results suggest that the levels of p27, Skp2 and Cks1 are strongly or solely regulated by proteasomal degradation. Finally, an inverse relationship of low p27 and high Cks1 in the nucleus was shown in patients in normal proliferative endometrium and grade I-III ECAs whereas differentiated secretory endometrium showed the reverse. These studies implicate Cdh1 as the master regulator of TGF-β-induced preservation of p27 tumor suppressor activity. Thus, Cdh1 is a potential therapeutic target for ECA and other human cancers showing an inverse relationship between Cks1/Skp2 and p27 and/or dysregulated TGF-β signaling.

  10. Src-Like adaptor protein (SLAP) binds to the receptor tyrosine kinase Flt3 and modulates receptor stability and downstream signaling.

    Science.gov (United States)

    Kazi, Julhash U; Rönnstrand, Lars

    2012-01-01

    Fms-like tyrosine kinase 3 (Flt3) is an important growth factor receptor in hematopoiesis. Gain-of-function mutations of the receptor contribute to the transformation of acute myeloid leukemia (AML). Src-like adaptor protein (SLAP) is an interaction partner of the E3 ubiquitin ligase Cbl that can regulate receptor tyrosine kinases-mediated signal transduction. In this study, we analyzed the role of SLAP in signal transduction downstream of the type III receptor tyrosine kinase Flt3. The results show that upon ligand stimulation SLAP stably associates with Flt3 through multiple phosphotyrosine residues in Flt3. SLAP constitutively interacts with oncogenic Flt3-ITD and co-localizes with Flt3 near the cell membrane. This association initiates Cbl-dependent receptor ubiquitination and degradation. Depletion of SLAP expression by shRNA in Flt3-transfected Ba/F3 cells resulted in a weaker activation of FL-induced PI3K-Akt and MAPK signaling. Meta-analysis of microarray data from patient samples suggests that SLAP mRNA is differentially expressed in different cancers and its expression was significantly increased in patients carrying the Flt3-ITD mutation. Thus, our data suggest a novel role of SLAP in different cancers and in modulation of receptor tyrosine kinase signaling apart from its conventional role in regulation of receptor stability.

  11. Src-Like adaptor protein (SLAP binds to the receptor tyrosine kinase Flt3 and modulates receptor stability and downstream signaling.

    Directory of Open Access Journals (Sweden)

    Julhash U Kazi

    Full Text Available Fms-like tyrosine kinase 3 (Flt3 is an important growth factor receptor in hematopoiesis. Gain-of-function mutations of the receptor contribute to the transformation of acute myeloid leukemia (AML. Src-like adaptor protein (SLAP is an interaction partner of the E3 ubiquitin ligase Cbl that can regulate receptor tyrosine kinases-mediated signal transduction. In this study, we analyzed the role of SLAP in signal transduction downstream of the type III receptor tyrosine kinase Flt3. The results show that upon ligand stimulation SLAP stably associates with Flt3 through multiple phosphotyrosine residues in Flt3. SLAP constitutively interacts with oncogenic Flt3-ITD and co-localizes with Flt3 near the cell membrane. This association initiates Cbl-dependent receptor ubiquitination and degradation. Depletion of SLAP expression by shRNA in Flt3-transfected Ba/F3 cells resulted in a weaker activation of FL-induced PI3K-Akt and MAPK signaling. Meta-analysis of microarray data from patient samples suggests that SLAP mRNA is differentially expressed in different cancers and its expression was significantly increased in patients carrying the Flt3-ITD mutation. Thus, our data suggest a novel role of SLAP in different cancers and in modulation of receptor tyrosine kinase signaling apart from its conventional role in regulation of receptor stability.

  12. 微种植体初期稳定性的影响因素%Factors affecting primary stability of mini-implant anchorage

    Institute of Scientific and Technical Information of China (English)

    鲁颖娟; 常少海

    2013-01-01

    Mini implant anchorage for the orthodontic treatment is an effective method, the primary stability is critical in the achievement of reliable anchorage. Therefore, it is the purpose of this review to summarize the cur-rent literature on the primary stability of mini-implant anchorage, in order to improve overall implant success.%  微种植体支抗技术是正畸治疗中一种有效和理想的方法,其初期稳定性是获得可靠支抗的必要条件。本文就影响微种植体支抗初期稳定性的患者因素、微种植体因素和操作因素等研究进展作一综述,以提高微种植体支抗的成功率。

  13. The Factors Affecting the Primary Stability of Mini-implant Anchorage%影响微种植体支抗初期稳定性的因素

    Institute of Scientific and Technical Information of China (English)

    王硕; 贺娇娇; 刘畅

    2015-01-01

    The use of mini-implants anchorage for the orthodontic and orthopedic treatment is an effec-tive and ideal method.It enlarges the treatment scope in clinic for its stability and efficiency .According to the implantation site and the quality of local bone tissue,it is essential to select the appropriate size of the mini-implants,implantation angle and implantation method for establishing adequate initial stability .Considerable researches have been done to investigate the initial stability of orthodontic mini-implants.Here is to make a review of the influencing factors of the primary stability of orthodontic mini-implants.%利用微种植体作为支抗装置进行正畸和矫形治疗是一种高效、理想的方法。微种植体支抗的应用使临床可矫治的范围大大增加。根据植入部位和局部骨组织的质量,适当选择微种植体的尺寸与植入角度和植入方式对建立足够的初期稳定性至关重要。许多学者对微种植体支抗的初期稳定性进行了临床及试验研究。该文就影响微种植体支抗初期稳定性的因素进行综述。

  14. Analysis of SAT type foot-and-mouth disease virus capsid proteins and the identification of putative amino acid residues affecting virus stability.

    Directory of Open Access Journals (Sweden)

    Francois F Maree

    Full Text Available Foot-and-mouth disease virus (FMDV initiates infection by adhering to integrin receptors on target cells, followed by cell entry and disassembly of the virion through acidification within endosomes. Mild heating of the virions also leads to irreversible dissociation into pentamers, a characteristic linked to reduced vaccine efficacy. In this study, the structural stability of intra- and inter-serotype chimeric SAT2 and SAT3 virus particles to various conditions including low pH, mild temperatures or high ionic strength, was compared. Our results demonstrated that while both the SAT2 and SAT3 infectious capsids displayed different sensitivities in a series of low pH buffers, their stability profiles were comparable at high temperatures or high ionic strength conditions. Recombinant vSAT2 and intra-serotype chimeric viruses were used to map the amino acid differences in the capsid proteins of viruses with disparate low pH stabilities. Four His residues at the inter-pentamer interface were identified that change protonation states at pH 6.0. Of these, the H145 of VP3 appears to be involved in interactions with A141 in VP3 and K63 in VP2, and may be involved in orientating H142 of VP3 for interaction at the inter-pentamer interfaces.

  15. Paddy Soil Stability and Mechanical Properties as Affected by Long-Term Application of Chemical Fertilizer and Animal Manure in Subtropical China

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Wet stability, penetration resistance (PR), and tensile strength (TS) of paddy soils under a fertilization experiment for 22 years were determined to elucidate the function of soil organic matter in paddy soil stabilization. The treatments included no fertilization (CK), normal chemical fertilization (NPK), double the NPK application rates (2NPK), and NPK mixed with organic manure (NPK+OM). Compared with CK, fertilization increased soil organic carbon (SOC) and soil porosity. The results of soil aggregate fragmentation degree (SAFD) showed that fast wetting by water was the key fragmentation mechanism. Among the treatments, the NPK+OM treatment had the largest size of water-stable aggregates and greatest normal mean weight diameter (NMWD) (P ≤ 0.05), but the lowest PR and TS in both cultivated horizon (Ap) and plow pan. The CK and 2NPK treatments were measured with PR > 2.0 MPa and friability index < 0.20,respectively, in the Ap horizon, suggesting that the soils was mechanically unfavourable to root growth and tillage. In the plow pan, the fertilization treatments had greater TS and PR than in CK. TS and PR of the tested soil aggregates were negatively correlated to SOC content and soil porosity. This study suggested that chemical fertilization could cause deterioration of mechanical properties while application of organic manure could improve soil stability and mechanical properties.

  16. Analysis of SAT type foot-and-mouth disease virus capsid proteins and the identification of putative amino acid residues affecting virus stability.

    Science.gov (United States)

    Maree, Francois F; Blignaut, Belinda; de Beer, Tjaart A P; Rieder, Elizabeth

    2013-01-01

    Foot-and-mouth disease virus (FMDV) initiates infection by adhering to integrin receptors on target cells, followed by cell entry and disassembly of the virion through acidification within endosomes. Mild heating of the virions also leads to irreversible dissociation into pentamers, a characteristic linked to reduced vaccine efficacy. In this study, the structural stability of intra- and inter-serotype chimeric SAT2 and SAT3 virus particles to various conditions including low pH, mild temperatures or high ionic strength, was compared. Our results demonstrated that while both the SAT2 and SAT3 infectious capsids displayed different sensitivities in a series of low pH buffers, their stability profiles were comparable at high temperatures or high ionic strength conditions. Recombinant vSAT2 and intra-serotype chimeric viruses were used to map the amino acid differences in the capsid proteins of viruses with disparate low pH stabilities. Four His residues at the inter-pentamer interface were identified that change protonation states at pH 6.0. Of these, the H145 of VP3 appears to be involved in interactions with A141 in VP3 and K63 in VP2, and may be involved in orientating H142 of VP3 for interaction at the inter-pentamer interfaces. PMID:23717387

  17. A novel Rho-dependent pathway that drives interaction of fascin-1 with p-Lin-11/Isl-1/Mec-3 kinase (LIMK 1/2 to promote fascin-1/actin binding and filopodia stability

    Directory of Open Access Journals (Sweden)

    Jayo Asier

    2012-08-01

    Full Text Available Abstract Background Fascin-1 is an actin crosslinking protein that is important for the assembly of cell protrusions in neurons, skeletal and smooth muscle, fibroblasts, and dendritic cells. Although absent from most normal adult epithelia, fascin-1 is upregulated in many human carcinomas, and is associated with poor prognosis because of its promotion of carcinoma cell migration, invasion, and metastasis. Rac and Cdc42 small guanine triphosphatases have been identified as upstream regulators of the association of fascin-1 with actin, but the possible role of Rho has remained obscure. Additionally, experiments have been hampered by the inability to measure the fascin-1/actin interaction directly in intact cells. We investigated the hypothesis that fascin-1 is a functional target of Rho in normal and carcinoma cells, using experimental approaches that included a novel fluorescence resonance energy transfer (FRET/fluorescence lifetime imaging (FLIM method to measure the interaction of fascin-1 with actin. Results Rho activity modulates the interaction of fascin-1 with actin, as detected by a novel FRET method, in skeletal myoblasts and human colon carcinoma cells. Mechanistically, Rho regulation depends on Rho kinase activity, is independent of the status of myosin II activity, and is not mediated by promotion of the fascin/PKC complex. The p-Lin-11/Isl-1/Mec-3 kinases (LIMK, LIMK1 and LIMK2, act downstream of Rho kinases as novel binding partners of fascin-1, and this complex regulates the stability of filopodia. Conclusions We have identified a novel activity of Rho in promoting a complex between fascin-1 and LIMK1/2 that modulates the interaction of fascin-1 with actin. These data provide new mechanistic insight into the intracellular coordination of contractile and protrusive actin-based structures. During the course of the study, we developed a novel FRET method for analysis of the fascin-1/actin interaction, with potential general

  18. 植物蛋白饮料稳定性影响因素和分析方法的研究%Study on the affected factors and analysis method of stability of plant protein beverage

    Institute of Scientific and Technical Information of China (English)

    周超进; 何锦风; 蒲彪

    2011-01-01

    植物蛋白饮料中蛋白沉淀、脂肪上浮问题,严重影响了产品质量.本文综合叙述了环境压力和饮料自身各因素对植物蛋白饮料稳定性的影响,并介绍了一些常用快速的稳定性分析方法.%The effect of sediment protein and fat separation on the quality of plant protein beverage was significant. The factors including environmental stresses and inside factors affecting the stability of plant protein beverage were comprehensively described ,the regular and fast technologies of determining stability were introduced.

  19. A novel p53-binding domain in CUL7.

    Science.gov (United States)

    Kasper, Jocelyn S; Arai, Takehiro; DeCaprio, James A

    2006-09-15

    CUL7 is a member of the cullin RING ligase family and forms an SCF-like complex with SKP1 and FBXW8. CUL7 is required for normal mouse embryonic development and cellular proliferation, and is highly homologous to PARC, a p53-associated, parkin-like cytoplasmic protein. We determined that CUL7, in a manner similar to PARC, can bind directly to p53 but does not affect p53 expression. We identified a discrete, co-linear domain in CUL7 that is conserved in PARC and HERC2, and is necessary and sufficient for p53-binding. The presence of p53 stabilized expression of this domain and we demonstrate that this p53-binding domain of CUL7 contributes to the cytoplasmic localization of CUL7. The results support the model that p53 plays a role in regulation of CUL7 activity. PMID:16875676

  20. EHD3 Protein Is Required for Tubular Recycling Endosome Stabilization, and an Asparagine-Glutamic Acid Residue Pair within Its Eps15 Homology (EH) Domain Dictates Its Selective Binding to NPF Peptides.

    Science.gov (United States)

    Bahl, Kriti; Xie, Shuwei; Spagnol, Gaelle; Sorgen, Paul; Naslavsky, Naava; Caplan, Steve

    2016-06-24

    An elaborate network of dynamic lipid membranes, termed tubular recycling endosomes (TRE), coordinates the process of endocytic recycling in mammalian cells. The C-terminal Eps15 homology domain (EHD)-containing proteins have been implicated in the bending and fission of TRE, thus regulating endocytic recycling. EHD proteins have an EH domain that interacts with proteins containing an NPF motif. We found that NPF-containing EHD1 interaction partners such as molecules interacting with CasL-like1 (MICAL-L1) and Syndapin2 are essential for TRE biogenesis. Also crucial for TRE biogenesis is the generation of phosphatidic acid, an essential lipid component of TRE that serves as a docking point for MICAL-L1 and Syndapin2. EHD1 and EHD3 have 86% amino acid identity; they homo- and heterodimerize and partially co-localize to TRE. Despite their remarkable identity, they have distinct mechanistic functions. EHD1 induces membrane vesiculation, whereas EHD3 supports TRE biogenesis and/or stabilization by an unknown mechanism. While using phospholipase D inhibitors (which block the conversion of glycerophospholipids to phosphatidic acid) to deplete cellular TRE, we observed that, upon inhibitor washout, there was a rapid and dramatic regeneration of MICAL-L1-marked TRE. Using this "synchronized" TRE biogenesis system, we determined that EHD3 is involved in the stabilization of TRE rather than in their biogenesis. Moreover, we identify the residues Ala-519/Asp-520 of EHD1 and Asn-519/Glu-520 of EHD3 as defining the selectivity of these two paralogs for NPF-containing binding partners, and we present a model to explain the atomic mechanism and provide new insight for their differential roles in vesiculation and tubulation, respectively. PMID:27189942

  1. Binding Procurement

    Science.gov (United States)

    Rao, Gopalakrishna M.; Vaidyanathan, Hari

    2007-01-01

    This viewgraph presentation reviews the use of the binding procurement process in purchasing Aerospace Flight Battery Systems. NASA Engineering and Safety Center (NESC) requested NASA Aerospace Flight Battery Systems Working Group to develop a set of guideline requirements document for Binding Procurement Contracts.

  2. Long-term culture and cryopreservation does not affect the stability and functionality of human embryonic stem cell-derived hepatocyte-like cells.

    Science.gov (United States)

    Mandal, Arundhati; Raju, Sheena; Viswanathan, Chandra

    2016-02-01

    Human embryonic stem cells (hESCs) are predicted to be an unlimited source of hepatocytes which can pave the way for applications such as cell replacement therapies or as a model of human development or even to predict the hepatotoxicity of drug compounds. We have optimized a 23-d differentiation protocol to generate hepatocyte-like cells (HLCs) from hESCs, obtaining a relatively pure population which expresses the major hepatic markers and is functional and mature. The stability of the HLCs in terms of hepato-specific marker expression and functionality was found to be intact even after an extended period of in vitro culture and cryopreservation. The hESC-derived HLCs have shown the capability to display sensitivity and an alteration in the level of CYP enzyme upon drug induction. This illustrates the potential of such assays in predicting the hepatotoxicity of a drug compound leading to advancement of pharmacology.

  3. Microtubular stability affects pVHL-mediated regulation of HIF-1alpha via the p38/MAPK pathway in hypoxic cardiomyocytes.

    Directory of Open Access Journals (Sweden)

    Miao Teng

    Full Text Available BACKGROUND: Our previous research found that structural changes of the microtubule network influence glycolysis in cardiomyocytes by regulating the hypoxia-inducible factor (HIF-1α during the early stages of hypoxia. However, little is known about the underlying regulatory mechanism of the changes of HIF-1α caused by microtubule network alternation. The von Hippel-Lindau tumor suppressor protein (pVHL, as a ubiquitin ligase, is best understood as a negative regulator of HIF-1α. METHODOLOGY/PRINCIPAL FINDINGS: In primary rat cardiomyocytes and H9c2 cardiac cells, microtubule-stabilization was achieved by pretreating with paclitaxel or transfection of microtubule-associated protein 4 (MAP4 overexpression plasmids and microtubule-depolymerization was achieved by pretreating with colchicine or transfection of MAP4 siRNA before hypoxia treatment. Recombinant adenovirus vectors for overexpressing pVHL or silencing of pVHL expression were constructed and transfected in primary rat cardiomyocytes and H9c2 cells. With different microtubule-stabilizing and -depolymerizing treaments, we demonstrated that the protein levels of HIF-1α were down-regulated through overexpression of pVHL and were up-regulated through knockdown of pVHL in hypoxic cardiomyocytes. Importantly, microtubular structure breakdown activated p38/MAPK pathway, accompanied with the upregulation of pVHL. In coincidence, we found that SB203580, a p38/MAPK inhibitor decreased pVHL while MKK6 (Glu overexpression increased pVHL in the microtubule network altered-hypoxic cardiomyocytes and H9c2 cells. CONCLUSIONS/SIGNIFICANCE: This study suggests that pVHL plays an important role in the regulation of HIF-1α caused by the changes of microtubular structure and the p38/MAPK pathway participates in the process of pVHL change following microtubule network alteration in hypoxic cardiomyocytes.

  4. Factors affecting the stability of mini-implants%影响微种植体支抗稳定性的相关因素

    Institute of Scientific and Technical Information of China (English)

    林仰东; 吴也可

    2015-01-01

    BACKGROUND:Mini-implants are widely applied in the clinical treatment of orthodontics and orthognathics, because they can provide absolute skeletal anchorage. However, the relatively high failure rates have always been their major drawback, and how to improve the success rates of mini-implants becomes the main research direction in recent years. OBJECTIVE:To summarize the factors influencing the stability of mini-implants. METHODS:A computer-based search of Wanfang, VIP and PubMed databases was performed using the keywords of “mini-implants, stability, success rate, osseointegration” in Chinese and English. RESULTS AND CONCLUSION:Mibni-implants are an effective means of anchorage control. In clinics, the factors such as implant design, health status of patients, implantation methods and regions, loading patterns and maintenance after implantation wil al have an influence on the stability and success rates of mini-implants. To improve the success rate of the mini-implants, the selection of appropriate implant area is necessary in clinical applications, for example, thicker cortical bone and higher mini-implants are recommended clinicaly; using reasonable and loading implants, studies have shown that non-scored mini-implants is beneficial to reduce the dropout rate of mini-implants during early orthodontic loading; maintenance during healing periods after implantation is emphasized, and currently, stress loading on the mini-implants is preferred immediately after implantation or earlier, which can have a better success rate.%背景:微种植体因能提供骨内绝对支抗而被广泛应用于正畸、正颌的临床治疗中,然而脱落率较高一直是其主要缺点,如何提高微种植体的成功率成为近年来的主要研究方向。目的:总结影响微种植体稳定性的因素。方法:应用计算机检索万方数据库、维普数据库及PubMed数据库,检索关键词为“微种植体,稳定性,成功

  5. Genetics Home Reference: mannose-binding lectin deficiency

    Science.gov (United States)

    ... Health Conditions mannose-binding lectin deficiency mannose-binding lectin deficiency Enable Javascript to view the expand/collapse ... PDF Open All Close All Description Mannose-binding lectin deficiency is a condition that affects the immune ...

  6. The selective glucocorticoid receptor antagonist ORG 34116 decreases immobility time in the forced swim test and affects cAMP-responsive element-binding protein phosphorylation in rat brain.

    Science.gov (United States)

    Bachmann, Cornelius G; Bilang-Bleuel, Alicia; De Carli, Sonja; Linthorst, Astrid C E; Reul, Johannes M H M

    2005-01-01

    Glucocorticoid receptor (GR) antagonists can block the retention of the immobility response in the forced swimming test. Recently, we showed that forced swimming evokes a distinct spatiotemporal pattern of cAMP-responsive element-binding protein (CREB) phosphorylation in the dentate gyrus (DG) and neocortex. In the present study, we found that chronic treatment of rats with the selective GR antagonist ORG 34116 decreased the immobility time in the forced swim test, increased baseline levels of phosphorylated CREB (P-CREB) in the DG and neocortex and affected the forced swimming-induced changes in P-CREB levels in a time- and site-specific manner. Overall, we observed that, in control rats, forced swimming evoked increases in P-CREB levels in the DG and neocortex, whereas in ORG 34116-treated animals a major dephosphorylation of P-CREB was observed. These observations underscore an important role of GRs in the control of the phosphorylation state of CREB which seems to be of significance for the immobility response in the forced swim test and extend the molecular mechanism of action of GRs in the brain.

  7. Different sources of omega-3 polyunsaturated fatty acids affects apparent digestibility, tissue deposition, and tissue oxidative stability in growing female rats

    Directory of Open Access Journals (Sweden)

    Benedito Vagner A

    2011-10-01

    Full Text Available Abstract Background Numerous health benefits associated with increased omega-3 polyunsaturated fatty acid (n-3 PUFA consumption has lead to an increasing variety of available n-3 PUFA sources. However, sources differ in the type, amount, and structural form of the n-3 PUFAs. Therefore, the objective of this study was to determine the effect of different sources of ω-3 PUFAs on digestibility, tissue deposition, eicosanoid metabolism, and oxidative stability. Methods Female Sprague-Dawley rats (age 28 d were randomly assigned (n = 10/group to be fed a high fat 12% (wt diet consisting of either corn oil (CO or n-3 PUFA rich flaxseed (FO, krill (KO, menhaden (MO, salmon (SO or tuna (TO oil for 8 weeks. Rats were individually housed in metabolic cages to determine fatty acid digestibility. Diet and tissue fatty acid composition was analyzed by gas chromatography and lipid classes using thin layer chromatography. Eicosanoid metabolism was determined by measuring urinary metabolites of 2-series prostaglandins (PGs and thromoboxanes (TXBs using enzyme immunoassays. Oxidative stability was assessed by measuring thiobarbituric acid reactive substances (TBARS and total antioxidant capacity (TAC using colorimetric assays. Gene expression of antioxidant defense enzymes was determined by real time quantitative polymerase chain reaction (RT-qPCR. Results Rats fed KO had significantly lower DHA digestibility and brain DHA incorporation than SO and TO-fed rats. Of the n-3 PUFA sources, rats fed SO and TO had the highest n-3 PUFAs digestibility and in turn, tissue accretion. Higher tissue n-3 LC-PUFAs had no significant effect on 2-series PG and TXB metabolites. Despite higher tissue n-3 LC-PUFA deposition, there was no increase in oxidation susceptibility indicated by no significant increase in TBARS or decrease in TAC and gene expression of antioxidant defense enzymes, in SO or TO-fed rats. Conclusions On the basis that the optimal n-3 PUFA sources should

  8. Affecting Factor Analysis and Control Technique of Open-pit Slope Stability in Sijiaying Iron Mine%研山铁矿边坡稳定性影响因素分析及控制技术

    Institute of Scientific and Technical Information of China (English)

    张树东

    2015-01-01

    The stability of open pit slope is the key factor affecting the mine production security. Based on the results of field investigation,it shows that slope lithology,water,and mining disturbance are the main three factors affecting the stability of Mine. The slope is divided to three areas by comprehensively considering the slope stability of rock and earth mass and the re-inforcement measures of whole-length bonding bolt,anchor wire technology,steel mesh+spray anchor net are taken to strengthen the slope stability. Based on the actual situation of the slope,some treatment measures are taken,such as full-length grouted bolt,pre-stressed cable,hanging shotcrete. Based on the pre-blasting technology theory,the pre-blasting parameter of the Yans-han Iron Mine was designed and brought into the field operations. The results show that the parameters greatly reduced blasting vibration and damage to the slope step,and then significantly improve the slope stability. The research lays a good foundation for the safety production of the mine.%露天边坡的稳定是决定矿山安全生产的关键因素。基于研山铁矿边坡工程地质特征现场调查结果,得出边坡岩性、水以及开采扰动是影响矿区边坡稳定性的三大主要因素。综合考虑边坡岩土体破碎情况将边坡自西向东划分为3个分区,根据各区边坡实际状况,分别采用了全长黏结锚杆支护、预应力锚索、挂网喷射混凝土等防护治理措施。基于预裂爆破技术原理,对研山铁矿进行了预裂爆破参数设计及现场试验,结果表明,设计的爆破参数不仅大幅度降低了爆破震动,减小了对台阶损伤破坏,极大地增强了边坡的稳定性,为矿山安全生产奠定了基础。

  9. On Clinical Stability Factors Affecting Micro Implant Anchorage%影响微种植钉支抗的临床稳定性因素研究

    Institute of Scientific and Technical Information of China (English)

    包晨刚

    2014-01-01

    Objective To investigate the stability of micro implant as reinforcing anchorage method in the clinical application,at the same time to analyze the related factors of the success,to provide the reference for the clinical work in the future. Methods 53 patients were implanted 171 micro screws, observation period of 1 years,the influence of age,gender,the mandibular plane angle,periodontitis,periodontal tissue swelling history on stability of micro implant were analyzed. Results The total success rate of 53 patients with wrong micro implant was 90. 57%(48/53),the oral hygiene status,patient’ s periodontal tissue swelling,periodontitis,mandibular plane angle history are independent factors of micro implant survival rate,the effect of the age,gender and micro implant design factors on micro screw success rate had no significant difference,it was not statistically significant (P > 0. 05). Conclusion Patients with micro implant as reinforcing anchorage means should pay attention to keeping the mouth clean, physicians should design planting scheme according to the mandibular plane angle, avoid the periodontal tissue swelling occurs in order to improve the success rate of micro implant.%目的:探讨微型种植钉作为增强支抗手段在临床应用中的稳定性,同时分析影响其成功率的相关因素,为今后的临床工作提供参考.方法53例错颌患者共植入微型种植钉171枚,观察期1 a,并分析年龄、性别、下颌平面角、牙周组织肿胀、牙周炎史等因素对微型种植钉稳定性的影响.结果本组53例错颌患者的微型种植钉总成功率为90.57%(48/53),其中患者的口腔卫生状况、牙周组织肿胀、牙周炎史、下颌平面角等是微型种植钉成活率的独立影响因素,而且患者的年龄、性别以及微型种植钉的设计因素对微型种植钉成功率的影响无显著性差异,不具有统计学意义(P>0.05).结论采用微型种植钉作为增强支抗手段的患者要注意

  10. Oxidative stability and antioxidant enzyme activities of dry-cured bacons as affected by the partial substitution of NaCl with KCl.

    Science.gov (United States)

    Wu, Haizhou; Yan, Wenjing; Zhuang, Hong; Huang, Mingming; Zhao, Jianying; Zhang, Jianhao

    2016-06-15

    This study investigated the influence of partial substitution of NaCl with KCl on protein and lipid oxidation as well as antioxidant enzyme activities in dry-cured bacons during processing. The partial substitution was 0% KCl (I), 40% KCl (II), and 70% KCl (III). Compared with 0% KCl (I), the substitution of 40% NaCl with KCl did not significantly influence the protein and lipid oxidation and antioxidant enzyme activities. The bacons that were treated with 70% KCl treatment (III) showed increased lipid oxidation and antioxidant enzyme GSH-Px activity, whereas samples treated with formulas I and II showed higher protein oxidation and antioxidant enzyme catalase activity. These results demonstrate that the substitution of NaCl with KCl by more than 40% may significantly affect protein and lipid oxidation and that for the substitution of NaCl in further processed meat products with other chloride salts, salt content is very important for control of protein and lipid biochemical changes in finished products. PMID:26868571

  11. Affection of the rotor-flux error on the induction motor full-order observer stability%转子磁链误差对感应电机观测器稳定性影响

    Institute of Scientific and Technical Information of China (English)

    许思猛; 陈冲

    2012-01-01

    The rotor flux error affection on the stability of the induction motor full-order speed adaptive rotor flux observer was studied using the voltage model. The positive-real property of the forward path transfer function of the observer equivalent error system was analyzed. Stability domain border equations in ω1 -ωs plane were derived. A modified rotor flux error model excluding a pure integrator was suggested. Affection of the modified model on open-loop zeros plots of the linearized equivalent speed control system was investigated, and the stability region distribution in all motor operation modes was studied. Research results indicate the stability region is enlarged by amplifying the rotor flux error. The observer with the modified model is stable in the low-speed region with regenerative loads but unstable in low-speed motoring mode. Simulation results illustrate the adaptive observer with combined speed adaptive laws is stable in all motor operation modes.%利用转子磁链电压模型研究转子磁链误差对感应电动机全阶转速自适应转子磁链观测器稳定性影响.通过研究观测器等效误差系统前向通道传递函数正实性,得到观测器在ω1-ωs平面中稳定区域边界方程.提出不舍纯积分器的新型转子磁链误差模型,通过分析该模型对线性化等效转速控制系统开环零点分布影响,研究不同工况下观测器稳定区域分布.研究结果表明增大转子磁链误差能够扩大稳定区域,所提出的模型解决了低速再生发电工况时观测器稳定问题,但在低速电动工况时观测器不稳定.仿真结果表明组合应用不同转速自适应律观测器在所有工况下均能稳定.

  12. Dynamic conformations of nucleophosmin (NPM1 at a key monomer-monomer interface affect oligomer stability and interactions with granzyme B.

    Directory of Open Access Journals (Sweden)

    Wei D Duan-Porter

    Full Text Available Nucleophosmin (NPM1 is an abundant, nucleolar tumor antigen with important roles in cell proliferation and putative contributions to oncogenesis. Wild-type NPM1 forms pentameric oligomers through interactions at the amino-terminal core domain. A truncated form of NPM1 found in some hepatocellular carcinoma tissue formed an unusually stable oligomer and showed increased susceptibility to cleavage by granzyme B. Initiation of translation at the seventh methionine generated a protein (M7-NPM that shared all these properties. We used deuterium exchange mass spectrometry (DXMS to perform a detailed structural analysis of wild-type NPM1 and M7-NPM, and found dynamic conformational shifts or local "unfolding" at a specific monomer-monomer interface which included the β-hairpin "latch." We tested the importance of interactions at the β-hairpin "latch" by replacing a conserved tyrosine in the middle of the β-hairpin loop with glutamic acid, generating Y67E-NPM. Y67E-NPM did not form stable oligomers and further, prevented wild-type NPM1 oligomerization in a dominant-negative fashion, supporting the critical role of the β-hairpin "latch" in monomer-monomer interactions. Also, we show preferential cleavage by granzyme B at one of two available aspartates (either D161 or D122 in M7-NPM and Y67E-NPM, whereas wild-type NPM1 was cleaved at both sites. Thus, we observed a correlation between the propensity to form oligomers and granzyme B cleavage site selection in nucleophosmin proteins, suggesting that a small change at an important monomer-monomer interface can affect conformational shifts and impact protein-protein interactions.

  13. Production and stability of chlorine dioxide in organic acid solutions as affected by pH, type of acid, and concentration of sodium chlorite, and its effectiveness in inactivating Bacillus cereus spores.

    Science.gov (United States)

    Kim, Hoikyung; Kang, Youngjee; Beuchat, Larry R; Ryu, Jee-Hoon

    2008-12-01

    We studied the production and stability of chlorine dioxide (ClO(2)) in organic acid solutions and its effectiveness in killing Bacillus cereus spores. Sodium chlorite (5000, 10,000, or 50,000 microg/ml) was added to 5% acetic, citric, or lactic acid solution, adjusted to pH 3.0, 4.0, 5.0, or 6.0, and held at 21 degrees C for up to 14 days. The amount of ClO(2) produced was higher as the concentration of sodium chlorite was increased and as the pH of the acid solutions was decreased. However, the stability in production of ClO(2) was enhanced by increasing the pH of the organic acid solutions. To evaluate the lethal activity of ClO(2) produced in various acid solutions as affected by acidulant and pH, suspensions of B. cereus spores were treated at 21 degrees C for 1, 3, 5, or 10 min in hydrochloric acid or organic acid solutions (pH 3.0, 4.0, 5.0, or 6.0) containing ClO(2) at concentrations of 100, 50, or 25 microg/ml. Populations of viable spores treated with ClO(2) at concentrations of 100 or 50 microg/ml in organic acid solutions decreased more rapidly than populations treated with the same concentrations of ClO(2) in HCl. Rates of inactivation tended to increase with higher pH of ClO(2) solutions. Results show that ClO(2) formed in organic acid solutions has higher stability and is more lethal to B. cereus spores than ClO(2) formed at the same concentration in HCl solution. This finding emphasizes the benefits of using organic acid solutions to prepare ClO(2) intended for use as an antimicrobial.

  14. Vibrational Softening of a Protein on Ligand Binding

    Energy Technology Data Exchange (ETDEWEB)

    Balog, Erica [Semmelweis University, Budapest, Hungary; Perahia, David [Ecole Normale Superieure de Cachan, Cachan, France; Smith, Jeremy C [ORNL; Merzel, Franci [National Institute of Chemistry, Solvenia

    2011-01-01

    Neutron scattering experiments have demonstrated that binding of the cancer drug methotrexate softens the low-frequency vibrations of its target protein, dihydrofolate reductase (DHFR). Here, this softening is fully reproduced using atomic detail normal-mode analysis. Decomposition of the vibrational density of states demonstrates that the largest contributions arise from structural elements of DHFR critical to stability and function. Mode-projection analysis reveals an increase of the breathing-like character of the affected vibrational modes consistent with the experimentally observed increased adiabatic compressibility of the protein on complexation.

  15. Dissection of the Critical Binding Determinants of Cellular Retinoic Acid Binding Protein II by Mutagenesis and Fluorescence Binding Assay

    OpenAIRE

    Vasileiou, Chrysoula; Lee, Kin Sing Stephen; Crist, Rachael M.; Vaezeslami, Soheila; Goins, Sarah M.; Geiger, James H.; Borhan, Babak

    2009-01-01

    The binding of retinoic acid to mutants of Cellular Retinoic Acid Binding Protein II (CRABPII) was evaluated to better understand the importance of the direct protein/ligand interactions. The important role of Arg111 for the correct structure and function of the protein was verified and other residues that directly affect retinoic acid binding have been identified. Furthermore, retinoic acid binding to CRABPII mutants that lack all previously identified interacting amino acids was rescued by ...

  16. In vitro and in silico investigations of the binding interactions between chlorophenols and trypsin

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yan-Qing, E-mail: wyqing76@126.com [Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Yancheng City 224002, Jiangsu Province (China); Institute of Applied Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng City 224002, Jiangsu Province (China); Tan, Chun-Yun [Institute of Applied Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng City 224002, Jiangsu Province (China); Zhuang, Shu-Lin [Institute of Environmental Science, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058 (China); Zhai, Peng-Zhan; Cui, Yun; Zhou, Qiu-Hua; Zhang, Hong-Mei [Institute of Applied Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng City 224002, Jiangsu Province (China); Fei, Zhenghao [Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Yancheng City 224002, Jiangsu Province (China); Institute of Applied Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng City 224002, Jiangsu Province (China)

    2014-08-15

    Graphical abstract: - Highlights: • Binding interactions of five chlorophenols with trypsin were investigated. • The number of chlorine atoms of chlorophenols partly affected the binding ability of them to trypsin. • Noncovalent interactions stabilized the trypsin–chlorophenols complexes. • There was the one main binding site of trypsin for chlorophenols. - Abstract: Being the first-degree toxic pollutants, chlorophenols (CP) have potential carcinogenic and mutagenic activity and toxicity. Since there still lacks studies on molecular interactions of chlorophenols with trypsin, one major binding target of many exogenous environmental pollutants, the binding interactions between five chlorophenols, 2-CP, 2,6-DCP, 2,4,6-TCP, 2,4,6-TCP, 2,3,4,6-TCP and PCP and trypsin were characterized by the combination of multispectroscopic techniques and molecular modeling. The chlorophenols bind at the one main site of trypsin and the binding induces the changes of microenvironment and global conformations of trypsin. Different number of chloride atoms significantly affects the binding and the binding constants K{sub A} ranks as K{sub A} (2-CP) < K{sub A} (2,6-DCP) ≈ K{sub A} (2,4,6-TCP) < K{sub A} (2,3,4,6-TCP) < K{sub A} (PCP). These chlorophenols interacts with trypsin mainly through hydrophobic interactions and via hydrogen bonding interactions and aromatic–aromatic π–π stacking interaction. Our results offer insights into the binding mechanism of chlorophenols with trypsin and provide important information for possible toxicity risk of chlorophenols to human health.

  17. Quantification of the total Na,K-ATPase concentration in atria and ventricles from mammalian species by measuring 3H-ouabain binding to intact myocardial samples. Stability to short term ischemia reperfusion

    DEFF Research Database (Denmark)

    Schmidt, T A; Svendsen, Jesper Hastrup; Haunsø, S;

    2011-01-01

    Na,K-ATPase concentration was measured by vanadate facilitated 3H-ouabain binding to intact samples taken from various parts of porcine and canine myocardium. In porcine and canine heart 3H-ouabain binding site concentration in ventricles was 1.4-2.5 times larger than in atria. Evaluation of 3H-o...

  18. Triazatriangulene as binding group for molecular electronics

    DEFF Research Database (Denmark)

    Wei, Zhongming; Wang, Xintai; Borges, Anders;

    2014-01-01

    The triazatriangulene (TATA) ring system was investigated as a binding group for tunnel junctions of molecular wires on gold surfaces. Self-assembled monolayers (SAMs) of TATA platforms with three different lengths of phenylene wires were fabricated, and their electrical conductance was recorded ...... with its high stability and directionality make this binding group very attractive for molecular electronic measurements and devices. (Figure Presented)....

  19. Duplex structural differences and not 2′-hydroxyls explain the more stable binding of HIV-reverse transcriptase to RNA-DNA versus DNA-DNA

    OpenAIRE

    Olimpo, Jeffrey T.; DeStefano, Jeffrey J

    2010-01-01

    Human immunodeficiency virus reverse transcriptase (HIV-RT) binds more stably in binary complexes with RNA–DNA versus DNA–DNA. Current results indicate that only the -2 and -4 RNA nucleotides (-1 hybridized to the 3′ recessed DNA base) are required for stable binding to RNA–DNA, and even a single RNA nucleotide conferred significantly greater stability than DNA–DNA. Replacing 2′- hydroxyls on pivotal RNA bases with 2′-O-methyls did not affect stability, indicating that interactions between hy...

  20. Methods for Improving Aptamer Binding Affinity

    OpenAIRE

    Hijiri Hasegawa; Nasa Savory; Koichi Abe; Kazunori Ikebukuro

    2016-01-01

    Aptamers are single stranded oligonucleotides that bind a wide range of biological targets. Although aptamers can be isolated from pools of random sequence oligonucleotides using affinity-based selection, aptamers with high affinities are not always obtained. Therefore, further refinement of aptamers is required to achieve desired binding affinities. The optimization of primary sequences and stabilization of aptamer conformations are the main approaches to refining the binding properties of a...

  1. Towards the classification of DYT6 dystonia mutants in the DNA-binding domain of THAP1.

    Science.gov (United States)

    Campagne, Sébastien; Muller, Isabelle; Milon, Alain; Gervais, Virginie

    2012-10-01

    The transcription factor THAP1 (THanatos Associated Protein 1) has emerged recently as the cause of DYT6 primary dystonia, a type of rare, familial and mostly early-onset syndrome that leads to involuntary muscle contractions. Many of the mutations described in the DYT6 patients fall within the sequence-specific DNA-binding domain (THAP domain) of THAP1 and are believed to negatively affect DNA binding. Here, we have used an integrated approach combining spectroscopic (NMR, fluorescence, DSF) and calorimetric (ITC) methods to evaluate the effect of missense mutations, within the THAP domain, on the structure, stability and DNA binding. Our study demonstrates that none of the mutations investigated failed to bind DNA and some of them even bind DNA stronger than the wild-type protein. However, some mutations could alter DNA-binding specificity. Furthermore, the most striking effect is the decrease of stability observed for mutations at positions affecting the zinc coordination, the hydrophobic core or the C-terminal AVPTIF motif, with unfolding temperatures ranging from 46°C for the wild-type to below 37°C for two mutations. These findings suggest that reduction in population of folded protein under physiological conditions could also account for the disease. PMID:22844099

  2. Fosfato e micorriza na estabilidade de agregados em amostras de latossolos cultivados e não-cultivados Aggregate stability in two cropped and no-cropped Oxisols as affected by phosphate addition and mycorrhiza

    Directory of Open Access Journals (Sweden)

    Júlio César Azevedo Nóbrega

    2001-11-01

    Full Text Available Nos trópicos, existe escassez de informação quanto à contribuição de espécies fúngicas do solo na formação e estabilização de agregados. Este estudo teve como objetivo avaliar o efeito do histórico de uso, níveis de P, de inoculação micorrízica e cultivo com braquiária e soja em casa de vegetação, sobre o diâmetro médio geométrico dos agregados (DMG, o índice de floculação das partículas, a matéria seca das raízes, a colonização micorrízica e o comprimento total de hifas, em amostras de Latossolo Vermelho distrófico e Latossolo Vermelho distroférrico. Amostras dos dois solos, previamente cultivados por longos períodos, e de solos não-cultivados, foram trazidas para casa de vegetação, submetidas a inoculação, e a dois níveis de P, e então cultivadas com braquiária e soja, em dois cultivos sucessivos. Os resultados mostraram que o solo previamente cultivado apresentou menor comprimento total de hifas, menor estabilidade de agregados (menor diâmetro médio de agregados e menor índice de floculação. A inoculação propiciou maior estabilidade dos agregados, e este efeito é condicionado ao nível de P do solo e ao histórico de uso. A presença de P promoveu, indiretamente, maior agregação, por propiciar maior comprimento total das hifas e matéria seca de raízes.In the tropics there is little information on the contribution of soil microorganisms on aggregate stability in the soils. Soil management, crop and fertilization can affect the fungi specie in soil, and also affect aggregate stability. This study attempted to evaluate the effect of earlier cropping, phosphate, inoculation with AMF, and brachiaria and soybean on the geometric mean diameter (GMD, particle flocculation index, root dry matter, and total hyphal length, in dystrophic Red Latosol and dystroferric Red Latosol (both Oxisols. Samples of both soils under natural condition and previously cultivated were brought to the green house and

  3. Cable Stability

    CERN Document Server

    Bottura, L

    2014-01-01

    Superconductor stability is at the core of the design of any successful cable and magnet application. This chapter reviews the initial understanding of the stability mechanism, and reviews matters of importance for stability such as the nature and magnitude of the perturbation spectrum and the cooling mechanisms. Various stability strategies are studied, providing criteria that depend on the desired design and operating conditions.

  4. Influence of surface charge, binding site residues and glycosylation on Thielavia terrestris cutinase biochemical characteristics.

    Science.gov (United States)

    Shirke, Abhijit N; Basore, Danielle; Holton, Samantha; Su, An; Baugh, Evan; Butterfoss, Glenn L; Makhatadze, George; Bystroff, Christopher; Gross, Richard A

    2016-05-01

    Cutinases are esterases of industrial importance for applications in recycling and surface modification of polyesters. The cutinase from Thielavia terrestris (TtC) is distinct in terms of its ability to retain its stability and activity in acidic pH. Stability and activity in acidic pHs are desirable for esterases as the pH of the reaction tends to go down with the generation of acid. The pH stability and activity are governed by the charged state of the residues involved in catalysis or in substrate binding. In this study, we performed the detailed structural and biochemical characterization of TtC coupled with surface charge analysis to understand its acidic tolerance. The stability of TtC in acidic pH was rationalized by evaluating the contribution of charge interactions to the Gibbs free energy of unfolding at varying pHs. The activity of TtC was found to be limited by substrate binding affinity, which is a function of the surface charge. Additionally, the presence of glycosylation affects the biochemical characteristics of TtC owing to steric interactions with residues involved in substrate binding. PMID:26758295

  5. Einstein universes stabilized

    OpenAIRE

    Scholz, Erhard

    2007-01-01

    The hypothesis that gravitational self-binding energy may be the source for the vacuum energy term of cosmology is studied in a Newtonian Ansatz. For spherical spaces the attractive force of gravitation and the negative pressure of the vacuum energy term form a self stabilizing system under very reasonable restrictions for the parameters, among them a characteristic coefficient \\beta of self energy. In the Weyl geometric approach to cosmological redshift, Einstein-Weyl universes with observat...

  6. ATP binding to the pseudokinase domain of JAK2 is critical for pathogenic activation.

    Science.gov (United States)

    Hammarén, Henrik M; Ungureanu, Daniela; Grisouard, Jean; Skoda, Radek C; Hubbard, Stevan R; Silvennoinen, Olli

    2015-04-14

    Pseudokinases lack conserved motifs typically required for kinase activity. Nearly half of pseudokinases bind ATP, but only few retain phosphotransfer activity, leaving the functional role of nucleotide binding in most cases unknown. Janus kinases (JAKs) are nonreceptor tyrosine kinases with a tandem pseudokinase-kinase domain configuration, where the pseudokinase domain (JAK homology 2, JH2) has important regulatory functions and harbors mutations underlying hematological and immunological diseases. JH2 of JAK1, JAK2, and TYK2 all bind ATP, but the significance of this is unclear. We characterize the role of nucleotide binding in normal and pathogenic JAK signaling using comprehensive structure-based mutagenesis. Disruption of JH2 ATP binding in wild-type JAK2 has only minor effects, and in the presence of type I cytokine receptors, the mutations do not affect JAK2 activation. However, JH2 mutants devoid of ATP binding ameliorate the hyperactivation of JAK2 V617F. Disrupting ATP binding in JH2 also inhibits the hyperactivity of other pathogenic JAK2 mutants, as well as of JAK1 V658F, and prevents induction of erythrocytosis in a JAK2 V617F myeloproliferative neoplasm mouse model. Molecular dynamic simulations and thermal-shift analysis indicate that ATP binding stabilizes JH2, with a pronounced effect on the C helix region, which plays a critical role in pathogenic activation of JAK2. Taken together, our results suggest that ATP binding to JH2 serves a structural role in JAKs, which is required for aberrant activity of pathogenic JAK mutants. The inhibitory effect of abrogating JH2 ATP binding in pathogenic JAK mutants may warrant novel therapeutic approaches. PMID:25825724

  7. Influence of 3‧-3‧ inversion of polarity site within d(TGGGGT) on inter quartet cation binding

    Science.gov (United States)

    Šket, Primož; Korbar, Tjaša; Plavec, Janez

    2014-10-01

    Stability, dynamics and function of nucleic acids are affected by nature of cations that are involved in interaction with specific functionalities. Introduction of inversion of polarity sites represents a very useful and chemically accessible backbone modification, which can alter the binding affinity of cations. NMR study on cation binding between G-quartets in tetramolecular G-quadruplex adopted by d(5‧TGG3‧-3‧GGT5‧) with 3‧-3‧ inversion of polarity sites in the middle of G-tract showed existence of two different G-quadruplex forms with all strands in parallel orientation, where all guanine residues adopt anti conformation around glycosidic bonds in the presence of 15NH4+ ions. In one of the forms all three binding sites are equally populated, while in the second form the binding site next to the inversion of polarity site is not fully populated by 15NH4+ ions.

  8. Food Fortification Stability Study

    Science.gov (United States)

    Sirmons, T. A.; Cooper, M. R.; Douglas, G. L.

    2016-01-01

    This study aims to assess the stability of vitamin content, sensory acceptability and color variation in fortified spaceflight foods over a period of 2 years. Findings will identify optimal formulation, processing, and storage conditions to maintain stability and acceptability of commercially available fortification nutrients. Changes in food quality are being monitored to indicate whether fortification affects quality over time (compared to the unfortified control), thus indicating their potential for use on long-duration missions.

  9. Numerical Simulation on Landslide Stability Affected by Seepage Field Variation Caused by Tunnel Excavation%隧洞开挖渗流场变化对滑坡稳定性的影响数值模拟分析

    Institute of Scientific and Technical Information of China (English)

    张凡; 韩爱果; 任光明; 杜飞; 吴龙科; 詹可

    2015-01-01

    The aim of this research is to investigate in landslide’s seepage field,slope deformation and stability af-fected by tunnel excavation.On the basis of analysing the physical and mechanical and water physical properties of a landslide slope,we simulated the variation of groundwater level and seepage field before and after tunnel excava-tion using 3D finite difference software Modflow.Furthermore,by employing Geo-Studio,we analyzed the stability and deformation of landslide after water level changed in natural and excavation conditions.Results reveal that the groundwater seepage field changed after tunnel excavation,and obvious water inflow was found at the excavation ar-ea.As a result,the groundwater level decreased about 20m and apparent “sinkholes”appeared in the excavation area.The change of groundwater level was mainly reflected in the front edge of landslide.The deformation of 2 #secondary sliding body,which caused the deformation of 1 #secondary sliding body,exacerbated under the com-bined actions of weakened sliding resistance and increased effective stress.The maximum slope deformation of sec-ondary landslide above the tunnel reached 1 2.42 cm,but the stability changed slightly.%为研究隧洞开挖对滑坡渗流场、坡体变形及稳定性的影响,在对某滑坡滑体物理力学及水理性质进行研究的基础上,采用 Modflow 有限元差分三维软件对隧洞开挖前后的地下水位进行数值模拟计算,分析隧洞开挖后渗流场的变化,并以此结合 Geo-Studio 软件对滑坡处于天然及开挖情况下水位变化后的稳定性及变形进行了分析研究。结果表明:隧洞开挖后地下水渗流场发生改变,隧洞开挖处产生明显涌水现象,开挖2 a 后地下水位降低约20 m,开挖区形成明显“落水洞”,地下水位变化主要体现在滑坡前缘;隧洞上部2#次级滑体在抗滑力减弱和有效应力增大的双重作用下变形加剧,其下滑带动1#

  10. Efficiency of the pTF-FC2 pas Poison-Antidote Stability System in Escherichia coli Is Affected by the Host Strain, and Antidote Degradation Requires the Lon Protease

    OpenAIRE

    Smith, Anthony S. G.; Rawlings, Douglas E

    1998-01-01

    The stabilization of a test plasmid by the proteic, poison-antidote plasmid addiction system (pas) of plasmid pTF-FC2 was host strain dependent, with a 100-fold increase in stability in Escherichia coli CSH50, a 2.5-fold increase in E. coli JM105, and no detectable stabilization in E. coli strains JM107 and JM109. The lethality of the PasB toxin was far higher in the E. coli strains in which the pas was most effective. Models for the way in which poison-antidote systems stabilize plasmids req...

  11. Structural stability, microbial biomass and community composition of sediments affected by the hydric dynamics of an urban stormwater infiltration basin. Dynamics of physical and microbial characteristics of stormwater sediment.

    Science.gov (United States)

    Badin, Anne Laure; Monier, Armelle; Volatier, Laurence; Geremia, Roberto A; Delolme, Cécile; Bedell, Jean-Philippe

    2011-05-01

    The sedimentary layer deposited at the surface of stormwater infiltration basins is highly organic and multicontaminated. It undergoes considerable moisture content fluctuations due to the drying and inundation cycles (called hydric dynamics) of these basins. Little is known about the microflora of the sediments and its dynamics; hence, the purpose of this study is to describe the physicochemical and biological characteristics of the sediments at different hydric statuses of the infiltration basin. Sediments were sampled at five time points following rain events and dry periods. They were characterized by physical (aggregation), chemical (nutrients and heavy metals), and biological (total, bacterial and fungal biomasses, and genotypic fingerprints of total bacterial and fungal communities) parameters. Data were processed using statistical analyses which indicated that heavy metal (1,841 μg/g dry weight (DW)) and organic matter (11%) remained stable through time. By contrast, aggregation, nutrient content (NH₄⁺, 53-717 μg/g DW), pH (6.9-7.4), and biological parameters were shown to vary with sediment water content and sediment biomass, and were higher consecutive to stormwater flows into the basin (up to 7 mg C/g DW) than during dry periods (0.6 mg C/g DW). Coinertia analysis revealed that the structure of the bacterial communities is driven by the hydric dynamics of the infiltration basin, although no such trend was found for fungal communities. Hydric dynamics more than rain events appear to be more relevant for explaining variations of aggregation, microbial biomass, and shift in the microbial community composition. We concluded that the hydric dynamics of stormwater infiltration basins greatly affects the structural stability of the sedimentary layer, the biomass of the microbial community living in it and its dynamics. The decrease in aggregation consecutive to rewetting probably enhances access to organic matter (OM), explaining the consecutive release

  12. Factors affecting stability of activated sludge process for sorbitol wastewater treatment%山梨醇废水生物处理工程稳定运行的影响因素分析

    Institute of Scientific and Technical Information of China (English)

    赵印; 吴育津; 顾向阳; 沈标

    2009-01-01

    In the present paper factors affecting the stability of activated sludge process for sorbitol wastewater treatment were analyzed. Results showed that organic shock loads, excessive input of siliceous marl or Ni~(2+) ion constituted major factors affecting sorbitol wastewater treatment efficiency and effluent quality. Intermittent and continuous shock loading had been observed during the 5-month operation of sorbitol wastewater treatment system using activated sludge process. Intermittent shock loading showed no adverse effects on effluent quality whereas continuous shock loading led to lower chemical oxygen demand ( COD) removal rate with effluent COD concentration higher than discharge standards. Inferior effluent quality could also result from input of excessive amounts of siliceous marl or Ni~(2+) to the process wastewater. In order to achieve long-term stable operation of sorbitol wastewater treatment system, leakage of siliceous marl or Ni~(2+) into process wastewater has to be prevented through strengthening facility operation and management.%根据工程运行数据对影响山梨醇废水生物处理工程稳定运行的因素进行了系统分析.结果发现:影响废水处理效率和出水水质的因素主要有有机负荷冲击、高浓度硅藻土和Ni~(2+)毒性负荷冲击.有机负荷冲击有间歇性冲击和连续性冲击两种形式,间歇性负荷冲击对系统处理效能没有不利影响,但连续性负荷冲击时化学需氧量(COD)去除率明显下降,出水水质严重超标.高浓度硅藻土和Ni~(2+)冲击对出水水质也有较大影响,且持续时间较长.因此,加强生产设备的操作和管理,杜绝硅藻土和Ni~(2+)泄漏进入工艺废水,是山梨醇废水工程长期稳定运行的必要条件.

  13. Coronary-Heart-Disease-Associated Genetic Variant at the COL4A1/COL4A2 Locus Affects COL4A1/COL4A2 Expression, Vascular Cell Survival, Atherosclerotic Plaque Stability and Risk of Myocardial Infarction.

    Science.gov (United States)

    Yang, Wei; Ng, Fu Liang; Chan, Kenneth; Pu, Xiangyuan; Poston, Robin N; Ren, Meixia; An, Weiwei; Zhang, Ruoxin; Wu, Jingchun; Yan, Shunying; Situ, Haiteng; He, Xinjie; Chen, Yequn; Tan, Xuerui; Xiao, Qingzhong; Tucker, Arthur T; Caulfield, Mark J; Ye, Shu

    2016-07-01

    Genome-wide association studies have revealed an association between coronary heart disease (CHD) and genetic variation on chromosome 13q34, with the lead single nucleotide polymorphism rs4773144 residing in the COL4A2 gene in this genomic region. We investigated the functional effects of this genetic variant. Analyses of primary cultures of vascular smooth muscle cells (SMCs) and endothelial cells (ECs) from different individuals showed a difference between rs4773144 genotypes in COL4A2 and COL4A1 expression levels, being lowest in the G/G genotype, intermediate in A/G and highest in A/A. Chromatin immunoprecipitation followed by allelic imbalance assays of primary cultures of SMCs and ECs that were of the A/G genotype revealed that the G allele had lower transcriptional activity than the A allele. Electrophoretic mobility shift assays and luciferase reporter gene assays showed that a short DNA sequence encompassing the rs4773144 site interacted with a nuclear protein, with lower efficiency for the G allele, and that the G allele sequence had lower activity in driving reporter gene expression. Analyses of cultured SMCs from different individuals demonstrated that cells of the G/G genotype had higher apoptosis rates. Immunohistochemical and histological examinations of ex vivo atherosclerotic coronary arteries from different individuals disclosed that atherosclerotic plaques with the G/G genotype had lower collagen IV abundance and thinner fibrous cap, a hallmark of unstable, rupture-prone plaques. A study of a cohort of patients with angiographically documented coronary artery disease showed that patients of the G/G genotype had higher rates of myocardial infarction, a phenotype often caused by plaque rupture. These results indicate that the CHD-related genetic variant at the COL4A2 locus affects COL4A2/COL4A1 expression, SMC survival, and atherosclerotic plaque stability, providing a mechanistic explanation for the association between the genetic variant and CHD

  14. STRUCTURAL STABILITY OF ALUMINOSILICATE INORGANIC POLYMERS: INFLUENCE OF THE PREPARATION PROCEDURE

    Directory of Open Access Journals (Sweden)

    Libor Kobera

    2011-12-01

    Full Text Available The stability of amorphous aluminosilicate inorganic polymer (AIP systems with regard to the structural role of water molecules incorporated in inorganic matrix is discussed. Innovative approach to preparation of amorphous AIP systems with identical chemical composition but differing in structural and mechanical behavior is introduced. It is shown that even small changes in the manufacture dramatically affect mechanical properties and the overall structural stability of AIP systems. If the required quantity of water is admixed to the reaction mixture during the initial step of AIPs synthesis the resulting amorphous aluminosilicate matrix undergoes extensive crystallization (zeolitization. On the other hand, if the amount of water is added to the reaction mixture during the last step of the preparation procedure, the inorganic matrix exhibits long-term stability without any structural defects. To find the structural reasons of the observed behavior a combination of traditional solid state NMR (1H and 29Si MAS NMR, 29Si CP/MAS NMR, 29Si inverse-T1-filtered NMR, XRPD and TGA measurements were used. The applied experiments revealed that the structural stability of AIPs can be attributed to the tight binding of water molecules into the inorganic matrix. The structural stability of the prepared amorphous AIP systems thus seems to be affected by the extent of hydration i.e. the strength of binding water into the inorganic framework.

  15. Stability of p53 homologs.

    Directory of Open Access Journals (Sweden)

    Tobias Brandt

    Full Text Available Most proteins have not evolved for maximal thermal stability. Some are only marginally stable, as for example, the DNA-binding domains of p53 and its homologs, whose kinetic and thermodynamic stabilities are strongly correlated. Here, we applied high-throughput methods using a real-time PCR thermocycler to study the stability of several full-length orthologs and paralogs of the p53 family of transcription factors, which have diverse functions, ranging from tumour suppression to control of developmental processes. From isothermal denaturation fluorimetry and differential scanning fluorimetry, we found that full-length proteins showed the same correlation between kinetic and thermodynamic stability as their isolated DNA-binding domains. The stabilities of the full-length p53 orthologs were marginal and correlated with the temperature of their organism, paralleling the stability of the isolated DNA-binding domains. Additionally, the paralogs p63 and p73 were significantly more stable and long-lived than p53. The short half-life of p53 orthologs and the greater persistence of the paralogs may be biologically relevant.

  16. Ganglioside binding bobath technique affect the results of rehabilitation for children with cerebral palsy%神经节苷酯结合Bobath技术对脑瘫儿康复影响效果

    Institute of Scientific and Technical Information of China (English)

    李熠; 李哲; 赖新波; 叶耀华

    2015-01-01

    Objective To investigate the influence effect of ganglioside binding Bobath technique spastic cerebral palsy children rehabilitation.MethodsSelect 90 cases of spastic cerebral palsy children from February 2013 to October 2014 in our hospital,randomly divide them to Ganglioside group,Bobath group and ganglioside binding Bobath group,after treatment,testing and compared three groups of children with surface electromyography,three-dimensional gait,assessing treatment effect.ResultsAfter treatment,the three groups of children with RMS,iEMG,AEMG,CR values were improved,but the degree of improvement ganglioside binding Bobath group was significantly better than ganglioside group,bobath group,and the value comparison between the two groups had statistical significance(P<0.05);After treatment,the three groups of children walking speed,stride inferior side,dominant side stride length were improved,but the degree of improvement ganglioside binding Bobath group was significantly better than ganglioside group, Bobath group,and the value comparison between the two groups had statistical significance(P<0.05).ConclusionThe ganglioside binding Bobath treatment of children with cerebral palsy children can improve surface electromyography, three-dimensional gait value, can help children with rehabilitation, which has a substantial clinical curative effect and is worthy of clinical application widely.%目的:探讨神经节苷脂结合Bobath技术对痉挛性脑瘫儿康复影响效果。方法选取2013年2月~2014年10月我院收治90例痉挛性脑瘫儿随机分为神经节苷脂组、Bobath组和神经节苷脂结合Bobath组,治疗后检测并比较三组患儿表面肌电、三维步态,评定治疗效果。结果三组患儿治疗后RMS、iEMG、AEMG、CR值均有改善,但神经节苷脂结合Bobath组改善程度明显优于神经节苷脂组、Bobath组,两组间各值比较有统计学意义(P<0.05);三组患儿治疗后步速、劣势侧跨步、优

  17. Analyzing binding data.

    Science.gov (United States)

    Motulsky, Harvey J; Neubig, Richard R

    2010-07-01

    Measuring the rate and extent of radioligand binding provides information on the number of binding sites, and their affinity and accessibility of these binding sites for various drugs. This unit explains how to design and analyze such experiments.

  18. Binding capacity: cooperativity and buffering in biopolymers.

    Science.gov (United States)

    Di Cera, E; Gill, S J; Wyman, J

    1988-01-01

    The group of linkage potentials resulting from the energy of a physicochemical system expressed per mol of a reference component, say a polyfunctional macromolecule, leads to the concept of binding capacity. This concept applies equally to both chemical and physical ligands and opens the way to consideration of higher-order linkage relationships. It provides a means of exploring the consequences of thermodynamic stability on generalized binding phenomena in biopolymers. PMID:3422436

  19. Identification of an Allosteric Binding Site on Human Lysosomal Alpha-Galactosidase Opens the Way to New Pharmacological Chaperones for Fabry Disease

    Science.gov (United States)

    den-Haan, Helena; Pérez-Sánchez, Horacio; Del Prete, Rosita; Liguori, Ludovica; Cimmaruta, Chiara; Lukas, Jan; Andreotti, Giuseppina

    2016-01-01

    Personalized therapies are required for Fabry disease due to its large phenotypic spectrum and numerous different genotypes. In principle, missense mutations that do not affect the active site could be rescued with pharmacological chaperones. At present pharmacological chaperones for Fabry disease bind the active site and couple a stabilizing effect, which is required, to an inhibitory effect, which is deleterious. By in silico docking we identified an allosteric hot-spot for ligand binding where a drug-like compound, 2,6-dithiopurine, binds preferentially. 2,6-dithiopurine stabilizes lysosomal alpha-galactosidase in vitro and rescues a mutant that is not responsive to a mono-therapy with previously described pharmacological chaperones, 1-deoxygalactonojirimycin and galactose in a cell based assay. PMID:27788225

  20. Structural Bases for the Regulation of CO Binding in the Archaeal Protoglobin from Methanosarcina acetivorans.

    Directory of Open Access Journals (Sweden)

    Lesley Tilleman

    Full Text Available Studies of CO ligand binding revealed that two protein states with different ligand affinities exist in the protoglobin from Methanosarcina acetivorans (in MaPgb*, residue Cys(E20101 was mutated to Ser. The switch between the two states occurs upon the ligation of MaPgb*. In this work, site-directed mutagenesis was used to explore the role of selected amino acids in ligand sensing and stabilization and in affecting the equilibrium between the "more reactive" and "less reactive" conformational states of MaPgb*. A combination of experimental data obtained from electronic and resonance Raman absorption spectra, CO ligand-binding kinetics, and X-ray crystallography was employed. Three amino acids were assigned a critical role: Trp(60B9, Tyr(61B10, and Phe(93E11. Trp(60B9 and Tyr(61B10 are involved in ligand stabilization in the distal heme pocket; the strength of their interaction was reflected by the spectra of the CO-ligated MaPgb* and by the CO dissociation rate constants. In contrast, Phe(93E11 is a key player in sensing the heme-bound ligand and promotes the rotation of the Trp(60B9 side chain, thus favoring ligand stabilization. Although the structural bases of the fast CO binding rate constant of MaPgb* are still unclear, Trp(60B9, Tyr(61B10, and Phe(93E11 play a role in regulating heme/ligand affinity.

  1. Affect on Boiler Economy and Stability by Blended Coal Combustion of Biomass Boiler%生物质锅炉混煤掺烧对锅炉经济性及稳定性的影响

    Institute of Scientific and Technical Information of China (English)

    肖志前; 宋杰; 宋景慧

    2015-01-01

    Based on biomass direct combustion power generation technology,field industrial environment experiment was conducted by taking coal as main additive for studying affect on boiler economy and stability by burning different varieties and variable proportion coals of biomass direct combustion boiler,so as to determine varieties of blending combustion coal and reasonable proportion. Research results indicate that relative to direct combustion biomass,it is able to improve boiler heating efficiency and reduce heat loss by burning blending coal. Experiment indicates that with blending combustion propor-tion of 20% calorific value coal,boiler heating efficiency improves 2.34% over than that of direct combustion biomass. Af-ter burning blending coal,boiler on-load capability and combustion condition improves with increase of proportion of blend-ing coal,and then it is able to keep stable combustion and improve utilization efficiency of biomass.%基于生物质直燃发电技术,以煤作为主要添加剂进行现场工业环境试验,研究生物质直燃锅炉掺烧不同品种、不同比例煤后对锅炉经济性及稳定性的影响,以确定掺烧煤的品种和合理比例。研究结果表明:相对于纯燃生物质,掺烧煤可以提高锅炉热效率,降低锅炉热损失。试验表明,在20%热值烟煤掺烧比例下锅炉热效率比纯燃生物质提高2.34%。在掺烧煤后,锅炉带负荷能力、燃烧状况都随掺煤比例的提高而提高,进而可以进一步稳定燃烧,提高生物质的利用效率。

  2. Equilibrium binding studies of mono, di and triisocyanide ligands on Au powder surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Ontko, A.

    1997-10-08

    The author`s group has previously shown that isocyanides are readily adsorbed from solutions to Au powder and bind to the Au surface in an end-on fashion through the terminal carbon. Later work demonstrated that the equilibrium constants for the reversible adsorption of electronically inequivalent isocyanides could be obtained using the Langmuir isotherm technique. This dissertation describes two projects completed which complement the initial findings of this group. Initially, several alkylisocyanides were synthesized to examine the effect of tail length on Au powder adsorption. It was observed that the length of the alkyl chain affected not only the Au surface binding affinity, but also the rate of surface saturation and saturation coverage values. Direct competition studies were also studied using a {sup 13}C-labeled isocyanide. These studies demonstrated the stabilization afforded by substrate-substrate packing forces in SAM`s formed by the longer chain isocyanides. In a second study, di and triisocyanides were synthesized to determine the effect that the length of the connecting link and the number of isocyanide groups (as points of attachment) have on Au adsorption stability. The work in this area describes the binding modes, relative binding affinities and surface coverage values for a series of flexible alkyl and xylyldiisocyanides on Au powder surfaces. This report contains only the introductory material, and general summary. Two chapters have been processed separately. 56 refs.

  3. Bacterial periplasmic sialic acid-binding proteins exhibit a conserved binding site

    Energy Technology Data Exchange (ETDEWEB)

    Gangi Setty, Thanuja [Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065 (India); Cho, Christine [Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109 (United States); Govindappa, Sowmya [Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065 (India); Apicella, Michael A. [Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109 (United States); Ramaswamy, S., E-mail: ramas@instem.res.in [Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065 (India)

    2014-07-01

    Structure–function studies of sialic acid-binding proteins from F. nucleatum, P. multocida, V. cholerae and H. influenzae reveal a conserved network of hydrogen bonds involved in conformational change on ligand binding. Sialic acids are a family of related nine-carbon sugar acids that play important roles in both eukaryotes and prokaryotes. These sialic acids are incorporated/decorated onto lipooligosaccharides as terminal sugars in multiple bacteria to evade the host immune system. Many pathogenic bacteria scavenge sialic acids from their host and use them for molecular mimicry. The first step of this process is the transport of sialic acid to the cytoplasm, which often takes place using a tripartite ATP-independent transport system consisting of a periplasmic binding protein and a membrane transporter. In this paper, the structural characterization of periplasmic binding proteins from the pathogenic bacteria Fusobacterium nucleatum, Pasteurella multocida and Vibrio cholerae and their thermodynamic characterization are reported. The binding affinities of several mutations in the Neu5Ac binding site of the Haemophilus influenzae protein are also reported. The structure and the thermodynamics of the binding of sugars suggest that all of these proteins have a very well conserved binding pocket and similar binding affinities. A significant conformational change occurs when these proteins bind the sugar. While the C1 carboxylate has been identified as the primary binding site, a second conserved hydrogen-bonding network is involved in the initiation and stabilization of the conformational states.

  4. Bacterial periplasmic sialic acid-binding proteins exhibit a conserved binding site

    International Nuclear Information System (INIS)

    Structure–function studies of sialic acid-binding proteins from F. nucleatum, P. multocida, V. cholerae and H. influenzae reveal a conserved network of hydrogen bonds involved in conformational change on ligand binding. Sialic acids are a family of related nine-carbon sugar acids that play important roles in both eukaryotes and prokaryotes. These sialic acids are incorporated/decorated onto lipooligosaccharides as terminal sugars in multiple bacteria to evade the host immune system. Many pathogenic bacteria scavenge sialic acids from their host and use them for molecular mimicry. The first step of this process is the transport of sialic acid to the cytoplasm, which often takes place using a tripartite ATP-independent transport system consisting of a periplasmic binding protein and a membrane transporter. In this paper, the structural characterization of periplasmic binding proteins from the pathogenic bacteria Fusobacterium nucleatum, Pasteurella multocida and Vibrio cholerae and their thermodynamic characterization are reported. The binding affinities of several mutations in the Neu5Ac binding site of the Haemophilus influenzae protein are also reported. The structure and the thermodynamics of the binding of sugars suggest that all of these proteins have a very well conserved binding pocket and similar binding affinities. A significant conformational change occurs when these proteins bind the sugar. While the C1 carboxylate has been identified as the primary binding site, a second conserved hydrogen-bonding network is involved in the initiation and stabilization of the conformational states

  5. Effects of PEG size on structure, function and stability of PEGylated BSA.

    Science.gov (United States)

    Plesner, Bitten; Fee, Conan J; Westh, Peter; Nielsen, Anders D

    2011-10-01

    The effects of PEGylation on the structural, thermal and functional stability of bovine serum albumin (BSA) were investigated using BSA and 6 linear mono-PEGylated BSA compounds. The secondary and tertiary structure of BSA measured by circular dichroism (CD) was independent of PEGylation. In contrast, the thermal stability of BSA was affected by PEGylation. The apparent unfolding temperature T(max) measured by differential scanning calorimetry (DSC) decreased with PEGylation, whereas the temperature of aggregation, T(agg), measured by dynamic light scattering (DLS) increased with PEGylation. The unfolding temperature and the temperature of aggregation were both independent of the molecular weight of the PEG chain. Possible functional changes of BSA after PEGylation were measured by Isothermal Titration Calorimetry (ITC), where the binding of sodium dodecyl sulphate (SDS) to BSA and PEGylated BSA was analysed. At 25°C, two distinct classes of binding sites (high affinity and low affinity) for BSA and one class of binding site (low affinity) for PEGylated BSA were identified. The binding isotherm was modelled assuming independence and thermodynamic equivalence of the sites within each class. From the present biophysical characterisation, it is concluded that after PEGylation BSA appears to be unaffected structurally (secondary and tertiary structure), slightly destabilised thermally (unfolding temperature), stabilised kinetically (temperature of aggregation) and has an altered functionality (binding profile). These biophysical characteristics are all independent of the molecular weight of the attached polymer chain.

  6. Structure and stability of a DNA triple helix in solution: NMR studies on d(T) sub 6 ter dot d(T) sub 6 and its complex with a minor groove binding drug

    Energy Technology Data Exchange (ETDEWEB)

    Umemoto, Kimiko; Sarma, Mukti H.; Gupta, Goutam; Luo, Jia; Sarma, Ramaswamy H. (State Univ. of New York, Albany (USA))

    1990-05-23

    The possibility of both Watson-Crick and Hoogsteen A{center dot}T pairs can result in a triple helical structure for d(T){sub 6}{center dot}d(A){sub 6}{center dot}d(T){sub 6} in solution. In the triple helix the Watson-Crick paired T strand can run antiparallel, while the Hoogsteen paired T strand can run parallel to the A strand. On the basis of 1D/2D NMR studies, we have characterized the structural properties of the triple helix in terms of (a) nature of H-bonding, (b) chain conformations and relative chain orientations, (c) location of triplets T{center dot}A{center dot}T with respect to the helix axis, and (d) effects of NaCl and MgCl{sub 2}. In addition, we experimentally demonstrate that a minor groove specific drug Dst2 (a distamycin analogue) can bind to the triple helix. We show that the nature of thermal transition is altered by Dst2 binding; i.e., the host triple helix shows triple {yields} coil (monophasic) transition in the absence of Dst2, while in its presence the helix shows a triplex {yields} duplex {yields} coil (biphasic) transition.

  7. Affective Urbanism

    DEFF Research Database (Denmark)

    Samson, Kristine

    . Under these circumstances affective aesthetics operate strategically within the urban field of interests, capital flows and desires of the social. This ‘affective urbanism’ (Anderson & Holden 2008) is linked to a society influenced by new kinds of information flows, where culture is mediated and enacted...... and cultural festivals, both practices indicate that design is implemented as means of creating affective spaces in the city. Both cases show how immaterial production of affects and emotions in the city can be seen in relation to economic potential and urban development. Finally, I will discuss whether urban......Urban design and architecture are increasingly used as material and affective strategies for setting the scene, for manipulation and the production of urban life: The orchestration of atmospheres, the framing and staging of urban actions, the programming for contemplation, involvement, play...

  8. Taxol-stabilized microtubules promote the formation of filaments from unmodified full-length Tau in vitro

    OpenAIRE

    Duan, Aranda R.; Goodson, Holly V.

    2012-01-01

    Tau is a neuronal protein that stabilizes the microtubule (MT) network, but it also forms filaments associated with Alzheimer's disease. Understanding Tau–MT and Tau–Tau interactions would help to establish Tau function in health and disease. For many years, literature reports on Tau–MT binding behavior and affinity have remained surprisingly contradictory (e.g., 10-fold variation in Tau–MT affinity). Tau–Tau interactions have also been investigated, but whether MTs might affect Tau filament ...

  9. Einstein universes stabilized

    CERN Document Server

    Scholz, Erhard

    2007-01-01

    The hypothesis that gravitational self-binding energy may be the source for the vacuum energy term of cosmology is studied in a Newtonian Ansatz. For spherical spaces the attractive force of gravitation and the negative pressure of the vacuum energy term form a self stabilizing system under very reasonable restrictions for the parameters, among them a characteristic coefficient \\beta of self energy. In the Weyl geometric approach to cosmological redshift, Einstein-Weyl universes with observational restrictions of the curvature parameters are dynamically stable, if \\beta is about 40 % smaller than in the exact Newton Ansatz or if the space geometry is elliptical.

  10. Affective Maps

    DEFF Research Database (Denmark)

    Salovaara-Moring, Inka

    . In particular, mapping environmental damage, endangered species, and human made disasters has become one of the focal point of affective knowledge production. These ‘more-than-humangeographies’ practices include notions of species, space and territory, and movement towards a new political ecology. This type...... of environmental knowledge production. It uses InfoAmazonia, the databased platform on Amazon rainforests, as an example of affective geo-visualization within information mapping that enhances embodiment in the experience of the information. Amazonia is defined as a digitally created affective (map)space within...

  11. Ensuring Stability

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    "Stable"will be a key word for China’s economy in 2012.That’s the beat set at the annual Central Economic Work Conference held in Beijing on December 12-14,which reviewed this year’s development and mapped out plans for the next year.Policymakers at the conference decided to keep macroeconomic policies stable,seek a stable and relatively fast economic growth,stabilize consumer prices and maintain social stability in 2012.On the basis of stability,the government will transform the development model,deepen reform and improve people’s livelihood.

  12. Against Stabilization

    Directory of Open Access Journals (Sweden)

    Roger Mac Ginty

    2012-11-01

    Full Text Available This is a polemic against the concept and practice of stabilization as practiced by leading states from the global north in peace support interventions. It is not an argument against stability. Instead, it depicts stabilization as an essentially conservative doctrine that runs counter to its stated aims of enhancing local participation and legitimacy. It is an agenda of control that privileges notions of assimilation with international (western standards and mainstreams the military into peace-support operations. As a result, the value of peace is undercut.

  13. [Influence of liquid ceramic additive on binding of heavy metal during the vitrification of fly ash from municipal solid waste incinerator].

    Science.gov (United States)

    Li, Run-dong; Nie, Yong-feng; Li, Ai-min; Wang, Lei; Chi, Yong; Cen, Ke-fa

    2004-09-01

    Vitrification process can effectively control the leachability of heavy metals in fly ash generated from municipal solid waste incinerator (MWSI). The use of liquid ceramic (LC) additive as a heavy metal chemical stabilization agent was evaluated for MSWI fly ash. The residuals of chromium, lead and zinc in slag increase by different degree with liquid ceramic additive at 1400 degrees C, while those of cadmium and copper decreases. The migrating characteristic of nickel is hardly affected by the additive less than 10%. The volatilization of Cr and Zn occurs after 61 minute with 10% addition of LC, and the binding efficiency of Cr decreases with increasing of melting temperature. The results indicate that the binding efficiency of heavy metals was affected greatly by LC additive and showed significant differences according to type of heavy metal during melting process. The short melting time (no longer than 33 min) is useful to obtain high binding efficiency of heavy metals. PMID:15623047

  14. Signatures of RNA binding proteins globally coupled to effective microRNA target sites

    DEFF Research Database (Denmark)

    Jacobsen, Anders; Wen, Jiayu; Marks, Debora S;

    2010-01-01

    in 3' untranslated regions (UTRs) correlate with expression changes following transfection of small RNAs. The most significantly overrepresented motifs in down-regulated mRNAs are two novel U-rich motifs (URMs), UUUUAAA and UUUGUUU, recently discovered as binding sites for the ELAVL4 (also known as Hu......D) RNA-BP. Surprisingly, the most significantly overrepresented motif in up-regulated mRNAs is the heptanucleotide AU-rich element (ARE), UAUUUAU, which is known to affect mRNA stability via at least 20 different RNA-BPs. We show that destabilization mediated by the transfected miRNA is generally...

  15. Protein stability: a crystallographer’s perspective

    Energy Technology Data Exchange (ETDEWEB)

    Deller, Marc C., E-mail: mdeller@stanford.edu [Stanford University, Shriram Center, 443 Via Ortega, Room 097, MC5082, Stanford, CA 94305-4125 (United States); Kong, Leopold [National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Building 8, Room 1A03, 8 Center Drive, Bethesda, MD 20814 (United States); Rupp, Bernhard [k.-k. Hofkristallamt, 91 Audrey Place, Vista, CA 92084 (United States); Medical University of Innsbruck, Schöpfstrasse 41, A-6020 Innsbruck (Austria)

    2016-01-26

    An understanding of protein stability is essential for optimizing the expression, purification and crystallization of proteins. In this review, discussion will focus on factors affecting protein stability on a somewhat practical level, particularly from the view of a protein crystallographer. Protein stability is a topic of major interest for the biotechnology, pharmaceutical and food industries, in addition to being a daily consideration for academic researchers studying proteins. An understanding of protein stability is essential for optimizing the expression, purification, formulation, storage and structural studies of proteins. In this review, discussion will focus on factors affecting protein stability, on a somewhat practical level, particularly from the view of a protein crystallographer. The differences between protein conformational stability and protein compositional stability will be discussed, along with a brief introduction to key methods useful for analyzing protein stability. Finally, tactics for addressing protein-stability issues during protein expression, purification and crystallization will be discussed.

  16. Evidence for an intrinsic binding force between dodecaborate dianions and receptors with hydrophobic binding pockets.

    Science.gov (United States)

    Warneke, Jonas; Jenne, Carsten; Bernarding, Johannes; Azov, Vladimir A; Plaumann, Markus

    2016-05-01

    A gas phase binding study revealed strong intrinsic intermolecular interactions between dianionic halogenated closo-dodecaborates [B12X12](2-) and several neutral organic receptors. Oxidation of a tetrathiafulvalene host allowed switching between two host-guest binding modes in a supramolecular complex. Complexes of β-cyclodextrin with [B12F12](2-) show remarkable stability in the gas phase and were successfully tested as carriers for the delivery of boron clusters into cancer cells. PMID:27087168

  17. Affect Regulation

    DEFF Research Database (Denmark)

    Pedersen, Signe Holm; Poulsen, Stig Bernt; Lunn, Susanne

    2014-01-01

    Gergely and colleagues’ state that their Social Biofeedback Theory of Parental Affect Mirroring” can be seen as a kind of operationalization of the classical psychoanalytic concepts of holding, containing and mirroring. This article examines to what extent the social biofeedback theory of parenta...

  18. Total iron binding capacity

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/article/003489.htm Total iron binding capacity To use the sharing features on this page, please enable JavaScript. Total iron binding capacity (TIBC) is a blood test to ...

  19. The microtubule-stabilizing agent discodermolide competitively inhibits the binding of paclitaxel (Taxol) to tubulin polymers, enhances tubulin nucleation reactions more potently than paclitaxel, and inhibits the growth of paclitaxel-resistant cells.

    Science.gov (United States)

    Kowalski, R J; Giannakakou, P; Gunasekera, S P; Longley, R E; Day, B W; Hamel, E

    1997-10-01

    The lactone-bearing polyhydroxylated alkatetraene (+)-discodermolide, which was isolated from the sponge Discodermia dissoluta, induces the polymerization of purified tubulin with and without microtubule-associated proteins or GTP, and the polymers formed are stable to cold and calcium. These effects are similar to those of paclitaxel (Taxol), but discodermolide is more potent. We confirmed that these properties represent hypernucleation phenomena; we obtained lower tubulin critical concentrations and shorter polymers with discodermolide than paclitaxel under a variety of reaction conditions. Furthermore, we demonstrated that discodermolide is a competitive inhibitor with [3H]paclitaxel in binding to tubulin polymer, with an apparent Ki value of 0.4 microM. Multidrug-resistant human colon and ovarian carcinoma cells overexpressing P-glycoprotein, which are 900- and 2800-fold resistant to paclitaxel, respectively, relative to the parental lines, retained significant sensitivity to discodermolide (25- and 89-fold more resistant relative to the parental lines). Ovarian carcinoma cells that are 20-30-fold more resistant to paclitaxel than the parental line on the basis of expression of altered beta-tubulin polypeptides retained nearly complete sensitivity to discodermolide. The effects of discodermolide on the reorganization of the microtubules of Potorous tridactylis kidney epithelial cells were examined at different times. Intracellular microtubules were reorganized into bundles in interphase cells much more rapidly after discodermolide treatment compared with paclitaxel treatment. A variety of spindle aberrations were observed after treatment with both drugs. The proportions of the different types of aberration were different for the two drugs and changed with the length of drug treatment.

  20. Understanding the roles of Lys33 and Arg45 in the binding-site stability of LjLTP10, an LTP related to drought stress in Lotus japonicus.

    Science.gov (United States)

    Valenzuela-Riffo, Felipe; Tapia, Gerardo; Parra-Palma, Carolina; Morales-Quintana, Luis

    2015-10-01

    In Lotus japonicus, as in most plants, long-chain fatty acids are important components of cuticular wax, one of the principal functions of which is to act as a barrier to water loss in response to drought stress. It is thought that lipid transfer proteins (LTPs) are involved in the process of cuticle formation. We previously described LjLTP10 as an LTP involved in cuticle formation during acclimation response to drought stress in L. japonicus. The structural model of LjLTP10 had two residues (K33 and R45) in the hydrophobic cavity, although the role of these residues was unclear. In the present work, we investigated the molecular mechanism involved in the transport of lipid precursors in L. japonicus and clarified the importance of the residues K33 and R45. First, in silico site-directed mutagenesis studies were carried out on the LjLTP10 structure. Structural analysis showed that LjLTP10 mutants possess similar structures but their hydrophobic cavities are somewhat different. Unfavorable energies for the interactions of the mutant proteins with different ligands were found by molecular docking and molecular dynamics simulations. We also examined the contributions of energetic parameters to the free energy of the protein-ligand complex using the MM-GBSA method. Results showed that the different complexes present similar, favorable van der Waals interactions, whereas electrostatic interactions were not favored in the mutant structures. Our study indicates that the residues K33 and R45 play a crucial role in maintaining the binding pocket structure required for lipid transport. PMID:26404479

  1. Acyl-coenzyme A binding protein (ACBP)

    DEFF Research Database (Denmark)

    Kragelund, B B; Knudsen, J; Poulsen, F M

    1999-01-01

    Acyl-coenzyme A binding proteins are known from a large group of eukaryote species and to bind a long chain length acyl-CoA ester with very high affinity. Detailed biochemical mapping of ligand binding properties has been obtained as well as in-depth structural studies on the bovine apo-protein...... and of the complex with palmitoyl-CoA using NMR spectroscopy. In the four alpha-helix bundle structure, a set of 21 highly conserved residues present in more that 90% of all known sequences of acyl-coenzyme A binding proteins constitutes three separate mini-cores. These residues are predominantly located...... at the helix-helix interfaces. From studies of a large set of mutant proteins the role of the conserved residues has been related to structure, function, folding and stability....

  2. Acyl-coenzyme A binding protein, ACBP

    DEFF Research Database (Denmark)

    Kragelund, Birthe Brandt; Knudsen, J.; Poulsen, Flemming

    1999-01-01

    Acyl-coenzyme A binding proteins are known from a large group of eukaryote species and to bind a long chain length acyl-CoA ester with very high affinity. Detailed biochemical mapping of ligand binding properties has been obtained as well as in-depth structural studies on the bovine apo-protein...... and of the complex with palmitoyl-CoA using NMR spectroscopy. In the four a-helix bundle structure, a set of 21 highly conserved residues present in more that 90% of all known sequences of acyl-coenzyme A binding proteins constitutes three separate mini-cores. These residues are predominantly located at the helix......-helix interfaces. From studies of a large set of mutant proteins the role of the conserved residues has been related to structure, function, folding and stability....

  3. Tau Induces Cooperative Taxol Binding to Microtubules

    Science.gov (United States)

    Ross, Jennifer; Santangelo, Christian; Victoria, Makrides; Fygenson, Deborah

    2004-03-01

    Taxol and tau are two ligands which stabilize the microtubule (MT) lattice. Taxol is an anti-mitotic drug that binds β tubulin in the MT interior. Tau is a MT-associated protein that binds both α and β tubulin on the MT exterior. Both taxol and tau reduce MT dynamics and promote tubulin polymerization. Tau alone also acts as a buttress to bundle, stiffen, and space MTs. A structural study recently suggested that taxol and tau may interact by binding to the same site. Using fluorescence recovery after photobleaching, we find that tau induces taxol to bind MTs cooperatively depending on the tau concentration. We develop a model that correctly fits the data in the absence of tau and yields a measure of taxol cooperativity when tau is present.

  4. Geometries, stabilities, and electronic properties of Be-doped gold clusters: a density functional theory study

    Institute of Scientific and Technical Information of China (English)

    Chen Dong-Dong; Kuang Xiao-Yu; Zhao Ya-Ru; Shao Peng; Li Yan-Fang

    2011-01-01

    We have systematically investigated the geometrical structures, relative stabilities and electronic properties of small bimetallic AunBe (n = 1, 2, ..., 8) clusters using a density functional method at BP86 level. The optimized geometries reveal that the impurity beryllium atom dramatically affects the structures of the Aun clusters. The averaged binding energies, fragmentation energies, second-order difference of energies, the highest occupied-lowest unoccupied molecular orbital energy gaps and chemical hardness are investigated. All of them exhibit a pronounced odd-even alternation,manifesting that the clusters with even number of gold atoms possess relatively higher stabilities. Especially, the linear Au2Be cluster is magic cluster with the most stable chemical stability. According to the natural population analysis, it is found that charge-transferring direction between Au atom and Be atom changes at the size of n = 4.

  5. 供应商间产量调整策略对供应链稳定性的影响%Affects of Production Adjustment Strategy between Manufactures on Supply Chain Stability

    Institute of Scientific and Technical Information of China (English)

    何喜军; 武玉英

    2012-01-01

    Considering the information asymmetry among manufacturers in supply chain, the paper establishes the model based on dynamic game. In this model, the paper sets an adjustment mechanism of each manufacturer. According to differential equations, the singularity of the differential equations is solved. On this basis, the necessary and sufficient conditions of Nash equilibrium solution that has stability is given by testing the stability of the singularity based on stability conditions of the Hartman - Grobman theorem. Output strategy of each manufacturer and the evolutionary trends of profit are calculated based on the theory of iterative algorithm and Matlab. At last, the paper proposes some countermeasures and suggestions of the output coordination and stability among manufacturers in supply chain.%考虑供应链生产商之间的信息不对称,建立动态博弈模型,设定不同生产商的产量调整机制,建立微分方程组并求解方程组的奇点.在此基础上,利用Hartman-Grobman定理的稳定性判断条件,对奇点的稳定性进行检验,得出纳什均衡解具备稳定性的充分必要条件.利用matlab工具以及迭代计算的算法计算不同生产商之间的产量策略以及利润的演化趋势,从而为供应链中生产商之间的产量协调与稳定性提出建议和对策.

  6. Plant Hormone Binding Sites

    OpenAIRE

    Napier, Richard

    2004-01-01

    • Aims Receptors for plant hormones are becoming identified with increasing rapidity, although a frustrating number remain unknown. There have also been many more hormone‐binding proteins described than receptors. This Botanical Briefing summarizes what has been discovered about hormone binding sites, their discovery and descriptions, and will not dwell on receptor functions or activities except where these are relevant to understand binding.

  7. Analysis of binding heterogeneity.

    NARCIS (Netherlands)

    Nederlof, M.M.

    1992-01-01

    Binding heterogeneity, due to different functional groups on a reactive surface, plays an important role in the binding of small molecules or ions to many adsorbents, both in industrial processes and in natural environments. The binding heterogeneity is described by a distribution of affinity consta

  8. PARALLEL STABILIZATION

    Institute of Scientific and Technical Information of China (English)

    J.L.LIONS

    1999-01-01

    A new algorithm for the stabilization of (possibly turbulent, chaotic) distributed systems, governed by linear or non linear systems of equations is presented. The SPA (Stabilization Parallel Algorithm) is based on a systematic parallel decomposition of the problem (related to arbitrarily overlapping decomposition of domains) and on a penalty argument. SPA is presented here for the case of linear parabolic equations: with distrjbuted or boundary control. It extends to practically all linear and non linear evolution equations, as it will be presented in several other publications.

  9. Affective Networks

    Directory of Open Access Journals (Sweden)

    Jodi Dean

    2010-02-01

    Full Text Available This article sets out the idea of affective networks as a constitutive feature of communicative capitalism. It explores the circulation of intensities in contemporary information and communication networks, arguing that this circulation should be theorized in terms of the psychoanalytic notion of the drive. The article includes critical engagements with theorists such as Guy Debord, Jacques Lacan, Tiziana Terranova, and Slavoj Zizek.

  10. Analyzing radioligand binding data.

    Science.gov (United States)

    Motulsky, Harvey; Neubig, Richard

    2002-08-01

    Radioligand binding experiments are easy to perform, and provide useful data in many fields. They can be used to study receptor regulation, discover new drugs by screening for compounds that compete with high affinity for radioligand binding to a particular receptor, investigate receptor localization in different organs or regions using autoradiography, categorize receptor subtypes, and probe mechanisms of receptor signaling, via measurements of agonist binding and its regulation by ions, nucleotides, and other allosteric modulators. This unit reviews the theory of receptor binding and explains how to analyze experimental data. Since binding data are usually best analyzed using nonlinear regression, this unit also explains the principles of curve fitting with nonlinear regression.

  11. Molecular Binding Mechanism of TtgR Repressor to Antibiotics and Antimicrobials.

    Directory of Open Access Journals (Sweden)

    Ana Maria Fernandez-Escamilla

    Full Text Available A disturbing phenomenon in contemporary medicine is the prevalence of multidrug-resistant pathogenic bacteria. Efflux pumps contribute strongly to this antimicrobial drug resistance, which leads to the subsequent failure of clinical treatments. The TtgR protein of Pseudomonas putida is a HTH-type transcriptional repressor that controls expression of the TtgABC efflux pump, which is the main contributor to resistance against several antimicrobials and toxic compounds in this microbe. One of the main strategies to modulate the bacterial resistance is the rational modification of the ligand binding target site. We report the design and characterization of four mutants-TtgRS77A, TtgRE78A, TtgRN110A and TtgRH114A - at the active ligand binding site. The biophysical characterization of the mutants, in the presence and in the absence of different antimicrobials, revealed that TtgRN110A is the variant with highest thermal stability, under any of the experimental conditions tested. EMSA experiments also showed a different dissociation pattern from the operator for TtgRN110A, in the presence of several antimicrobials, making it a key residue in the TtgR protein repression mechanism of the TtgABC efflux pump. We found that TtgRE78A stability is the most affected upon effector binding. We also probe that one mutation at the C-terminal half of helix-α4, TtgRS77A, provokes a severe protein structure distortion, demonstrating the important role of this residue in the overall protein structure and on the ligand binding site. The data provide new information and deepen the understanding of the TtgR-effector binding mechanism and consequently the TtgABC efflux pump regulation mechanism in Pseudomonas putida.

  12. Stabilizing Movements

    DEFF Research Database (Denmark)

    Norbäck, Maria; Helin, Jenny; Raviola, Elena

    2014-01-01

    of turbulent times. Departing from a process perspective to organizational change and insights from Bakhtin's notion of ‘double-voicing’, which means that people borrow other people's words in their own talk, two main contributions are offered. First, we show how stability cannot be taken for granted...

  13. Before Stabilization

    DEFF Research Database (Denmark)

    Plesner, Ursula; Horst, Maja

    2013-01-01

    to the literature on the relationship between ICTs and organizing, but with a distinct focus on innovation communication and distributed innovation processes taking place before ICTs are stabilized, issues which cannot be captured by studies of diffusion and adaptation of new ICTs within single organizations....

  14. Macroeconomic stability

    DEFF Research Database (Denmark)

    Jespersen, Jesper

    2004-01-01

    It is demonstrated that full employment and sustainable development not necessarily are conflicting goals. On the other hand macroeconomic stability cannot be obtained without a deliberate labour sharing policy and a shift in the composition of private consumption away from traditional material...

  15. LATS1 tumor suppressor is a novel actin-binding protein and negative regulator of actin polymerization

    Institute of Scientific and Technical Information of China (English)

    Stacy Visser-Grieve; Zhonghua Zhou; Yi-Min She; He Huang; Terry D Cyr; Tian Xu; Xiaolong Yang

    2011-01-01

    Dear Editor,The LATS tumor suppressor,conserved from Drosophila (dlats) to humans (LATS1,LATS2),plays a vital role in maintaining cellular homeostasis in humans since loss of either LATS1 or LATS2 leads to the development of numerous cancer types such as breast cancer and leukemia [1].Apart from its roles as a Ser/Thr kinase within the emerging Hippo pathway regulating cell proliferation and apoptosis,ultimately leading to the control of organ size and tumorigenesis [2],LATS is also implicated in a broad range of functions including regulation of genetic stability,transcription,and protein stability [1 ].Recently,tumor suppressors have also been shown to affect the later stages of tumorigenesis,including metastasis.Among this group of metastasis regulators are genes that can directly affect actin dynamics by binding to F-actin,such as the tumor suppressors p53 [3],NF2 [4] and APC [5].

  16. The bovine papillomavirus 1 E2 protein contains two activation domains: one that interacts with TBP and another that functions after TBP binding.

    Science.gov (United States)

    Steger, G; Ham, J; Lefebvre, O; Yaniv, M

    1995-01-16

    The E2 transactivator of bovine papillomavirus type-1 is unable to activate minimal promoters in vivo that contain only E2 binding sites and a TATA box. This block can be overcome by over-expression of human TATA binding protein (TBP) or by the addition of either SP1 binding sites or an initiator element to the promoter, suggesting that the binding of TFIID may normally be a rate-limiting step for activation by E2. Surprisingly, purified E2 and TBP bind co-operatively to DNA in vitro when the sites are closely spaced. E2 does not affect the on rate of association but reduces the off rate. The E2 region responsible for this effect is located in the hinge region that links the classic transactivation and DNA binding domains. We demonstrate that the TBP stabilizing domain contributes in vivo to co-operativity with co-expressed TBP and to activation of the major late minimal promoter (MLP) containing E2 sites. In contrast, promoters with SP1 sites are activated to wild-type levels by such a mutant. This promoter specificity is also evident in vitro. A truncated E2 mutant, lacking the classic transactivation domain but containing the TBP stabilizing domain, stimulates transcription of the MLP in vitro, but does not activate promoters with SP1 sites. In conclusion, our results show that the E2 transactivation domain has a modular structure. We have identified one domain which probably acts at an early step in the assembly of the pre-initiation complex and which is involved in reducing the dissociation rate of bound TBP in vitro. The classic N-terminal activation domain of E2 might affect one or several step(s) in the assembly of the preinitiation complex occurring after the binding of TFIID. PMID:7835344

  17. Dendrimers bind antioxidant polyphenols and cisplatin drug.

    Directory of Open Access Journals (Sweden)

    Amine Abderrezak

    Full Text Available Synthetic polymers of a specific shape and size play major role in drug delivery systems. Dendrimers are unique synthetic macromolecules of nanometer dimensions with a highly branched structure and globular shape with potential applications in gene and drug delivery. We examine the interaction of several dendrimers of different compositions mPEG-PAMAM (G3, mPEG-PAMAM (G4 and PAMAM (G4 with hydrophilic and hydrophobic drugs cisplatin, resveratrol, genistein and curcumin at physiological conditions. FTIR and UV-visible spectroscopic methods as well as molecular modeling were used to analyse drug binding mode, the binding constant and the effects of drug complexation on dendrimer stability and conformation. Structural analysis showed that cisplatin binds dendrimers in hydrophilic mode via Pt cation and polymer terminal NH(2 groups, while curcumin, genistein and resveratrol are located mainly in the cavities binding through both hydrophobic and hydrophilic contacts. The overall binding constants of durg-dendrimers are ranging from 10(2 M(-1 to 10(3 M(-1. The affinity of dendrimer binding was PAMAM-G4>mPEG-PAMAM-G4>mPEG-PAMAM-G3, while the order of drug-polymer stability was curcumin>cisplatin>genistein>resveratrol. Molecular modeling showed larger stability for genisten-PAMAM-G4 (ΔG = -4.75 kcal/mol than curcumin-PAMAM-G4 ((ΔG = -4.53 kcal/mol and resveratrol-PAMAM-G4 ((ΔG = -4.39 kcal/mol. Dendrimers might act as carriers to transport hydrophobic and hydrophilic drugs.

  18. 农村留守妇女的婚姻稳定感及其影响因素--以湖南省为例%The Sense of Married Stability for the Women Staying Alone in Rural Hometown and Its Affecting factors:An Analysis of Hunan Province

    Institute of Scientific and Technical Information of China (English)

    陈飞强

    2014-01-01

    Based on the data from a survey of the married women staying alone hometown in the rural areas of Hunan province, this study explores the sense of marriage stability of these left-behind married women and its influencing factors. It is found that the sense of marriage stability of these women is still at a high level. The factors affecting the marriage stability includes the bullied experiences, relations with elders, family living satisfaction,communication frequency with husband working far away, the home-visiting frequency of husband, whom her husband transfer his earnings to, worries about fading of marriage commitment, and changes in marital relation with husband working away from home all affect the feeling of marriage stability.%通过对“湖南省农村留守妇女调查”数据的分析,本研究探讨了农村留守妇女的婚姻稳定感及其影响因素。研究发现,农村留守妇女的婚姻稳定感处于较高的水平;就其影响因素而言,有无被欺凌的情况、与家里长辈的相处情况、家庭生活满意度、丈夫打工期间的联系频率、探亲频率、丈夫汇钱时是否直接汇给自己、是否担心婚姻感情会发生变化、丈夫外出打工后夫妻感情的变化等变量对农村留守妇女的婚姻稳定感都有显著的影响。

  19. Effects of cytosine methylation on transcription factor binding sites

    KAUST Repository

    Medvedeva, Yulia A

    2014-03-26

    Background: DNA methylation in promoters is closely linked to downstream gene repression. However, whether DNA methylation is a cause or a consequence of gene repression remains an open question. If it is a cause, then DNA methylation may affect the affinity of transcription factors (TFs) for their binding sites (TFBSs). If it is a consequence, then gene repression caused by chromatin modification may be stabilized by DNA methylation. Until now, these two possibilities have been supported only by non-systematic evidence and they have not been tested on a wide range of TFs. An average promoter methylation is usually used in studies, whereas recent results suggested that methylation of individual cytosines can also be important.Results: We found that the methylation profiles of 16.6% of cytosines and the expression profiles of neighboring transcriptional start sites (TSSs) were significantly negatively correlated. We called the CpGs corresponding to such cytosines " traffic lights" We observed a strong selection against CpG " traffic lights" within TFBSs. The negative selection was stronger for transcriptional repressors as compared with transcriptional activators or multifunctional TFs as well as for core TFBS positions as compared with flanking TFBS positions.Conclusions: Our results indicate that direct and selective methylation of certain TFBS that prevents TF binding is restricted to special cases and cannot be considered as a general regulatory mechanism of transcription. 2013 Medvedeva et al.; licensee BioMed Central Ltd.

  20. The complex interplay between ligand binding and conformational structure of the folate binding protein (folate receptor)

    DEFF Research Database (Denmark)

    Holm, Jan; Bruun, Susanne Wrang; Hansen, Steen I.

    2015-01-01

    , and the binding induces a conformational change with formation of hydrophilic and stable holo-FBP. Holo-FBP exhibits a ligand-mediated concentration-dependent self-association into multimers of great thermal and chemical stability due to strong intermolecular forces. Both ligand and FBP are thus protected against...

  1. Glycolipid binding preferences of Shiga toxin variants.

    Directory of Open Access Journals (Sweden)

    Sayali S Karve

    Full Text Available The major virulence factor of Shiga toxin producing E. coli, is Shiga toxin (Stx, an AB5 toxin that consists of a ribosomal RNA-cleaving A-subunit surrounded by a pentamer of receptor-binding B subunits. The two major isoforms, Stx1 and Stx2, and Stx2 variants (Stx2a-h significantly differ in toxicity. The exact reason for this toxicity difference is unknown, however different receptor binding preferences are speculated to play a role. Previous studies used enzyme linked immunosorbent assay (ELISA to study binding of Stx1 and Stx2a toxoids to glycolipid receptors. Here, we studied binding of holotoxin and B-subunits of Stx1, Stx2a, Stx2b, Stx2c and Stx2d to glycolipid receptors globotriaosylceramide (Gb3 and globotetraosylceramide (Gb4 in the presence of cell membrane components such as phosphatidylcholine (PC, cholesterol (Ch and other neutral glycolipids. In the absence of PC and Ch, holotoxins of Stx2 variants bound to mixtures of Gb3 with other glycolipids but not to Gb3 or Gb4 alone. Binding of all Stx holotoxins significantly increased in the presence of PC and Ch. Previously, Stx2a has been shown to form a less stable B-pentamer compared to Stx1. However, its effect on glycolipid receptor binding is unknown. In this study, we showed that even in the absence of the A-subunit, the B-subunits of both Stx1 and Stx2a were able to bind to the glycolipids and the more stable B-pentamer formed by Stx1 bound better than the less stable pentamer of Stx2a. B-subunit mutant of Stx1 L41Q, which shows similar stability as Stx2a B-subunits, lacked glycolipid binding, suggesting that pentamerization is more critical for binding of Stx1 than Stx2a.

  2. [Affective dependency].

    Science.gov (United States)

    Scantamburlo, G; Pitchot, W; Ansseau, M

    2013-01-01

    Affective dependency is characterized by emotional distress (insecure attachment) and dependency to another person with a low self-esteem and reassurance need. The paper proposes a reflection on the definition of emotional dependency and the confusion caused by various denominations. Overprotective and authoritarian parenting, cultural and socio-environmental factors may contribute to the development of dependent personality. Psychological epigenetic factors, such as early socio-emotional trauma could on neuronal circuits in prefronto-limbic regions that are essential for emotional behaviour.We also focus on the interrelations between dependent personality, domestic violence and addictions. The objective for the clinician is to propose a restoration of self-esteem and therapeutic strategies focused on autonomy. PMID:23888587

  3. [Affective dependency].

    Science.gov (United States)

    Scantamburlo, G; Pitchot, W; Ansseau, M

    2013-01-01

    Affective dependency is characterized by emotional distress (insecure attachment) and dependency to another person with a low self-esteem and reassurance need. The paper proposes a reflection on the definition of emotional dependency and the confusion caused by various denominations. Overprotective and authoritarian parenting, cultural and socio-environmental factors may contribute to the development of dependent personality. Psychological epigenetic factors, such as early socio-emotional trauma could on neuronal circuits in prefronto-limbic regions that are essential for emotional behaviour.We also focus on the interrelations between dependent personality, domestic violence and addictions. The objective for the clinician is to propose a restoration of self-esteem and therapeutic strategies focused on autonomy.

  4. Interaction of zinc and cobalt with dipeptides and their DNA binding studies

    Indian Academy of Sciences (India)

    P Rabindra Reddy; M Radhika; K Srinivas Rao

    2004-06-01

    Interactions of zinc and cobalt with peptides cysteinylglycine and histidylglycine have been studied. The binding modes were identified and geometry assigned. Stabilities of these complexes and their ability to bind DNA have been investigated. It is demonstrated that only zinc complexes bind DNA as compared to cobalt complexes.

  5. Hydrogen binding effect on charged P2 ( = 1-7) clusters

    Indian Academy of Sciences (India)

    Zhicong Fang; Xiangjun Kuang

    2013-11-01

    An all-electron (AE) calculation of the hydrogen binding effect on charged phosphorus clusters has been performed under the framework of density functional theory (DFT). Compared with the P$^{\\pm}_{2n}$ ( = 1-7) clusters, the HP$^{\\pm}_{2n}$ ( = 1-7), cluster has shorter average P-P bond length, larger binding energy and HOMOLUMO gap (HLG), higher chemical hardness and frequency of P-P mode. After binding with one hydrogen atom, the electronic structure is changed from open electronic shell to closed electronic shell. Geometrical stability, chemical stability and electronic stability are strengthened. These stability enhancements may be simply understood considering the electron pairing effect.

  6. Ehlers-Danlos Syndrome type IV: a multi-exon deletion in one of the two COL3A1 alleles affecting structure, stability, and processing of type III procollagen

    Energy Technology Data Exchange (ETDEWEB)

    Superti-Furga, A.; Gugler, E.; Gitzelmann, R.; Steinmann, B.

    1988-05-05

    The authors have studied a patient with severe, dominantly inherited Ehlers-Danlos syndrome type IV. The results indicate that this patient carries a deletion of 3.3 kilobase pairs in the triple helical coding domain of one of the two alleles for the pro-..cap alpha..-chains of type III collagen (COL3A1). His cultured skin fibroblasts contain equal amounts of normal length mRNA and of mRNA shortened by approximately 600 bases, and synthesize both normal and shortened pro-..cap alpha..1(III)-chains. In procollagen molecules containing one or more shortened chains, a triple helix is formed with a length of only about 780 amino acids. The mutant procollagen molecules have decreased thermal stability, are less efficiently secreted, and are not processed as their normal counterpart. The deletion in this family is the first mutation to be described in COL3A1.

  7. Plutonium stabilization and packaging system

    International Nuclear Information System (INIS)

    This document describes the functional design of the Plutonium Stabilization and Packaging System (Pu SPS). The objective of this system is to stabilize and package plutonium metals and oxides of greater than 50% wt, as well as other selected isotopes, in accordance with the requirements of the DOE standard for safe storage of these materials for 50 years. This system will support completion of stabilization and packaging campaigns of the inventory at a number of affected sites before the year 2002. The package will be standard for all sites and will provide a minimum of two uncontaminated, organics free confinement barriers for the packaged material

  8. Python bindings for libcloudph++

    OpenAIRE

    Jarecka, Dorota; Arabas, Sylwester; Del Vento, Davide

    2015-01-01

    This technical note introduces the Python bindings for libcloudph++. The libcloudph++ is a C++ library of algorithms for representing atmospheric cloud microphysics in numerical models. The bindings expose the complete functionality of the library to the Python users. The bindings are implemented using the Boost.Python C++ library and use NumPy arrays. This note includes listings with Python scripts exemplifying the use of selected library components. An example solution for using the Python ...

  9. DNS & Bind Cookbook

    CERN Document Server

    Liu, Cricket

    2011-01-01

    The DNS & BIND Cookbook presents solutions to the many problems faced by network administrators responsible for a name server. Following O'Reilly's popular problem-and-solution cookbook format, this title is an indispensable companion to DNS & BIND, 4th Edition, the definitive guide to the critical task of name server administration. The cookbook contains dozens of code recipes showing solutions to everyday problems, ranging from simple questions, like, "How do I get BIND?" to more advanced topics like providing name service for IPv6 addresses. It's full of BIND configuration files that yo

  10. Python bindings for libcloudph++

    CERN Document Server

    Jarecka, Dorota; Del Vento, Davide

    2015-01-01

    This technical note introduces the Python bindings for libcloudph++. The libcloudph++ is a C++ library of algorithms for representing atmospheric cloud microphysics in numerical models. The bindings expose the complete functionality of the library to the Python users. The bindings are implemented using the Boost.Python C++ library and use NumPy arrays. This note includes listings with Python scripts exemplifying the use of selected library components. An example solution for using the Python bindings to access libcloudph++ from Fortran is presented.

  11. Spectroscopic and thermodynamic studies on the binding of sanguinarine and berberine to triple and double helical DNA and RNA structures.

    Science.gov (United States)

    Das, Suman; Kumar, Gopinatha Suresh; Ray, Arghya; Maiti, Motilal

    2003-04-01

    A comparative study on the interaction of sanguinarine and berberine with DNA and RNA triplexes and their parent duplexes was performed, by using a combination of spectrophotometric, UV thermal melting, circular dichroic and thermodynamic techniques. Formation of the DNA and RNA triplexes was confirmed from UV-melting and circular dichroic measurements. The interaction process was characterized by increase of thermal melting temperature, perturbation in circular dichroic spectrum and the typical hypochromic and bathochromic effects in the absorption spectrum. Scatchard analysis indicated that both the alkaloids bound to the triplex and duplex structures in a non-cooperative manner and the binding was stronger to triplexes than to parent duplexes. Thermal melting studies further indicated that sanguinarine stabilized the Hoogsteen base paired third strand of both DNA and RNA triplexes more tightly compared to their Watson-Crick strands, while berberine stabilized the third strand only without affecting the Watson-Crick strand. However, sanguinarine stabilized the parent duplexes while no stabilization was observed with berberine under identical conditions. Circular dichroic studies were also consistent with the observation that perturbations of DNA and RNA triplexes were more compared to their parent duplexes in presence of the alkaloids. Thermodynamic data revealed that binding of sanguinarine and berberine to triplexes (T.AxT and U.AxU) and duplexes (A.T and A.U) showed negative enthalpy changes and positive entropy changes but that of sanguinarine to C.GxC(+) triplex and G.C duplex exhibited negative enthalpy and negative entropy changes. Taken together, these results suggest that both sanguinarine and berberine can bind and stabilize the DNA and RNA triplexes more strongly than their respective parent duplexes. PMID:12643773

  12. Conformational changes in dopamine transporter intracellular regions upon cocaine binding and dopamine translocation

    Science.gov (United States)

    Dehnes, Yvette; Shan, Jufang; Beuming, Thijs; Shi, Lei; Weinstein, Harel; Javitch, Jonathan A.

    2014-01-01

    The dopamine transporter (DAT), a member of the neurotransmitter:sodium symporter family, mediates the reuptake of dopamine at the synaptic cleft. DAT is the primary target for psychostimulants such as cocaine and amphetamine. We previously demonstrated that cocaine binding and dopamine transport alter the accessibility of Cys342 in the third intracellular loop (IL3). To study the conformational changes associated with the functional mechanism of the transporter, we made cysteine substitution mutants, one at a time, from Phe332 to Ser351 in IL3 of the background DAT construct, X7C, in which 7 endogenous cysteines were mutated. The accessibility of the 20 engineered cysteines to polar charged sulfhydryl reagents was studied in the absence and presence of cocaine or dopamine. Of the 11 positions that reacted with methanethiosulfonate ethyl ammonium, as evidenced by inhibition of ligand binding, 5 were protected against this inhibition by cocaine and dopamine (S333C, S334C, N336C, M342C and T349C), indicating that reagent accessibility is affected by conformational changes associated with inhibitor and substrate binding. In some of the cysteine mutants, transport activity is disrupted, but can be rescued by the presence of zinc, most likely because the distribution between inward- and outward-facing conformations is restored by zinc binding. The experimental data were interpreted in the context of molecular models of DAT in both the inward- and outward-facing conformations. Differences in the solvent accessible surface area for individual IL3 residues calculated for these states correlate well with the experimental accessibility data, and suggest that protection by ligand binding results from the stabilization of the outward-facing configuration. Changes in the residue interaction networks observed from the molecular dynamics simulations also revealed the critical roles of several positions during the conformational transitions. We conclude that the IL3 region of DAT

  13. Designed metalloprotein stabilizes a semiquinone radical.

    Science.gov (United States)

    Ulas, Gözde; Lemmin, Thomas; Wu, Yibing; Gassner, George T; DeGrado, William F

    2016-04-01

    Enzymes use binding energy to stabilize their substrates in high-energy states that are otherwise inaccessible at ambient temperature. Here we show that a de novo designed Zn(II) metalloprotein stabilizes a chemically reactive organic radical that is otherwise unstable in aqueous media. The protein binds tightly to and stabilizes the radical semiquinone form of 3,5-di-tert-butylcatechol. Solution NMR spectroscopy in conjunction with molecular dynamics simulations show that the substrate binds in the active site pocket where it is stabilized by metal-ligand interactions as well as by burial of its hydrophobic groups. Spectrochemical redox titrations show that the protein stabilized the semiquinone by reducing the electrochemical midpoint potential for its formation via the one-electron oxidation of the catechol by approximately 400 mV (9 kcal mol(-1)). Therefore, the inherent chemical properties of the radical were changed drastically by harnessing its binding energy to the metalloprotein. This model sets the basis for designed enzymes with radical cofactors to tackle challenging chemistry. PMID:27001731

  14. Designed metalloprotein stabilizes a semiquinone radical

    Science.gov (United States)

    Ulas, Gözde; Lemmin, Thomas; Wu, Yibing; Gassner, George T.; Degrado, William F.

    2016-04-01

    Enzymes use binding energy to stabilize their substrates in high-energy states that are otherwise inaccessible at ambient temperature. Here we show that a de novo designed Zn(II) metalloprotein stabilizes a chemically reactive organic radical that is otherwise unstable in aqueous media. The protein binds tightly to and stabilizes the radical semiquinone form of 3,5-di-tert-butylcatechol. Solution NMR spectroscopy in conjunction with molecular dynamics simulations show that the substrate binds in the active site pocket where it is stabilized by metal-ligand interactions as well as by burial of its hydrophobic groups. Spectrochemical redox titrations show that the protein stabilized the semiquinone by reducing the electrochemical midpoint potential for its formation via the one-electron oxidation of the catechol by approximately 400 mV (9 kcal mol-1). Therefore, the inherent chemical properties of the radical were changed drastically by harnessing its binding energy to the metalloprotein. This model sets the basis for designed enzymes with radical cofactors to tackle challenging chemistry.

  15. Expression of Nucleolin Affects Microtubule Dynamics.

    Directory of Open Access Journals (Sweden)

    Xavier Gaume

    Full Text Available Nucleolin is present in diverse cellular compartments and is involved in a variety of cellular processes from nucleolar structure and function to intracellular trafficking, cell adhesion and migration. Recently, nucleolin has been localized at the mature centriole where it is involved in microtubule nucleation and anchoring. Although this new function of nucleolin linked to microtubule regulation has been identified, the global effects of nucleolin on microtubule dynamics have not been addressed yet. In the present study, we analyzed the roles of nucleolin protein levels on global microtubule dynamics by tracking the EB3 microtubule plus end binding protein in live cells. We have found that during microtubule growth phases, nucleolin affects both the speed and life time of polymerization and by analyzing catastrophe events, we showed that nucleolin reduces catastrophe frequency. This new property of nucleolin was then confirmed in a cold induced microtubule depolymerization experiment in which we have found that cold resistant microtubules were totally destabilized in nucleolin depleted cells. Altogether, our data demonstrate a new function of nucleolin on microtubule stabilization, thus bringing novel insights into understanding the multifunctional properties of nucleolin in healthy and cancer cells.

  16. Expression of Nucleolin Affects Microtubule Dynamics.

    Science.gov (United States)

    Gaume, Xavier; Place, Christophe; Delage, Helene; Mongelard, Fabien; Monier, Karine; Bouvet, Philippe

    2016-01-01

    Nucleolin is present in diverse cellular compartments and is involved in a variety of cellular processes from nucleolar structure and function to intracellular trafficking, cell adhesion and migration. Recently, nucleolin has been localized at the mature centriole where it is involved in microtubule nucleation and anchoring. Although this new function of nucleolin linked to microtubule regulation has been identified, the global effects of nucleolin on microtubule dynamics have not been addressed yet. In the present study, we analyzed the roles of nucleolin protein levels on global microtubule dynamics by tracking the EB3 microtubule plus end binding protein in live cells. We have found that during microtubule growth phases, nucleolin affects both the speed and life time of polymerization and by analyzing catastrophe events, we showed that nucleolin reduces catastrophe frequency. This new property of nucleolin was then confirmed in a cold induced microtubule depolymerization experiment in which we have found that cold resistant microtubules were totally destabilized in nucleolin depleted cells. Altogether, our data demonstrate a new function of nucleolin on microtubule stabilization, thus bringing novel insights into understanding the multifunctional properties of nucleolin in healthy and cancer cells. PMID:27309529

  17. Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species.

    Directory of Open Access Journals (Sweden)

    Robert K Bradley

    2010-03-01

    Full Text Available Changes in gene expression play an important role in evolution, yet the molecular mechanisms underlying regulatory evolution are poorly understood. Here we compare genome-wide binding of the six transcription factors that initiate segmentation along the anterior-posterior axis in embryos of two closely related species: Drosophila melanogaster and Drosophila yakuba. Where we observe binding by a factor in one species, we almost always observe binding by that factor to the orthologous sequence in the other species. Levels of binding, however, vary considerably. The magnitude and direction of the interspecies differences in binding levels of all six factors are strongly correlated, suggesting a role for chromatin or other factor-independent forces in mediating the divergence of transcription factor binding. Nonetheless, factor-specific quantitative variation in binding is common, and we show that it is driven to a large extent by the gain and loss of cognate recognition sequences for the given factor. We find only a weak correlation between binding variation and regulatory function. These data provide the first genome-wide picture of how modest levels of sequence divergence between highly morphologically similar species affect a system of coordinately acting transcription factors during animal development, and highlight the dominant role of quantitative variation in transcription factor binding over short evolutionary distances.

  18. A new zinc binding fold underlines the versatility of zinc binding modules in protein evolution.

    Science.gov (United States)

    Sharpe, Belinda K; Matthews, Jacqueline M; Kwan, Ann H Y; Newton, Anthea; Gell, David A; Crossley, Merlin; Mackay, Joel P

    2002-05-01

    Many different zinc binding modules have been identified. Their abundance and variety suggests that the formation of zinc binding folds might be relatively common. We have determined the structure of CH1(1), a 27-residue peptide derived from the first cysteine/histidine-rich region (CH1) of CREB binding protein (CBP). This peptide forms a highly ordered zinc-dependent fold that is distinct from known folds. The structure differs from a subsequently determined structure of a larger region from the CH3 region of CBP, and the CH1(1) fold probably represents a nonphysiologically active form. Despite this, the fold is thermostable and tolerant to both multiple alanine mutations and changes in the zinc-ligand spacing. Our data support the idea that zinc binding domains may arise frequently. Additionally, such structures may prove useful as scaffolds for protein design, given their stability and robustness.

  19. The N-terminal hybrid binding domain of RNase HI from Thermotoga maritima is important for substrate binding and Mg2+-dependent activity.

    Science.gov (United States)

    Jongruja, Nujarin; You, Dong-Ju; Kanaya, Eiko; Koga, Yuichi; Takano, Kazufumi; Kanaya, Shigenori

    2010-11-01

    Thermotoga maritima ribonuclease H (RNase H) I (Tma-RNase HI) contains a hybrid binding domain (HBD) at the N-terminal region. To analyze the role of this HBD, Tma-RNase HI, Tma-W22A with the single mutation at the HBD, the C-terminal RNase H domain (Tma-CD) and the N-terminal domain containing the HBD (Tma-ND) were overproduced in Escherichia coli, purified and biochemically characterized. Tma-RNase HI prefers Mg(2+) to Mn(2+) for activity, and specifically loses most of the Mg(2+)-dependent activity on removal of the HBD and 87% of it by the mutation at the HBD. Tma-CD lost the ability to suppress the RNase H deficiency of an E. coli rnhA mutant, indicating that the HBD is responsible for in vivo RNase H activity. The cleavage-site specificities of Tma-RNase HI are not significantly changed on removal of the HBD, regardless of the metal cofactor. Binding analyses of the proteins to the substrate using surface plasmon resonance indicate that the binding affinity of Tma-RNase HI is greatly reduced on removal of the HBD or the mutation. These results indicate that there is a correlation between Mg(2+)-dependent activity and substrate binding affinity. Tma-CD was as stable as Tma-RNase HI, indicating that the HBD is not important for stability. The HBD of Tma-RNase HI is important not only for substrate binding, but also for Mg(2+)-dependent activity, probably because the HBD affects the interaction between the substrate and enzyme at the active site, such that the scissile phosphate group of the substrate and the Mg(2+) ion are arranged ideally.

  20. Melanin-binding radiopharmaceuticals

    Energy Technology Data Exchange (ETDEWEB)

    Packer, S; Fairchild, R G; Watts, K P; Greenberg, D; Hannon, S J

    1980-01-01

    The scope of this paper is limited to an analysis of the factors that are important to the relationship of radiopharmaceuticals to melanin. While the authors do not attempt to deal with differences between melanin-binding vs. melanoma-binding, a notable variance is assumed. (PSB)

  1. DNS BIND Server Configuration

    Directory of Open Access Journals (Sweden)

    Radu MARSANU

    2011-01-01

    Full Text Available After a brief presentation of the DNS and BIND standard for Unix platforms, the paper presents an application which has a principal objective, the configuring of the DNS BIND 9 server. The general objectives of the application are presented, follow by the description of the details of designing the program.

  2. Axisymmetric annular curtain stability

    International Nuclear Information System (INIS)

    A temporal stability analysis was carried out to investigate the stability of an axially moving viscous annular liquid jet subject to axisymmetric disturbances in surrounding co-flowing viscous gas media. We investigated in this study the effects of inertia, surface tension, the gas-to-liquid density ratio, the inner-to-outer radius ratio and the gas-to-liquid viscosity ratio on the stability of the jet. With an increase in inertia, the growth rate of the unstable disturbances is found to increase. The dominant (or most unstable) wavenumber decreases with increasing Reynolds number for larger values of the gas-to-liquid viscosity ratio. However, an opposite tendency for the most unstable wavenumber is predicted for small viscosity ratio in the same inertia range. The surrounding gas density, in the presence of viscosity, always reduces the growth rate, hence stabilizing the flow. There exists a critical value of the density ratio above which the flow becomes stable for very small viscosity ratio, whereas for large viscosity ratio, no stable flow appears in the same range of the density ratio. The curvature has a significant destabilizing effect on the thin annular jet, whereas for a relatively thick jet, the maximum growth rate decreases as the inner radius increases, irrespective of the surrounding gas viscosity. The degree of instability increases with Weber number for a relatively large viscosity ratio. In contrast, for small viscosity ratio, the growth rate exhibits a dramatic dependence on the surface tension. There is a small Weber number range, which depends on the viscosity ratio, where the flow is stable. The viscosity ratio always stabilizes the flow. However, the dominant wavenumber increases with increasing viscosity ratio. The range of unstable wavenumbers is affected only by the curvature effect. (paper)

  3. Serum albumin ligand binding volumes using high pressure denaturation

    International Nuclear Information System (INIS)

    Highlights: ► We use pressure shift assay to study the thermodynamics of decanoate and dodecanoate ligand binding to human serum albumin. ► Pressure shift assay provides information on ligand binding volumes. ► The ligands stabilized human serum albumin against both pressure and temperature denaturation. ► ANS is a strong human serum albumin stabilizer and competes with lipids for the same binding sites. - Abstract: The pressure shift assay (PSA, also termed either PressureFluor or differential pressure fluorimetry) was used to study the thermodynamics of decanoate and dodecanoate lipid binding to human serum albumin (HSA) in the temperature range from 25 °C to 80 °C and the pressure range from 0.1 MPa to 400 MPa. The ligands stabilized HSA against both pressure and temperature denaturation. The P–T phase diagram for HSA bound to saturated fatty acids is shown. Pressure induced HSA denaturation reversibility is demonstrated via either intrinsic tryptophan or extrinsic probe 1,8-anilinonaphthalene sulfonate (ANS) fluorescence. The effect of guanidinium in a PSA was studied. PSA provides information on ligand binding volumes. The volume changes from protein–ligand binding are thermodynamically important and could be used in designing compounds with specific volumetric binding properties.

  4. Sequence similarity between the erythrocyte binding domain of the Plasmodium vivax Duffy binding protein and the V3 loop of HIV-1 strain MN reveals a functional heparin binding motif involved in binding to the Duffy antigen receptor for chemokines

    Directory of Open Access Journals (Sweden)

    Bolton Michael J

    2011-11-01

    Full Text Available Abstract Background The HIV surface glycoprotein gp120 (SU, gp120 and the Plasmodium vivax Duffy binding protein (PvDBP bind to chemokine receptors during infection and have a site of amino acid sequence similarity in their binding domains that often includes a heparin binding motif (HBM. Infection by either pathogen has been found to be inhibited by polyanions. Results Specific polyanions that inhibit HIV infection and bind to the V3 loop of X4 strains also inhibited DBP-mediated infection of erythrocytes and DBP binding to the Duffy Antigen Receptor for Chemokines (DARC. A peptide including the HBM of PvDBP had similar affinity for heparin as RANTES and V3 loop peptides, and could be specifically inhibited from heparin binding by the same polyanions that inhibit DBP binding to DARC. However, some V3 peptides can competitively inhibit RANTES binding to heparin, but not the PvDBP HBM peptide. Three other members of the DBP family have an HBM sequence that is necessary for erythrocyte binding, however only the protein which binds to DARC, the P. knowlesi alpha protein, is inhibited by heparin from binding to erythrocytes. Heparitinase digestion does not affect the binding of DBP to erythrocytes. Conclusion The HBMs of DBPs that bind to DARC have similar heparin binding affinities as some V3 loop peptides and chemokines, are responsible for specific sulfated polysaccharide inhibition of parasite binding and invasion of red blood cells, and are more likely to bind to negative charges on the receptor than cell surface glycosaminoglycans.

  5. The Case against Binding Interest Arbitration.

    Science.gov (United States)

    Ecker, Charles I.

    1984-01-01

    The author contends that districts should reject binding interest arbitration as a means of resolving an impasse in contract negotiations, charging that it hampers good faith bargaining, adversely affects fiscal and operational management of the school system, and diminishes the governing role of the board of education. (MJL)

  6. How does real affect affect affect recognition in speech?

    NARCIS (Netherlands)

    Truong, Khiet Phuong

    2009-01-01

    The aim of the research described in this thesis was to develop speech-based affect recognition systems that can deal with spontaneous (‘real’) affect instead of acted affect. Several affect recognition experiments with spontaneous affective speech data were carried out to investigate what combinati

  7. Moral Hazard and Stability

    DEFF Research Database (Denmark)

    Tumennasan, Norovsambuu

    2014-01-01

    Economists perceive moral hazard as an undesirable problem because it undermines efficiency. Carefully designed contracts can mitigate the moral hazard problem, but this assumes that a team is already formed. This paper demonstrates that these contracts are sometimes the reason why teams do...... not form. Formally, we study the team formation problem in which the agents’ efforts are not verifiable and the size of teams does not exceed quota r . We show that if the team members cannot make transfers, then moral hazard affects stability positively in a large class of games. For example, a stable...

  8. Regulating the stability of TGFβ receptors and Smads

    Institute of Scientific and Technical Information of China (English)

    Peter L(o)nn; Anita Morén; Erna Raja; Markus Dahl; Aristidis Moustakas

    2009-01-01

    Transforming growth factor β(TGFβ)controls cellular behavior in embryonic and adult tissues.TGFβ binding to serine/threonine kinase receptors on the plasma membrane activates Smad molecules and additional signaling proteins that together regulate gene expression.In this review,mechanisms and models that aim at explaining the coordination between several components of the signaling network downstream of TGFβ are presented.We discuss how the activity and duration of TGFβ receptor/Smad signaling can be regulated by post-transIational modifications that affect the stability of key proteins in the pathway.We highlight links between these mechanisms and human diseases,such as tissue fibrosis and cancer

  9. Salivary concentrations of urea released from a chewing gum containing urea and how these affect the urea content of gel-stabilized plaques and their pH after exposure to sucrose.

    Science.gov (United States)

    Dawes, C; Dibdin, G H

    2001-01-01

    The objectives were to: (1) determine the salivary concentrations of urea during 20 min chewing of a sugar-free gum containing 30 mg of urea; (2) measure the degree to which this urea would diffuse into a gel-stabilized plaque; (3) study the effect of the urea on the fall and subsequent rise in pH (Stephan curve) on exposure to 10% sucrose for 1 min; (4) model the measurements 2 and 3 mathematically. In point 1, the salivary urea concentration of the 12 subjects peaked at 47 mmol/l in the first 2 min of gum chewing, falling within 15 min to the unstimulated salivary concentration of 3.4 mmol/l. Recovery of urea from the saliva averaged 81.5%. 'Plaques' of 1% agarose or 67% dead bacteria in agarose accumulated urea from the saliva roughly as expected, whereas those plaques containing 8% live and 59% dead Streptococcus vestibularis showed negligible accumulation. Computer modelling showed this difference to be due to urease of live bacteria breaking down the urea as rapidly as it entered the plaque. Simulation of the effect of gum chewing subsequent to initiation of a Stephan curve in the latter type of plaque showed a rapid rise in pH but then a fall again on return to unstimulated conditions. This fall had not been seen in previous studies, with Streptococcus oralis, nor was it predicted by the computer modelling. Neither experimental simulation nor computer modelling suggested that chewing urea-containing gum before exposure to sucrose would have any effect on a subsequent Stephan curve. Thus chewing gum is only likely to inhibit caries when it is chewed after consumption of fermentable carbohydrate, rather than before.

  10. Ligand binding and thermostability of different allosteric states of the insulin zinc-hexamer

    DEFF Research Database (Denmark)

    Huus, Kasper; Havelund, Svend; Olsen, Helle B;

    2006-01-01

    The influence of ligand binding and conformation state on the thermostability of hexameric zinc-insulin was studied by differential scanning calorimetry (DSC). The insulin hexamer exists in equilibrium between the forms T6, T3R3, and R6. Phenolic ligands induce and stabilize the T3R3- and R6-states...... which are further stabilized by binding of certain anions that do not stabilize the T6-state. It was shown that the thermostability of the resorcinol-stabilized R6-state was significantly higher than that of the T6-state. Further analysis showed that phenol- and m-cresol-stabilized R6-hexamer loses...

  11. Stabilizing brokerage.

    Science.gov (United States)

    Stovel, Katherine; Golub, Benjamin; Milgrom, Eva M Meyersson

    2011-12-27

    A variety of social and economic arrangements exist to facilitate the exchange of goods, services, and information over gaps in social structure. Each of these arrangements bears some relationship to the idea of brokerage, but this brokerage is rarely like the pure and formal economic intermediation seen in some modern markets. Indeed, for reasons illuminated by existing sociological and economic models, brokerage is a fragile relationship. In this paper, we review the causes of instability in brokerage and identify three social mechanisms that can stabilize fragile brokerage relationships: social isolation, broker capture, and organizational grafting. Each of these mechanisms rests on the emergence or existence of supporting institutions. We suggest that organizational grafting may be the most stable and effective resolution to the tensions inherent in brokerage, but it is also the most institutionally demanding.

  12. STABILIZED OSCILLATOR

    Science.gov (United States)

    Jessen, P.L.; Price, H.J.

    1958-03-18

    This patent relates to sine-wave generators and in particular describes a generator with a novel feedback circuit resulting in improved frequency stability. The generator comprises two triodes having a common cathode circuit connected to oscillate at a frequency and amplitude at which the loop galn of the circutt ls unity, and another pair of triodes having a common cathode circuit arranged as a conventional amplifier. A signal is conducted from the osciliator through a frequency selective network to the amplifier and fed back to the osciliator. The unique feature of the feedback circuit is the amplifier operates in the nonlinear portion of its tube characteristics thereby providing a relatively constant feedback voltage to the oscillator irrespective of the amplitude of its input signal.

  13. 大规模风电集中接入对电力系统暂态功角稳定性的影响(二):影响因素分析%Impact of Large-scale Wind Power Centralized Integration on Transient Angle Stability of Power Systems-Part II:Factors Affecting Transient Angle Stability

    Institute of Scientific and Technical Information of China (English)

    汤蕾; 沈沉; 张雪敏

    2015-01-01

    该文作为2篇系列文章的第2篇,重点分析双馈风机组成的大规模风电场集中接入电力系统后影响系统暂态功角稳定性的关键因素。在第1篇文章理论分析的基础上,根据扩展等面积定则,讨论了同步机出力调整、风电渗透率和风电场选址等因素起主导作用时,电力系统暂态功角稳定性的变化。然后,从暂态功角稳定的角度出发,总结出风电接入情况下指导电力系统规划和调度的一般规律。最后,通过在双机互联系统上进行的数值仿真验证所提规律的正确性。结果表明,从本质上看,各种因素的变化如果有助于减小前向机群的有功出力,则有助于提高电力系统的暂态功角稳定水平。%As the second part of this two-part paper, this paper focused on the factors that had impacts on the transient angle stability of power systems with large-scale wind power farms consisted of doubly-fed induction generators (DFIG). Based on the theoretic analysis in the first part of this paper, how wind power penetration influenced power system transient angle stability was discussed according to the extended equal area criterion when the factors, such as the synchronous generator dispatch pattern, the siting of wind farms and the wind power penetration rate, played a leading role. Then general rules for power system planning and dispatching considering transient angle stability of power systems with high wind power penetration rate were summarized. Finally, the proposed rules were verified by simulations on a two-machine power system. The results show that in essence, if the variation of the factors helps reduce the active power of synchronous generators of which the power angle swings forward, it is beneficial to transient angle stability of power systems.

  14. The fission yeast RNA binding protein Mmi1 regulates meiotic genes by controlling intron specific splicing and polyadenylation coupled RNA turnover.

    Directory of Open Access Journals (Sweden)

    Huei-Mei Chen

    Full Text Available The polyA tails of mRNAs are monitored by the exosome as a quality control mechanism. We find that fission yeast, Schizosaccharomyces pombe, adopts this RNA quality control mechanism to regulate a group of 30 or more meiotic genes at the level of both splicing and RNA turnover. In vegetative cells the RNA binding protein Mmi1 binds to the primary transcripts of these genes. We find the novel motif U(U/C/GAAAC highly over-represented in targets of Mmi1. Mmi1 can specifically regulate the splicing of particular introns in a transcript: it inhibits the splicing of introns that are in the vicinity of putative Mmi1 binding sites, while allowing the splicing of other introns that are far from such sites. In addition, binding of Mmi1, particularly near the 3' end, alters 3' processing to promote extremely long polyA tails of up to a kilobase. The hyperadenylated transcripts are then targeted for degradation by the nuclear exonuclease Rrp6. The nuclear polyA binding protein Pab2 assists this hyperadenylation-mediated RNA decay. Rrp6 also targets other hyperadenylated transcripts, which become hyperadenylated in an unknown, but Mmi1-independent way. Thus, hyperadenylation may be a general signal for RNA degradation. In addition, binding of Mmi1 can affect the efficiency of 3' cleavage. Inactivation of Mmi1 in meiosis allows meiotic expression, through splicing and RNA stabilization, of at least 29 target genes, which are apparently constitutively transcribed.

  15. Zinc ions bind to and inhibit activated protein C

    DEFF Research Database (Denmark)

    Zhu, Tianqing; Ubhayasekera, Wimal; Nickolaus, Noëlle;

    2010-01-01

    fold enhanced, presumably due to the Ca2+-induced conformational change affecting the conformation of the Zn2+-binding site. The inhibition mechanism was non-competitive both in the absence and presence of Ca2+. Comparisons of sequences and structures suggested several possible sites for zinc binding...

  16. Crystal Structure of a Bacterial Topoisomerase IB in Complex with DNA Reveals a Secondary DNA Binding Site

    Energy Technology Data Exchange (ETDEWEB)

    Patel, Asmita; Yakovleva, Lyudmila; Shuman, Stewart; Mondragón, Alfonso (NWU); (SKI)

    2010-10-22

    Type IB DNA topoisomerases (TopIB) are monomeric enzymes that relax supercoils by cleaving and resealing one strand of duplex DNA within a protein clamp that embraces a {approx}21 DNA segment. A longstanding conundrum concerns the capacity of TopIB enzymes to stabilize intramolecular duplex DNA crossovers and form protein-DNA synaptic filaments. Here we report a structure of Deinococcus radiodurans TopIB in complex with a 12 bp duplex DNA that demonstrates a secondary DNA binding site located on the surface of the C-terminal domain. It comprises a distinctive interface with one strand of the DNA duplex and is conserved in all TopIB enzymes. Modeling of a TopIB with both DNA sites suggests that the secondary site could account for DNA crossover binding, nucleation of DNA synapsis, and generation of a filamentous plectoneme. Mutations of the secondary site eliminate synaptic plectoneme formation without affecting DNA cleavage or supercoil relaxation.

  17. Mutational analysis of the high-affinity zinc binding site validates a refined human dopamine transporter homology model.

    Directory of Open Access Journals (Sweden)

    Thomas Stockner

    Full Text Available The high-resolution crystal structure of the leucine transporter (LeuT is frequently used as a template for homology models of the dopamine transporter (DAT. Although similar in structure, DAT differs considerably from LeuT in a number of ways: (i when compared to LeuT, DAT has very long intracellular amino and carboxyl termini; (ii LeuT and DAT share a rather low overall sequence identity (22% and (iii the extracellular loop 2 (EL2 of DAT is substantially longer than that of LeuT. Extracellular zinc binds to DAT and restricts the transporter's movement through the conformational cycle, thereby resulting in a decrease in substrate uptake. Residue H293 in EL2 praticipates in zinc binding and must be modelled correctly to allow for a full understanding of its effects. We exploited the high-affinity zinc binding site endogenously present in DAT to create a model of the complete transmemberane domain of DAT. The zinc binding site provided a DAT-specific molecular ruler for calibration of the model. Our DAT model places EL2 at the transporter lipid interface in the vicinity of the zinc binding site. Based on the model, D206 was predicted to represent a fourth co-ordinating residue, in addition to the three previously described zinc binding residues H193, H375 and E396. This prediction was confirmed by mutagenesis: substitution of D206 by lysine and cysteine affected the inhibitory potency of zinc and the maximum inhibition exerted by zinc, respectively. Conversely, the structural changes observed in the model allowed for rationalizing the zinc-dependent regulation of DAT: upon binding, zinc stabilizes the outward-facing state, because its first coordination shell can only be completed in this conformation. Thus, the model provides a validated solution to the long extracellular loop and may be useful to address other aspects of the transport cycle.

  18. Communication routes in ARID domains between distal residues in helix 5 and the DNA-binding loops.

    Directory of Open Access Journals (Sweden)

    Gaetano Invernizzi

    2014-09-01

    Full Text Available ARID is a DNA-binding domain involved in several transcriptional regulatory processes, including cell-cycle regulation and embryonic development. ARID domains are also targets of the Human Cancer Protein Interaction Network. Little is known about the molecular mechanisms related to conformational changes in the family of ARID domains. Thus, we have examined their structural dynamics to enrich the knowledge on this important family of regulatory proteins. In particular, we used an approach that integrates atomistic simulations and methods inspired by graph theory. To relate these properties to protein function we studied both the free and DNA-bound forms. The interaction with DNA not only stabilizes the conformations of the DNA-binding loops, but also strengthens pre-existing paths in the native ARID ensemble for long-range communication to those loops. Residues in helix 5 are identified as critical mediators for intramolecular communication to the DNA-binding regions. In particular, we identified a distal tyrosine that plays a key role in long-range communication to the DNA-binding loops and that is experimentally known to impair DNA-binding. Mutations at this tyrosine and in other residues of helix 5 are also demonstrated, by our approach, to affect the paths of communication to the DNA-binding loops and alter their native dynamics. Overall, our results are in agreement with a scenario in which ARID domains exist as an ensemble of substates, which are shifted by external perturbation, such as the interaction with DNA. Conformational changes at the DNA-binding loops are transmitted long-range by intramolecular paths, which have their heart in helix 5.

  19. Communication routes in ARID domains between distal residues in helix 5 and the DNA-binding loops.

    Science.gov (United States)

    Invernizzi, Gaetano; Tiberti, Matteo; Lambrughi, Matteo; Lindorff-Larsen, Kresten; Papaleo, Elena

    2014-09-01

    ARID is a DNA-binding domain involved in several transcriptional regulatory processes, including cell-cycle regulation and embryonic development. ARID domains are also targets of the Human Cancer Protein Interaction Network. Little is known about the molecular mechanisms related to conformational changes in the family of ARID domains. Thus, we have examined their structural dynamics to enrich the knowledge on this important family of regulatory proteins. In particular, we used an approach that integrates atomistic simulations and methods inspired by graph theory. To relate these properties to protein function we studied both the free and DNA-bound forms. The interaction with DNA not only stabilizes the conformations of the DNA-binding loops, but also strengthens pre-existing paths in the native ARID ensemble for long-range communication to those loops. Residues in helix 5 are identified as critical mediators for intramolecular communication to the DNA-binding regions. In particular, we identified a distal tyrosine that plays a key role in long-range communication to the DNA-binding loops and that is experimentally known to impair DNA-binding. Mutations at this tyrosine and in other residues of helix 5 are also demonstrated, by our approach, to affect the paths of communication to the DNA-binding loops and alter their native dynamics. Overall, our results are in agreement with a scenario in which ARID domains exist as an ensemble of substates, which are shifted by external perturbation, such as the interaction with DNA. Conformational changes at the DNA-binding loops are transmitted long-range by intramolecular paths, which have their heart in helix 5.

  20. Formation and characterization of iron-binding phosphorylated human-like collagen as a potential iron supplement

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Jianjun; Chen, Fei; Fan, Daidi, E-mail: fandaidi@nwu.edu.cn; Zhu, Chenhui; Ma, Xiaoxuan; Xue, Wenjiao

    2013-10-01

    Iron incorporated into food can induce precipitation and unwanted interaction with other components in food. Iron-binding proteins represent a possibility to avoid these problems and other side effects, as the iron is protected. However, there are several technical problems associated with protein–iron complex formation. In this paper, the iron-binding phosphorylated human-like collagen (Fe-G6P-HLC) was prepared under physiological conditions through phosphorylated modification. One molecule of Fe-G6P-HLC possesses about 24 atoms of Fe. Spectroscopy analysis, differential scanning calorimetry (DSC) and equilibrium dialysis techniques were employed to investigate the characteristics of the Fe-G6P-HLC. The binding sites (n{sub b}) and apparent association constant (K{sub app}) between iron and phosphorylated HLC were measured at n{sub b} = 23.7 and log K{sub app} = 4.57, respectively. The amount of iron (Fe{sup 2+} sulfate) binding to phosphorylated HLC was found to be a function of pH and phosphate content. In addition, the solubility and thermal stability of HLC were not significantly affected. The results should facilitate the utilization of HLC as a bioactive iron supplement in the food and medical industry and provide an important theoretical evidence for the application of HLC chelates. - Highlights: • The iron-binding phosphorylated human-like collagen (Fe-G6P-HLC) was prepared. • One molecule of Fe-G6P-HLC possesses about 24 atoms of Fe. • The binding properties could be modulated through alterations in pH and phosphate content presented in HLC. • A novel strategy for preparing iron-binding proteins was provided.

  1. Formation and characterization of iron-binding phosphorylated human-like collagen as a potential iron supplement

    International Nuclear Information System (INIS)

    Iron incorporated into food can induce precipitation and unwanted interaction with other components in food. Iron-binding proteins represent a possibility to avoid these problems and other side effects, as the iron is protected. However, there are several technical problems associated with protein–iron complex formation. In this paper, the iron-binding phosphorylated human-like collagen (Fe-G6P-HLC) was prepared under physiological conditions through phosphorylated modification. One molecule of Fe-G6P-HLC possesses about 24 atoms of Fe. Spectroscopy analysis, differential scanning calorimetry (DSC) and equilibrium dialysis techniques were employed to investigate the characteristics of the Fe-G6P-HLC. The binding sites (nb) and apparent association constant (Kapp) between iron and phosphorylated HLC were measured at nb = 23.7 and log Kapp = 4.57, respectively. The amount of iron (Fe2+ sulfate) binding to phosphorylated HLC was found to be a function of pH and phosphate content. In addition, the solubility and thermal stability of HLC were not significantly affected. The results should facilitate the utilization of HLC as a bioactive iron supplement in the food and medical industry and provide an important theoretical evidence for the application of HLC chelates. - Highlights: • The iron-binding phosphorylated human-like collagen (Fe-G6P-HLC) was prepared. • One molecule of Fe-G6P-HLC possesses about 24 atoms of Fe. • The binding properties could be modulated through alterations in pH and phosphate content presented in HLC. • A novel strategy for preparing iron-binding proteins was provided

  2. Topographical changes of ground surface affected by the Tarim Desert Highway

    Institute of Scientific and Technical Information of China (English)

    LI Shengyu; LEI Jiaqiang; XU Xinwen; WANG Lixin; ZHOU Zhibin; LI Hongzhong

    2006-01-01

    The Tarim Desert Highway is the longest highway crossing the mobile desert in the world. The highway and its sand protection system were established in 1995. This great project must have significant effect on the aeolian environment in its neighborhoods. In 2004, we investigated the topographic changes of ground surface within the sand protection system and its external adjacent area in the hinterland of the Taklimakan Desert. The results showed that (i) the original topographic patterns of ground surface were greatly changed, and erosion as well as deposition was distributed clearly on the ground surface, affected by the road and its sand protection system; (ii) sediment deposited in the sand protection system gradually heightened the ground surface, but each part in the system changed differently: in the sand-blocking belt, a transverse sand ridge was formed in the same direction as the upright sand barrier; in the sand-binding belt, sediment was aggraded on the original surface in a certain thickness; at the initial stages since the establishment of the sand protection system, erosion had taken place in the un-stabilized area named by the deposition belt between the sand-blocking belt and the sand-binding belt, the inner of sand-binding belt, the windward slope of dunes in the sand-binding belt, and the neighboring leeward area of the sand protection system.

  3. SHBG (Sex Hormone Binding Globulin)

    Science.gov (United States)

    ... as: Testosterone-estrogen Binding Globulin; TeBG Formal name: Sex Hormone Binding Globulin Related tests: Testosterone , Free Testosterone, ... I should know? How is it used? The sex hormone binding globulin (SHBG) test may be used ...

  4. CD36 binds oxidized low density lipoprotein (LDL) in a mechanism dependent upon fatty acid binding.

    Science.gov (United States)

    Jay, Anthony G; Chen, Alexander N; Paz, Miguel A; Hung, Justin P; Hamilton, James A

    2015-02-20

    The association of unesterified fatty acid (FA) with the scavenger receptor CD36 has been actively researched, with focuses on FA and oxidized low density lipoprotein (oxLDL) uptake. CD36 has been shown to bind FA, but this interaction has been poorly characterized to date. To gain new insights into the physiological relevance of binding of FA to CD36, we characterized FA binding to the ectodomain of CD36 by the biophysical method surface plasmon resonance. Five structurally distinct FAs (saturated, monounsaturated (cis and trans), polyunsaturated, and oxidized) were pulsed across surface plasmon resonance channels, generating association and dissociation binding curves. Except for the oxidized FA HODE, all FAs bound to CD36, with rapid association and dissociation kinetics similar to HSA. Next, to elucidate the role that each FA might play in CD36-mediated oxLDL uptake, we used a fluorescent oxLDL (Dii-oxLDL) live cell assay with confocal microscopy imaging. CD36-mediated uptake in serum-free medium was very low but greatly increased when serum was present. The addition of exogenous FA in serum-free medium increased oxLDL binding and uptake to levels found with serum and affected CD36 plasma membrane distribution. Binding/uptake of oxLDL was dependent upon the FA dose, except for docosahexaenoic acid, which exhibited binding to CD36 but did not activate the uptake of oxLDL. HODE also did not affect oxLDL uptake. High affinity FA binding to CD36 and the effects of each FA on oxLDL uptake have important implications for protein conformation, binding of other ligands, functional properties of CD36, and high plasma FA levels in obesity and type 2 diabetes.

  5. Control Design for an Inertially Stabilized Rifle

    OpenAIRE

    White, Alejandro Porter

    2007-01-01

    An alternate method for mitigating the depredating physiological affects of a soldiers marksmanship due to combat stressors can be achieved through the design and implementation of a active stabilization system for small arms weapons. The INSTAR system is an innovative active stabilization system designed to decouple the shooterâ s disturbance effects from the barrel movement. The INSTAR system uses an piezoelectric actuator separating the barrel of the rifle from its stock to stabilize barr...

  6. Sulfo-SMCC Prevents Annealing of Taxol-Stabilized Microtubules In Vitro

    CERN Document Server

    Prabhune, Meenakshi; Schmidt, Christoph F

    2015-01-01

    Microtubule structure and functions have been widely studied in vitro and in cells. Research has shown that cysteines on tubulin play a crucial role in the polymerization of microtubules. Here, we show that blocking sulfhydryl groups of cysteines in taxol-stabilized polymerized microtubules with a commonly used chemical crosslinker prevents temporal end-to-end annealing of microtubules in vitro. This can dramatically affect the length distribution of the microtubules. The crosslinker sulfosuccinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate, sulfo-SMCC, consists of a maleimide and a N-hydroxysuccinimide ester group to bind to sulfhydryl groups and primary amines, respectively. Interestingly, addition of a maleimide dye alone does not show the same prevention of annealing in stabilized microtubules. This study shows that the sulfhydryl groups of cysteines of tubulin that are vital for the polymerization are also important for the subsequent annealing of microtubules.

  7. The readiness potential reflects intentional binding

    Directory of Open Access Journals (Sweden)

    Han-Gue eJo

    2014-06-01

    Full Text Available When a voluntary action is causally linked with a sensory outcome, the action and its consequent effect are perceived as being closer together in time. This effect is called intentional binding. Although many experiments were conducted on this phenomenon, the underlying neural mechanisms are not well understood. While intentional binding is specific to voluntary action, we presumed that preconscious brain activity (the readiness potential, RP, which occurs before an action is made, might play an important role in this binding effect. In this study, the brain dynamics were recorded with electroencephalography (EEG and analyzed in single-trials in order to estimate whether intentional binding is correlated with the early neural processes. Moreover, we were interested in different behavioral performance between meditators and non-meditators since meditators are expected to be able to keep attention more consistently on a task. Thus, we performed the intentional binding paradigm with twenty mindfulness meditators and compared them to matched controls. Although, we did not observe a group effect on either behavioral data or EEG recordings, we found that self-initiated movements following ongoing negative deflections of slow cortical potentials (SCPs result in a stronger binding effect compared to positive potentials, especially regarding the perceived time of the consequent effect. Our results provide the first direct evidence that the early neural activity within the range of SCPs affects perceived time of a sensory outcome that is caused by intentional action.

  8. The readiness potential reflects intentional binding.

    Science.gov (United States)

    Jo, Han-Gue; Wittmann, Marc; Hinterberger, Thilo; Schmidt, Stefan

    2014-01-01

    When a voluntary action is causally linked with a sensory outcome, the action and its consequent effect are perceived as being closer together in time. This effect is called intentional binding. Although many experiments were conducted on this phenomenon, the underlying neural mechanisms are not well understood. While intentional binding is specific to voluntary action, we presumed that preconscious brain activity (the readiness potential, RP), which occurs before an action is made, might play an important role in this binding effect. In this study, the brain dynamics were recorded with electroencephalography (EEG) and analyzed in single-trials in order to estimate whether intentional binding is correlated with the early neural processes. Moreover, we were interested in different behavioral performance between meditators and non-meditators since meditators are expected to be able to keep attention more consistently on a task. Thus, we performed the intentional binding paradigm with 20 mindfulness meditators and compared them to matched controls. Although, we did not observe a group effect on either behavioral data or EEG recordings, we found that self-initiated movements following ongoing negative deflections of slow cortical potentials (SCPs) result in a stronger binding effect compared to positive potentials, especially regarding the perceived time of the consequent effect. Our results provide the first direct evidence that the early neural activity within the range of SCPs affects perceived time of a sensory outcome that is caused by intentional action.

  9. Factors Affecting Biological Stability of Drinking Water Distribution Systems%超滤工艺出水管网生物稳定性影响因素研究

    Institute of Scientific and Technical Information of China (English)

    李春敏; 李星; 杨艳玲; 相坤; 赵乐乐; 郭栋

    2013-01-01

    Annular biofilm reactor was used to simulate water distribution system carrying effluent from biological activated carbon/ultrafiltration process. The effects of shear force, pipe materials and AOC on biofilm biomass on coupons as well as the relationship of the effluent turbidity and biofilm to suspended bacteria were investigated. The results showed that the effluent concentration of AOC decreased with the increase in biomass on coupons. The maximum biomasses on coupons with 100 r/min and 50 r/min in stainless steel pipe and copper pipe were of the same order of magnitude. In stainless steel pipe, the amount of suspended bacteria was the major factor affecting the effluent turbidity level. In addition, the biomass on biofilm had the positive correlation with the amount of suspended bacteria.%以活性炭/超滤出水为试验水样,采用生物膜培养反应器(BAR)模拟实际给水管网,研究了剪切力、管材以及水中可同化有机碳(AOC)对挂片生物膜上生物量的影响,以及反应器出水浊度、生物膜与悬浮菌的关系.结果表明,反应器出水AOC浓度随着挂片上生物量的增加而减少;在不锈钢管和铜管中,转速分别为100、50 r/min下挂片上最大生物量在同一数量级上;在不锈钢给水管中,悬浮菌是影响浊度的主要因素,悬浮菌量的多少影响反应器出水浊度的高低;生物膜上生物量与悬浮菌量有相同的变化趋势.

  10. Characterization of the DNA binding properties of polyomavirus capsid protein

    Science.gov (United States)

    Chang, D.; Cai, X.; Consigli, R. A.; Spooner, B. S. (Principal Investigator)

    1993-01-01

    The DNA binding properties of the polyomavirus structural proteins VP1, VP2, and VP3 were studied by Southwestern analysis. The major viral structural protein VP1 and host-contributed histone proteins of polyomavirus virions were shown to exhibit DNA binding activity, but the minor capsid proteins VP2 and VP3 failed to bind DNA. The N-terminal first five amino acids (Ala-1 to Lys-5) were identified as the VP1 DNA binding domain by genetic and biochemical approaches. Wild-type VP1 expressed in Escherichia coli (RK1448) exhibited DNA binding activity, but the N-terminal truncated VP1 mutants (lacking Ala-1 to Lys-5 and Ala-1 to Cys-11) failed to bind DNA. The synthetic peptide (Ala-1 to Cys-11) was also shown to have an affinity for DNA binding. Site-directed mutagenesis of the VP1 gene showed that the point mutations at Pro-2, Lys-3, and Arg-4 on the VP1 molecule did not affect DNA binding properties but that the point mutation at Lys-5 drastically reduced DNA binding affinity. The N-terminal (Ala-1 to Lys-5) region of VP1 was found to be essential and specific for DNA binding, while the DNA appears to be non-sequence specific. The DNA binding domain and the nuclear localization signal are located in the same N-terminal region.

  11. Structural Basis for Binding of RNA and Cofactor by a KsgA Methyltransferase

    Energy Technology Data Exchange (ETDEWEB)

    Tu, Chao; Tropea, Joseph E.; Austin, Brian P.; Court, Donald L.; Waugh, David S.; Ji, Xinhua; (NCI)

    2009-03-27

    Among methyltransferases, KsgA and the reaction it catalyzes are conserved throughout evolution. However, the specifics of substrate recognition by the enzyme remain unknown. Here we report structures of Aquifex aeolicus KsgA, in its ligand-free form, in complex with RNA, and in complex with both RNA and S-adenosylhomocysteine (SAH, reaction product of cofactor S-adenosylmethionine), revealing critical structural information on KsgA-RNA and KsgA-SAH interactions. Moreover, the structures show how conformational changes that occur upon RNA binding create the cofactor-binding site. There are nine conserved functional motifs (motifs IVIII and X) in KsgA. Prior to RNA binding, motifs I and VIII are flexible, each exhibiting two distinct conformations. Upon RNA binding, the two motifs become stabilized in one of these conformations, which is compatible with the binding of SAH. Motif X, which is also stabilized upon RNA binding, is directly involved in the binding of SAH.

  12. CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins.

    Science.gov (United States)

    Khorshid, Mohsen; Rodak, Christoph; Zavolan, Mihaela

    2011-01-01

    The stability, localization and translation rate of mRNAs are regulated by a multitude of RNA-binding proteins (RBPs) that find their targets directly or with the help of guide RNAs. Among the experimental methods for mapping RBP binding sites, cross-linking and immunoprecipitation (CLIP) coupled with deep sequencing provides transcriptome-wide coverage as well as high resolution. However, partly due to their vast volume, the data that were so far generated in CLIP experiments have not been put in a form that enables fast and interactive exploration of binding sites. To address this need, we have developed the CLIPZ database and analysis environment. Binding site data for RBPs such as Argonaute 1-4, Insulin-like growth factor II mRNA-binding protein 1-3, TNRC6 proteins A-C, Pumilio 2, Quaking and Polypyrimidine tract binding protein can be visualized at the level of the genome and of individual transcripts. Individual users can upload their own sequence data sets while being able to limit the access to these data to specific users, and analyses of the public and private data sets can be performed interactively. CLIPZ, available at http://www.clipz.unibas.ch, aims to provide an open access repository of information for post-transcriptional regulatory elements.

  13. Discodermolide interferes with the binding of tau protein to microtubules.

    Science.gov (United States)

    Kar, Santwana; Florence, Gordon J; Paterson, Ian; Amos, Linda A

    2003-03-27

    We investigated whether discodermolide, a novel antimitotic agent, affects the binding to microtubules of tau protein repeat motifs. Like taxol, the new drug reduces the proportion of tau that pellets with microtubules. Despite their differing structures, discodermolide, taxol and tau repeats all bind to a site on beta-tubulin that lies within the microtubule lumen and is crucial in controlling microtubule assembly. Low concentrations of tau still bind strongly to the outer surfaces of preformed microtubules when the acidic C-terminal regions of at least six tubulin dimers are available for interaction with each tau molecule; otherwise binding is very weak.

  14. Field investigation of keyblock stability

    Energy Technology Data Exchange (ETDEWEB)

    Yow, J.L. Jr.

    1985-04-01

    Discontinuities in a rock mass can intersect an excavation surface to form discrete blocks (keyblocks) which can be unstable. This engineering problem is divided into two parts: block identification, and evaluation of block stability. One stable keyblock and thirteen fallen keyblocks were observed in field investigations at the Nevada Test Site. Nine blocks were measured in detail sufficient to allow back-analysis of their stability. Measurements included block geometry, and discontinuity roughness and compressive strength. Back-analysis correctly predicted stability or failure in all but two cases. These two exceptions involved situations that violated the stress assumptions of the stability calculations. Keyblock faces correlated well with known joint set orientations. The effect of tunnel orientation on keyblock frequency was apparent. Back-analysis of physical models successfully predicted block pullout force for two-dimensional models of unit thickness. Two-dimensional (2D) and three-dimensional (3D) analytic models for the stability of simple pyramidal keyblocks were examined. Calculated stability is greater for 3D analyses than for 2D analyses. Calculated keyblock stability increases with larger in situ stress magnitudes, larger lateral stress ratios, and larger shear strengths. Discontinuity stiffness controls block displacement more strongly than it does stability itself. Large keyblocks are less stable than small ones, and stability increases as blocks become more slender. Rock mass temperature decreases reduce the confining stress magnitudes and can lead to failure. The pattern of stresses affecting each block face explains conceptually the occurrence of pyramidal keyblocks that are truncated near their apex.

  15. Field investigation of keyblock stability

    International Nuclear Information System (INIS)

    Discontinuities in a rock mass can intersect an excavation surface to form discrete blocks (keyblocks) which can be unstable. This engineering problem is divided into two parts: block identification, and evaluation of block stability. One stable keyblock and thirteen fallen keyblocks were observed in field investigations at the Nevada Test Site. Nine blocks were measured in detail sufficient to allow back-analysis of their stability. Measurements included block geometry, and discontinuity roughness and compressive strength. Back-analysis correctly predicted stability or failure in all but two cases. These two exceptions involved situations that violated the stress assumptions of the stability calculations. Keyblock faces correlated well with known joint set orientations. The effect of tunnel orientation on keyblock frequency was apparent. Back-analysis of physical models successfully predicted block pullout force for two-dimensional models of unit thickness. Two-dimensional (2D) and three-dimensional (3D) analytic models for the stability of simple pyramidal keyblocks were examined. Calculated stability is greater for 3D analyses than for 2D analyses. Calculated keyblock stability increases with larger in situ stress magnitudes, larger lateral stress ratios, and larger shear strengths. Discontinuity stiffness controls block displacement more strongly than it does stability itself. Large keyblocks are less stable than small ones, and stability increases as blocks become more slender. Rock mass temperature decreases reduce the confining stress magnitudes and can lead to failure. The pattern of stresses affecting each block face explains conceptually the occurrence of pyramidal keyblocks that are truncated near their apex

  16. Heart-type fatty acid binding protein for the assessment of the short-term prognosis in acute pulmonary embolism patients with hemodynamic stability on admission%心脏型脂肪酸结合蛋白对人院时血流动力学稳定的急性肺栓塞患者短期预后的评估

    Institute of Scientific and Technical Information of China (English)

    陈勇; 刘双; 郭伟; 王增智

    2013-01-01

    目的 探讨心脏型脂肪酸结合蛋白(H-FABP)对入院时血流动力学稳定的急性肺栓塞患者短期预后评估的临床意义.方法 筛选2009年12月至2010年12月在北京安贞医院就诊并被确诊的入院时血流动力学稳定的急性肺栓塞患者156例,其中符合纳入标准90例,男37例,女53例,平均年龄(61.1±14.6)岁,留取溶栓或抗凝前的外周静脉血标本,应用双抗体夹心酶联免疫吸附法测定H-FABP浓度,非均相免疫法测定肌钙蛋白Ⅰ(cTnI)、N-末端脑钠肽前体(NT-proBNP)浓度,所有患者随访30 d,根据随访结果分为复杂临床过程组(7例)和简单临床过程组(83例),结果采用Mann-Whitney U检验、x2检验、x2检验的连续性校正及logistic回归进行分析.结果 复杂临床过程组H-FABP水平高于简单临床过程组(U =54.000,P<0.01);ROC曲线获得H-FABP的最佳预后截值为7 μg/L,H-FABP、cTnI和NT-proBNP三者之间AUC比较差异无统计学意义;单变量logistic回归分析发现H-FABP≥6 μg,/L、心率≥106次/min和晕厥(均P<0.01)可预测血流动力学稳定的急性肺栓塞患者短期不良预后;多变量logistic回归分析发现仅H-FABP≥6 μg/L和晕厥(均P<0.05)仍是独立预测因素;cTnI或NT-proBNP联合H-FABP可提高对血流动力学稳定的急性肺栓塞患者治疗30 d的预测价值.结论 单独应用H-FABP或H-FABP联合其他临床资料,可对入院时血流动力学稳定的急性肺栓塞患者治疗30 d的预后进行评估,H-FABP作为预后评估可能优于cTnI和NT-proBNP.%Objective To explore the clinical value of heart-type fatty acid binding protein (H-FABP)for the assessment of the short-term prognosis in acute pulmonary embolism (APE)patients with hemodynamic stability on admission.Method A total of 156 APE patients with hemodynamic stability on admission were hospitalized in Beijing Anzhen hospital from December 2009 to December 2010,and the final study population comprised 90

  17. Influence of target concentration and background binding on in vitro selection of affinity reagents.

    Directory of Open Access Journals (Sweden)

    Jinpeng Wang

    Full Text Available Nucleic acid-based aptamers possess many useful features that make them a promising alternative to antibodies and other affinity reagents, including well-established chemical synthesis, reversible folding, thermal stability and low cost. However, the selection process typically used to generate aptamers (SELEX often requires significant resources and can fail to yield aptamers with sufficient affinity and specificity. A number of seminal theoretical models and numerical simulations have been reported in the literature offering insights into experimental factors that govern the effectiveness of the selection process. Though useful, these previous models have not considered the full spectrum of experimental factors or the potential impact of tuning these parameters at each round over the course of a multi-round selection process. We have developed an improved mathematical model to address this important question, and report that both target concentration and the degree of non-specific background binding are critical determinants of SELEX efficiency. Although smaller target concentrations should theoretically offer superior selection outcome, we show that the level of background binding dramatically affect the target concentration that will yield maximum enrichment at each round of selection. Thus, our model enables experimentalists to determine appropriate target concentrations as a means for protocol optimization. Finally, we perform a comparative analysis of two different selection methods over multiple rounds of selection, and show that methods with inherently lower background binding offer dramatic advantages in selection efficiency.

  18. Binding of Industrial Deposits of Heavy Metals and Arsenic in the Soil by 3-Aminopropyltrimethoxysilane

    Directory of Open Access Journals (Sweden)

    Grzesiak Piotr

    2014-06-01

    Full Text Available The results of the research studies concerning binding of heavy metals and arsenic (HM+As, occurring in soils affected by emissions from Głogów Copper Smelter and Refinery, by silane nanomaterial have been described. The content of heavy metals and arsenic was determined by AAS and the effectiveness of heavy metals and arsenic binding by 3-Aminopropyltrimethoxysilane was examined. The total leaching level of impurities in those fractions was 73.26% Cu, 74.7% – Pb, 79.5% Zn, 65.81% – Cd and 55.55% As. The studies demonstrated that the total binding of heavy metals and arsenic with nanomaterial in all fractions was about as follows: 20.5% Cu, 9.5% Pb, 7.1% Zn, 25.3% Cd and 10.89% As. The results presented how the safety of food can be cultivated around industrial area, as the currently used soil stabilization technique of HM by soil pH does not guarantee their stable blocking in a sorptive complex.

  19. Changes of conformation and aggregation state induced by binding of lanthanide ions to insulin

    Institute of Scientific and Technical Information of China (English)

    程驿; 李荣昌; 王夔

    2002-01-01

    To clarify the mechanism of lanthanide ions (Ln3+) on the across-membrane transport of insulin and subsequent reducing blood glucose, the interactions of Ln3+ with Zn-insulin and Zn-free insulin are investigated by spectroscopic methods. The results reveal that the binding of Ln3+ to insulin can induce its structure changes from secondary to quaternary structure, depending on the Ln3+ concentration. In the lower concentration, it triggers the conformational changes of insulin monomer in the binding region with insulin receptor (B(24-30)). It would affect insulin-insulin receptor interaction. Moreover, Ln3+ binding promotes the assembly of insulin monomer from dimer to polymer. The potency of Ln3+ in inducing insulin's aggregation is stronger than that of Zn2+. Furthermore, the aggregation can be reversed partly by EDTA-treatment, indicating that it is not due to denaturation. Similar to Zn2+ effect, Ln3+ can stabilize insulin hexamer in a certain range of concentration, but is stronger than the former.

  20. Changes of conformation and aggregation state induced by binding of lanthanide ions to insulin

    Institute of Scientific and Technical Information of China (English)

    程驿; 李荣昌; 王夔

    2002-01-01

    To clarify the mechanism of lanthanide ions (Ln3+) on the across-membrane transport of insulin and subsequent reducing blood glucose, the interactions of Ln3+with Zn-insulin and Zn-free insulin are investigated by spectroscopic methods. The results reveal that the binding of Ln3+ to insulin can induce its structure changes from secondary to quaternary structure, depending on the Ln3+ concentration. In the lower concentration, it triggers the conformational changes of insulin monomer in the binding region with insulin receptor (B(24-30)). It would affect insulin-insulin receptor interaction. Moreover, Ln3+ binding promotes the assembly of insulin monomer from dimer to polymer. The potency of Ln3+ in inducing insulin’s aggregation is stronger than that of Zn2+. Furthermore, the aggregation can be reversed partly by EDTA-treatment, indicating that it is not due to denaturation. Similar to Zn2+ effect, Ln3+ can stabilize insulin hexamer in a certain range of concentration, but is stronger than the former.

  1. An external sodium ion binding site controls allosteric gating in TRPV1 channels.

    Science.gov (United States)

    Jara-Oseguera, Andres; Bae, Chanhyung; Swartz, Kenton J

    2016-01-01

    TRPV1 channels in sensory neurons are integrators of painful stimuli and heat, yet how they integrate diverse stimuli and sense temperature remains elusive. Here, we show that external sodium ions stabilize the TRPV1 channel in a closed state, such that removing the external ion leads to channel activation. In studying the underlying mechanism, we find that the temperature sensors in TRPV1 activate in two steps to favor opening, and that the binding of sodium to an extracellular site exerts allosteric control over temperature-sensor activation and opening of the pore. The binding of a tarantula toxin to the external pore also exerts control over temperature-sensor activation, whereas binding of vanilloids influences temperature-sensitivity by largely affecting the open/closed equilibrium. Our results reveal a fundamental role of the external pore in the allosteric control of TRPV1 channel gating and provide essential constraints for understanding how these channels can be tuned by diverse stimuli. PMID:26882503

  2. Sex Differences in Serotonin 1 Receptor Binding in Rat Brain

    Science.gov (United States)

    Fischette, Christine T.; Biegon, Anat; McEwen, Bruce S.

    1983-10-01

    Male and female rats exhibit sex differences in binding by serotonin 1 receptors in discrete areas of the brain, some of which have been implicated in the control of ovulation and of gonadotropin release. The sex-specific changes in binding, which occur in response to the same hormonal (estrogenic) stimulus, are due to changes in the number of binding sites. Castration alone also affects the number of binding sites in certain areas. The results lead to the conclusion that peripheral hormones modulate binding by serotonin 1 receptors. The status of the serotonin receptor system may affect the reproductive capacity of an organism and may be related to sex-linked emotional disturbances in humans.

  3. Thermodynamic characterization of proflavine–DNA binding through microcalorimetric studies

    International Nuclear Information System (INIS)

    Highlights: • Energetics of the interaction of proflavine with DNA has been studied. • The binding reaction was favored by both negative enthalpy and positive entropy. • Enthalpy–entropy compensation phenomenon was observed. • Non-polyelectrolytic forces played a dominant role in the binding process. • Proflavine enhanced the thermal stability of DNA remarkably. - Abstract: The interaction of an important acridine dye, proflavine hydrochloride, with double stranded DNA was investigated using isothermal titration calorimetry and differential scanning calorimetry. The equilibrium constant for the binding reaction was calculated to be (1.60 ± 0.04) · 105 · M−1 at T = 298.15 K. The binding of proflavine hydrochloride to DNA was favored by both negative enthalpy and positive entropy contributions to the Gibbs energy. The equilibrium constant for the binding reaction decreased with increasing temperature. The standard molar enthalpy change became increasingly negative while the standard molar entropy change became less positive with rise in temperature. However, the standard molar Gibbs free energy change varied marginally suggesting the occurrence of enthalpy–entropy compensation phenomenon. The binding reaction was dominated by non-polyelectrolytic forces which remained virtually unchanged at all the salt concentrations studied. The binding also significantly increased the thermal stability of DNA against thermal denaturation

  4. The inhibition of anti-DNA binding to DNA by nucleic acid binding polymers.

    Directory of Open Access Journals (Sweden)

    Nancy A Stearns

    Full Text Available Antibodies to DNA (anti-DNA are the serological hallmark of systemic lupus erythematosus (SLE and can mediate disease pathogenesis by the formation of immune complexes. Since blocking immune complex formation can attenuate disease manifestations, the effects of nucleic acid binding polymers (NABPs on anti-DNA binding in vitro were investigated. The compounds tested included polyamidoamine dendrimer, 1,4-diaminobutane core, generation 3.0 (PAMAM-G3, hexadimethrine bromide, and a β-cylodextrin-containing polycation. As shown with plasma from patients with SLE, NABPs can inhibit anti-DNA antibody binding in ELISA assays. The inhibition was specific since the NABPs did not affect binding to tetanus toxoid or the Sm protein, another lupus autoantigen. Furthermore, the polymers could displace antibody from preformed complexes. Together, these results indicate that NABPs can inhibit the formation of immune complexes and may represent a new approach to treatment.

  5. Nitrogen enrichment weakens ecosystem stability through decreased species asynchrony and population stability in a temperate grassland.

    Science.gov (United States)

    Zhang, Yunhai; Loreau, Michel; Lü, Xiaotao; He, Nianpeng; Zhang, Guangming; Han, Xingguo

    2016-04-01

    Biodiversity generally promotes ecosystem stability. To assess whether the diversity-stability relationship observed under ambient nitrogen (N) conditions still holds under N enriched conditions, we designed a 6-year field experiment to test whether the magnitude and frequency of N enrichment affects ecosystem stability and its relationship with species diversity in a temperate grassland. Results of this experiment showed that the frequency of N addition had no effect on either the temporal stability of ecosystem and population or the relationship between diversity and stability. Nitrogen addition decreased ecosystem stability significantly through decreases in species asynchrony and population stability. Species richness was positively associated with ecosystem stability, but no significant relationship between diversity and the residuals of ecosystem stability was detected after controlling for the effects of the magnitude of N addition, suggesting collinearity between the effects of N addition and species richness on ecosystem stability, with the former prevailing over the latter. Both population stability and the residuals of population stability after controlling for the effects of the magnitude of N addition were positively associated with ecosystem stability, indicating that the stabilizing effects of component populations were still present after N enrichment. Our study supports the theory predicting that the effects of environmental factors on ecosystem functioning are stronger than those of biodiversity. Understanding such mechanisms is important and urgent to protect biodiversity in mediating ecosystem functioning and services in the face of global changes. PMID:26511538

  6. [Water binding of adsorptive immobilized lipases].

    Science.gov (United States)

    Loose, S; Meusel, D; Muschter, A; Ruthe, B

    1990-01-01

    It is supposed that not only the total water content of lipase preparations but more their state of water binding is of technological importance in enzymatic interesterification reactions in systems nearly free from water. The isotherms at 65 degrees C of two microbial lipases immobilized on various adsorbents as well as different adsorbents themselves are shown. The water binding capacity in the range of water content of technological interest decreases from the anion exchange resin Amberlyst A 21 via nonpolar adsorbent Amberlite XAD-2 to kieselguhr Celite 545. It is demonstrated that water binding by lipases is depending on temperature but is also affected by adsorptive immobilization. Adsorptive immobilized lipases show hysteresis, which is very important for preparing a definite water content of the enzyme preparations. PMID:2325750

  7. Mechanical unfolding of ribose binding protein and its comparison with other periplasmic binding proteins.

    Science.gov (United States)

    Kotamarthi, Hema Chandra; Narayan, Satya; Ainavarapu, Sri Rama Koti

    2014-10-01

    Folding and unfolding studies on large, multidomain proteins are still rare despite their high abundance in genomes of prokaryotes and eukaryotes. Here, we investigate the unfolding properties of a 271 residue, two-domain ribose binding protein (RBP) from the bacterial periplasm using single-molecule force spectroscopy. We observe that RBP predominately unfolds via a two-state pathway with an unfolding force of ∼80 pN and an unfolding contour length of ∼95 nm. Only a small population (∼15%) of RBP follows three-state pathways. The ligand binding neither increases the mechanical stability nor influences the unfolding flux of RBP through different pathways. The kinetic partitioning between two-state and three-state pathways, which has been reported earlier for other periplasmic proteins, is also observed in RBP, albeit to a lesser extent. These results provide important insights into the mechanical stability and unfolding processes of large two-domain proteins and highlight the contrasting features upon ligand binding. Protein structural topology diagrams are used to explain the differences in the mechanical unfolding behavior of RBP with other periplasmic binding proteins.

  8. Probing the Kinetic Stabilities of Friedreich’s Ataxia Clinical Variants Using a Solid Phase GroEL Chaperonin Capture Platform

    Directory of Open Access Journals (Sweden)

    Ana R. Correia

    2014-10-01

    Full Text Available Numerous human diseases are caused by protein folding defects where the protein may become more susceptible to degradation or aggregation. Aberrant protein folding can affect the kinetic stability of the proteins even if these proteins appear to be soluble in vivo. Experimental discrimination between functional properly folded and misfolded nonfunctional conformers is not always straightforward at near physiological conditions. The differences in the kinetic behavior of two initially folded frataxin clinical variants were examined using a high affinity chaperonin kinetic trap approach at 25 °C. The kinetically stable wild type frataxin (FXN shows no visible partitioning onto the chaperonin. In contrast, the clinical variants FXN-p.Asp122Tyr and FXN-p.Ile154Phe kinetically populate partial folded forms that tightly bind the GroEL chaperonin platform. The initially soluble FXN-p.Ile154Phe variant partitions onto GroEL more rapidly and is more kinetically liable. These differences in kinetic stability were confirmed using differential scanning fluorimetry. The kinetic and aggregation stability differences of these variants may lead to the distinct functional impairments described in Friedreich’s ataxia, the neurodegenerative disease associated to frataxin functional deficiency. This chaperonin platform approach may be useful for identifying small molecule stabilizers since stabilizing ligands to frataxin variants should lead to a concomitant decrease in chaperonin binding.

  9. Tritiated imipramine binding sites are decreased in the frontal cortex of suicides

    International Nuclear Information System (INIS)

    Binding characteristics of tritiated imipramine were determined in the frontal cortex of suicides and well-matched controls. Maximal binding was significantly lower in brains from the suicides. This finding is consistent with reports of decreased tritiated imipramine binding in the platelets of patients diagnosed as having a major affective disorder

  10. [Prognosis of affinity change of the TATA-binding protein to TATA-boxes upon polymorphisms of the human gene promoter TATA boxes].

    Science.gov (United States)

    Ponomarenko, P M; Ponomarenko, M P; Drachkova, I A; Lysova, M V; Arshinova, T V; Savinkova, L K; Kolchanov, N A

    2009-01-01

    TATA-binding protein (TBP) is a subunit of basal transcription factor TFIID that recognizes and binds to the TATA-box on TATA-containing promoters of class II genes, and starts assembling RNA polymerase II basal transcription complex. It is shown in many works that the sequence of TATA-box with its flanking regions affects the level of basal and activated transcription. TATA-box polymorphisms and human hereditary diseases associated with them show that TBP/TATA interaction may indirectly affect gene regulation in vivo. The object of this work is to determine changes in the TBP/TATA affinity upon polymorphisms in TATA-boxes of human gene promoters. We assess changes in TBP/TATA affinities in silico by using our formula of equilibrium TBP/TATA binding upon four consecutive steps: nonspecific binding sliding braking (stopping) stabilization. Our prognoses agree with known examples of TATA-box polymorphisms and human hereditary diseases associated with them. PMID:19548537

  11. Cellulose binding domain proteins

    Energy Technology Data Exchange (ETDEWEB)

    Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc (Davis, CA); Doi, Roy (Davis, CA)

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  12. Sequential memory: Binding dynamics

    Science.gov (United States)

    Afraimovich, Valentin; Gong, Xue; Rabinovich, Mikhail

    2015-10-01

    Temporal order memories are critical for everyday animal and human functioning. Experiments and our own experience show that the binding or association of various features of an event together and the maintaining of multimodality events in sequential order are the key components of any sequential memories—episodic, semantic, working, etc. We study a robustness of binding sequential dynamics based on our previously introduced model in the form of generalized Lotka-Volterra equations. In the phase space of the model, there exists a multi-dimensional binding heteroclinic network consisting of saddle equilibrium points and heteroclinic trajectories joining them. We prove here the robustness of the binding sequential dynamics, i.e., the feasibility phenomenon for coupled heteroclinic networks: for each collection of successive heteroclinic trajectories inside the unified networks, there is an open set of initial points such that the trajectory going through each of them follows the prescribed collection staying in a small neighborhood of it. We show also that the symbolic complexity function of the system restricted to this neighborhood is a polynomial of degree L - 1, where L is the number of modalities.

  13. Lectin binding in meningiomas.

    Science.gov (United States)

    Kleinert, R; Radner, H

    1987-01-01

    Forty-two meningiomas of different morphological sub-type were examined to determine their pattern of binding to 11 different lectins which characterize cell surface components such as carbohydrate residues. Histiocytic and xanthoma cells within meningiomas could be demonstrated with six different lectins: wheat germ agglutinin (WGA), peanut agglutinin (PNA) Bauhinia purpurea agglutinin (BPA), Helix pomatia agglutinin (HPA), Vicia fava agglutinin (VFA) and Soyabean agglutinin (SBA). Vascular elements including endothelial cells and intimal cells, bound Ulex europaeus agglutinin type 1 (UEA 1), WGA and HPA. The fibrous stroma in fibrous and fibroblastic meningiomas bound PNA, Laburnum alpinum agglutinin (LAA) and SBA. Tumour cells in meningotheliomatous meningiomas and some areas of anaplastic meningiomas bound Concanavalin A, PNA, LAA and VFA whereas tumour cells in fibrous and fibroblastic meningiomas bound BPA, LAA and VFA. Lectin binding has proved to be of value in detecting histiocytic and xanthoma cells together with vascular elements within meningiomas. In addition, the different lectin binding patterns allow different histological sub-types of meningioma to be distinguished although the biological significance of the binding patterns is unclear. PMID:3658105

  14. Partitioning of metals in different binding phases of tropical estuarine sediments: importance of metal chemistry

    Digital Repository Service at National Institute of Oceanography (India)

    Chakraborty, P.; Chakraborty, S.; Vudamala, K.; Sarkar, Arindam; Nath, B.N.

    Distribution of metals in different binding phases of estuarine sediments provides chemically significant description of metal–sediment interactions. This study describes the influences of ligand field stabilization energy (LFSE), Jahn–Teller effect...

  15. Technical factors affecting cup stability in bone impaction grafting.

    NARCIS (Netherlands)

    Bolder, S.B.T.; Verdonschot, N.J.J.; Schreurs, B.W.

    2007-01-01

    Favourable long-term clinical results can be achieved by the bone impaction technique in bone stock deficient acetabuli. Originally, firm impaction of manually prepared bone grafts using a rongeur was performed. An alternative technique for producing bone grafts is reaming from the pelvic wall or fe

  16. Mutations increasing exposure of a receptor binding site epitope in the soluble and oligomeric forms of the caprine arthritis-encephalitis lentivirus envelope glycoprotein.

    Science.gov (United States)

    Hötzel, Isidro; Cheevers, William P

    2005-09-01

    The caprine arthritis-encephalitis (CAEV) and ovine maedi-visna (MVV) viruses are resistant to antibody neutralization, a feature shared with all other lentiviruses. Whether the CAEV gp135 receptor binding site(s) (RBS) in the functional surface envelope glycoprotein (Env) is protected from antibody binding, allowing the virus to resist neutralization, is not known. Two CAEV gp135 regions were identified by extrapolating a gp135 structural model that could affect binding of antibodies to the RBS: the V1 region and a short sequence analogous in position to the human immunodeficiency virus type 1 gp120 loop B postulated to be located between two major domains of CAEV gp135. Mutation of isoleucine-166 to alanine in the putative loop B of gp135 increased the affinity of soluble gp135 for the CAEV receptor(s) and goat monoclonal antibody (Mab) F7-299 which recognizes an epitope overlapping the gp135 RBS. The I166A mutation also stabilized or exposed the F7-299 epitope in anionic detergent buffers, indicating that the I166A mutation induces conformational changes and stabilizes the RBS of soluble gp135 and enhances Mab F7-299 binding. In contrast, the affinity of a V1 deletion mutant of gp135 for the receptor and Mab F7-299 and its structural stability did not differ from that of the wild-type gp135. However, both the I166A mutation and the V1 deletion of gp135 increased cell-to-cell fusion activity and binding of Mab F7-299 to the oligomeric Env. Therefore, the CAEV gp135 RBS is protected from antibody binding by mechanisms both dependent and independent of Env oligomerization which are disrupted by the V1 deletion and the I166A mutation, respectively. In addition, we found a correlation between side-chain beta-branching at amino acid position 166 and binding of Mab F7-299 to oligomeric Env and cell-to-cell fusion, suggesting local secondary structure constraints in the region around isoleucine-166 as one determinant of gp135 RBS exposure and antibody binding. PMID

  17. Mutations increasing exposure of a receptor binding site epitope in the soluble and oligomeric forms of the caprine arthritis-encephalitis lentivirus envelope glycoprotein

    International Nuclear Information System (INIS)

    The caprine arthritis-encephalitis (CAEV) and ovine maedi-visna (MVV) viruses are resistant to antibody neutralization, a feature shared with all other lentiviruses. Whether the CAEV gp135 receptor binding site(s) (RBS) in the functional surface envelope glycoprotein (Env) is protected from antibody binding, allowing the virus to resist neutralization, is not known. Two CAEV gp135 regions were identified by extrapolating a gp135 structural model that could affect binding of antibodies to the RBS: the V1 region and a short sequence analogous in position to the human immunodeficiency virus type 1 gp120 loop B postulated to be located between two major domains of CAEV gp135. Mutation of isoleucine-166 to alanine in the putative loop B of gp135 increased the affinity of soluble gp135 for the CAEV receptor(s) and goat monoclonal antibody (Mab) F7-299 which recognizes an epitope overlapping the gp135 RBS. The I166A mutation also stabilized or exposed the F7-299 epitope in anionic detergent buffers, indicating that the I166A mutation induces conformational changes and stabilizes the RBS of soluble gp135 and enhances Mab F7-299 binding. In contrast, the affinity of a V1 deletion mutant of gp135 for the receptor and Mab F7-299 and its structural stability did not differ from that of the wild-type gp135. However, both the I166A mutation and the V1 deletion of gp135 increased cell-to-cell fusion activity and binding of Mab F7-299 to the oligomeric Env. Therefore, the CAEV gp135 RBS is protected from antibody binding by mechanisms both dependent and independent of Env oligomerization which are disrupted by the V1 deletion and the I166A mutation, respectively. In addition, we found a correlation between side-chain β-branching at amino acid position 166 and binding of Mab F7-299 to oligomeric Env and cell-to-cell fusion, suggesting local secondary structure constraints in the region around isoleucine-166 as one determinant of gp135 RBS exposure and antibody binding

  18. Salt Effects on the Conformational Stability of the Visual G-Protein-Coupled Receptor Rhodopsin

    Science.gov (United States)

    Reyes-Alcaraz, Arfaxad; Martínez-Archundia, Marlet; Ramon, Eva; Garriga, Pere

    2011-01-01

    Membrane protein stability is a key parameter with important physiological and practical implications. Inorganic salts affect protein stability, but the mechanisms of their interactions with membrane proteins are not completely understood. We have undertaken the study of a prototypical G-protein-coupled receptor, the α-helical membrane protein rhodopsin from vertebrate retina, and explored the effects of inorganic salts on the thermal decay properties of both its inactive and photoactivated states. Under high salt concentrations, rhodopsin significantly increased its activation enthalpy change for thermal bleaching, whereas acid denaturation affected the formation of a denatured loose-bundle state for both the active and inactive conformations. This behavior seems to correlate with changes in protonated Schiff-base hydrolysis. However, chromophore regeneration with the 11-cis-retinal chromophore and MetarhodopsinII decay kinetics were slower only in the presence of sodium chloride, suggesting that in this case, the underlying phenomenon may be linked to the activation of rhodopsin and the retinal release processes. Furthermore, the melting temperature, determined by means of circular dichroism and differential scanning calorimetry measurements, was increased in the presence of high salt concentrations. The observed effects on rhodopsin could indicate that salts favor electrostatic interactions in the retinal binding pocket and indirectly favor hydrophobic interactions at the membrane protein receptor core. These effects can be exploited in applications where the stability of membrane proteins in solution is highly desirable. PMID:22261069

  19. Stabilization of antibody fragments in adverse environments.

    Science.gov (United States)

    Dooley, H; Grant, S D; Harris, W J; Porter, A J

    1998-08-01

    Antibody fragments have the potential to be used as sensitive and specific binding agents in a broad range of industrial applications. Genetic manipulation has been used to design a series of antibody fragment configurations with a flexible linker and/or a disulphide bond between the heavy chain and light chain of an antibody fragment against the herbicide atrazine. The thermostability and stability to a range of denaturants, polar and non-polar solvents, surfactants and proteases have been compared. It has been found that a novel antibody fragment construct (STAB: stabilized antibody) containing both a flexible linker and a disulphide bond can be effectively produced and shows greatly improved stability in these diverse environments. These STABs should be useful in environmental diagnostics and remediation, and may provide a generic approach for stabilizing antibody fragments in formulations containing detergents and penetrants for topical application in the pharmaceutical and cosmetic industries.

  20. Tetrapyrrole binding affinity of the murine and human p22HBP heme-binding proteins.

    Science.gov (United States)

    Micaelo, Nuno M; Macedo, Anjos L; Goodfellow, Brian J; Félix, Vítor

    2010-11-01

    We present the first systematic molecular modeling study of the binding properties of murine (mHBP) and human (hHBP) p22HBP protein (heme-binding protein) with four tetrapyrrole ring systems belonging to the heme biosynthetic pathway: iron protoporphyrin IX (HEMIN), protoporphyrin IX (PPIX), coproporphyrin III (CPIII), coproporphyrin I (CPI). The relative binding affinities predicted by our computational study were found to be similar to those observed experimentally, providing a first rational structural analysis of the molecular recognition mechanism, by p22HBP, toward a number of different tetrapyrrole ligands. To probe the structure of these p22HBP protein complexes, docking, molecular dynamics and MM-PBSA methodologies supported by experimental NMR ring current shift data have been employed. The tetrapyrroles studied were found to bind murine p22HBP with the following binding affinity order: HEMIN> PPIX> CPIII> CPI, which ranged from -22.2 to -6.1 kcal/mol. In general, the protein-tetrapyrrole complexes are stabilized by non-bonded interactions between the tetrapyrrole propionate groups and basic residues of the protein, and by the preferential solvation of the complex compared to the unbound components. PMID:20800521

  1. Exploration of the binding mode between (-)-zampanolide and tubulin using docking and molecular dynamics simulation.

    Science.gov (United States)

    Liao, Si-Yan; Mo, Guang-Quan; Chen, Jin-Can; Zheng, Kang-Cheng

    2014-02-01

    The binding mode of (-)-zampanolide (ZMP) to tubulin was investigated using docking, molecular dynamics (MD) simulation, and binding free-energy calculations. The docking studies validated the experimental results indicating that the paclitaxel site is the binding site for (-)-ZMP. The 18 ns MD simulation shows the docking mode has changed a lot, whereas it offers more reliable binding data. MM-PBSA binding free-energy calculations further confirmed the results of the MD simulation. The study revealed that hydrophobic interactions play an important role in stabilizing the binding, and the strong hydrogen bond formed with Asp224 enhances the affinity for tubulin. Meanwhile, the results support the assumption that (-)-ZMP can be attacked by His227, leading to a nucleophilic reaction and covalent binding. These theoretical results lead to a greater understanding of the mechanism of action of binding to tubulin, and will therefore aid the design of new compounds with higher affinities for tubulin. PMID:24478043

  2. Isothermal Titration Calorimetry Measurements of Metal Ions Binding to Proteins.

    Science.gov (United States)

    Quinn, Colette F; Carpenter, Margaret C; Croteau, Molly L; Wilcox, Dean E

    2016-01-01

    ITC measurements involving metal ions are susceptible to a number of competing reactions (oxidation, precipitation, and hydrolysis) and coupled reactions involving the buffer and protons. Stabilization and delivery of the metal ion as a well-defined and well-characterized complex with the buffer, or a specific ligand, can suppress undesired solution chemistry and, depending on the stability of the metal complex, allow accurate measurements of higher affinity protein-binding sites. This requires, however, knowledge of the thermodynamics of formation of the metal complex and accounting for its contribution to the experimentally measured values (KITC and ΔHITC) through a post hoc analysis that provides the condition-independent binding thermodynamics (K, ΔG(o), ΔH, ΔS, and ΔCP). This analysis also quantifies the number of protons that are displaced when the metal ion binds to the protein.

  3. Improved assay for measuring heparin binding to bull sperm

    International Nuclear Information System (INIS)

    The binding of heparin to sperm has been used to study capacitation and to rank relative fertility of bulls. Previous binding assays were laborious, used 107 sperm per assay point, and required large amounts of radiolabeled heparin. A modified heparin-binding assay is described that used only 5 x 104 cells per incubation well and required reduced amounts of [3H] heparin. The assay was performed in 96-well Millititer plates, enabling easy incubation and filtering. Dissociation constants and concentrations of binding sites did not differ if analyzed by Scatchard plots, Woolf plots, or by log-logit transformed weighted nonlinear least squares regression, except in the case of outliers. In such cases, Scatchard analysis was more sensitive to outliers. Nonspecific binding was insignificant using nonlinear logistic fit regression and a proportion graph. The effects were tested of multiple free-thawing of sperm in either a commercial egg yolk extender, 40 mM Tris buffer with 8% glycerol, or 40 mM Tris buffer without glycerol. Freeze-thawing in extender did not affect the dissociation constant or the concentration of binding sites. However, freeze-thawing three times in 40 mM Tris reduced the concentration of binding sites and lowered the dissociation constant (raised the affinity). The inclusion of glycerol in the 40 mM Tris did not significantly affect the estimated dissociation constant or the concentration of binding sites as compared to 40 mM Tris without glycerol

  4. Voting behavior and budget stability

    OpenAIRE

    Cristina Vicente; Ana-María Ríos; María-Dolores Guillamón

    2013-01-01

    The aim of this paper is to analyze how the implementation of the Budgetary Stability Law has affectedPolitical Budget Cycles generated by Spanish local governments. Specifically, we study whether the evolutionof debt, budget deficit, capital spending and current spending over the electoral cycle has changed after theintroduction of this law. We use a sample of 132 Spanish municipalities with more than 50,000 inhabitants(including the provincial capitals) during the period 1995‑2009. Our resu...

  5. Plutonium inventories for stabilization and stabilized materials

    Energy Technology Data Exchange (ETDEWEB)

    Williams, A.K.

    1996-05-01

    The objective of the breakout session was to identify characteristics of materials containing plutonium, the need to stabilize these materials for storage, and plans to accomplish the stabilization activities. All current stabilization activities are driven by the Defense Nuclear Facilities Safety Board Recommendation 94-1 (May 26, 1994) and by the recently completed Plutonium ES&H Vulnerability Assessment (DOE-EH-0415). The Implementation Plan for accomplishing stabilization of plutonium-bearing residues in response to the Recommendation and the Assessment was published by DOE on February 28, 1995. This Implementation Plan (IP) commits to stabilizing problem materials within 3 years, and stabilizing all other materials within 8 years. The IP identifies approximately 20 metric tons of plutonium requiring stabilization and/or repackaging. A further breakdown shows this material to consist of 8.5 metric tons of plutonium metal and alloys, 5.5 metric tons of plutonium as oxide, and 6 metric tons of plutonium as residues. Stabilization of the metal and oxide categories containing greater than 50 weight percent plutonium is covered by DOE Standard {open_quotes}Criteria for Safe Storage of Plutonium Metals and Oxides{close_quotes} December, 1994 (DOE-STD-3013-94). This standard establishes criteria for safe storage of stabilized plutonium metals and oxides for up to 50 years. Each of the DOE sites and contractors with large plutonium inventories has either started or is preparing to start stabilization activities to meet these criteria.

  6. Trapped particle stability for the kinetic stabilizer

    Science.gov (United States)

    Berk, H. L.; Pratt, J.

    2011-08-01

    A kinetically stabilized axially symmetric tandem mirror (KSTM) uses the momentum flux of low-energy, unconfined particles that sample only the outer end-regions of the mirror plugs, where large favourable field-line curvature exists. The window of operation is determined for achieving magnetohydrodynamic (MHD) stability with tolerable energy drain from the kinetic stabilizer. Then MHD stable systems are analysed for stability of the trapped particle mode. This mode is characterized by the detachment of the central-cell plasma from the kinetic-stabilizer region without inducing field-line bending. Stability of the trapped particle mode is sensitive to the electron connection between the stabilizer and the end plug. It is found that the stability condition for the trapped particle mode is more constraining than the stability condition for the MHD mode, and it is challenging to satisfy the required power constraint. Furthermore, a severe power drain may arise from the necessary connection of low-energy electrons in the kinetic stabilizer to the central region.

  7. On hovercraft overwater heave stability

    Science.gov (United States)

    Hinchey, M. J.; Sullivan, P. A.

    1993-05-01

    The dynamic heave stability of an air cushion vehicle or hovercraft hovering over deep water without forward motion is investigated analytically. The principal feature of the analysis is the modeling of the motion of the water surface beneath the cushion caused by fluctuations in the pressure of the cushion or cavity air. This surface motion interacts with the vehicle dynamics by modulating both the volume and exit flow area of the cushion. For analytical simplicity, the geometry chosen for study is a 2D section of a rigid wall plenum chamber; this enables exploitation of classical linear wave formulas developed by Lamb for the surface motion generated by a spatially uniform surface pressure oscillating sinusoidally in time. To assess stability characteristics, the Nyquist criterion is applied to the linearized equations. Results are presented for two cases: one is representative of a small test vehicle, and the other of a large ice-breaking platform. They show that the water surface motion significantly affects stability through both of the proposed mechanisms, with cushion exit flow area modulation usually being more important. A feature of the results is that as the weight of a vehicle decreases many stability transitions occur. This suggests that simple guidelines for avoiding instability may not exist, so that stability augmentation devices may be required for vehicles designed to hover for extended periods over water.

  8. Copper binding ligands: production by marine plankton and characterization by ESI-MS

    Science.gov (United States)

    Orians, K.; Ross, A.; Lawrence, M.; Ikonomou, M.

    2003-04-01

    Organic complexation affects the bioavailability and distribution of copper in the surface ocean. The cyanobacterium Synechococcus sp. PCC 7002 was cultured in the lab and subjected to near-toxic Cu concentrations. Strong Cu-binding ligands were produced under these conditions, as found for other species of Synechococcus. The copper-binding ligand produced had a log K'cond. (log conditional stability constant) of 12.2, similar to the natural ligands found in the surface ocean. The amount of ligand produced was proportional to the amount of copper present. Isolation and concentration of these compounds for characterization by electrospray mass spectrometry (ESI-MS) provides information about the structure of the organic ligands and their metal-ion complexes. Using model ligands, we'll show that ligands can be characterized by ESI-MS and that the location of the copper binding site can be determined in complex molecules. We'll also present results of copper-complexing ligands extracted from the coastal waters of British Columbia. Ligand concentrations are higher at low salinity and in surface waters, indicating that these ligands are produced in surface waters and/or delivered to the region via the Fraser River. Analysis of the extracts with highest UV absorbance identified two Cu2+ ligands of molecular weight 259 and 264. The mass and isotopic distributions are consistent with dipeptides and tripeptides containing two metal-binding amino groups. This result is consistent with the findings of other studies attempting to characterize Cu2+ ligands in seawater. The structure of the identified ligand is similar to that of rhodotorulic acid (a microbial siderophore), glutathione, and phytochelatins, indicating that small peptides and related compounds can act as strong, specific metal chelators in natural waters

  9. Sequence-selective DNA binding with cell-permeable oligoguanidinium-peptide conjugates.

    Science.gov (United States)

    Mosquera, Jesús; Sánchez, Mateo I; Valero, Julián; de Mendoza, Javier; Vázquez, M Eugenio; Mascareñas, José L

    2015-03-21

    Conjugation of a short peptide fragment from a bZIP protein to an oligoguanidinium tail results in a DNA-binding miniprotein that selectively interacts with composite sequences containing the peptide-binding site next to an A/T-rich tract. In addition to stabilizing the complex with the target DNA, the oligoguanidinium unit also endows the conjugate with cell internalization properties.

  10. Current trends to measure implant stability.

    Science.gov (United States)

    Swami, Vasanthi; Vijayaraghavan, Vasantha; Swami, Vinit

    2016-01-01

    Implant stability plays a critical role for successful osseointegration. Successful osseointegration is a prerequisite for functional dental implants. Continuous monitoring in an objective and qualitative manner is important to determine the status of implant stability. Implant stability is measured at two different stages: Primary and secondary. Primary stability comes from mechanical engagement with cortical bone. Secondary stability is developed from regeneration and remodeling of the bone and tissue around the implant after insertion and affected by the primary stability, bone formation and remodelling. The time of functional loading is dependent upon the implant stability. Historically the gold standard method to evaluate stability were microscopic or histologic analysis, radiographs, however due to invasiveness of these methods and related ethical issues various other methods have been proposed like cutting torque resistance, reverse torque analysis, model analysis etc. It is, therefore, of an utmost importance to be able to access implant stability at various time points and to project a long term prognosis for successful therapy. Therefore this review focuses on the currently available methods for evaluation of implant stability.

  11. [The effect of cocaine on binding of tricyclic antidepressives in the synaptic plasma membranes in the brain].

    Science.gov (United States)

    Bures, P; Krulík, R; Fisar, Z; Fuksová, K

    1993-10-01

    Effect of cocaine on binding of 3H-imipramine, 3H-desmethylimipramine, 3H-didesmethylimipramine and 3H-amitriptyline to brain synaptic plasma membranes (SPM) was studied. Binding of methylated tricyclic antidepressants was more affected. Cocaine inhibits 3H-imipramine binding at concentrations higher than 10(-5) mol/l. Binding stimulated by phosphatidylserine was affected more significantly. PMID:8269521

  12. Folding thermodynamics of c-Myb DNA-binding domain in correlation with its α-helical contents.

    Science.gov (United States)

    Inaba, Satomi; Fukada, Harumi; Oda, Masayuki

    2016-01-01

    The conformational and thermal stabilities of the minimum functional unit for c-Myb DNA-binding domain, tandem repeat 2 and 3 (R2R3), were analyzed under different pH conditions, ranging from 4.0 to 7.5, using circular dichroism and differential scanning calorimetry. Secondary structure analysis showed that the solution pH largely affects the conformational stability of the protein domain. Of all conditions analyzed, the α-helical content was maximal at pH 6.5, and the thermal stability was highest at pH 5.0. Thermodynamic parameters for thermal unfolding of R2R3 were determined using differential scanning calorimetry, and the origin of folding thermodynamics at the different pHs and its correlation with the α-helical content were further analyzed. It should be noted that the α-helical content correlates well with the enthalpy change in the pH range from 4.5 to 7.5, suggesting that the strength of hydrogen bonds and salt bridges needed for maintenance of helical structure is related to enthalpy in the native state. Under physiological pH conditions, c-Myb R2R3 exists in the enthalpically unstable but entropically stable state. Due to loss of rigid structure and high stability, the protein can now obtain structural flexibility, befitting its function.

  13. Monomeric rhodopsin is the minimal functional unit required for arrestin binding*

    OpenAIRE

    Tsukamoto, Hisao; Sinha, Abhinav; DeWitt, Mark; Farrens, David L.

    2010-01-01

    We have tested if arrestin binding requires the G protein-coupled receptor (GPCR) be a dimer or multimer. To do this, we encapsulated single rhodopsin molecules into nanoscale phospholipids particles (so called nanodiscs) and measured their ability to bind arrestin. Our data clearly show that both visual arrestin and β-arrestin 1 can bind to monomeric rhodopsin and stabilize the active metarhodopsin II form. Interestingly, we find the monomeric rhodopsin in nanodiscs has a higher affinity for...

  14. Arctic Submarine Slope Stability

    Science.gov (United States)

    Winkelmann, D.; Geissler, W.

    2010-12-01

    Submarine landsliding represents aside submarine earthquakes major natural hazard to coastal and sea-floor infrastructure as well as to coastal communities due to their ability to generate large-scale tsunamis with their socio-economic consequences. The investigation of submarine landslides, their conditions and trigger mechanisms, recurrence rates and potential impact remains an important task for the evaluation of risks in coastal management and offshore industrial activities. In the light of a changing globe with warming oceans and rising sea-level accompanied by increasing human population along coasts and enhanced near- and offshore activities, slope stability issues gain more importance than ever before. The Arctic exhibits the most rapid and drastic changes and is predicted to change even faster. Aside rising air temperatures, enhanced inflow of less cooled Atlantic water into the Arctic Ocean reduces sea-ice cover and warms the surroundings. Slope stability is challenged considering large areas of permafrost and hydrates. The Hinlopen/Yermak Megaslide (HYM) north of Svalbard is the first and so far only reported large-scale submarine landslide in the Arctic Ocean. The HYM exhibits the highest headwalls that have been found on siliciclastic margins. With more than 10.000 square kilometer areal extent and app. 2.400 cubic kilometer of involved sedimentary material, it is one of the largest exposed submarine slides worldwide. Geometry and age put this slide in a special position in discussing submarine slope stability on glaciated continental margins. The HYM occurred 30 ka ago, when the global sea-level dropped by app. 50 m within less than one millennium due to rapid onset of global glaciation. It probably caused a tsunami with circum-Arctic impact and wave heights exceeding 130 meters. The HYM affected the slope stability field in its neighbourhood by removal of support. Post-megaslide slope instability as expressed in creeping and smaller-scaled slides are

  15. Ligand photo-isomerization triggers conformational changes in iGluR2 ligand binding domain.

    Directory of Open Access Journals (Sweden)

    Tino Wolter

    Full Text Available Neurological glutamate receptors bind a variety of artificial ligands, both agonistic and antagonistic, in addition to glutamate. Studying their small molecule binding properties increases our understanding of the central nervous system and a variety of associated pathologies. The large, oligomeric multidomain membrane protein contains a large and flexible ligand binding domains which undergoes large conformational changes upon binding different ligands. A recent application of glutamate receptors is their activation or inhibition via photo-switchable ligands, making them key systems in the emerging field of optochemical genetics. In this work, we present a theoretical study on the binding mode and complex stability of a novel photo-switchable ligand, ATA-3, which reversibly binds to glutamate receptors ligand binding domains (LBDs. We propose two possible binding modes for this ligand based on flexible ligand docking calculations and show one of them to be analogues to the binding mode of a similar ligand, 2-BnTetAMPA. In long MD simulations, it was observed that transitions between both binding poses involve breaking and reforming the T686-E402 protein hydrogen bond. Simulating the ligand photo-isomerization process shows that the two possible configurations of the ligand azo-group have markedly different complex stabilities and equilibrium binding modes. A strong but slow protein response is observed after ligand configuration changes. This provides a microscopic foundation for the observed difference in ligand activity upon light-switching.

  16. THEORETICAL CONSIDERATIONS OF PRICE STABILITY AS PART OF THE FINANCIAL STABILITY

    Directory of Open Access Journals (Sweden)

    Magdalena RĂDULESCU

    2012-09-01

    Full Text Available Currently there are many authors who consider that the only objective of the central bank should be the price stability and between the respective objective and financial stability there is incompatibility. As far we are concerned, we subscribe the idea that between price stability and financial stability there are complementarities. And a strong argument in the favour of this position is also historical. Actually, many older or newer facts show that banking crises were often caused by the unfavourable macroeconomic situation coupled with the bad macroeconomic policies carried by the authorities. But, a monetary policy that aims the price stability reduces this risk. The truth is that the central banks have a series of tools that allow them to act for achieving both the objective of price stability, and that of the stability of financial sector. Although the financial stability is not, usually, an explicit objective for the modern central bank, the systematic financial instability can cancel their performances in achieving their major final objective: the price stability. Being that, because of the need that it creates to inject additional liquidity into the banking system, a crisis of the banking sector may directly affect the monetary stability. Here the mentioned complementarities arise between price stability and financial stability, although the achievement of the first does not necessarily involve the assurance of the last.

  17. Trapped Particle Stability for the Kinetic Stabilizer

    CERN Document Server

    Berk, H L

    2011-01-01

    A kinetically stabilized axially symmetric tandem mirror (KSTM) uses the momentum flux of low-energy, unconfined particles that sample only the outer end-regions of the mirror plugs, where large favorable field-line curvature exists. The window of operation is determined for achieving MHD stability with tolerable energy drain from the kinetic stabilizer. Then MHD stable systems are analyzed for stability of the trapped particle mode. This mode is characterized by the detachment of the central-cell plasma from the kinetic stabilizer region without inducing field-line bending. Stability of the trapped particle mode is sensitive to the electron connection between the stabilizer and the end plug. It is found that the stability condition for the trapped particle mode is more constraining than the stability condition for the MHD mode, and it is challenging to satisfy the required power constraint. Furthermore a severe power drain may arise from the necessary connection of low-energy electrons in the kinetic stabili...

  18. Binding of fluorescent lanthanides to rat liver mitochondrial membranes and calcium ion-binding proteins.

    Science.gov (United States)

    Mikkelsen, R B; Wallach, D F

    1976-05-21

    (1) Tb3+ binding to mitochondrial membranes can be monitored by enhanced ion fluorescence at 545 nm with excitation at 285 nm. At low protein concentrations (less than 30 mug/ml) no inner filter effects are observed. (2) This binding is localized at the external surface of the inner membrane and is unaffected by inhibitors of respiration or oxidative phosphorylation. (3) A soluble Ca2+ binding protein isolated according to Lehninger, A.L. ((1971) Biochem. Biophys. Res. Commun. 42, 312-317) also binds Tb3+ with enhanced ion fluorescence upon excitation at 285 nm. The excitation spectrum of the isolated protein and of the intact mitochondria are indicative of an aromatic amino acid at the cation binding site. (4) Further characterization of the Tb3+-protein interaction revealed that there is more than one binding site per protein molecule and that these sites are clustered (less than 20 A). Neuraminidase treatment or organic solvent extraction of the protein did not affect fluorescent Tb3+ binding. (5) pH dependency studies of Tb3+ binding to the isolated protein or intact mitochondria demonstrated the importance of an ionizable group of pK greater than 6. At pH less than 7.5 the amount of Tb3+ bound to the isolated protein decreased with increase in pH as monitored by Tb3+ fluorescence. With intact mitochondria the opposite occurred with a large increase in Tb3+ fluorescence at higher pH. This increase was not observed when the mitochondria were preincubated with antimycin A and rotenone. PMID:6061

  19. A GBP 130 derived peptide from Plasmodium falciparum binds to human erythrocytes and inhibits merozoite invasion in vitro

    OpenAIRE

    Jorge E Suarez; Mauricio Urquiza; Hernando Curtidor; Rodriguez, Luis E.; Marisol Ocampo; Elizabeth Torres; Fanny Guzman; Manuel Elkin Patarroyo

    2000-01-01

    The malarial GBP 130 protein binds weakly to intact human erythrocytes; the binding sites seem to be located in the repeat region and this region's antibodies block the merozoite invasion. A peptide from this region (residues from 701 to 720) which binds to human erythrocytes was identified. This peptide named 2220 did not bind to sialic acid; the binding site on human erythrocyte was affected by treatment with trypsin but not by chymotrypsin. The peptide was able to inhibit Plasmodium falcip...

  20. Identification of sucrose synthase as an actin-binding protein

    Science.gov (United States)

    Winter, H.; Huber, J. L.; Huber, S. C.; Davies, E. (Principal Investigator)

    1998-01-01

    Several lines of evidence indicate that sucrose synthase (SuSy) binds both G- and F-actin: (i) presence of SuSy in the Triton X-100-insoluble fraction of microsomal membranes (i.e. crude cytoskeleton fraction); (ii) co-immunoprecipitation of actin with anti-SuSy monoclonal antibodies; (iii) association of SuSy with in situ phalloidin-stabilized F-actin filaments; and (iv) direct binding to F-actin, polymerized in vitro. Aldolase, well known to interact with F-actin, interfered with binding of SuSy, suggesting that a common or overlapping binding site may be involved. We postulate that some of the soluble SuSy in the cytosol may be associated with the actin cytoskeleton in vivo.