Sample records for binding profile study

  1. Comparative study of heparin-binding proteins profile of Murrah buffalo (Bubalus bubalis semen

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    S. S. Ramteke


    Full Text Available Aim: The experiment was conducted to study the total seminal plasma protein (TSPP and heparin-binding proteins (HBPs in relation to initial semen quality of buffalo bull. Materials and Methods: Semen from two Murrah buffalo bulls (bull no. 605 and 790 with mass motility of ≥3+ were used for the study and categorized into three groups (Group I- Mass motility 3+, Group II- Mass motility 4+ and Group III- Mass motility 5+. Seminal plasma from semen was separated by centrifugation. HBPs was isolated and purified from heparin-agarose affinity column by modified elution buffer. TSPP and isolated HBPs concentration was estimated by Lowry’s method. The purified HBPs were resolved on Sodium dodecyl sulfate polyacrylamide gel electrophoresis to check the protein profile of two bulls. Results: The mean values of TSPP concentrations in bull no. 605 and 790 in Group I, II and III were 30.64±0.12, 31.66±0.09, 32.53±0.19 and 28.51±0.09, 29.49±0.15, 30.45±0.17 mg/mL, respectively. The mean values of HBPs concentrations in bull no. 605 and 790 in Group I, II and III were 3.11±0.07, 3.32±0.06, 3.46±0.08 and 2.51±0.08, 2.91±0.05, 3.10±0.03 mg/mL, respectively. Both the values of TSPP and HBPs were significantly higher (p<0.01 in bull no. 605 when compared to 790 in all the three groups. 31 kDa HBP was more intensely present in bull no. 605, thus may indicate its superiority over bull no. 790 in relation to fertility potential. Conclusion: TSPP and HBPs shows variation in concentration with respect to initial semen quality. Furthermore, presence of fertility related 31 kDa HBPs in one of the bull may be an indication of high fertility of a bull. In future, in-vivo and in-vitro correlative study on larger basis is needed for the establishment of fertility-related HBPs in semen which might establish criteria for selection of buffalo bull with high fertility potential.

  2. Relating the shape of protein binding sites to binding affinity profiles: is there an association?

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    Bitter István


    Full Text Available Abstract Background Various pattern-based methods exist that use in vitro or in silico affinity profiles for classification and functional examination of proteins. Nevertheless, the connection between the protein affinity profiles and the structural characteristics of the binding sites is still unclear. Our aim was to investigate the association between virtual drug screening results (calculated binding free energy values and the geometry of protein binding sites. Molecular Affinity Fingerprints (MAFs were determined for 154 proteins based on their molecular docking energy results for 1,255 FDA-approved drugs. Protein binding site geometries were characterized by 420 PocketPicker descriptors. The basic underlying component structure of MAFs and binding site geometries, respectively, were examined by principal component analysis; association between principal components extracted from these two sets of variables was then investigated by canonical correlation and redundancy analyses. Results PCA analysis of the MAF variables provided 30 factors which explained 71.4% of the total variance of the energy values while 13 factors were obtained from the PocketPicker descriptors which cumulatively explained 94.1% of the total variance. Canonical correlation analysis resulted in 3 statistically significant canonical factor pairs with correlation values of 0.87, 0.84 and 0.77, respectively. Redundancy analysis indicated that PocketPicker descriptor factors explain 6.9% of the variance of the MAF factor set while MAF factors explain 15.9% of the total variance of PocketPicker descriptor factors. Based on the salient structures of the factor pairs, we identified a clear-cut association between the shape and bulkiness of the drug molecules and the protein binding site descriptors. Conclusions This is the first study to investigate complex multivariate associations between affinity profiles and the geometric properties of protein binding sites. We found that

  3. Is there a link between selectivity and binding thermodynamics profiles? (United States)

    Tarcsay, Ákos; Keserű, György M


    Thermodynamics of ligand binding is influenced by the interplay between enthalpy and entropy contributions of the binding event. The impact of these binding free energy components, however, is not limited to the primary target only. Here, we investigate the relationship between binding thermodynamics and selectivity profiles by combining publicly available data from broad off-target assay profiling and the corresponding thermodynamics measurements. Our analysis indicates that compounds binding their primary targets with higher entropy contributions tend to hit more off-targets compared with those ligands that demonstrated enthalpy-driven binding.

  4. Fluorescence Correlation Spectroscopy in Drug Discovery: Study of Alexa532-Endothelin 1 Binding to the Endothelin ETA Receptor to Describe the Pharmacological Profile of Natural Products

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    Catherina Caballero-George


    Full Text Available Fluorescence correlation spectroscopy and the newly synthesized Alexa532-ET1 were used to study the dynamics of the endothelin ETA receptor-ligand complex alone and under the influence of a semisynthetic selective antagonist and a fungal extract on living A10 cells. Dose-dependent increase of inositol phosphate production was seen for Alexa532-ET1, and its binding was reduced to 8% by the selective endothelin ETA antagonist BQ-123, confirming the specific binding of Alexa532-ET1 to the endothelin ETA receptor. Two different lateral mobilities of the receptor-ligand complexes within the cell membrane were found allowing the discrimination of different states for this complex. BQ-123 showed a strong binding affinity to the “inactive” receptor state characterized by the slow diffusion time constant. A similar effect was observed for the fungal extract, which completely displaced Alexa532-ET1 from its binding to the “inactive” receptor state. These findings suggest that both BQ-123 and the fungal extract act as inverse agonists.

  5. Concentration profiles of actin-binding molecules in lamellipodia (United States)

    Falcke, Martin


    Motile cells form lamellipodia in the direction of motion, which are flat membrane protrusions containing an actin filament network. The network flows rearward relative to the leading edge of the lamellipodium due to actin polymerization at the front. Thus, actin binding molecules are subject to transport towards the rear of the cell in the bound state and diffuse freely in the unbound state. We analyze this reaction-diffusion-advection process with respect to the concentration profiles of these species and provide an analytic approximation for them. Network flow may cause a depletion zone of actin binding molecules close to the leading edge. The existence of such zone depends on the free molecule concentration in the cell body, on the ratio of the diffusion length to the distance bound molecules travel rearward with the flow before dissociating, and the ratio of the diffusion length to the width of the region with network flow and actin binding. Our calculations suggest the existence of depletion zones for the F-actin cross-linkers filamin and α-actinin in fish keratocytes (and other cell types), which is in line with the small elastic moduli of the F-actin network close to the leading edge found in measurements of the force motile cells are able to exert.

  6. Transcriptome Profiling of Pediatric Core Binding Factor AML.

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    Chih-Hao Hsu

    Full Text Available The t(8;21 and Inv(16 translocations disrupt the normal function of core binding factors alpha (CBFA and beta (CBFB, respectively. These translocations represent two of the most common genomic abnormalities in acute myeloid leukemia (AML patients, occurring in approximately 25% pediatric and 15% of adult with this malignancy. Both translocations are associated with favorable clinical outcomes after intensive chemotherapy, and given the perceived mechanistic similarities, patients with these translocations are frequently referred to as having CBF-AML. It remains uncertain as to whether, collectively, these translocations are mechanistically the same or impact different pathways in subtle ways that have both biological and clinical significance. Therefore, we used transcriptome sequencing (RNA-seq to investigate the similarities and differences in genes and pathways between these subtypes of pediatric AMLs. Diagnostic RNA from patients with t(8;21 (N = 17, Inv(16 (N = 14, and normal karyotype (NK, N = 33 were subjected to RNA-seq. Analyses compared the transcriptomes across these three cytogenetic subtypes, using the NK cohort as the control. A total of 1291 genes in t(8;21 and 474 genes in Inv(16 were differentially expressed relative to the NK controls, with 198 genes differentially expressed in both subtypes. The majority of these genes (175/198; binomial test p-value < 10(-30 are consistent in expression changes among the two subtypes suggesting the expression profiles are more similar between the CBF cohorts than in the NK cohort. Our analysis also revealed alternative splicing events (ASEs differentially expressed across subtypes, with 337 t(8;21-specific and 407 Inv(16-specific ASEs detected, the majority of which were acetylated proteins (p = 1.5 x 10(-51 and p = 1.8 x 10(-54 for the two subsets. In addition to known fusions, we identified and verified 16 de novo fusions in 43 patients, including three fusions involving NUP98 in six

  7. Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles. (United States)

    Brender, Jeffrey R; Zhang, Yang


    The formation of protein-protein complexes is essential for proteins to perform their physiological functions in the cell. Mutations that prevent the proper formation of the correct complexes can have serious consequences for the associated cellular processes. Since experimental determination of protein-protein binding affinity remains difficult when performed on a large scale, computational methods for predicting the consequences of mutations on binding affinity are highly desirable. We show that a scoring function based on interface structure profiles collected from analogous protein-protein interactions in the PDB is a powerful predictor of protein binding affinity changes upon mutation. As a standalone feature, the differences between the interface profile score of the mutant and wild-type proteins has an accuracy equivalent to the best all-atom potentials, despite being two orders of magnitude faster once the profile has been constructed. Due to its unique sensitivity in collecting the evolutionary profiles of analogous binding interactions and the high speed of calculation, the interface profile score has additional advantages as a complementary feature to combine with physics-based potentials for improving the accuracy of composite scoring approaches. By incorporating the sequence-derived and residue-level coarse-grained potentials with the interface structure profile score, a composite model was constructed through the random forest training, which generates a Pearson correlation coefficient >0.8 between the predicted and observed binding free-energy changes upon mutation. This accuracy is comparable to, or outperforms in most cases, the current best methods, but does not require high-resolution full-atomic models of the mutant structures. The binding interface profiling approach should find useful application in human-disease mutation recognition and protein interface design studies.

  8. Orbital momentum profiles and binding energy spectra for the complete valence shell of molecular fluorine

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Y.; Brion, C.E. [British Columbia Univ., Vancouver, BC (Canada). Dept. of Chemistry; Brunger, M.J.; Zhao, K.; Grisogono, A.M.; Braidwood, S.; Weigold, E. [Flinders Univ. of South Australia, Adelaide, SA (Australia). Electronic Structure of Materials Centre; Chakravorty, S.J.; Davidson, E.R. [Indiana Univ., Bloomington, IN (United States). Dept. of Chemistry; Sgamellotti, A. [Univ di Perugia (Italy). Dipartimento di Chimica; von Niessen, W. [Technische Univ. Braunschweig (Germany). Inst fuer Physikalische


    The first electronic structural study of the complete valence shell binding energy spectrum of molecular fluorine, encompassing both the outer and inner valence regions, is reported. These binding energy spectra as well as the individual orbital momentum profiles have been measured using an energy dispersive multichannel electron momentum spectrometer at a total energy of 1500 eV, with an energy resolution of 1.5 eV and a momentum resolution of 0.1 a.u. The measured binding energy spectra in the energy range of 14-60 eV are compared with the results of ADC(4) many-body Green`s function and also direct-Configuration Interaction (CI) and MRSD-CI calculations. The experimental orbital electron momentum profiles are compared with SCF theoretical profiles calculated using the target Hartree-Fock approximation with a range of basis sets and with Density Functional Theory predictions in the target Kohn-Sham approximation with non-local potentials. The truncated (aug-cc-pv5z) Dunning basis sets were used for the Density Functional Theory calculations which also include some treatment of correlation via the exchange and correlation potentials. Comparisons are also made with the full ion-neutral overlap amplitude calculated with MRSD-CI wave functions. Large, saturated basis sets (199-GTO) were employed for both the high level SCF near Hartree-Fock limit and MRSD-CI calculations to investigate the effects of electron correlation and relaxation. 66 refs., 9 tabs., 9 figs.

  9. Design and synthesis of ATP-based nucleotide analogues and profiling of nucleotide-binding proteins

    NARCIS (Netherlands)

    Wolters, Justina. C.; Roelfes, Gerard; Poolman, Bert


    Two nucleotide-based probes were designed and synthesized in order to enrich samples for specific classes of proteins by affinity-based protein profiling. We focused on the profiling of adenine nucleotide-binding proteins. Two properties were considered in the design of the probes: the bait needs to

  10. Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: The Stockholm Atherosclerosis Gene Expression (STAGE) study

    KAUST Repository

    Hägg, Sara


    Environmental exposures filtered through the genetic make-up of each individual alter the transcriptional repertoire in organs central to metabolic homeostasis, thereby affecting arterial lipid accumulation, inflammation, and the development of coronary artery disease (CAD). The primary aim of the Stockholm Atherosclerosis Gene Expression (STAGE) study was to determine whether there are functionally associated genes (rather than individual genes) important for CAD development. To this end, two-way clustering was used on 278 transcriptional profiles of liver, skeletal muscle, and visceral fat (n =66/tissue) and atherosclerotic and unaffected arterial wall (n =40/tissue) isolated from CAD patients during coronary artery bypass surgery. The first step, across all mRNA signals (n =15,042/12,621 RefSeqs/genes) in each tissue, resulted in a total of 60 tissue clusters (n= 3958 genes). In the second step (performed within tissue clusters), one atherosclerotic lesion (n =49/48) and one visceral fat (n =59) cluster segregated the patients into two groups that differed in the extent of coronary stenosis (P=0.008 and P=0.00015). The associations of these clusters with coronary atherosclerosis were validated by analyzing carotid atherosclerosis expression profiles. Remarkably, in one cluster (n =55/54) relating to carotid stenosis (P =0.04), 27 genes in the two clusters relating to coronary stenosis were confirmed (n= 16/17, P<10 -27and-30). Genes in the transendothelial migration of leukocytes (TEML) pathway were overrepresented in all three clusters, referred to as the atherosclerosis module (A-module). In a second validation step, using three independent cohorts, the Amodule was found to be genetically enriched with CAD risk by 1.8-fold (P<0.004). The transcription co-factor LIM domain binding 2 (LDB2) was identified as a potential high-hierarchy regulator of the A-module, a notion supported by subnetwork analysis, by cellular and lesion expression of LDB2, and by the

  11. Multi-organ expression profiling uncovers a gene module in coronary artery disease involving transendothelial migration of leukocytes and LIM domain binding 2: the Stockholm Atherosclerosis Gene Expression (STAGE study.

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    Sara Hägg


    Full Text Available Environmental exposures filtered through the genetic make-up of each individual alter the transcriptional repertoire in organs central to metabolic homeostasis, thereby affecting arterial lipid accumulation, inflammation, and the development of coronary artery disease (CAD. The primary aim of the Stockholm Atherosclerosis Gene Expression (STAGE study was to determine whether there are functionally associated genes (rather than individual genes important for CAD development. To this end, two-way clustering was used on 278 transcriptional profiles of liver, skeletal muscle, and visceral fat (n = 66/tissue and atherosclerotic and unaffected arterial wall (n = 40/tissue isolated from CAD patients during coronary artery bypass surgery. The first step, across all mRNA signals (n = 15,042/12,621 RefSeqs/genes in each tissue, resulted in a total of 60 tissue clusters (n = 3958 genes. In the second step (performed within tissue clusters, one atherosclerotic lesion (n = 49/48 and one visceral fat (n = 59 cluster segregated the patients into two groups that differed in the extent of coronary stenosis (P = 0.008 and P = 0.00015. The associations of these clusters with coronary atherosclerosis were validated by analyzing carotid atherosclerosis expression profiles. Remarkably, in one cluster (n = 55/54 relating to carotid stenosis (P = 0.04, 27 genes in the two clusters relating to coronary stenosis were confirmed (n = 16/17, P<10(-27 and-30. Genes in the transendothelial migration of leukocytes (TEML pathway were overrepresented in all three clusters, referred to as the atherosclerosis module (A-module. In a second validation step, using three independent cohorts, the A-module was found to be genetically enriched with CAD risk by 1.8-fold (P<0.004. The transcription co-factor LIM domain binding 2 (LDB2 was identified as a potential high-hierarchy regulator of the A-module, a notion supported by subnetwork analysis, by cellular and lesion expression of LDB2

  12. Expression profile and ligand-binding characterization of odorant-binding protein 2 in Batocera horsfieldi (Hope) (United States)

    Odorant-binding proteins (OBPs) are important components in insect olfactory systems that transport semiochemicals through the aqueous sensillum lymph to surface of olfactory receptor neurons. In this study, we cloned the cDNA of odorant-binding protein 2 (BhorOBP2) in Batocera horsfieldi (Hope) and...

  13. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

    DEFF Research Database (Denmark)

    Portales-Casamar, Elodie; Thongjuea, Supat; Kwon, Andrew T


    JASPAR ( is the leading open-access database of matrix profiles describing the DNA-binding patterns of transcription factors (TFs) and other proteins interacting with DNA in a sequence-specific manner. Its fourth major release is the largest expansion of the core database...

  14. Theoretical Compton profile anisotropies in molecules and solids. VI. Compton profile anisotropies and chemical binding

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    Matcha, R.L.; Pettitt, B.M.


    An interesting empirical relationship between zero point Compton profile anisotropies (0) and nuclear charges is noted. It is shown that, for alkali halide molecules AB, to a good approximation (0) =N ln(Z/sub b//Z/sub a/).

  15. DNA binding studies of tartrazine food additive. (United States)

    Kashanian, Soheila; Zeidali, Sahar Heidary


    The interaction of native calf thymus DNA with tartrazine in 10 mM Tris-HCl aqueous solution at neutral pH 7.4 was investigated. Tartrazine is a nitrous derivative and may cause allergic reactions, with a potential of toxicological risk. Also, tartrazine induces oxidative stress and DNA damage. Its DNA binding properties were studied by UV-vis and circular dichroism spectra, competitive binding with Hoechst 33258, and viscosity measurements. Tartrazine molecules bind to DNA via groove mode as illustrated by hyperchromism in the UV absorption band of tartrazine, decrease in Hoechst-DNA solution fluorescence, unchanged viscosity of DNA, and conformational changes such as conversion from B-like to C-like in the circular dichroism spectra of DNA. The binding constants (K(b)) of DNA with tartrazine were calculated at different temperatures. Enthalpy and entropy changes were calculated to be +37 and +213 kJ mol(-1), respectively, according to the Van't Hoff equation, which indicated that the reaction is predominantly entropically driven. Also, tartrazine does not cleave plasmid DNA. Tartrazine interacts with calf thymus DNA via a groove interaction mode with an intrinsic binding constant of 3.75 × 10(4) M(-1).

  16. Distinct expression profiles and different functions of odorant binding proteins in Nilaparvata lugens Stal.

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    Peng He

    Full Text Available BACKGROUND: Odorant binding proteins (OBPs play important roles in insect olfaction. The brown planthopper (BPH, Nilaparvata lugens Stål (Delphacidae, Auchenorrhyncha, Hemiptera is one of the most important rice pests. Its monophagy (only feeding on rice, wing form (long and short wing variation, and annual long distance migration (seeking for rice plants of high nutrition imply that the olfaction would play a central role in BPH behavior. However, the olfaction related proteins have not been characterized in this insect. METHODOLOGY/PRINCIPAL FINDINGS: Full length cDNA of three OBPs were obtained and distinct expression profiles were revealed regarding to tissue, developmental stage, wing form and gender for the first time for the species. The results provide important clues in functional differentiation of these genes. Binding assays with 41 compounds demonstrated that NlugOBP3 had markedly higher binding ability and wider binding spectrum than the other two OBPs. Terpenes and Ketones displayed higher binding while Alkanes showed no binding to the three OBPs. Focused on NlugOBP3, RNA interference experiments showed that NlugOBP3 not only involved in nymph olfaction on rice seedlings, but also had non-olfactory functions, as it was closely related to nymph survival. CONCLUSIONS: NlugOBP3 plays important roles in both olfaction and survival of BPH. It may serve as a potential target for developing behavioral disruptant and/or lethal agent in N. lugens.

  17. Determination of solvation and binding site profile within electropolymerised poly(pyrrole-N-propionic acid)

    DEFF Research Database (Denmark)

    Glidle, A.; Swann, M.J.; Gadegaard, Nikolaj


    Specular neutron reflectivity measurements were performed on electropolymerised films of poly(pyrrole-N-propionic acid) to determine the degree to which the solvents are capable of supporting biological macromolecules can penetrate the polymer film. The permeation profile of Ni2+ ions which chela...... to the polymer's carboxylic acid moieties for subsequent modified protein binding was also determined. (C) 2000 Elsevier Science B.V. All rights reserved....

  18. DNA methylation profiling of primary neuroblastoma tumors using methyl-CpG-binding domain sequencing. (United States)

    Decock, Anneleen; Ongenaert, Maté; Van Criekinge, Wim; Speleman, Frank; Vandesompele, Jo


    Comprehensive genome-wide DNA methylation studies in neuroblastoma (NB), a childhood tumor that originates from precursor cells of the sympathetic nervous system, are scarce. Recently, we profiled the DNA methylome of 102 well-annotated primary NB tumors by methyl-CpG-binding domain (MBD) sequencing, in order to identify prognostic biomarker candidates. In this data descriptor, we give details on how this data set was generated and which bioinformatics analyses were applied during data processing. Through a series of technical validations, we illustrate that the data are of high quality and that the sequenced fragments represent methylated genomic regions. Furthermore, genes previously described to be methylated in NB are confirmed. As such, these MBD sequencing data are a valuable resource to further study the association of NB risk factors with the NB methylome, and offer the opportunity to integrate methylome data with other -omic data sets on the same tumor samples such as gene copy number and gene expression, also publically available.

  19. 'Perfectly' curvilinear profiles for binding as determined by ITC may in fact be multiphasic

    CERN Document Server

    Nissen, Per


    In a structural analysis of the proteasome activator PafE in Mycobacterium tuberculosis, the binding of the activator or shorter constructs to the 20S proteasome core particle (20S CP) or derivatives was measured by isothermal titration calorimetry (Bai et al. Proc Natl Acad Sci USA 113: E1983-E1992. 2016). The data were fitted by the authors by nonlinear least squares to give curvilinear profiles that, at least in part, appear to fit the data very well. However, reanalysis of the data shows that the profiles are much better (P < 0.001) represented as multiphasic, i.e. by a series of straight lines separated by discontinuous transitions, often in the form jumps, than by the conventional curvilinear profiles.

  20. DNA binding protein identification by combining pseudo amino acid composition and profile-based protein representation (United States)

    Liu, Bin; Wang, Shanyi; Wang, Xiaolong


    DNA-binding proteins play an important role in most cellular processes. Therefore, it is necessary to develop an efficient predictor for identifying DNA-binding proteins only based on the sequence information of proteins. The bottleneck for constructing a useful predictor is to find suitable features capturing the characteristics of DNA binding proteins. We applied PseAAC to DNA binding protein identification, and PseAAC was further improved by incorporating the evolutionary information by using profile-based protein representation. Finally, Combined with Support Vector Machines (SVMs), a predictor called iDNAPro-PseAAC was proposed. Experimental results on an updated benchmark dataset showed that iDNAPro-PseAAC outperformed some state-of-the-art approaches, and it can achieve stable performance on an independent dataset. By using an ensemble learning approach to incorporate more negative samples (non-DNA binding proteins) in the training process, the performance of iDNAPro-PseAAC was further improved. The web server of iDNAPro-PseAAC is available at

  1. Teachers' Entrepreneurial Profile: Case Study (United States)

    Stettiner, Caio Flavio; Formigoni, Alexandre; Filho, Mário Pereira Roque; de Camargo, Mauricio Ortiz; Moia, Roberto Padilha


    This article was prepared in order to investigate whether the teachers working in a Business Administration BA degree have an entrepreneurial profile, with the aim of finding whether such teachers are able to support the Pedagogical Proposal of the Institution to which they belong to in what concerns the requirement of the course and also the…

  2. JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

    DEFF Research Database (Denmark)

    Mathelier, Anthony; Fornes, Oriol; Arenillas, David J;


    JASPAR ( is an open-access database storing curated, non-redundant transcription factor (TF) binding profiles representing transcription factor binding preferences as position frequency matrices for multiple species in six taxonomic groups. For this 2016 release, we...

  3. Thermodynamics of ligand binding to acyl-coenzyme A binding protein studied by titration calorimetry

    DEFF Research Database (Denmark)

    Færgeman, Nils J.; Sigurskjold, B W; Kragelund, B B


    Ligand binding to recombinant bovine acyl-CoA binding protein (ACBP) was examined using isothermal microcalorimetry. Microcalorimetric measurements confirm that the binding affinity of acyl-CoA esters for ACBP is strongly dependent on the length of the acyl chain with a clear preference for acyl......-CoA esters containing more than eight carbon atoms and that the 3'-phosphate of the ribose accounts for almost half of the binding energy. Binding of acyl-CoA esters, with increasing chain length, to ACBP was clearly enthalpically driven with a slightly unfavorable entropic contribution. Accessible surface...... areas derived from the measured enthalpies were compared to those calculated from sets of three-dimensional solution structures and showed reasonable correlation, confirming the enthalphically driven binding. Binding of dodecanoyl-CoA to ACBP was studied at various temperatures and was characterized...

  4. Probabilistic Inference on Multiple Normalized Signal Profiles from Next Generation Sequencing: Transcription Factor Binding Sites

    KAUST Repository

    Wong, Ka-Chun


    With the prevalence of chromatin immunoprecipitation (ChIP) with sequencing (ChIP-Seq) technology, massive ChIP-Seq data has been accumulated. The ChIP-Seq technology measures the genome-wide occupancy of DNA-binding proteins in vivo. It is well-known that different DNA-binding protein occupancies may result in a gene being regulated in different conditions (e.g. different cell types). To fully understand a gene\\'s function, it is essential to develop probabilistic models on multiple ChIP-Seq profiles for deciphering the gene transcription causalities. In this work, we propose and describe two probabilistic models. Assuming the conditional independence of different DNA-binding proteins\\' occupancies, the first method (SignalRanker) is developed as an intuitive method for ChIP-Seq genome-wide signal profile inference. Unfortunately, such an assumption may not always hold in some gene regulation cases. Thus, we propose and describe another method (FullSignalRanker) which does not make the conditional independence assumption. The proposed methods are compared with other existing methods on ENCODE ChIP-Seq datasets, demonstrating its regression and classification ability. The results suggest that FullSignalRanker is the best-performing method for recovering the signal ranks on the promoter and enhancer regions. In addition, FullSignalRanker is also the best-performing method for peak sequence classification. We envision that SignalRanker and FullSignalRanker will become important in the era of next generation sequencing. FullSignalRanker program is available on the following website:∼wkc/FullSignalRanker/ © 2015 IEEE.

  5. 哺乳动物转录因子DNA结合谱%DNA-binding profiles of mammalian transcription factors

    Institute of Scientific and Technical Information of China (English)

    谷光明; 王进科


    The differential gene expression is the molecular base of development and responses to stimuli of organisms. Transcription factors (TFs) play important regulatory roles in this kind of differential gene expression. Therefore, to elucidate how these TFs regulate the complex differential gene expression, it is necessary to identify all target genes of them and construct the gene transcription regulatory network controlled by them. DNA binding is a key step for TFs regulating gene transcription. Therefore, in order to identify their target genes, it is indispensable to identify all possible DNA sequences that can be recognized and bound by TFs at the molecular level of their interactions with DNA, i.e., construction of the DNA-binding profiles of TFs. In recent years, along with the development of DNA microarray and high-throughput DNA sequencing techniques, there appeared some revolutionary new techniques for constructing DNA-binding profiles of TFs, which greatly promotes studies in this field. These techniques include ChlP-chip and ChlP-Seq for constructing in vivo DNA-binding profiles of TFs, dsDNA microarray, SELEX-SAGE, Bind-n-Seq, MMP-SELEX, EMSA-Seq, and HiTS-FLIP for constructing in vitro DNA-binding profiles of TFs. This paper reviewed these techniques.%基因差异表达是生物发育和对刺激作出应答的分子基础,转录因子在这种基因差异表达中发挥着重要的调控作用.因此,要弄清楚转录因子调控基因差异表达的机理,就必须鉴定出它们全部的靶基因并构建其操纵的转录调控网络.对基因组DNA的序列特异性结合是转录因子调控基因转录的关键环节.因此,要鉴定转录因子的靶基因,就必须从它们与DNA相互作用的分子水平,鉴定它们能够识别并结合的全部DNA序列,即转录因子DNA结合谱.近年来随着DNA微阵列芯片和高通量DNA测序技术的产生和快速发展,出现了建立转录因子体内及体外DNA结合谱的一系列革命性的

  6. The spinal precerebellar nuclei: calcium binding proteins and gene expression profile in the mouse. (United States)

    Fu, YuHong; Sengul, Gulgun; Paxinos, George; Watson, Charles


    We have localized the spinocerebellar neuron groups in C57BL/6J mice by injecting the retrograde neuronal tracer Fluoro-Gold into the cerebellum and examined the distribution of SMI 32 and the calcium-binding proteins (CBPs), calbindin-D-28K (Cb), calretinin (Cr), and parvalbumin (Pv) in the spinal precerebellar nuclei. The spinal precerebellar neuron clusters identified were the dorsal nucleus, central cervical nucleus, lumbar border precerebellar nucleus, lumbar precerebellar nucleus, and sacral precerebellar nucleus. Some dispersed neurons in the deep dorsal horn and spinal laminae 6-8 also projected to the cerebellum. Cb, Cr, Pv, and SMI 32 were present in all major spinal precerebellar nuclei and Pv was the most commonly observed CBP. A number of genes expressed in hindbrain precerebellar nuclei are also expressed in spinal precerebellar groups, but there were some differences in gene expression profile between the different spinal precerebellar nuclei, pointing to functional diversity amongst them.

  7. Biochemical profiling of histone binding selectivity of the yeast bromodomain family.

    Directory of Open Access Journals (Sweden)

    Qiang Zhang

    Full Text Available BACKGROUND: It has been shown that molecular interactions between site-specific chemical modifications such as acetylation and methylation on DNA-packing histones and conserved structural modules present in transcriptional proteins are closely associated with chromatin structural changes and gene activation. Unlike methyl-lysine that can interact with different protein modules including chromodomains, Tudor and MBT domains, as well as PHD fingers, acetyl-lysine (Kac is known thus far to be recognized only by bromodomains. While histone lysine acetylation plays a crucial role in regulation of chromatin-mediated gene transcription, a high degree of sequence variation of the acetyl-lysine binding site in the bromodomains has limited our understanding of histone binding selectivity of the bromodomain family. Here, we report a systematic family-wide analysis of 14 yeast bromodomains binding to 32 lysine-acetylated peptides derived from known major acetylation sites in four core histones that are conserved in eukaryotes. METHODOLOGY: The histone binding selectivity of purified recombinant yeast bromodomains was assessed by using the native core histones in an overlay assay, as well as N-terminally biotinylated lysine-acetylated histone peptides spotted on streptavidin-coated nitrocellulose membrane in a dot blot assay. NMR binding analysis further validated the interactions between histones and selected bromodomain. Structural models of all yeast bromodomains were built using comparative modeling to provide insights into the molecular basis of their histone binding selectivity. CONCLUSIONS: Our study reveals that while not all members of the bromodomain family are privileged to interact with acetylated-lysine, identifiable sequence features from those that bind histone emerge. These include an asparagine residue at the C-terminus of the third helix in the 4-helix bundle, negatively charged residues around the ZA loop, and preponderance of aromatic

  8. Neutralization and Binding Profile of Monoclonal Antibodies Generated Against Influenza A H1N1 Viruses. (United States)

    Shembekar, Nachiket; Mallajosyula, Vamsee V Aditya; Malik, Ankita; Saini, Ashok; Varadarajan, Raghavan; Gupta, Satish Kumar


    Monoclonal antibodies (MAbs) provide scope for the development of better therapeutics and diagnostic tools. Herein, we describe the binding and neutralization profile(s) for a panel of murine MAbs generated against influenza A H1N1 viruses elicited by immunization with pandemic H1 recombinant hemagglutinin (rHA)/whole virus or seasonal H1 rHA. Neutralizing MAbs, MA-2070 and MA-M, were obtained after pandemic A/California/07/2009 (H1N1) virus/rHA immunization(s). Both MAbs reacted specifically with rHA from A/California/07/2009 and A/England/195/2009 in ELISA. MA-2070 bound rHA of A/California/07/2009 with high affinity (KD = 51.36 ± 9.20 nM) and exhibited potent in vitro neutralization (IC50 = 2.50 μg/mL). MA-2070 bound within the stem domain of HA. MA-M exhibited both hemagglutination inhibition (HI, 1.50 μg/mL) and in vitro neutralization (IC50 = 0.66 μg/mL) activity against the pandemic A/California/07/2009 virus and showed higher binding affinity (KD = 9.80 ± 0.67 nM) than MA-2070. MAb, MA-H generated against the seasonal A/Solomon Islands/03/2006 (H1N1) rHA binds within the head domain and bound the seasonal H1N1 (A/Solomon Islands/03/2006 and A/New Caledonia/20/1990) rHAs with high affinity (KD; 0.72-8.23 nM). MA-H showed high HI (2.50 μg/mL) and in vitro neutralization (IC50 = 2.61 μg/mL) activity against the A/Solomon Islands/03/2006 virus. All 3 MAbs failed to react in ELISA with rHA from various strains of H2N2, H3N2, H5N1, H7N9, and influenza virus B, suggesting their specificity for either pandemic or seasonal H1N1 influenza virus. The MAbs reported here may be useful in developing diagnostic assays.

  9. Presence of a highly efficient binding to bacterial contamination can distort data from binding studies

    Energy Technology Data Exchange (ETDEWEB)

    Balcar, V.J. (Department of Anatomy, University of Sydney, N.S.W. (Australia))


    {sup 3}HGABA at low concentrations (5-10 nM) was bound by what appeared to be a GABA receptor binding site in bacterial contamination originating from a batch of distilled water. Under experimental conditions similar to those usually employed in {sup 3}HGABA binding studies, the apparent binding displayed a very high specific component and a high efficiency in terms of {sup 3}HGABA bound per mg of protein. The binding was blocked by muscimol but not by isoguvacine, SR95531 and nipecotic acid. These characteristics suggest that the presence of such spurious binding in the experiments using 3H-labeled ligands in brain homogenates may not always be very obvious and, moreover, it can result in subtle, but serious, distortions of data from such studies, which may not be immediately recognized.

  10. In silico mechanistic profiling to probe small molecule binding to sulfotransferases. (United States)

    Martiny, Virginie Y; Carbonell, Pablo; Lagorce, David; Villoutreix, Bruno O; Moroy, Gautier; Miteva, Maria A


    Drug metabolizing enzymes play a key role in the metabolism, elimination and detoxification of xenobiotics, drugs and endogenous molecules. While their principal role is to detoxify organisms by modifying compounds, such as pollutants or drugs, for a rapid excretion, in some cases they render their substrates more toxic thereby inducing severe side effects and adverse drug reactions, or their inhibition can lead to drug-drug interactions. We focus on sulfotransferases (SULTs), a family of phase II metabolizing enzymes, acting on a large number of drugs and hormones and showing important structural flexibility. Here we report a novel in silico structure-based approach to probe ligand binding to SULTs. We explored the flexibility of SULTs by molecular dynamics (MD) simulations in order to identify the most suitable multiple receptor conformations for ligand binding prediction. Then, we employed structure-based docking-scoring approach to predict ligand binding and finally we combined the predicted interaction energies by using a QSAR methodology. The results showed that our protocol successfully prioritizes potent binders for the studied here SULT1 isoforms, and give new insights on specific molecular mechanisms for diverse ligands' binding related to their binding sites plasticity. Our best QSAR models, introducing predicted protein-ligand interaction energy by using docking, showed accuracy of 67.28%, 78.00% and 75.46%, for the isoforms SULT1A1, SULT1A3 and SULT1E1, respectively. To the best of our knowledge our protocol is the first in silico structure-based approach consisting of a protein-ligand interaction analysis at atomic level that considers both ligand and enzyme flexibility, along with a QSAR approach, to identify small molecules that can interact with II phase dug metabolizing enzymes.

  11. Reversible albumin-binding GH possesses a potential once-weekly treatment profile in adult growth hormone deficiency

    DEFF Research Database (Denmark)

    Rasmussen, Michael Højby; Janukonyté, Jurgita; Klose, Marianne


    assessment was performed prior to initiating treatment at the next dose level of NNC0195-0092. Daily GH treatment was discontinued 14 days before the trial start. Blood samples were drawn for assessment of safety, pharmacokinetics, pharmacodynamics (IGF-1 and IGF-binding protein-3) profiles...... for the active control group. CONCLUSION: Four once-weekly doses of NNC0195-0092 (dose range 0.02-0.12 mg/kg) administered to adult patients with GH deficiency were well tolerated, and IGF-1 profiles were consistent with a once-weekly treatment profile. No clinically significant safety and tolerability signals...

  12. Profiling of β-lactam selectivity for penicillin-binding proteins in Streptococcus pneumoniae D39. (United States)

    Kocaoglu, Ozden; Tsui, Ho-Ching T; Winkler, Malcolm E; Carlson, Erin E


    Selective fluorescent β-lactam chemical probes enable the visualization of the transpeptidase activity of penicillin-binding proteins (PBPs) at different stages of bacterial cell division. To facilitate the development of new fluorescent probes for PBP imaging, we evaluated 20 commercially available β-lactams for selective PBP inhibition in an unencapsulated derivative of the D39 strain of Streptococcus pneumoniae. Live cells were treated with β-lactam antibiotics at different concentrations and subsequently incubated with Bocillin FL (Boc-FL; fluorescent penicillin) to saturate uninhibited PBPs. Fluorophore-labeled PBPs were visualized by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and fluorescence scanning. Among 20 compounds tested, carbapenems (doripenem and meropenem) were coselective for PBP1a, PBP2x, and PBP3, while six of the nine penicillin compounds were coselective for PBP2x and PBP3. In contrast, the seven cephalosporin compounds tested display variability in their PBP-binding profiles. Three cephalosporin compounds (cefoxitin, cephalexin, and cefsulodin) and the monobactam aztreonam exhibited selectivity for PBP3, while only cefuroxime (a cephalosporin) was selective for PBP2x. Treatment of S. pneumoniae cultures with a sublethal concentration of cefuroxime that inhibited 60% of PBP2x activity and less than 20% of the activity of other PBPs resulted in formation of elongated cells. In contrast, treatment of S. pneumoniae cultures with concentrations of aztreonam and cefoxitin that inhibited up to 70% of PBP3 activity and less than 30% of other PBPs resulted in no discernible morphological changes. Additionally, correlation of the MIC and IC50s for each PBP, with the exception of faropenem, amdinocillin (mecillinam), and 6-APA, suggests that pneumococcal growth inhibition is primarily due to the inhibition of PBP2x.

  13. A Comprehensive Evaluation of the Activity and Selectivity Profile of Ligands for RGD-binding Integrins (United States)

    Kapp, Tobias G.; Rechenmacher, Florian; Neubauer, Stefanie; Maltsev, Oleg V.; Cavalcanti-Adam, Elisabetta A.; Zarka, Revital; Reuning, Ute; Notni, Johannes; Wester, Hans-Jürgen; Mas-Moruno, Carlos; Spatz, Joachim; Geiger, Benjamin; Kessler, Horst


    Integrins, a diverse class of heterodimeric cell surface receptors, are key regulators of cell structure and behaviour, affecting cell morphology, proliferation, survival and differentiation. Consequently, mutations in specific integrins, or their deregulated expression, are associated with a variety of diseases. In the last decades, many integrin-specific ligands have been developed and used for modulation of integrin function in medical as well as biophysical studies. The IC50-values reported for these ligands strongly vary and are measured using different cell-based and cell-free systems. A systematic comparison of these values is of high importance for selecting the optimal ligands for given applications. In this study, we evaluate a wide range of ligands for their binding affinity towards the RGD-binding integrins αvβ3, αvβ5, αvβ6, αvβ8, α5β1, αIIbβ3, using homogenous ELISA-like solid phase binding assay. PMID:28074920

  14. Evaluation of intestinal phosphate binding to improve the safety profile of oral sodium phosphate bowel cleansing.

    Directory of Open Access Journals (Sweden)

    Stef Robijn

    Full Text Available Prior to colonoscopy, bowel cleansing is performed for which frequently oral sodium phosphate (OSP is used. OSP results in significant hyperphosphatemia and cases of acute kidney injury (AKI referred to as acute phosphate nephropathy (APN; characterized by nephrocalcinosis are reported after OSP use, which led to a US-FDA warning. To improve the safety profile of OSP, it was evaluated whether the side-effects of OSP could be prevented with intestinal phosphate binders. Hereto a Wistar rat model of APN was developed. OSP administration (2 times 1.2 g phosphate by gavage with a 12h time interval induced bowel cleansing (severe diarrhea and significant hyperphosphatemia (21.79 ± 5.07 mg/dl 6h after the second OSP dose versus 8.44 ± 0.97 mg/dl at baseline. Concomitantly, serum PTH levels increased fivefold and FGF-23 levels showed a threefold increase, while serum calcium levels significantly decreased from 11.29 ± 0.53 mg/dl at baseline to 8.68 ± 0.79 mg/dl after OSP. OSP administration induced weaker NaPi-2a staining along the apical proximal tubular membrane. APN was induced: serum creatinine increased (1.5 times baseline and nephrocalcinosis developed (increased renal calcium and phosphate content and calcium phosphate deposits on Von Kossa stained kidney sections. Intestinal phosphate binding (lanthanum carbonate or aluminum hydroxide was not able to attenuate the OSP induced side-effects. In conclusion, a clinically relevant rat model of APN was developed. Animals showed increased serum phosphate levels similar to those reported in humans and developed APN. No evidence was found for an improved safety profile of OSP by using intestinal phosphate binders.


    Directory of Open Access Journals (Sweden)



    Full Text Available BACKGROUND Lipid abnormalities are common in diabetes mellitus and play an important role in acceleration of atherosclerosis leading to increased cardiovascular diseases. Due to increasing burden of diabetes, it is becoming important to identify dyslipidaemia in high-risk state for diabetes especially prediabetes so that early intervention can reduce cardiovascular risk. AIM To study lipid profile in prediabetes individuals. METHODS This study was a cross-sectional case control study which included 107 prediabetes and 101 healthy controls. Lipid profile of prediabetes and controls were measured and statistically analysed. RESULT Total cholesterol, LDL, triglycerides, VLDL, TG/HDL ratio, and LDL/HDL ratio were significantly high whereas HDL was significantly low in prediabetes subjects as compared to controls. CONCLUSION This study showed significant lipid abnormalities in prediabetes subjects. Because of these they are at high risk of developing atherosclerotic cardiovascular diseases. Therefore, proper screening and appropriate therapy of these conditions becomes important.

  16. Studies on the binding of amylopectin sulfate with gastric mucin. (United States)

    Kim, Y S; Bella, A; Whitehead, J S; Isaacs, R; Remer, L


    Amylopectin sulfate, a sulfated polysaccharide that has an antipeptic property, was examined for its ability to bind gastric mucins. After chemically cross-linking the amylopectin sulfate into an insoluble gel, its binding with mucins isolated from antral and fundic mucosa of canine stomachs was studied with chromatography. A component present in both mucin fractions bound to the amylopectin sulfate gel below pH 4.5. This binding was reversible, and the complex dissociated above pH 5. Similar binding properties were found with soluble amylopectin sulfate. The component of the mucine which bound to amylopectin sulfate differed from the one which did not bind in its electrophoretic mobility and in its higher proportion of basic amino acids and a lower hexosamine, serine, and threonine content. This study suggests that amylopectin sulfate may bind to gastric mucins only under conditions of low pH.

  17. AFM studies of nonspecific binding of enzyme on DNA

    Institute of Scientific and Technical Information of China (English)

    张益; 谢恒月; 等


    Atomic force microscope(AFM) is used to study restriction endonuclease digestion of plasmid DNA,pWRr plasmid DNA is digested by Hind Ⅲ,and the specific and the nonspecific binding of the restriction endonuclease are imaged,and the biological function of the enzyme binding to nonspecific sites is discussed.In addition,it is found that nonspecific binding of Hind ǚ could not induce the DNA characteristic bending angle.

  18. Profiling of methyltransferases and other S-adenosyl-L-homocysteine-binding Proteins by Capture Compound Mass Spectrometry (CCMS). (United States)

    Lenz, Thomas; Poot, Peter; Gräbner, Olivia; Glinski, Mirko; Weinhold, Elmar; Dreger, Mathias; Köster, Hubert


    cofactor SAM is used by further enzymes transferring other parts of the cofactor or initiating radical reactions as well as because of its chemical instability (12), SAH is an ideal selectivity function for a CC to target MTases. Here, we report the utility of the SAH-CC and CCMS by profiling MTases and other SAH-binding proteins from the strain DH5α of Escherichia coli (E. coli), one of the best-characterized prokaryotes, which has served as the preferred model organism in countless biochemical, biological, and biotechnological studies. Photo-activated crosslinking enhances yield and sensitivity of the experiment, and the specificity can be readily tested for in competition experiments using an excess of free SAH.

  19. Toxicity and Binding Profile of Lectins from the Genus Canavalia on Brine Shrimp

    Directory of Open Access Journals (Sweden)

    Francisco Vassiliepe Sousa Arruda


    Full Text Available Lectins are sugar-binding proteins widely distributed in nature with many biological functions. Although many lectins have a remarkable biotechnological potential, some of them can be cytotoxic. Thus, the aim of this study was to assess the toxicity of five lectins, purified from seeds of different species of Canavalia genus. In order to determine the toxicity, assays with Artemia nauplii were performed. In addition, a fluorescence assay was carried out to evaluate the binding of lectins to Artemia nauplii. In order to verify the relationship between the structure of lectins and their cytotoxic effect, structural analysis was carried out to evaluate the volume of the carbohydrate recognition domain (CRD of each lectin. The results showed that all lectins exhibited different toxicities and bound to a similar area in the digestive tract of Artemia nauplii. Concerning the structural analysis, differences in spatial arrangement and volume of CRD may explain the variation of the toxicity exhibited by each lectin. To this date, this is the first study that establishes a link between toxicity and structure of CRD from Diocleinae lectins.

  20. Toxicity and binding profile of lectins from the Genus canavalia on brine shrimp. (United States)

    Arruda, Francisco Vassiliepe Sousa; Melo, Arthur Alves; Vasconcelos, Mayron Alves; Carneiro, Romulo Farias; Barroso-Neto, Ito Liberato; Silva, Suzete Roberta; Pereira-Junior, Francisco Nascimento; Nagano, Celso Shiniti; Nascimento, Kyria Santiago; Teixeira, Edson Holanda; Saker-Sampaio, Silvana; Sousa Cavada, Benildo; Sampaio, Alexandre Holanda


    Lectins are sugar-binding proteins widely distributed in nature with many biological functions. Although many lectins have a remarkable biotechnological potential, some of them can be cytotoxic. Thus, the aim of this study was to assess the toxicity of five lectins, purified from seeds of different species of Canavalia genus. In order to determine the toxicity, assays with Artemia nauplii were performed. In addition, a fluorescence assay was carried out to evaluate the binding of lectins to Artemia nauplii. In order to verify the relationship between the structure of lectins and their cytotoxic effect, structural analysis was carried out to evaluate the volume of the carbohydrate recognition domain (CRD) of each lectin. The results showed that all lectins exhibited different toxicities and bound to a similar area in the digestive tract of Artemia nauplii. Concerning the structural analysis, differences in spatial arrangement and volume of CRD may explain the variation of the toxicity exhibited by each lectin. To this date, this is the first study that establishes a link between toxicity and structure of CRD from Diocleinae lectins.

  1. Understanding lignin-degrading reactions of ligninolytic enzymes: binding affinity and interactional profile. (United States)

    Chen, Ming; Zeng, Guangming; Tan, Zhongyang; Jiang, Min; Li, Hui; Liu, Lifeng; Zhu, Yi; Yu, Zhen; Wei, Zhen; Liu, Yuanyuan; Xie, Gengxin


    Previous works have demonstrated that ligninolytic enzymes mediated effective degradation of lignin wastes. The degrading ability greatly relied on the interactions of ligninolytic enzymes with lignin. Ligninolytic enzymes mainly contain laccase (Lac), lignin peroxidase (LiP) and manganese peroxidase (MnP). In the present study, the binding modes of lignin to Lac, LiP and MnP were systematically determined, respectively. Robustness of these modes was further verified by molecular dynamics (MD) simulations. Residues GLU460, PRO346 and SER113 in Lac, residues ARG43, ALA180 and ASP183 in LiP and residues ARG42, HIS173 and ARG177 in MnP were most crucial in binding of lignin, respectively. Interactional analyses showed hydrophobic contacts were most abundant, playing an important role in the determination of substrate specificity. This information is an important contribution to the details of enzyme-catalyzed reactions in the process of lignin biodegradation, which can be used as references for designing enzyme mutants with a better lignin-degrading activity.

  2. Understanding lignin-degrading reactions of ligninolytic enzymes: binding affinity and interactional profile.

    Directory of Open Access Journals (Sweden)

    Ming Chen

    Full Text Available Previous works have demonstrated that ligninolytic enzymes mediated effective degradation of lignin wastes. The degrading ability greatly relied on the interactions of ligninolytic enzymes with lignin. Ligninolytic enzymes mainly contain laccase (Lac, lignin peroxidase (LiP and manganese peroxidase (MnP. In the present study, the binding modes of lignin to Lac, LiP and MnP were systematically determined, respectively. Robustness of these modes was further verified by molecular dynamics (MD simulations. Residues GLU460, PRO346 and SER113 in Lac, residues ARG43, ALA180 and ASP183 in LiP and residues ARG42, HIS173 and ARG177 in MnP were most crucial in binding of lignin, respectively. Interactional analyses showed hydrophobic contacts were most abundant, playing an important role in the determination of substrate specificity. This information is an important contribution to the details of enzyme-catalyzed reactions in the process of lignin biodegradation, which can be used as references for designing enzyme mutants with a better lignin-degrading activity.

  3. Steered molecular dynamics study of inhibitor binding in the internal binding site in dehaloperoxidase-hemoglobin. (United States)

    Zhang, Zhisen; Santos, Andrew P; Zhou, Qing; Liang, Lijun; Wang, Qi; Wu, Tao; Franzen, Stefan


    The binding free energy of 4-bromophenol (4-BP), an inhibitor that binds in the internal binding site in dehaloperoxidase-hemoglobin (DHP) was calculated using Molecular Dynamics (MD) methods combined with pulling or umbrella sampling. The effects of systematic changes in the pulling speed, pulling force constant and restraint force constant on the calculated potential of mean force (PMF) are presented in this study. The PMFs calculated using steered molecular dynamics (SMD) were validated by umbrella sampling (US) in the strongly restrained regime. A series of restraint force constants ranging from 1000 down to 5 kJ/(mol nm(2)) were used in SMD simulations. This range was validated using US, however noting that weaker restraints give rise to a broader sampling of configurations. This comparison was further tested by a pulling simulation conducted without any restraints, which was observed to have a value closest to the experimentally measured free energy for binding of 4-BP to DHP based on ultraviolet-visible (UV-vis) and resonance Raman spectroscopies. The protein-inhibitor system is well suited for fundamental study of free energy calculations because the DHP protein is relatively small and the inhibitor is quite rigid. Simulation configuration structures are compared to the X-ray crystallography structures of the binding site of 4-BP in the distal pocket above the heme.

  4. Plasma TNF binding capacity profiles during treatment with etanercept in rheumatoid arthritis

    DEFF Research Database (Denmark)

    Gudbrandsdottir, S; Bliddal, H; Petri, A;


    Etanercept (Enbrel) induces a rapid and sustained decline in disease activity in the majority of patients with refractory rheumatoid arthritis (RA). In these patients neutralization of TNFalpha and lymphotoxin (LT), previously termed TNFbeta is mediated by etanercept itself, as well as by naturally...... occurring soluble TNF receptors. However, the clinical response to treatment with etanercept may vary. Previously, pharmacokinetic studies have focused on the molar concentrations of etanercept, but very little is known about the kinetics of bioactive etanercept in patients treated with etanercept....... The purpose of this study was to evaluate kinetics, including inter- and intraindividual variations of the total TNF binding capacity, in RA patients who were on a standard treatment schedule with etanercept....

  5. Profiling of Concanavalin A-Binding Glycoproteins in Human Hepatic Stellate Cells Activated with Transforming Growth Factor-β1

    Directory of Open Access Journals (Sweden)

    Yannan Qin


    Full Text Available Glycoproteins play important roles in maintaining normal cell functions depending on their glycosylations. Our previous study indicated that the abundance of glycoproteins recognized by concanavalin A (ConA was increased in human hepatic stellate cells (HSCs following activation by transforming growth factor-β1 (TGF-β1; however, little is known about the ConA-binding glycoproteins (CBGs of HSCs. In this study, we employed a targeted glycoproteomics approach using lectin-magnetic particle conjugate-based liquid chromatography-tandem mass spectrometry to compare CBG profiles between LX-2 HSCs with and without activation by TGF-β1, with the aim of discovering novel CBGs and determining their possible roles in activated HSCs. A total of 54 and 77 proteins were identified in the quiescent and activated LX-2 cells, respectively. Of the proteins identified, 14.3% were glycoproteins and 73.3% were novel potential glycoproteins. Molecules involved in protein processing in the endoplasmic reticulum (e.g., calreticulin and calcium signaling (e.g., 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase β-2 [PLCB2] were specifically identified in activated LX-2 cells. Additionally, PLCB2 expression was upregulated in the cytoplasm of the activated LX-2 cells, as well as in the hepatocytes and sinusoidal cells of liver cirrhosis tissues. In conclusion, the results of this study may aid future investigations to find new molecular mechanisms involved in HSC activation and antifibrotic therapeutic targets.

  6. Further studies on the neuroleptic profile of manassantin A. (United States)

    Rao, K V; Puri, V N; el-Sawaf, H A


    In an earlier preliminary study, manassantin A, a neolignoid from Saururus cernuus was found to show neuroleptic type activity in mice when given by the i.p. route. It blocked the stereotypy and hyperactivity caused by amphetamine at doses comparable to those of haloperidol, but unlike the latter, did not show catalepsy or ptosis at atoxic doses. In the present study, a more detailed comparison of manassantin A with haloperidol and in some cases with chlorpromazine and reserpine using a variety of neuroleptic parameters and by various routes of administration is described. Results of the present study clearly show that the drug is readily absorbed from various routes of administration and shows many of the patterns of neuroleptic activity. Manassantin A was comparable to haloperidol in many of the tests but unlike the latter, did not produce antiadrenergic or anticholinergic effects. Manassantin A was found to bind weakly to calf caudate membranes (IC50 3500 nM) while haloperidol (IC50 5 nM) and chlorpromazine (IC50 50 nM) inhibited [3H]haloperidol binding. Manassantin A also did not affect the dopamine-induced adenylate cyclase activity in rat caudate nuclei (IC50 greater than 10,000 nM) while haloperidol (IC50 700 nM) and chlorpromazine (IC50 350 nM) inhibited the enzyme synthesis. These biochemical and behavioral tests suggest that manassantin A exhibits a selective neuroleptic profile and may be considered to behave as an atypical agent.

  7. Profiling of drug binding proteins by monolithic affinity chromatography in combination with liquid chromatography-tandem mass spectrometry. (United States)

    Zhang, Xuepei; Wang, Tongdan; Zhang, Hanzhi; Han, Bing; Wang, Lishun; Kang, Jingwu


    A new approach for proteome-wide profiling drug binding proteins by using monolithic capillary affinity chromatography in combination with HPLC-MS/MS is reported. Two immunosuppresive drugs, namely FK506 and cyclosporin A, were utilized as the experimental models for proof-of-concept. The monolithic capillary affinity columns were prepared through a single-step copolymerization of the drug derivatives with glycidyl methacrylate and ethylene dimethacrylate. The capillary chromatography with the affinity monolithic column facilitates the purification of the drug binding proteins from the cell lysate. By combining the capillary affinity column purification and the shot-gun proteomic analysis, totally 33 FK506- and 32 CsA-binding proteins including all the literature reported target proteins of these two drugs were identified. Among them, two proteins, namely voltage-dependent anion-selective channel protein 1 and serine/threonine-protein phosphatase PGAM5 were verified by using the recombinant proteins. The result supports that the monolithic capillary affinity chromatography is likely to become a valuable tool for profiling of binding proteins of small molecular drugs as well as bioactive compounds.

  8. In vitro DNA binding studies of Aspartame, an artificial sweetener. (United States)

    Kashanian, Soheila; Khodaei, Mohammad Mehdi; Kheirdoosh, Fahimeh


    A number of small molecules bind directly and selectively to DNA, by inhibiting replication, transcription or topoisomerase activity. In this work the interaction of native calf thymus DNA (CT-DNA) with Aspartame (APM), an artificial sweeteners was studied at physiological pH. DNA binding study of APM is useful to understand APM-DNA interaction mechanism and to provide guidance for the application and design of new and safer artificial sweeteners. The interaction was investigated using spectrophotometric, spectrofluorometric competition experiment and circular dichroism (CD). Hypochromism and red shift are shown in UV absorption band of APM. A strong fluorescence quenching reaction of DNA to APM was observed and the binding constants (Kf) of DNA with APM and corresponding number of binding sites (n) were calculated at different temperatures. Thermodynamic parameters, enthalpy changes (ΔH) and entropy changes (ΔS) were calculated to be +181kJmol(-1) and +681Jmol(-1)K(-1) according to Van't Hoff equation, which indicated that reaction is predominantly entropically driven. Moreover, spectrofluorometric competition experiment and circular dichroism (CD) results are indicative of non-intercalative DNA binding nature of APM. We suggest that APM interacts with calf thymus DNA via groove binding mode with an intrinsic binding constant of 5×10(+4)M(-1).

  9. Molecular modeling and competition binding study of Br-noscapine and colchicine provides insight into noscapinoid-tubulin binding site


    Naik, Pradeep K.; Santoshi, Seneha; Rai, Ankit; Joshi, Harish C.


    We have previously discovered the tubulin-binding anti-cancer properties of noscapine and its derivatives (noscapinoids). Here, we present three lines of evidence that noscapinoids bind at or near the well studied colchicine binding site of tubulin: 1) In silico molecular docking studies of Br-noscapine and noscapine yield highest docking score with the well characterised colchicine-binding site from the co-crystal structure; 2) the molecular mechanics-generalized Born/surface area (MM-GB/SA)...

  10. Binding Equilibrium Studies Between Co2+ and HAS or BSA

    Institute of Scientific and Technical Information of China (English)


    @@ Introduction Up to now,the interactions of Cu2+,Ni2+ and Zn2+ with serum albumin have been extensively studied[1-3].However,the interaction of serum with Co2+ has rarely been studied.Our study of Co2+-HSA by means of charge transfer spectra indicated that the metal center took an octahedron configuration and the binding site was probably located at the tripeptide segment of the N-terminal of albumin[4].Sadler et al.[5]has reported that the binding site of Co2+ in HSA is located at the tripeptide segment of HSA involving the four nitrogen atoms and a carboxyl oxygen atom of Aspl.In this paper the interaction of HSA and BSA with Co2+ at physiological pH is further studied by equilibrium dialysis.The number of binding sites and the cooperation among the binding sites are reported.According to the equilibrium dialysis results and the study of competition between Co2+ and Cu2+,Ca2+ or Zn2+ to be bound to HSA or BSA,it is suggested that there are three strong binding sites in both HSA and BSA.The possible locations of the strong binding sites of Co2+ in HSA and BSA have also been determined.

  11. Competing binding of metal ions with protein studied by microdialysis

    Institute of Scientific and Technical Information of China (English)

    GUO; Ming(郭明); KONG; Liang(孔亮); MAO; Xiqin(毛希琴); LI; Xin(历欣); ZOU; Hanfa(邹汉法)


    A method has been established to study the competing binding of metal ions with protein by a combined technique of microdialysis with high performance liquid chromatography (HPLC). Ni2+, Cd2+, Zn2+, Cu2+ and human serum albumin (HSA) were chosen as model metal ions and protein. The experimental results show that Ni2+ and Cu2+ share a common primary binding site on HSA, and Zn2+ and Cd2+ share a different common primary binding site from them, but there is a common multi-metal binding site for all of those four metal ions. This method show advantages of fast sampling, easily to be operated and especially to be useful when ideal spectroscopic probes are not available for the study of interaction between protein and metal ions.

  12. Alkaloid metabolite profiles by GC/MS and acetylcholinesterase inhibitory activities with binding-mode predictions of five Amaryllidaceae plants. (United States)

    Cortes, Natalie; Alvarez, Rafael; Osorio, Edison H; Alzate, Fernando; Berkov, Strahil; Osorio, Edison


    Acetylcholinesterase (AChE) enzymatic inhibition is an important target for the management of Alzheimer disease (AD) and AChE inhibitors are the mainstay drugs for its treatment. In order to discover new sources of potent AChE inhibitors, a combined strategy is presented based on AChE-inhibitory activity and chemical profiles by GC/MS, together with in silico studies. The combined strategy was applied on alkaloid extracts of five Amaryllidaceae species that grow in Colombia. Fifty-seven alkaloids were detected using GC/MS, and 21 of them were identified by comparing their mass-spectral fragmentation patterns with standard reference spectra in commercial and private library databases. The alkaloid extracts of Zephyranthes carinata exhibited a high level of inhibitory activity (IC50 = 5.97 ± 0.24 μg/mL). Molecular modeling, which was performed using the structures of some of the alkaloids present in this extract and the three-dimensional crystal structures of AChE derived from Torpedo californica, disclosed their binding configuration in the active site of this AChE. The results suggested that the alkaloids 3-epimacronine and lycoramine might be of interest for AChE inhibition. Although the galanthamine group is known for its potential utility in treating AD, the tazettine-type alkaloids should be evaluated to find more selective compounds of potential benefit for AD.

  13. L-Rhamnose-binding lectins (RBLs) in channel catfish, Ictalurus punctatus: Characterization and expression profiling in mucosal tissues. (United States)

    Thongda, Wilawan; Li, Chao; Luo, Yupeng; Beck, Benjamin H; Peatman, Eric


    Rhamnose-binding lectins (RBLs) have recently emerged as important molecules in the context of innate immunity in teleost fishes. Previously, using RNA-seq technology, we observed marked up-regulation of a RBL in channel catfish (Ictalurus punctatus) gill following a challenge with the bacterial pathogen Flavobacterium columnare. Furthermore, the magnitude of RBL up-regulation positively correlated with disease susceptibility. Moving forward from these findings, we wished to more broadly understand RBL function, diversity, and expression kinetics in channel catfish. Therefore, in the present study we characterized the RBL gene family present in select channel catfish tissues and profiled family member expression after challenge with two different Gram-negative bacterial pathogens. Here, six RBLs were identified from channel catfish and were designated IpRBL1a, IpRBL1b, IpRBL1c, IpRBL3a, IpRBL3b, and IpRBL5a. These RBLs contained carbohydrate recognition domains (CRD) ranging from one to three domains and each CRD contained the conserved motifs of -YGR- and -DPC-. Despite a level of structural conservation, the catfish RBLs showed low full-length identity with RBLs from outside the order Siluriformes. IpRBL expression after bacterial infection varied depending on both pathogen and tissue type, suggesting that IpRBLs may exert disparate functions or exhibit distinct tissue-selective roles in the host immune response to bacterial pathogens.

  14. Identification and expression profile analysis of odorant binding protein and chemosensory protein genes in Bemisia tabaci MED by head transcriptome (United States)

    Zhang, Wei; Zhang, Xiaoman; Qu, Cheng; Tetreau, Guillaume; Sun, Lujuan; Zhou, Jingjiang


    Odorant binding proteins (OBPs) and chemosensory proteins (CSPs) of arthropods are thought to be involved in chemical recognition which regulates pivotal behaviors including host choice, copulation and reproduction. In insects, OBPs and CSPs located mainly in the antenna but they have not been systematically characterized yet in Bemisia tabaci which is a cryptic species complex and could damage more than 600 plant species. In this study, among the 106,893 transcripts in the head assembly, 8 OBPs and 13 CSPs were identified in B. tabaci MED based on head transcriptomes of adults. Phylogenetic analyses were conducted to investigate the relationships of B. tabaci OBPs and CSPs with those from several other important Hemipteran species, and the motif-patterns between Hemiptera OBPs and CSPs were also compared by MEME. The expression profiles of the OBP and CSP genes in different tissues of B. tabaci MED adults were analyzed by real-time qPCR. Seven out of the 8 OBPs found in B. tabaci MED were highly expressed in the head. Conversely, only 4 CSPs were enriched in the head, while the other nine CSPs were specifically expressed in other tissues. Our findings pave the way for future research on chemical recognition of B. tabaci at the molecular level. PMID:28166541

  15. Binding of several benzodiazepines to bovine serum albumin: Fluorescence study (United States)

    Machicote, Roberta G.; Pacheco, María E.; Bruzzone, Liliana


    The interactions of lorazepam, oxazepam and bromazepam with bovine serum albumin (BSA) were studied by fluorescence spectrometry. The Stern-Volmer quenching constants and corresponding thermodynamic parameters Δ H, Δ G and Δ S were calculated. The binding constants and the number of binding sites were also investigated. The distances between the donor (BSA) and the acceptors (benzodiazepines) were obtained according to fluorescence resonance energy transfer and conformational changes of BSA were observed from synchronous fluorescence spectra.

  16. Molecular modelling and competition binding study of Br-noscapine and colchicine provide insight into noscapinoid-tubulin binding site. (United States)

    Naik, Pradeep K; Santoshi, Seneha; Rai, Ankit; Joshi, Harish C


    We have previously discovered the tubulin-binding anti-cancer properties of noscapine and its derivatives (noscapinoids). Here, we present three lines of evidence that noscapinoids bind at or near the well studied colchicine binding site of tubulin: (1) in silico molecular docking studies of Br-noscapine and noscapine yield highest docking score with the well characterised colchicine-binding site from the co-crystal structure; (2) the molecular mechanics-generalized Born/surface area (MM-GB/SA) scoring results ΔΔG(bind-cald) for both noscapine and Br-noscapine (3.915 and 3.025 kcal/mol) are in reasonably good agreement with our experimentally determined binding affinity (ΔΔG(bind-Expt) of 3.570 and 2.988 kcal/mol, derived from K(d) values); and (3) Br-noscapine competes with colchicine binding to tubulin. The simplest interpretation of these collective data is that Br-noscapine binds tubulin at a site overlapping with, or very close to colchicine-binding site of tubulin. Although we cannot rule out a formal possibility that Br-noscapine might bind to a site distinct and distant from the colchicine-binding site that might negatively influence the colchicine binding to tubulin.

  17. Context influences on TALE-DNA binding revealed by quantitative profiling. (United States)

    Rogers, Julia M; Barrera, Luis A; Reyon, Deepak; Sander, Jeffry D; Kellis, Manolis; Joung, J Keith; Bulyk, Martha L


    Transcription activator-like effector (TALE) proteins recognize DNA using a seemingly simple DNA-binding code, which makes them attractive for use in genome engineering technologies that require precise targeting. Although this code is used successfully to design TALEs to target specific sequences, off-target binding has been observed and is difficult to predict. Here we explore TALE-DNA interactions comprehensively by quantitatively assaying the DNA-binding specificities of 21 representative TALEs to ∼5,000-20,000 unique DNA sequences per protein using custom-designed protein-binding microarrays (PBMs). We find that protein context features exert significant influences on binding. Thus, the canonical recognition code does not fully capture the complexity of TALE-DNA binding. We used the PBM data to develop a computational model, Specificity Inference For TAL-Effector Design (SIFTED), to predict the DNA-binding specificity of any TALE. We provide SIFTED as a publicly available web tool that predicts potential genomic off-target sites for improved TALE design.

  18. Study of binding glycyrrhetic acid to AT1 receptor

    Institute of Scientific and Technical Information of China (English)

    ZHANG; Fengyun; (张凤云); YUE; Baozhen; (岳保珍); HE; Shipeng; (贺师鹏)


    To analyze the binding of glycyrrhetic acid (GA) to angiotensin II type I (AT1) receptor and to explore the mechanisms underlying the binding, primary cell culture of rat vascular smooth muscle cell (VSMC), radioactive ligand-receptor binding assay, lascer confocal scanning microscope (LCSM), Northern blot, 3H-TdR incorporation DNA assay were used in this study. The results suggest that specific binding of GA to AT1 receptor (IC50 value was 35.0 μmol/L) increases intracellular [Ca2+]i of VSMC, activates transcription factor c-myc and promotes the proliferation of VSMC, therefore GA was probably an agonist of AT1 receptor, providing a new target for GA's pharmaceutical effects.

  19. Controlling Multivalent Binding through Surface Chemistry: Model Study on Streptavidin (United States)


    Although multivalent binding to surfaces is an important tool in nanotechnology, quantitative information about the residual valency and orientation of surface-bound molecules is missing. To address these questions, we study streptavidin (SAv) binding to commonly used biotinylated surfaces such as supported lipid bilayers (SLBs) and self-assembled monolayers (SAMs). Stability and kinetics of SAv binding are characterized by quartz crystal microbalance with dissipation monitoring, while the residual valency of immobilized SAv is quantified using spectroscopic ellipsometry by monitoring binding of biotinylated probes. Purpose-designed SAv constructs having controlled valencies (mono-, di-, trivalent in terms of biotin-binding sites) are studied to rationalize the results obtained on regular (tetravalent) SAv. We find that divalent interaction of SAv with biotinylated surfaces is a strict requirement for stable immobilization, while monovalent attachment is reversible and, in the case of SLBs, leads to the extraction of biotinylated lipids from the bilayer. The surface density and lateral mobility of biotin, and the SAv surface coverage are all found to influence the average orientation and residual valency of SAv on a biotinylated surface. We demonstrate how the residual valency can be adjusted to one or two biotin binding sites per immobilized SAv by choosing appropriate surface chemistry. The obtained results provide means for the rational design of surface-confined supramolecular architectures involving specific biointeractions at tunable valency. This knowledge can be used for the development of well-defined bioactive coatings, biosensors and biomimetic model systems. PMID:28234007

  20. Electron profile stiffness and critical gradient studies (United States)

    DeBoo, J. C.; Petty, C. C.; White, A. E.; Burrell, K. H.; Doyle, E. J.; Hillesheim, J. C.; Holland, C.; McKee, G. R.; Rhodes, T. L.; Schmitz, L.; Smith, S. P.; Wang, G.; Zeng, L.


    Electron profile stiffness was studied in DIII-D L-mode discharges by systematically varying the heat flux in a narrow region with electron cyclotron heating and measuring the local change produced in ∇Te. Electron stiffness was found to slowly increase with toroidal rotation velocity. A critical inverse temperature gradient scale length 1/LC ˜ 3 m-1 was identified at ρ =0.6 and found to be independent of rotation. Both the heat pulse diffusivity and the power balance diffusivity, the latter determined by integrating the measured dependence of the heat pulse diffusivity on -∇Te, were fit reasonably well by a model containing a critical inverse temperature gradient scale length and varying linearly with 1/LT above the threshold.

  1. A study of microbial profile modification

    Energy Technology Data Exchange (ETDEWEB)

    Bae, J.H.; Lee, H.O.


    A microbial profile modification method using spores was investigated. A halotolerant, spore-forming, biopolymer-producing mesophile was used in Berea cores with a specifically formulated nutrient package to reduce the permeability of the rock. The degree of permeability reduction varied widely depending on the stimulation protocols used. The incubation period had a significant impact on permeability reduction, and there appeared to be an optimum incubation time for maximum permeability reduction. The reduction persisted for many PV of brine injection and appeared very stable. For our microbes used in this study, the permeability reduction was about the same when the NaCl concentration was above 2 wt% in the range from 0 wt% to 10 wt%.

  2. Cohort Profile Update: The GAZEL Cohort Study. (United States)

    Goldberg, Marcel; Leclerc, Annette; Zins, Marie


    The original GAZEL cohort was composed of 20 625 employees of the French national gas and electricity companies (15 011 male employees then aged 40 to 50 years and 5614 women between 35 and 50 years old) at its inception in 1989. A Cohort Profile article was published in 2007. By the end of 2013, participants were aged 60-75, and almost all of them retired during follow-up. Accordingly, the main focus of research in the past decade was devoted to the study of the persistent, long-term effects of occupational exposures after retirement; of the transition between professionally active life and retirement; and on determinants of early ageing. Accordingly, in addition to the health, behavioural and social data collected yearly since the beginning of the follow-up, new data were thus collected on cognitive complaints, cognitive and physical functioning, limitations in daily activities, time use and social relationships of retirees. This update presents the main findings of research within the GAZEL Cohort Study during the past 7 years. Any research group, in France or elsewhere, can submit a research proposal to work on the GAZEL cohort. To do this, interested researchers should contact one of the principal investigators of the GAZEL Cohort Study.

  3. Curcumin Binding to Beta Amyloid: A Computational Study. (United States)

    Rao, Praveen P N; Mohamed, Tarek; Teckwani, Karan; Tin, Gary


    Curcumin, a chemical constituent present in the spice turmeric, is known to prevent the aggregation of amyloid peptide implicated in the pathophysiology of Alzheimer's disease. While curcumin is known to bind directly to various amyloid aggregates, no systematic investigations have been carried out to understand its ability to bind to the amyloid aggregates including oligomers and fibrils. In this study, we constructed computational models of (i) Aβ hexapeptide (16) KLVFFA(21) octamer steric-zipper β-sheet assembly and (ii) full-length Aβ fibril β-sheet assembly. Curcumin binding in these models was evaluated by molecular docking and molecular dynamics (MD) simulation studies. In both the models, curcumin was oriented in a linear extended conformation parallel to fiber axis and exhibited better stability in the Aβ hexapeptide (16) KLVFFA(21) octamer steric-zipper model (Ebinding  = -10.05 kcal/mol) compared to full-length Aβ fibril model (Ebinding  = -3.47 kcal/mol). Analysis of MD trajectories of curcumin bound to full-length Aβ fibril shows good stability with minimum Cα-atom RMSD shifts. Interestingly, curcumin binding led to marked fluctuations in the (14) HQKLVFFA(21) region that constitute the fibril spine with RMSF values ranging from 1.4 to 3.6 Å. These results show that curcumin binding to Aβ shifts the equilibrium in the aggregation pathway by promoting the formation of non-toxic aggregates.

  4. Molecular Characterization and Expression Profiling of Odorant-Binding Proteins in Apolygus lucorum.

    Directory of Open Access Journals (Sweden)

    Hai-Bin Yuan

    Full Text Available Apolygus lucorum (Meyer-Dür (Hemiptera: Miridae is one of the most important agricultural pests, with broad host range and cryptic feeding habits in China. Chemosensory behavior plays an important role in many crucial stages in the life of A. lucorum, such as the detection of sex pheromone cues during mate pursuit and fragrant odorants during flowering host plant localization. Odorant-binding proteins (OBPs are involved in the initial biochemical recognition steps in semiochemical perception. In the present study, a transcriptomics-based approach was used to identify potential OBPs in A. lucorum. In total, 38 putative OBP genes were identified, corresponding to 26 'classic' OBPs and 12 'Plus-C' OBPs. Phylogenetic analysis revealed that A. lucorum OBP proteins are more closely related to the OBP proteins of other mirid bugs as the same family OBP clustering together. Quantitative real-time PCR analysis for the first reported 23 AlucOBPs revealed that the expression level of 11 AlucOBP genes were significantly higher in antennae of both sexes than in other tissues. Three of them were male antennae-biased and six were female antennae-biased, suggesting their putative roles in the detection of female sex pheromones and host plant volatiles. In addition, three, four, two and one AlucOBPs had the highest degree of enrichment in the stylet, head, leg, and in abdomen tissues, respectively. Two other OBPs were ubiquitously expressed in the main tissues, including antennae, stylets, heads, legs and wings. Most orthologs had similar expression patterns, strongly indicating that these genes have the same function in olfaction and gustation.

  5. Cloning and expression profiling of odorant-binding proteins in the tarnished plant bug, Lygus lineolaris (United States)

    In insects, the perception and discrimination of odorants requires the involvement of odorant binding proteins (OBPs). To gain a better molecular understanding of olfaction in the agronomic pest, Lygus lineolaris (tarnished plant bug), we used a transcriptomics-based approach to identify potential ...

  6. In vitro DNA binding profile of enantiomeric dinuclear Cu(II)/Ni(II) complexes derived from l-/d-histidine-terepthaldehyde reduced Schiff base as potential chemotherapeutic agents. (United States)

    Yousuf, Imtiyaz; Arjmand, Farukh


    New chiral reduced Schiff base ligands, L1 and L2 derived from l-/d-histidine and terepthaldehyde, and their Cu(II) and Ni(II) dinuclear complexes 1 &2 (a and b) were synthesized and thoroughly characterized by various spectroscopic techniques. Comparative binding profile of both l-/d-enantiomeric Cu(II) and Ni(II) complexes with ct-DNA was studied by employing optical and spectroscopic techniques to evaluate their enantiopreferential selectivity towards molecular target DNA and thereby explore their relative chemotherapeutic potential. Quantitative assessment of DNA binding propensity was ascertained by calculating Kb, K and Ksv values of 1 &2 (a and b) which demonstrated higher binding affinity of l-enantiomeric Cu(II) complex, 1a and followed the order as 1a>1b>2a>2b. Scanning electron microscopy (SEM) was used to analyze the morphological changes of the DNA condensate in presence of complexes 1 (a and b). The SEM micrographs condensates revealed morphological transitions and formation of different structural features implicating the condensation process between the complexes and biomolecule occurred to form compact massive structures. The gel electrophoretic assay of complex 1a was carried out with pBR322 plasmid DNA which revealed an efficient cleaving ability of the complex via oxidative pathway with the involvement of singlet oxygen ((1)O2) and the superoxide anion (O2(•-)) radicals as the ROS responsible the cleavage reactions. Molecular docking studies of 1 (a and b) with DNA revealed selective recognition of G-C residues of the narrow minor groove of the DNA duplex and complex 1a demonstrated binding affinity towards DNA ascertained from its higher binding energy values. Furthermore, the cytotoxic assessment of 1a was examined on a panel of cancer cell lines of different histological origin employing SRB assay which revealed remarkably good cytotoxic activity towards HL60, HeLa and MCF7 cancer cell lines.


    Institute of Scientific and Technical Information of China (English)

    Thirawan Nipithakul; Ladawan Watthanachote; Nanticha Kalapat


    A preliminary study of using maleic anhydride copolymer for protein binding has been carried out.The polymeric films were prepared by compression of the purified resin and annealing the film to induce efficient back formation of the anhydride groups.The properties of the film surface were analyzed by attenuated total reflection Fourier transforms infrared spectroscopy and water contact angle measurements.The protein content was determined by Bradford assay.To obtain optimum conditions,immersion time for protein binding was examined.Results revealed that proteins can be successfully immobilized onto the film surface via covalent linkage.The efficiency of the covalent binding of the extractable protein to maleic anhydride-polyethylene film was estimated at 69.87 μtg/cm2,although the film had low anhydride content (3%) on the surface.

  8. Single-Molecule Studies of the Linker Histone H1 Binding to DNA and the Nucleosome. (United States)

    Yue, Hongjun; Fang, He; Wei, Sijie; Hayes, Jeffrey J; Lee, Tae-Hee


    Linker histone H1 regulates chromatin structure and gene expression. Investigating the dynamics and stoichiometry of binding of H1 to DNA and the nucleosome is crucial to elucidating its functions. Because of the abundant positive charges and the strong self-affinity of H1, quantitative in vitro studies of its binding to DNA and the nucleosome have generated results that vary widely and, therefore, should be interpreted in a system specific manner. We sought to overcome this limitation by developing a specially passivated microscope slide surface to monitor binding of H1 to DNA and the nucleosome at a single-molecule level. According to our measurements, the stoichiometry of binding of H1 to DNA and the nucleosome is very heterogeneous with a wide distribution whose averages are in reasonable agreement with previously published values. Our study also revealed that H1 does not dissociate from DNA or the nucleosome on a time scale of tens of minutes. We found that histone chaperone Nap1 readily dissociates H1 from DNA and superstoichiometrically bound H1 from the nucleosome, supporting a hypothesis whereby histone chaperones contribute to the regulation of the H1 profile in chromatin.

  9. Characterization of the novel progestin gestodene by receptor binding studies and transactivation assays. (United States)

    Fuhrmann, U; Slater, E P; Fritzemeier, K H


    Gestodene is a novel progestin used in oral contraceptives with an increased separation of progestogenic versus androgenic activity and a distinct antimineralocorticoid activity. This specific pharmacological profile of gestodene is defined by its pattern of binding affinities to a variety of steroid hormone receptors. In the present study the affinity of gestodene to the progesterone receptor (PR), the androgen receptor (AR), the glucocorticoid receptor (GR), the mineralocorticoid receptor (MR) and the estrogen receptor (ER) was re-evaluated by steroid binding assays and compared to those obtained for 3-keto-desogestrel and progesterone. The two synthetic progestins displayed identical high affinity to rabbit PR and similar marked binding to rat AR and GR, while progesterone showed high affinity to PR but only low binding to AR and GR. Furthermore, 3-keto-desogestrel exhibited almost no binding to MR, whereas gestodene, similar to progesterone, showed marked affinity to this receptor. In addition to receptor binding studies, transactivation assays were carried out to investigate the effects of gestodene on AR-, GR- and MR-mediated induction of transcription. In contrast to progesterone, which showed antiandrogenic activity, gestodene and 3-keto-desogestrel both exhibited androgenic activity. Furthermore, all three progestins exhibited weak GR-mediated antagonistic activity. In contrast to progesterone, which showed almost no glucocorticoid activity, gestodene and 3-keto-desogestrel showed weak glucocorticoid action. In addition, gestodene inhibited the aldosterone-induced reporter gene transcription, similar to progesterone, whereas unlike progesterone, gestodene did not induce reporter gene transcription. 3-Keto-desogestrel showed neither antimineralocorticoid nor mineralocorticoid action.

  10. Sequence-selective binding of phenazinium dyes phenosafranin and safranin O to guanine-cytosine deoxyribopolynucleotides: spectroscopic and thermodynamic studies. (United States)

    Saha, Ishita; Hossain, Maidul; Suresh Kumar, Gopinatha


    The sequence selectivity of the DNA binding of the phenazinium dyes phenosafranin and safranin O have been investigated with four sequence-specific deoxyribopolynucleotides from spectroscopic and calorimetric studies. The alternating guanine-cytosine sequence selectivity of the dyes has been revealed from binding affinity values, circular dichroism, thermal melting, competition dialysis, and calorimetric results. The binding affinities of both the dyes to the polynucleotides were of the order of 10(5) M(-1), but the values were higher for the guanine-cytosine polynucleotides over adenine-thymine ones. Phenosafranin had a higher binding affinity compared to safranin O. Isothermal titration calorimetric studies revealed that the binding reactions were exothermic and favored by negative enthalpy and predominantly large positive entropy contributions in all cases except poly(dA)·poly(dT) where the profile was anomalous. Although charged, nonpolyelectrolytic contribution was revealed to be dominant to the free energy of binding. The negative heat capacity values obtained from the temperature dependence of enthalpy changes, which were higher for phenosafranin compared to safranin O, suggested significant hydrophobic contribution to the binding process. In aggregate, the data presents evidence for the alternating guanine-cytosine base pair selectivity of these phenazinium dyes and a stronger binding of phenosafranin over safranin O.

  11. Structural and binding studies of SAP-1 protein with heparin. (United States)

    Yadav, Vikash K; Mandal, Rahul S; Puniya, Bhanwar L; Kumar, Rahul; Dey, Sharmistha; Singh, Sarman; Yadav, Savita


    SAP-1 is a low molecular weight cysteine protease inhibitor (CPI) which belongs to type-2 cystatins family. SAP-1 protein purified from human seminal plasma (HuSP) has been shown to inhibit cysteine and serine proteases and exhibit interesting biological properties, including high temperature and pH stability. Heparin is a naturally occurring glycosaminoglycan (with varied chain length) which interacts with a number of proteins and regulates multiple steps in different biological processes. As an anticoagulant, heparin enhances inhibition of thrombin by the serpin antithrombin III. Therefore, we have employed surface plasmon resonance (SPR) to improve our understanding of the binding interaction between heparin and SAP-1 (protease inhibitor). SPR data suggest that SAP-1 binds to heparin with a significant affinity (KD = 158 nm). SPR solution competition studies using heparin oligosaccharides showed that the binding of SAP-1 to heparin is dependent on chain length. Large oligosaccharides show strong binding affinity for SAP-1. Further to get insight into the structural aspect of interactions between SAP-1 and heparin, we used modelled structure of the SAP-1 and docked with heparin and heparin-derived polysaccharides. The results suggest that a positively charged residue lysine plays important role in these interactions. Such information should improve our understanding of how heparin, present in the reproductive tract, regulates cystatins activity.

  12. Binding equilibrium study between Mn( Ⅱ ) and HSA or BSA

    Institute of Scientific and Technical Information of China (English)

    LIANG, Hong; TU, Chu-Qiao; ZHANG, Hong-Zhi; SHEN, Xing-Can; ZHOU, Yong-Qia; SHEN, Pan-Wen


    The binding of Mn( Ⅱ ) to human serum allbumin (HSA) or bovine serum albumin (BSA) has been studied by equilibrium dialysis at physiological pH (7.43). The Scatchard analysis indicates that there are 1.8 and 1.9 strong binding sites of Mn( Ⅱ ) in HSA and BSA, respectively. The successive stobility constants which are reported for the first time are obtained by non-linear least-squares methods fitting Bjerrum formula.For both Mn( Ⅱ )-HSA and Mn( Ⅱ )-BSA systems, the order of magnitude of K1 was found to be 104. The analyses of Hill plots and free energy coupling show that the positive cooperative effect was found in both Mn( Ⅱ )-HSA and Mn(Ⅱ)-BSA systems. The results of Mn ( Ⅱ ) competing with Cu ( Ⅱ )、Zn( Ⅱ )、Cd( Ⅱ ) or Ca( Ⅱ ) to bind to HSA or BSA further support the conjecture that there are two strong binding sites of Mn( Ⅱ ) in both HSA and BSA. One is most probably located at the tripeptide segment of N-terminal sequence of HSA and BSA molecules involving four groups composed of nitrogen atoms, and the fifth coordination atom is the carboxyl oxygen of Asp1. The coordinated atoms of the other are most probably almost all oxygen atoms.

  13. Binding of beta-scorpion toxin: a physicochemical study. (United States)

    Jover, E; Bablito, J; Couraud, F


    The binding to rat brain synaptosomes of a beta-scorpion toxin, i.e., toxin II of Centruroides suffusus suffusus (Css II), was studied as a function of pH, temperature, and concentration of some monovalent and divalent cations. At 10 degrees C and pH 6.0, the specific binding of 125I-labeled Css II corresponds to a single class of noninteracting high-affinity binding sites (KD = 0.18 nM) with a capacity (4.2 pmol/mg of protein) that is almost identical with that generally accepted for saxitoxin. The equilibrium dissociation constant of beta-scorpion toxin is pH independent, but the maximum binding capacity is reduced with increasing pH. Li+, guanidinium, Ca2+, Mg2+, and Mn2+ modified the apparent KD of the 125I-labeled Css II toxin. The equilibrium dissociation constant varies markedly with the temperature. The van't Hoff plot of the data is curvilinear, corresponding to a standard free-energy change associated with an entropy-driven process. The association rate constant also varies considerably with the temperature whereas the Arrhenius plot is linear between 1 and 30 degrees C. The energy of activation determined from these data is 17.6 kcal/mol. These results support the hypothesis that a cluster of nonpolar amino acid residues present on one face of the molecule is involved in the toxin-receptor interaction.

  14. The mu1, mu2, delta, kappa opioid receptor binding profiles of methadone stereoisomers and morphine

    DEFF Research Database (Denmark)

    Kristensen, K; Christensen, C B; Christrup, Lona Louring


    The binding affinities of racemic methadone and its optical isomers R-methadone and S-methadone were evaluated for the opioid receptors mu1, mu2, delta and kappa, in comparison with that of morphine. The analgesic R-methadone had a 10-fold higher affinity for mu1 receptors than S-methadone (IC50 3.......0 nM and 26.4 nM, respectively). At the mu2 receptor, the IC50 value of R-methadone was 6.9 nM and 88 nM for S-methadone, respectively. As expected, R-methadone had twice the affinity for mu1 and mu2 receptors than the racemate. All of the compounds tested had low affinity for the delta and kappa...

  15. Theoretical studies of binding of mannose-binding protein to monosaccharides (United States)

    Aida-Hyugaji, Sachiko; Takano, Keiko; Takada, Toshikazu; Hosoya, Haruo; Kojima, Naoya; Mizuochi, Tsuguo; Inoue, Yasushi


    Binding properties of mannose-binding protein (MBP) to monosaccharides are discussed based on ab initio molecular orbital calculations for cluster models constructed. The calculated binding energies indicate that MBP has an affinity for N-acetyl- D-glucosamine, D-mannose, L-fucose, and D-glucose rather than D-galactose and N-acetyl- D-galactosamine, which is consistent with the biochemical experimental results. Electrostatic potential surfaces at the binding site of four monosaccharides having binding properties matched well with that of MBP. A vacant frontier orbital was found to be localized around the binding site of MBP, suggesting that MBP-monosaccharide interaction may occur through electrostatic and orbital interactions.

  16. Adenosine A2A receptor binding profile of two antagonists, ST1535 and KW6002: consideration on the presence of atypical adenosine A2A binding sites

    Directory of Open Access Journals (Sweden)

    Teresa Riccioni


    Full Text Available Adenosine A2A receptors seem to exist in typical (more in striatum and atypical (more in hippocampus and cortex subtypes. In the present study, we investigated the affinity of two adenosine A2A receptor antagonists, ST1535 [2 butyl -9-methyl-8-(2H-1,2,3-triazol 2-yl-9H-purin-6-xylamine] and KW6002 [(E-1,3-diethyl-8-(3,4-dimethoxystyryl-7-methyl-3,7-dihydro-1H-purine-2,6,dione] to the “typical” and “atypical” A2A binding sites. Affinity was determined by radioligand competition experiments in membranes from rat striatum and hippocampus. Displacement of the adenosine analog [3H]CGS21680 [2-p-(2-carboxyethylphenethyl-amino-5’-N-ethylcarbox-amidoadenosine] was evaluated in the absence or in the presence of either CSC [8-(3-chlorostyryl-caffeine], an adenosine A2A antagonist that pharmacologically isolates atypical binding sites, or DPCPX (8-cyclopentyl-1,3-dipropylxanthine, an adenosine A1 receptor antagonist that pharmacologically isolates typical binding site. ZM241385 [84-(2-[7-amino-2-(2-furyl [1,2,4]-triazol[2,3-a][1,3,5]triazin-5-yl amino]ethyl phenol] and SCH58261 [(5-amino-7-(β-phenylethyl-2-(8-furylpyrazolo(4,3-e-1,2,4-triazolo(1,5-c pyrimidine], two other adenosine A2A receptor antagonists, which were reported to differently bind to atypical and typical A2A receptors, were used as reference compounds. ST1535, KW6002, ZM241385 and SCH58261 displaced [3H]CGS21680 with higher affinity in striatum than in hippocampus. In hippocampus, no typical adenosine A2A binding was detected, and ST1535 was the only compound that occupied atypical A2A adenosine receptors. Present data are explained in terms of heteromeric association among adenosine A2A, A2B and A1 receptors, rather than with the presence of atypical A2A receptor subtype.

  17. Profiling metabolic networks to study cancer metabolism. (United States)

    Hiller, Karsten; Metallo, Christian M


    Cancer is a disease of unregulated cell growth and survival, and tumors reprogram biochemical pathways to aid these processes. New capabilities in the computational and bioanalytical characterization of metabolism have now emerged, facilitating the identification of unique metabolic dependencies that arise in specific cancers. By understanding the metabolic phenotype of cancers as a function of their oncogenic profiles, metabolic engineering may be applied to design synthetically lethal therapies for some tumors. This process begins with accurate measurement of metabolic fluxes. Here we review advanced methods of quantifying pathway activity and highlight specific examples where these approaches have uncovered potential opportunities for therapeutic intervention.

  18. Transduction of Glycan-Lectin Binding using Near Infrared Fluorescent Single Walled Carbon Nanotubes for Glycan Profiling (United States)

    Reuel, Nigel; Ahn, Jin-Ho; Kim, Jong-Ho; Zhang, Jingqing; Boghossian, Ardemis; Mahal, Lara; Strano, Michael


    In this work, we demonstrate a sensor array employing recombinant lectins as glycan recognition sites tethered via Histidine tags to Ni2+ complexes that act as fluorescent quenchers for semi-conducting single walled carbon nanotubes embedded in a chitosan to measure binding kinetics of model glycans. Two higher-affined glycan-lectin pairs are explored: fucose (Fuc) to PA-IIL and N-acetylglucosamine (GlcNAc) to GafD. The dissociation constants (KD) for these pairs as free glycans (106 and 19 μM respectively) and streptavidin-tethered (142 and 50 μM respectively) were found. The absolute detection limit for the current platform was found to be 2 μg of glycosylated protein or 100 ng of free glycan to 20 μg of lectin. Glycan detection is demonstrated at the single nanotube level (GlcNAc to GafD). Over a population of 1000 nanotubes, 289 of the SWNT sensors had signals strong enough to yield kinetic information (KD of 250 ± 10 μM). We are also able to identify the locations of ``strong-transducers'' on the basis of dissociation constant (4 sensors with KD 5% quench response). The ability to pinpoint strong-binding, single sensors is promising to build a nanoarray of glycan-lectin transducers as a method to profile glycans without protein labeling or glycan liberation pretreatment steps.

  19. Calorimetric study of binding of some disaccharides with crown ethers

    Energy Technology Data Exchange (ETDEWEB)

    Davydova, Olga I.; Lebedeva, Nataliya Sh.; Parfenyuk, Elena V


    Isothermal titration calorimetry has been applied to the determination of the thermodynamic parameters of binding of {beta}-lactose, {alpha},{alpha}-trehalose and sucrose with 15-crown-5 and 18-crown-6 in water at 298.15 K. The formation of 1:1 molecular associates has been found for the systems studied except 18-crown-6 and {beta}-lactose. The associates are preferentially or completely entropy stabilized. The most stable associate is formed between {alpha},{alpha}-trehalose and 18-crown-6. The obtained values of thermodynamic parameters of binding are discussed from the point of view of solute-solvent interactions as well as conformational and structural peculiarities of the disaccharides (DS) and crown ethers (CE)

  20. Insights into Coupled Folding and Binding Mechanisms from Kinetic Studies. (United States)

    Shammas, Sarah L; Crabtree, Michael D; Dahal, Liza; Wicky, Basile I M; Clarke, Jane


    Intrinsically disordered proteins (IDPs) are characterized by a lack of persistent structure. Since their identification more than a decade ago, many questions regarding their functional relevance and interaction mechanisms remain unanswered. Although most experiments have taken equilibrium and structural perspectives, fewer studies have investigated the kinetics of their interactions. Here we review and highlight the type of information that can be gained from kinetic studies. In particular, we show how kinetic studies of coupled folding and binding reactions, an important class of signaling event, are needed to determine mechanisms.

  1. Cognitive processes in criminal profile construction: a preliminary study. (United States)

    Kocsis, Richard N; Middledorp, Jenny; Try, Andrew C


    This study undertook an empirically based examination of the cognitive processes associated with the accurate construction of a criminal psychological profile. This was accomplished by comparing the abilities of profilers and nonprofilers in two simulated profiling exercises that measured both profile accuracy and an individual's performance on various tests of memory and comprehension related to the case materials presented in each exercise. The results of these experiments suggest that an incremental relationship exists between comprehension of the case materials and accuracy of the profiles generated. In addition, the findings provide some tentative indications that the comprehension of case material in a narrative (i.e., written) format is an integral cognitive function to proficient profiling.

  2. Global transcript profiling of transgenic plants constitutively overexpressing the RNA-binding protein AtGRP7

    Directory of Open Access Journals (Sweden)

    Hennig Lars


    Full Text Available Abstract Background The clock-controlled RNA-binding protein AtGRP7 influences circadian oscillations of its own transcript at the post-transcriptional level. To identify additional targets that are regulated by AtGRP7, transcript profiles of transgenic plants constitutively overexpressing AtGRP7 (AtGRP7-ox and wild type plants were compared. Results Approximately 1.4% of the transcripts represented on the Affymetrix ATH1 microarray showed changes in steady-state abundance upon AtGRP7 overexpression. One third of the differentially expressed genes are controlled by the circadian clock, and they show a distinct bias of their phase: The up-regulated genes preferentially peak around dawn, roughly opposite to the AtGRP7 peak abundance whereas the down-regulated genes preferentially peak at the end of the day. Further, transcripts responsive to abiotic and biotic stimuli were enriched among AtGRP7 targets. Transcripts encoding the pathogenesis-related PR1 and PR2 proteins were elevated in AtGRP7-ox plants but not in plants overexpressing AtGRP7 with a point mutation in the RNA-binding domain, indicating that the regulation involves RNA binding activity of AtGRP7. Gene set enrichment analysis uncovered components involved in ribosome function and RNA metabolism among groups of genes upregulated in AtGRP7-ox plants, consistent with its role in post-transcriptional regulation. Conclusion Apart from regulating a suite of circadian transcripts in a time-of-day dependent manner AtGRP7, both directly and indirectly, affects other transcripts including transcripts responsive to abiotic and biotic stimuli. This suggests a regulatory role of AtGRP7 in the output of the endogenous clock and a complex network of transcripts responsive to external stimuli downstream of the AtGRP7 autoregulatory circuit.

  3. (/sup 3/H)nitrobenzylthioinosine binding as a probe for the study of adenosine uptake sites in brain

    Energy Technology Data Exchange (ETDEWEB)

    Marangos, P.J.; Patel, J.; Clark-Rosenberg, R.; Martino, A.M.


    The binding of the potent adenosine uptake inhibitor (/sup 3/H)nitrobenzylthioinosine ((/sup 3/H)NBI) to brain membrane fractions was investigated. Reversible, saturable, specific, high-affinity binding was demonstrated in both rat and human brain. The KD in both was 0.15 nM with Bmax values of 140-200 fmol/mg protein. Linear Scatchard plots were routinely obtained, indicating a homogeneous population of binding sites in brain. The highest density of binding sites was found in the caudate and hypothalamus in both species. The binding site was heat labile and trypsin sensitive. Binding was also decreased by incubation of the membranes in 0.05% Triton X-100 and by treatment with dithiothreitol and iodoacetamide. Of the numerous salt and metal ions tested, only copper and zinc had significant effects on (/sup 3/H)NBI binding. The inhibitory potencies of copper and zinc were IC50 . 160 microM and 6 mM, respectively. Subcellular distribution studies revealed a high percentage of the (/sup 3/H)NBI binding sites on synaptosomes, indicating that these sites were present in the synaptic region. A study of the tissue distribution of the (/sup 3/H)NBI sites revealed very high densities of binding in erythrocyte, lung, and testis, with much lower binding densities in brain, kidney, liver, muscle, and heart. The binding affinity in the former group was approximately 1.5 nM, whereas that in the latter group was 0.15 nM, suggesting two types of binding sites. The pharmacologic profile of (/sup 3/H)NBI binding was consistent with its function as the adenosine transport site, distinct from the adenosine receptor, since thiopurines were very potent inhibitors of binding whereas adenosine receptor ligands, such as cyclohexyladenosine and 2-chloroadenosine, were three to four orders of magnitude less potent. (/sup 3/H)NBI binding in brain should provide a useful probe for the study of adenosine transport in the brain.

  4. A rapid screening method using DNA binding dyes to determine whether hair follicles have sufficient DNA for successful profiling. (United States)

    Haines, Alicia M; Linacre, Adrian


    We report a simple screening method to assess the viability of successful DNA profiling from single hair follicles. A total of 48 hair samples (shed and plucked) were collected from male and female donors and the root tips (0.5cm) were stained using one of three DNA binding dyes (EvaGreen™, Diamond™ Nucleic Acid Dye and RedSafe™) at 20× concentration. The hairs were subsequently viewed under a Nikon Optiphot fluorescent microscope to count the approximate number of nuclei in one plane of view. The hairs were then processed using either (1) a DNA extraction kit (QIAmp(®) Mini Kit) and then amplified using the AmpFLSTR(®) NGM™ kit, which amplifies 15 short tandem repeat (STR) loci plus the gender marker amelogenin, or (2) by direct PCR amplification using the same DNA profiling kit. Diamond™ dye had the lowest background signal and plucked hairs treated with this dye produced full DNA profiles when amplified directly and was chosen to screen a further 150 mixed hair samples. These hairs were separated into one of five categories (1, >100 nuclei; 1.5, 50-99 nuclei; 2, 1-49 nuclei; 2.5, no nuclei but high fluorescent signal; 3, no nuclei and very low fluorescent signal) from which 60 of the hairs were chosen to undergo direct amplification using the NGM™ kit. It was found that there was a direct correlation to the category designation and the ability to obtain a DNA profile up-loadable to the Australian DNA Database. Approximately 91% of category 1 hairs resulted in either a full or high partial (12-29 alleles) profile by direct PCR whereas about 78% of category 3 hairs exhibited no amplification. The results show that this method can be used to predict successful STR amplification from single hair follicles. It is a rapid, sensitive, cheap, non-destructive and easy to perform methodology applicable for screening multiple hairs in order to aid forensic investigators in predicting hairs that will yield DNA results.

  5. Molecular cloning, expression profile, odorant affinity, and stability of two odorant-binding proteins in Macrocentrus cingulum Brischke (Hymenoptera: Braconidae). (United States)

    Ahmed, Tofael; Zhang, Tiantao; Wang, Zhenying; He, Kanglai; Bai, Shuxiong


    The polyembryonic endoparasitoid wasp Macrocentrus cingulum Brischke (Hymenoptera: Braconidae) is deployed successfully as a biocontrol agent for corn pest insects from the Lepidopteran genus Ostrinia in Europe and throughout Asia, including Japan, Korea, and China. The odorants are recognized, bound, and solubilized by odorant-binding protein (OBP) in the initial biochemical recognition steps in olfaction that transport them across the sensillum lymph to initiate behavioral response. In the present study, we examine the odorant-binding effects on thermal stability of McinOBP2, McinOBP3, and their mutant form that lacks the third disulfide bonds. Real-time PCR experiments indicate that these two are expressed mainly in adult antennae, with expression levels differing by sex. Odorant-binding affinities of aldehydes, terpenoids, and aliphatic alcohols were measured with circular dichroism spectroscopy based on changes in the thermal stability of the proteins upon their affinities to odorants. The obtained results reveal higher affinity of trans-caryophelle, farnesene, and cis-3-Hexen-1-ol exhibits to both wild and mutant McinOBP2 and McinOBP3. Although conformational flexibility of the mutants and shape of binding cavity make differences in odorant affinity between the wild-type and mutant, it suggested that lacking the third disulfide bond in mutant proteins may have chance to incorrect folded structures that reduced the affinity to these odorants. In addition, CD spectra clearly indicate proteins enriched with α-helical content.

  6. Two ScFv antibody libraries derived from identical VL-VH framework with different binding site designs display distinct binding profiles. (United States)

    Huovinen, Tuomas; Syrjänpää, Markku; Sanmark, Hanna; Brockmann, Eeva-Christine; Azhayev, Alex; Wang, Qi; Vehniäinen, Markus; Lamminmäki, Urpo


    In directed evolution experiments, a single randomization scheme of an antibody gene does not provide optimal diversity for recognition of all sizes of antigens. In this study, we have expanded the recognition potential of our universal library, termed ScFvP, with a second distinct diversification scheme. In the second library, termed ScFvM, diversity was designed closer to the center of the antigen binding site in the same antibody framework as earlier. Also, the CDR-H3 loop structures were redesigned to be shorter, 5-12 aa and mostly without the canonical salt bridge between Arg106H and Asp116H to increase the flexibility of the loop and to allow more space in the center of the paratope for binding smaller targets. Antibodies were selected from the two libraries against various antigens separately and as a mixture. The origin and characteristics of the retrieved antibodies indicate that complementary diversity results in complementary functionality widening the spectrum of targets amenable for selection.

  7. Genome-wide profiling of peroxisome proliferator-activated receptor γ in primary epididymal, inguinal, and brown adipocytes reveals depot-selective binding correlated with gene expression

    DEFF Research Database (Denmark)

    Siersbæk, Majken; Loft, Anne; Jørgensen, Mads Malik Aagaard;


    epididymal, inguinal, and brown adipose tissues. While these PPARγ binding profiles are overall similar, there are clear depot-selective binding sites. Most PPARγ binding sites previously mapped in 3T3-L1 adipocytes can also be detected in primary adipocytes, but there are a large number of PPARγ binding...... sites that are specific to the primary cells, and these tend to be located in closed chromatin regions in 3T3-L1 adipocytes. The depot-selective binding of PPARγ is associated with highly depot-specific gene expression. This indicates that PPARγ plays a role in the induction of genes characteristic...... of different adipocyte lineages and that preadipocytes from different depots are differentially preprogrammed to permit PPARγ lineage-specific recruitment even when differentiated in vitro....


    Institute of Scientific and Technical Information of China (English)

    CHUJin-Shong; WANGYi-Fei


    The specific estrogen binding site for 17β-estradiol has been investigated on human spermatozoa by electron microscopec autoradiography. The results show that the binding sites were distributed over the surface of human spermatozoa: acrosomal cap, equatorial

  9. Profile control studies for JET optimised shear regime

    Energy Technology Data Exchange (ETDEWEB)

    Litaudon, X.; Becoulet, A.; Eriksson, L.G.; Fuchs, V.; Huysmans, G.; How, J.; Moreau, D.; Rochard, F.; Tresset, G.; Zwingmann, W. [Association Euratom-CEA, CEA/Cadarache, Dept. de Recherches sur la Fusion Controlee, DRFC, 13 - Saint-Paul-lez-Durance (France); Bayetti, P.; Joffrin, E.; Maget, P.; Mayorat, M.L.; Mazon, D.; Sarazin, Y. [JET Abingdon, Oxfordshire (United Kingdom); Voitsekhovitch, I. [Universite de Provence, LPIIM, Aix-Marseille 1, 13 (France)


    This report summarises the profile control studies, i.e. preparation and analysis of JET Optimised Shear plasmas, carried out during the year 1999 within the framework of the Task-Agreement (RF/CEA/02) between JET and the Association Euratom-CEA/Cadarache. We report on our participation in the preparation of the JET Optimised Shear experiments together with their comprehensive analyses and the modelling. Emphasis is put on the various aspects of pressure profile control (core and edge pressure) together with detailed studies of current profile control by non-inductive means, in the prospects of achieving steady, high performance, Optimised Shear plasmas. (authors)

  10. Characterization of Receptor Binding Profiles of Influenza A Viruses Using An Ellipsometry-Based Label-Free Glycan Microarray Assay Platform

    Directory of Open Access Journals (Sweden)

    Yiyan Fei


    Full Text Available A key step leading to influenza viral infection is the highly specific binding of a viral spike protein, hemagglutinin (HA, with an extracellular glycan receptor of a host cell. Detailed and timely characterization of virus-receptor binding profiles may be used to evaluate and track the pandemic potential of an influenza virus strain. We demonstrate a label-free glycan microarray assay platform for acquiring influenza virus binding profiles against a wide variety of glycan receptors. By immobilizing biotinylated receptors on a streptavidin-functionalized solid surface, we measured binding curves of five influenza A virus strains with 24 glycans of diverse structures and used the apparent equilibrium dissociation constants (avidity constants, 10–100 pM as characterizing parameters of viral receptor profiles. Furthermore by measuring binding kinetic constants of solution-phase glycans to immobilized viruses, we confirmed that the glycan-HA affinity constant is in the range of 10 mM and the reaction is enthalpy-driven.

  11. Liquid drops on a surface: Using density functional theory to calculate the binding potential and drop profiles and comparing with results from mesoscopic modelling (United States)

    Hughes, Adam P.; Thiele, Uwe; Archer, Andrew J.


    The contribution to the free energy for a film of liquid of thickness h on a solid surface due to the interactions between the solid-liquid and liquid-gas interfaces is given by the binding potential, g(h). The precise form of g(h) determines whether or not the liquid wets the surface. Note that differentiating g(h) gives the Derjaguin or disjoining pressure. We develop a microscopic density functional theory (DFT) based method for calculating g(h), allowing us to relate the form of g(h) to the nature of the molecular interactions in the system. We present results based on using a simple lattice gas model, to demonstrate the procedure. In order to describe the static and dynamic behaviour of non-uniform liquid films and drops on surfaces, a mesoscopic free energy based on g(h) is often used. We calculate such equilibrium film height profiles and also directly calculate using DFT the corresponding density profiles for liquid drops on surfaces. Comparing quantities such as the contact angle and also the shape of the drops, we find good agreement between the two methods. We also study in detail the effect on g(h) of truncating the range of the dispersion forces, both those between the fluid molecules and those between the fluid and wall. We find that truncating can have a significant effect on g(h) and the associated wetting behaviour of the fluid.

  12. Synthesis, Characterization, and DNA Binding Studies of Nanoplumbagin

    Directory of Open Access Journals (Sweden)

    Sheik Dawood Shahida Parveen


    Full Text Available The traditional anticancer medicine plumbagin (PLN was prepared as nanostructured material (nanoplumbagin, NPn1 from its commercial counterparts, simultaneously coencapsulating with cetyltrimethylammonium bromide or cyclodextrin as stabilizers using ultrasonication technique. Surface morphology of NPn analysed from atomic force microscopy (AFM indicates that NPn has tunable size between 75 nm and 100 nm with narrow particle size distribution. Its binding efficiency with herring sperm DNA was studied using spectral and electrochemical techniques and its efficiency was found to be more compared to the commercial microcrystalline plumbagin (PLN. DNA cleavage was also studied by gel electrophoresis. The observed results indicate that NPn1 has better solubility in aqueous medium and hence showed better bioavailability compared to its commercial counterparts.


    Directory of Open Access Journals (Sweden)

    Gulshan Lal Khanna


    Full Text Available The present study was conducted to study the morphological, physiological and biochemical characteristics of Indian National boxers as well as to assess the cardiovascular adaptation to graded exercise and actual boxing round. Two different studies were conducted. In the first study [N = 60, (junior boxers below-19 yrs, n = 30, (senior boxers-20-25 yrs, n = 30] different morphological, physiological and biochemical parameters were measured. In the second study (N = 21, Light Weight category- <54 kg, n = 7; Medium weight category <64 kg, n = 7 and Medium heavy weight category <75 kg, n = 7 cardiovascular responses were studied during graded exercise protocol and actual boxing bouts. Results showed a significantly higher (p < 0.05 stature, body mass, LBM, body fat and strength of back and grip in senior boxers compared to juniors. Moreover, the senior boxers possessed mesomorphic body conformation where as the juniors' possessed ectomorphic body conformation. Significantly lower (p < 0.05 aerobic capacity and anaerobic power were noted in junior boxers compared to seniors. Further, significantly higher (p < 0.05 maximal heart rates and recovery heart rates were observed in the seniors as compared to the juniors. Significantly higher maximum heart rates were noted during actual boxing compared to graded exercise. Blood lactate concentration was found to increase with the increase of workload during both graded exercise and actual boxing round. The senior boxers showed a significantly elevated (p < 0.05 levels of hemoblobin, blood urea, uric acid and peak lactate as compared to junior boxers. In the senior boxers significantly lower levels of total cholesterol, triglyceride and LDLC were observed as compared to junior boxers. No significant change has been noted in HDLC between the groups. The age and level of training in boxing has significant effect on Aerobic, anaerobic component. The study of physiological responses during graded exercise

  14. Study of CNC Grinding Machining Method About Isometric Polygon Profile

    Institute of Scientific and Technical Information of China (English)


    The formed principle and CNC grinding machining method of isometric polygonal profile are studied deeply and systematically. Equation about section curve of isometric polygon profile is set up by means of geometric principle. With the use of differential geometry theory, the curve is proved to be with geometric feature of convex curve. It is referred to as Isometric Polygonal Curve (IPC), because that is a kind of convex curve on which the distance between any parallel tangent lines is equal. Isometric Poly...

  15. Effects of the binding of a dextran derivative on fibroblast growth factor 2: secondary structure and receptor-binding studies. (United States)

    Bittoun, P; Bagheri-Yarmand, R; Chaubet, F; Crépin, M; Jozefonvicz, J; Fermandjian, S


    CMDB (carboxymethyldextran-benzylamide) are dextrans statistically substituted with carboxymethyl and benzylamide groups which can mimick some of the biological properties of heparin. It has previously been shown that CMDB inhibit autocrine growth of breast tumor cells (Bagheri-Yarmand et al., Biochem. Biophys. Res. Commun. 239: 424-428, 1997) and selectively displace fibroblast growth factor 2 (FGF-2) from its receptor. Here, we used circular dichroism and fluorescence anisotropy measurements to show that the conformation of FGF-2 was significantly altered upon its binding to CMDB and to short CMDB fragments prepared within this study. CMDB and fragments formed a stable 1:1 complex with FGF-2, with affinities being estimated as 20+/-10 nM from fluorescence anisotropy analysis. No such a complex was formed with insulin-like growth factor (IGF-1) or epidermal growth factor (EGF). CMDB competed with the FGF-2 receptor for binding to FGF-2 but did not disturb the binding of IGF-1 and EGF to their receptors. Thus, our results highlight the selectivity of CMDB and their fragments towards FGF-2. Heparin, however, competes with CMDB and their fragments for binding to FGF-2. The carboxymethyl and benzylamide groups of these molecules likely interact directly with a heparin-binding region of FGF-2. The resulting change in conformation disturbs the binding of FGF-2 to its receptor and consecutively its mitogenic activity.

  16. Toxicological profiles of selected synthetic cannabinoids showing high binding affinities to the cannabinoid receptor subtype CB₁. (United States)

    Koller, Verena J; Zlabinger, Gerhard J; Auwärter, Volker; Fuchs, Sabine; Knasmueller, Siegfried


    Products containing synthetic cannabinoids are consumed as a surrogate for marihuana due to their non-detectability with commonly used drug tests and their strong cannabimimetic effects. Because data concerning their toxicological properties are scarce, the cytotoxic, genotoxic, immunomodulatory, and hormonal activities of four naphthoylindole compounds (JWH-018, JWH-073, JWH-122 and JWH-210) and of one benzoylindole (AM-694) were studied in human cell lines and primary cells; tetrahydrocannabinol was included as the classical non-endogenous cannabinoid receptor ligand. All compounds induced damage to the cell membranes of buccal (TR146) and breast (MCF-7) derived cells at concentrations of ≥75-100 μM. No cytotoxic responses were seen in other assays which reflect mitochondrial damage, protein synthesis, and lysosomal activities. JWH-073 and JWH-122 induced DNA migration in buccal and liver cells (HepG2) in single cell gel electrophoresis assays, while JWH-210 was only in the latter cell line active. No estrogenic activities were detected in bone marrow cells (U2-OS), but all compounds caused anti-estrogenic effects at levels between 2.1 and 23.0 μM. Furthermore, no impact on cytokine release (i.e., on IL-10, IL-6, IL-12/23p40 and TNFα levels) was seen in LPS-stimulated human PBMCs, except with JWH-210 and JWH-122 which caused a decrease of TNFα and IL-12/23p40. All toxic effects were observed with concentrations higher than those expected in body fluids of users. Since genotoxic effects are in general linear over a wide concentration range and the exposure levels may be higher in epithelial cells than [corrected] in serum, further experimental work is required to find out if DNA damage takes place in drug users.

  17. Lunar seismic profiling experiment natural activity study (United States)

    Duennebier, F. K.


    The Lunar Seismic Experiment Natural Activity Study has provided a unique opportunity to study the high frequency (4-20 Hz) portion to the seismic spectrum on the moon. The data obtained from the LSPE was studied to evaluate the origin and importance of the process that generates thermal moonquakes and the characteristics of the seismic scattering zone at the lunar surface. The detection of thermal moonquakes by the LSPE array made it possible to locate the sources of many events and determine that they are definitely not generated by astronaut activities but are the result of a natural process on the moon. The propagation of seismic waves in the near-surface layers was studied in a qualitative manner. In the absence of an adequate theoretical model for the propagation of seismic waves in the moon, it is not possible to assign a depth for the scattering layer. The LSPE data does define several parameters which must be satisfied by any model developed in the future.

  18. Cohort profile: Shahroud Eye Cohort Study. (United States)

    Fotouhi, Akbar; Hashemi, Hassan; Shariati, Mohammad; Emamian, Mohammad Hassan; Yazdani, Kamran; Jafarzadehpur, Ebrahim; Koohian, Hassan; Khademi, Mohammad Reza; Hodjatjalali, Kamran; Kheirkhah, Ahmad; Chaman, Reza; Malihi, Sarvenaz; Mirzaii, Mehdi; Khabazkhoob, Mehdi


    The Shahroud Eye Cohort Study was set up to determine the prevalence and incidence of visual impairment and major eye conditions in the 40-64-year-old population of Shahroud as a Middle Eastern population. The first phase of the study was conducted in 2009-10. Using random cluster sampling, 6311 Shahroud inhabitants were invited for ophthalmologic examinations; of these, 5190 participants completed phase 1 (participation rate of 82.2%). All participants were interviewed to collect data on participants' demographics, occupation status, socioeconomic status, history of smoking, and medical and ophthalmic history, as well as history of medication, and the quality and duration of their insurance. DNA and plasma samples, as well as four dots of whole blood were collected from participants. Extensive optometric and ophthalmologic examinations were performed for each participant, including lensometry of current glasses, testing near and far visual acuity; determining objective and subjective refraction; eye motility; cycloplegic refraction; colour vision test; slit-lamp biomicroscopy and intraocular pressure measurement; direct and indirect fundoscopy; perimetry test; ocular biometry; corneal topography; lens and fundus photography; and the Schirmer's (1008 participants) and tear breakup time tests (1013 participants). The study data are available for collaborative research at Noor Ophthalmology Research Center, Tehran, Iran.

  19. Influence of the fluid structure on the binding potential: Comparing liquid drop profiles from density functional theory with results from mesoscopic theory (United States)

    Hughes, Adam P.; Thiele, Uwe; Archer, Andrew J.


    For a film of liquid on a solid surface, the binding potential g(h) gives the free energy as a function of the film thickness h and also the closely related (structural) disjoining pressure Π =-∂g /∂h . The wetting behaviour of the liquid is encoded in the binding potential and the equilibrium film thickness corresponds to the value at the minimum of g(h). Here, the method we developed in the work of Hughes et al. [J. Chem. Phys. 142, 074702 (2015)], and applied with a simple discrete lattice-gas model, is used with continuum density functional theory (DFT) to calculate the binding potential for a Lennard-Jones fluid and other simple liquids. The DFT used is based on fundamental measure theory and so incorporates the influence of the layered packing of molecules at the surface and the corresponding oscillatory density profile. The binding potential is frequently input in mesoscale models from which liquid drop shapes and even dynamics can be calculated. Here we show that the equilibrium droplet profiles calculated using the mesoscale theory are in good agreement with the profiles calculated directly from the microscopic DFT. For liquids composed of particles where the range of the attraction is much less than the diameter of the particles, we find that at low temperatures g(h) decays in an oscillatory fashion with increasing h, leading to highly structured terraced liquid droplets.

  20. Protein binding prodrugs : Synthesis and protein binding studies of didanonsine derivates


    Olberg, Dag Erlend


    A novel series of 5 -O-ester prodrugs of the anti-HIV drug 2 ,3 -dideoxyinosine (ddI,didanosine) were synthesized for the purpose of increasing protein binding. Hope was that these derivates would exhibit superior pharmacodynamic and pharmacokinetic properties against HIV-infection than the parent drug, didanosine. Ten compounds were synthesized, five fatty acid derivates and five dicarboxylic acid monoester derivates. The fatty acid- and dicarboxylic acid derivates had the sam...

  1. Study on Synthesis and Binding Ability of a New Anion Receptor Containing NH Binding Sites

    Institute of Scientific and Technical Information of China (English)

    QIAO,Yan-Hong; LIN,Hai; LIN,Hua-Kuan


    A new colorimetric recognition receptor 1 based on the dual capability containing NH binding sites of selectively sensing anionic guest species has been synthesized. Compared with other halide anions, its UV/Vis absorption spectrum in dimethyl sulfoxide showed the response toward the presence of fluoride anion with high selectivity,and also displayed dramatic color changes from colorless to yellow in the presence of TBAF (5 × 10-5 mol/L). The similar UV/Vis absorption spectrum change also occurred when 1 was treated with AcO- while a little change with H2PO-4 and OH-. Receptor 1 has almost not affinity abilities to Cl-, Br- and I-. The binding ability of receptor 1to fluoride with high selectivity over other halides contributes to the anion size and the ability of forming hydrogen bonding. While the different ability of binding with geometrically triangular (AcO-), tetrahedral (H2PO-4 ) and linear (OH-) anions maybe result from their geometry configuration.

  2. Studies of the silencing of Baculovirus DNA binding protein

    NARCIS (Netherlands)

    Quadt, I.; Lent, van J.W.M.; Knebel-Morsdorf, D.


    Baculovirus DNA binding protein (DBP) binds preferentially single-stranded DNA in vitro and colocalizes with viral DNA replication sites. Here, its putative role as viral replication factor has been addressed by RNA interference. Silencing of DBP in Autographa californica multiple nucleopolyhedrovir

  3. Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation

    Directory of Open Access Journals (Sweden)

    Ronne Hans


    Full Text Available Abstract Background The rate of mRNA transcription is controlled by transcription factors that bind to specific DNA motifs in promoter regions upstream of protein coding genes. Recent results indicate that not only the presence of a motif but also motif context (for example the orientation of a motif or its location relative to the coding sequence is important for gene regulation. Results In this study we present ContextFinder, a tool that is specifically aimed at identifying cases where motif context is likely to affect gene regulation. We used ContextFinder to examine the role of motif context in S. cerevisiae both for DNA binding by transcription factors and for effects on gene expression. For DNA binding we found significant patterns of motif location bias, whereas motif orientations did not seem to matter. Motif context appears to affect gene expression even more than it affects DNA binding, as biases in both motif location and orientation were more frequent in promoters of co-expressed genes. We validated our results against data on nucleosome positioning, and found a negative correlation between preferred motif locations and nucleosome occupancy. Conclusion We conclude that the requirement for stable binding of transcription factors to DNA and their subsequent function in gene regulation can impose constraints on motif context.

  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


    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. Host response transcriptional profiling reveals extracellular components and ABC (ATP-binding cassette transporters gene enrichment in typhoid fever-infected Nigerian children

    Directory of Open Access Journals (Sweden)

    Resau James H


    Full Text Available Abstract Background Salmonella enterica serovar Typhi (S. Typhi is a human-specific pathogen that causes typhoid fever, and remains a global health problem especially in developing countries. Its pathogenesis is complex and host response is poorly understood. In Africa, typhoid fever can be a major cause of morbidity in young infected children. The onset of the illness is insidious and clinical diagnosis is often unreliable. Gold standard blood culture diagnostic services are limited, thus rapid, sensitive, and affordable diagnostic test is essential in poor-resourced clinical settings. Routine typhoid fever vaccination is highly recommended but currently licensed vaccines provide only 55-75% protection. Recent epidemiological studies also show the rapid emergence of multi-drug resistant S. Typhi strains. High-throughput molecular technologies, such as microarrays, can dissect the molecular mechanisms of host responses which are S. Typhi-specific to provide a comprehensive genomic component of immunological responses and suggest new insights for diagnosis and treatment. Methods Global transcriptional profiles of S. Typhi-infected young Nigerian children were obtained from their peripheral blood and compared with that of other bacteremic infections using Agilent gene expression microarrays. The host-response profiles of the same patients in acute vs. convalescent phases were also determined. The top 96-100 differentially-expressed genes were identified and four genes were validated by quantitative real-time PCR. Gene clusters were obtained and functional pathways were predicted by DAVID (Database for Annotation, Visualization and Integrated Discovery. Results Transcriptional profiles from S. Typhi-infected children could be distinguished from those of other bacteremic infections. Enriched gene clusters included genes associated with extracellular peptides/components such as lipocalin (LCN2 and systemic immune response which is atypical in

  6. Label-Free LC-MS Profiling of Skeletal Muscle Reveals Heart-Type Fatty Acid Binding Protein as a Candidate Biomarker of Aerobic Capacity

    Directory of Open Access Journals (Sweden)

    Zulezwan A. Malik


    Full Text Available Two-dimensional gel electrophoresis provides robust comparative analysis of skeletal muscle, but this technique is laborious and limited by its inability to resolve all proteins. In contrast, orthogonal separation by SDS-PAGE and reverse-phase liquid chromatography (RPLC coupled to mass spectrometry (MS affords deep mining of the muscle proteome, but differential analysis between samples is challenging due to the greater level of fractionation and the complexities of quantifying proteins based on the abundances of their tryptic peptides. Here we report simple, semi-automated and time efficient (i.e., 3 h per sample proteome profiling of skeletal muscle by 1-dimensional RPLC electrospray ionisation tandem MS. Solei were analysed from rats (n = 5, in each group bred as either high- or low-capacity runners (HCR and LCR, respectively that exhibited a 6.4-fold difference (1,625 ± 112 m vs. 252 ± 43 m, p < 0.0001 in running capacity during a standardized treadmill test. Soluble muscle proteins were extracted, digested with trypsin and individual biological replicates (50 ng of tryptic peptides subjected to LC-MS profiling. Proteins were identified by triplicate LC-MS/MS analysis of a pooled sample of each biological replicate. Differential expression profiling was performed on relative abundances (RA of parent ions, which spanned three orders of magnitude. In total, 207 proteins were analysed, which encompassed almost all enzymes of the major metabolic pathways in skeletal muscle. The most abundant protein detected was type I myosin heavy chain (RA = 5,843 ± 897 and the least abundant protein detected was heat shock 70 kDa protein (RA = 2 ± 0.5. Sixteen proteins were significantly (p < 0.05 more abundant in HCR muscle and hierarchal clustering of the profiling data highlighted two protein subgroups, which encompassed proteins associated with either the respiratory chain or fatty acid oxidation. Heart-type fatty acid binding protein (FABPH was 1

  7. Analysis of the DNA-binding profile and function of TALE homeoproteins reveals their specialization and specific interactions with Hox genes/proteins. (United States)

    Penkov, Dmitry; Mateos San Martín, Daniel; Fernandez-Díaz, Luis C; Rosselló, Catalina A; Torroja, Carlos; Sánchez-Cabo, Fátima; Warnatz, H J; Sultan, Marc; Yaspo, Marie L; Gabrieli, Arianna; Tkachuk, Vsevolod; Brendolan, Andrea; Blasi, Francesco; Torres, Miguel


    The interactions of Meis, Prep, and Pbx1 TALE homeoproteins with Hox proteins are essential for development and disease. Although Meis and Prep behave similarly in vitro, their in vivo activities remain largely unexplored. We show that Prep and Meis interact with largely independent sets of genomic sites and select different DNA-binding sequences, Prep associating mostly with promoters and housekeeping genes and Meis with promoter-remote regions and developmental genes. Hox target sequences associate strongly with Meis but not with Prep binding sites, while Pbx1 cooperates with both Prep and Meis. Accordingly, Meis1 shows strong genetic interaction with Pbx1 but not with Prep1. Meis1 and Prep1 nonetheless coregulate a subset of genes, predominantly through opposing effects. Notably, the TALE homeoprotein binding profile subdivides Hox clusters into two domains differentially regulated by Meis1 and Prep1. During evolution, Meis and Prep thus specialized their interactions but maintained significant regulatory coordination.

  8. Study on Higher Efficiency Thermal Cycling Profile for HALT

    Institute of Scientific and Technical Information of China (English)

    TAO Jun-yong; CHU Wei-hua; CHEN Xun


    HALT (highly accelerated life test) is a new reliability test technique. This paper uses nonlinear finite element method to analyze the stress strain characteristic of solder joints of PQFP (plastic quad flat packaging) and BGA (ball grid array) under thermal cycle test, and studies influences of profile parameters of the thermal cycle, such as hot and cold soak temperature, hot and cold soak time and temperature change rate, on elastic strain range, accumulated plastic strain, fatigue life and test efficiency of two types of solder joints. Based on the above research and experimental verification, this paper presents the method to build an optimal thermal cycling profile for HALT of electronic components.

  9. Study of ion implantation profiles by the PIXE technique (United States)

    Midy, P.; Lagarde, G.; Brissaud, I.; Frontier, J. P.; Chaumont, J.


    The RBS technique is currently used with alpha particles as a non-destructive way of studying concentration depth profiles. This technique is especially convenient in characterizing heavy atom distributions inside a matrix of lighter elements, and its use is less convenient in the case of light elements in a matrix of heavier ones. On the other hand the probing depth is limited by the small range of alpha particles in the matrix. We present here a new procedure for determining ion implantation profiles by means of the PIXE technique and by varying the impinging proton energy. As an example, silicon ions of two energies have been implanted into pure titanium samples in order to obtain implantation profiles with a double peak. The results presented here are in good agreement with the calculations using the TRIM code.

  10. Case Studies: Profiles of Women Recovering from Drug Addiction. (United States)

    Miller, Suzanne M.


    Profiles two women over an eight-month study who abused alcohol and other drugs while pregnant and describes their recovery from the addiction. Examines, from an ecological framework, the women's experiences with drug addiction, treatment, and recovery, and recounts their situation through each. (JPS)

  11. A Diagnostic Profile of Gerstmann's Syndrome: A Case Study (United States)

    Naude, H.; Pretorius, E.


    The authors present a diagnostic profile of Gerstmann's syndrome, the subject being a girl, aged 10 years 3 months, right-handed, and at the time of this study in her fourth school year (Grade 4). The subject's verbal and non-verbal IQ scores and additional assessment data were analyzed and summative responses given. The Senior South African…

  12. Binding of (/sup 3/H)imipramine to human platelet membranes with compensation for saturable binding to filters and its implication for binding studies with brain membranes

    Energy Technology Data Exchange (ETDEWEB)

    Phillips, O.M.; Wood, K.M.; Williams, D.C.


    Apparent specific binding of (/sup 3/H)imipramine to human platelet membranes at high concentrations of imipramine showed deviation from that expected of a single binding site, a result consistent with a low-affinity binding site. The deviation was due to displaceable, saturable binding to the glass fibre filters used in the assays. Imipramine, chloripramine, desipramine, and fluoxetine inhibited binding to filters whereas 5-hydroxytryptamine and ethanol were ineffective. Experimental conditions were developed that eliminated filter binding, allowing assay of high- and low-affinity binding to membranes. Failure to correct for filter binding may lead to overestimation of binding parameters, Bmax and KD for high-affinity binding to membranes, and may also be misinterpreted as indicating a low-affinity binding component in both platelet and brain membranes. Low-affinity binding (KD less than 2 microM) of imipramine to human platelet membranes was demonstrated and its significance discussed.

  13. A tight-binding study of single-atom transistors. (United States)

    Ryu, Hoon; Lee, Sunhee; Fuechsle, Martin; Miwa, Jill A; Mahapatra, Suddhasatta; Hollenberg, Lloyd C L; Simmons, Michelle Y; Klimeck, Gerhard


    A detailed theoretical study of the electronic and transport properties of a single atom transistor, where a single phosphorus atom is embedded within a single crystal transistor architecture, is presented. Using a recently reported deterministic single-atom transistor as a reference, the electronic structure of the device is represented atomistically with a tight-binding model, and the channel modulation is simulated self-consistently with a Thomas-Fermi method. The multi-scale modeling approach used allows confirmation of the charging energy of the one-electron donor charge state and explains how the electrostatic environments of the device electrodes affects the donor confinement potential and hence extent in gate voltage of the two-electron charge state. Importantly, whilst devices are relatively insensitive to dopant ordering in the highly doped leads, a ∼1% variation of the charging energy is observed when a dopant is moved just one lattice spacing within the device. The multi-scale modeling method presented here lays a strong foundation for the understanding of single-atom device structures: essential for both classical and quantum information processing.

  14. Myosin binding protein-C slow: a multifaceted family of proteins with a complex expression profile in fast and slow twitch skeletal muscles. (United States)

    Ackermann, Maegen A; Kontrogianni-Konstantopoulos, Aikaterini


    Myosin Binding Protein-C slow (sMyBP-C) comprises a complex family of proteins expressed in slow and fast type skeletal muscles. Similar to its fast and cardiac counterparts, sMyBP-C functions to modulate the formation of actomyosin cross-bridges, and to organize and stabilize sarcomeric A- and M-bands. The slow form of MyBP-C was originally classified as a single protein, however several variants encoded by the single MYBPC1 gene have been recently identified. Alternative splicing of the 5' and 3' ends of the MYBPC1 transcript has led to the differential expression of small unique segments interspersed between common domains. In addition, the NH2-terminus of sMyBP-C undergoes complex phosphorylation. Thus, alternative splicing and phosphorylation appear to regulate the functional activities of sMyBP-C. sMyBP-C proteins are not restricted to slow twitch muscles, but they are abundantly expressed in fast twitch muscles, too. Using bioinformatic tools, we herein perform a systematic comparison of the known human and mouse sMyBP-C variants. In addition, using single fiber westerns and antibodies to a common region of all known sMyBP-C variants, we present a detailed and comprehensive characterization of the expression profile of sMyBP-C proteins in the slow twitch soleus and the fast twitch flexor digitorum brevis (FDB) mouse muscles. Our studies demonstrate for the first time that distinct sMyBP-C variants are co-expressed in the same fiber, and that their expression profile differs among fibers. Given the differential expression of sMyBP-C variants in single fibers, it becomes apparent that each variant or combination thereof may play unique roles in the regulation of actomyosin cross-bridges formation and the stabilization of thick filaments.

  15. Myosin Binding Protein-C Slow: a multifaceted family of proteins with a complex expression profile in fast and slow twitch skeletal muscles

    Directory of Open Access Journals (Sweden)

    Maegen A Ackermann


    Full Text Available Myosin Binding Protein-C slow (sMyBP-C comprises a complex family of proteins expressed in slow and fast type skeletal muscles. Similar to its fast and cardiac counterparts, sMyBP-C functions to modulate the formation of actomyosin cross-bridges, and to organize and stabilize sarcomeric A- and M-bands. The slow form of MyBP-C was originally classified as a single protein, however several variants encoded by the single MYBPC1 gene have been recently identified. Alternative splicing of the 5’ and 3’ ends of the MYBPC1 transcript has led to the differential expression of small unique segments interspersed between common domains. In addition, the NH2-terminus of sMyBP-C undergoes complex phosphorylation. Thus, alternative splicing and phosphorylation appear to regulate the functional activities of sMyBP-C. sMyBP-C proteins are not restricted to slow twitch muscles, but they are abundantly expressed in fast twitch muscles, too. Using bioinformatic tools, we herein perform a systematic comparison of the known human and mouse sMyBP-C variants. In addition, using single fiber westerns and antibodies to a common region of all known sMyBP-C variants, we present a detailed and comprehensive characterization of the expression profile of sMyBP-C proteins in the slow twitch soleus and the fast twitch flexor digitorum brevis (FDB mouse muscles. Our studies demonstrate for the first time that distinct sMyBP-C variants are co-expressed in the same fiber, and that their expression profile differs among fibers. Given the differential expression of sMyBP-C variants in single fibers, it becomes apparent that each variant or combination thereof may play unique roles in the regulation of actomyosin cross-bridges formation and the stabilization of thick filaments.

  16. Identification, expression profiling and fluorescence-based binding assays of a chemosensory protein gene from the Western flower thrips, Frankliniella occidentalis.

    Directory of Open Access Journals (Sweden)

    Zhi-Ke Zhang

    Full Text Available Using RT-PCR and RACE-PCR strategies, we cloned and identified a new chemosensory protein (FoccCSP from the Western flower thrips, Frankliniella occidentalis, a species for which no chemosensory protein (CSP has yet been identified. The FoccCSP gene contains a 387 bp open-reading frame encoding a putative protein of 128 amino acids with a molecular weight of 14.51 kDa and an isoelectric point of 5.41. The deduced amino acid sequence contains a putative signal peptide of 19 amino acid residues at the N-terminus, as well as the typical four-cysteine signature found in other insect CSPs. As FoccCSP is from a different order of insect than other known CSPs, the GenBank FoccCSP homolog showed only 31-50% sequence identity with them. A neighbor-joining tree was constructed and revealed that FoccCSP is in a group with CSPs from Homopteran insects (e.g., AgosCSP4, AgosCSP10, ApisCSP, and NlugCSP9, suggesting that these genes likely developed from a common ancestral gene. The FoccCSP gene expression profile of different tissues and development stages was measured by quantitative real-time PCR. The results of this analysis revealed this gene is predominantly expressed in the antennae and also highly expressed in the first instar nymph, suggesting a function for FoccCSP in olfactory reception and in particular life activities during the first instar nymph stage. We expressed recombinant FoccCSP protein in a prokaryotic expression system and purified FoccCSP protein by affinity chromatography using a Ni-NTA-Sepharose column. Using N-phenyl-1-naphthylamine (1-NPN as a fluorescent probe in fluorescence-based competitive binding assay, we determined the binding affinities of 19 volatile substances for FoccCSP protein. This analysis revealed that anisic aldehyde, geraniol and methyl salicylate have high binding affinities for FoccCSP, with KD values of 10.50, 15.35 and 35.24 μM, respectively. Thus, our study indicates that FoccCSP may play an important role in

  17. Cytotoxicity and binding profiles of activated Cry1Ac and Cry2Ab to three insect cell lines (United States)

    While Cry1Ac has been known to bind with larval midgut proteins cadherin, APN (amino peptidase N), ALP (alkaline phosphatase) and ABCC2 (ATP-binding cassette transporter subfamily C2), little is known about the receptors of Cry2Ab. To provide a clue to the receptors of Cry2Ab, we tested the baselin...

  18. Radiometric Study of Soil Profiles in the Infrared Band (United States)

    Ponomareva, T. V.; Ponomarev, E. I.


    The applicability of radiometric survey of soil profiles in the infrared range for the analysis of soil physical properties was studied. Radiometric data were obtained for different dates of the growing season for a number of soil profiles. The specificity of temperature profiles of texture-differentiated soils (Luvisols and Retisols) as related to weather conditions of the growing season was examined. The correlation analysis showed a close relationship between the air and surface soil temperatures and between the radiometric and thermodynamic soil temperatures in the upper 10 cm. In the studied profiles, the gradient of radiometric temperatures reached 0.5-0.8°C/cm in the humus horizons and sharply decreased at the depth of more than 15-20 cm. The gradient analysis of radiometric images made it possible to outline the boundaries of soil horizons. For the texture-differentiated soils, the most distinct boundaries were established between the gray-humus AY horizon and the underlying eluvial EL horizon in podzolic soils and between the AY horizon and the underlying humus-eluvial AEL horizon in gray soils.

  19. Alkane-induced expression, substrate binding profile, and immunolocalization of a cytochrome P450 encoded on the nifD excision element of Anabaena 7120

    Directory of Open Access Journals (Sweden)

    Fjetland Conrad R


    Full Text Available Abstract Background Alkanes have been hypothesized to act as universal inducers of bacterial cytochrome P450 gene expression. We tested this hypothesis on an unusual P450 gene (cyp110 found on a conserved 11 kilobase episomal DNA element of unknown function found in filamentous cyanobacteria. We also monitored the binding of potential substrates to the P450 protein and explored the distribution of P450 protein in vegetative cells and nitrogen-fixing heterocysts using immuno-electron microscopy. Results Hexadecane treatments resulted in a two-fold increase in mRNA, and a four-fold increase in P450 protein levels relative to control cultures. Hexane, octane and dodecane were toxic and induced substantial changes in membrane morphology. Long-chain saturated and unsaturated fatty acids were shown to bind the CYP110 protein using a spectroscopic spin-shift assay, but alkanes did not bind. CYP110 protein was detected in vegetative cells but not in differentiated heterocysts where nitrogen fixation occurs. Conclusion Hexadecane treatment was an effective inducer of CYP110 expression in cyanobacteria. Based on substrate binding profiles and amino acid sequence similarities it is hypothesized that CYP110 is a fatty acid ω-hydroxylase in photosynthetic cells. CYP110 was found associated with membrane fractions unlike other soluble microbial P450 proteins, and in this regard CYP110 more closely resembles eukarytotic P450s. Substrate stablization is an unlikely mechanism for alkane induction because alkanes did not bind to purified CYP110 protein.

  20. Large-scale integration of small molecule-induced genome-wide transcriptional responses, Kinome-wide binding affinities and cell-growth inhibition profiles reveal global trends characterizing systems-level drug action

    Directory of Open Access Journals (Sweden)

    Dusica eVidovic


    Full Text Available The Library of Integrated Network-based Cellular Signatures (LINCS project is a large-scale coordinated effort to build a comprehensive systems biology reference resource. The goals of the program include the generation of a very large multidimensional data matrix and informatics and computational tools to integrate, analyze, and make the data readily accessible. LINCS data include genome-wide transcriptional signatures, biochemical protein binding profiles, cellular phenotypic response profiles and various other datasets for a wide range of cell model systems and molecular and genetic perturbations. Here we present a partial survey of this data facilitated by data standards and in particular a robust compound standardization workflow; we integrated several types of LINCS signatures and analyzed the results with a focus on mechanism of action and chemical compounds. We illustrate how kinase targets can be related to disease models and relevant drugs. We identified some fundamental trends that appear to link Kinome binding profiles and transcriptional signatures to chemical information and biochemical binding profiles to transcriptional responses independent of chemical similarity. To fill gaps in the datasets we developed and applied predictive models. The results can be interpreted at the systems level as demonstrated based on a large number of signaling pathways. We can identify clear global relationships, suggesting robustness of cellular responses to chemical perturbation. Overall, the results suggest that chemical similarity is a useful measure at the systems level, which would support phenotypic drug optimization efforts. With this study we demonstrate the potential of such integrated analysis approaches and suggest prioritizing further experiments to fill the gaps in the current data.

  1. Experimental strategies for studying transcription factor-DNA binding specificities. (United States)

    Geertz, Marcel; Maerkl, Sebastian J


    Specific binding of transcription factors (TFs) determines in a large part the connectivity of gene regulatory networks as well as the quantitative level of gene expression. A multiplicity of both experimental and computational methods is currently used to discover and characterize the underlying TF-DNA interactions. Experimental methods can be further subdivided into in vitro- and in vivo-based approaches, each accenting different aspects of TF-binding events. In this review we summarize the flexibility and performance of a selection of both types of experimental methods. In conclusion, we argue that a serial combination of methods with different throughput and data type constitutes an optimal experimental strategy.

  2. Calcium binding to the purple membrane : A molecular dynamics study

    NARCIS (Netherlands)

    Wassenaar, Tsjerk A.; Daura, Xavier; Padros, Esteve; Mark, Alan E.


    The purple membrane (PM) is a specialized membrane patch found in halophilic archaea, containing the photoreceptor bacteriorhodopsin (bR). It is long known that calcium ions bind to the PM, but their position and role remain elusive to date. Molecular dynamics simulations in conjunction with a highl

  3. Tubulin binding, protein-bound conformation in solution, and antimitotic cellular profiling of noscapine and its derivatives. (United States)

    Bennani, Youssef L; Gu, Wenxin; Canales, Angeles; Díaz, Fernando J; Eustace, Brenda K; Hoover, Russell R; Jiménez-Barbero, Jesus; Nezami, Azin; Wang, Tiansheng


    Noscapine and its 7-hydroxy and 7-amino derivatives were characterized for their binding to tubulin. A solution NMR structure of these compounds bound to tubulin shows that noscapine and its 7-aniline derivative do not compete for the same binding site nor does its small molecule crystal structure match its tubulin-bound conformation. These compounds were also tested for their antiproliferative effects on a panel hepatocellular carcinoma cell lines.

  4. Profiling Dizziness in Older Primary Care Patients: An Empirical Study (United States)

    Dros, Jacquelien; Maarsingh, Otto R.; van der Windt, Daniëlle A. W. M.; Oort, Frans J.; ter Riet, Gerben; de Rooij, Sophia E. J. A.; Schellevis, François G.; van der Horst, Henriëtte E.; van Weert, Henk C. P. M.


    Background The diagnostic approach to dizzy, older patients is not straightforward as many organ systems can be involved and evidence for diagnostic strategies is lacking. A first differentiation in diagnostic subtypes or profiles may guide the diagnostic process of dizziness and can serve as a classification system in future research. In the literature this has been done, but based on pathophysiological reasoning only. Objective To establish a classification of diagnostic profiles of dizziness based on empirical data. Design Cross-sectional study. Participants and Setting 417 consecutive patients of 65 years and older presenting with dizziness to 45 primary care physicians in the Netherlands from July 2006 to January 2008. Methods We performed tests, including patient history, and physical and additional examination, previously selected by an international expert panel and based on an earlier systematic review. We used the results of these tests in a principal component analysis for exploration, data-reduction and finally differentiation into diagnostic dizziness profiles. Results Demographic data and the results of the tests yielded 221 variables, of which 49 contributed to the classification of dizziness into six diagnostic profiles, that may be named as follows: “frailty”, “psychological”, “cardiovascular”, “presyncope”, “non-specific dizziness” and “ENT”. These explained 32% of the variance. Conclusions Empirically identified components classify dizziness into six profiles. This classification takes into account the heterogeneity and multicausality of dizziness and may serve as starting point for research on diagnostic strategies and can be a first step in an evidence based diagnostic approach of dizzy older patients. PMID:21304984

  5. Profiling dizziness in older primary care patients: an empirical study.

    Directory of Open Access Journals (Sweden)

    Jacquelien Dros

    Full Text Available BACKGROUND: The diagnostic approach to dizzy, older patients is not straightforward as many organ systems can be involved and evidence for diagnostic strategies is lacking. A first differentiation in diagnostic subtypes or profiles may guide the diagnostic process of dizziness and can serve as a classification system in future research. In the literature this has been done, but based on pathophysiological reasoning only. OBJECTIVE: To establish a classification of diagnostic profiles of dizziness based on empirical data. DESIGN: Cross-sectional study. PARTICIPANTS AND SETTING: 417 consecutive patients of 65 years and older presenting with dizziness to 45 primary care physicians in the Netherlands from July 2006 to January 2008. METHODS: We performed tests, including patient history, and physical and additional examination, previously selected by an international expert panel and based on an earlier systematic review. We used the results of these tests in a principal component analysis for exploration, data-reduction and finally differentiation into diagnostic dizziness profiles. RESULTS: Demographic data and the results of the tests yielded 221 variables, of which 49 contributed to the classification of dizziness into six diagnostic profiles, that may be named as follows: "frailty", "psychological", "cardiovascular", "presyncope", "non-specific dizziness" and "ENT". These explained 32% of the variance. CONCLUSIONS: Empirically identified components classify dizziness into six profiles. This classification takes into account the heterogeneity and multicausality of dizziness and may serve as starting point for research on diagnostic strategies and can be a first step in an evidence based diagnostic approach of dizzy older patients.

  6. Study on migrants' profiles, drivers of migration and migratory trends


    ACHILLI, Luigi; FARGUES, Philippe; Salamonska, Justyna; TALÒ, Teresa


    This study analyses the socioeconomic background of migrants and refugees who have fled to Italy. It compiles information about their education level, work experience, skills, professional aspirations and future employment prospects. The aim of this research is to help policy-makers in Italy and across Europe get a current, in-depth profile of migrants, understand what drives them to leave home, what influences their decisions during their journey and how they can better integrate in Italy. ...

  7. Biotype Characterization, Developmental Profiling, Insecticide Response and Binding Property of Bemisia tabaci Chemosensory Proteins: Role of CSP in Insect Defense.

    Directory of Open Access Journals (Sweden)

    Guoxia Liu

    Full Text Available Chemosensory proteins (CSPs are believed to play a key role in the chemosensory process in insects. Sequencing genomic DNA and RNA encoding CSP1, CSP2 and CSP3 in the sweet potato whitefly Bemisia tabaci showed strong variation between B and Q biotypes. Analyzing CSP-RNA levels showed not only biotype, but also age and developmental stage-specific expression. Interestingly, applying neonicotinoid thiamethoxam insecticide using twenty-five different dose/time treatments in B and Q young adults showed that Bemisia CSP1, CSP2 and CSP3 were also differentially regulated over insecticide exposure. In our study one of the adult-specific gene (CSP1 was shown to be significantly up-regulated by the insecticide in Q, the most highly resistant form of B. tabaci. Correlatively, competitive binding assays using tryptophan fluorescence spectroscopy and molecular docking demonstrated that CSP1 protein preferentially bound to linoleic acid, while CSP2 and CSP3 proteins rather associated to another completely different type of chemical, i.e. α-pentyl-cinnamaldehyde (jasminaldehyde. This might indicate that some CSPs in whiteflies are crucial to facilitate the transport of fatty acids thus regulating some metabolic pathways of the insect immune response, while some others are tuned to much more volatile chemicals known not only for their pleasant odor scent, but also for their potent toxic insecticide activity.

  8. Biotype Characterization, Developmental Profiling, Insecticide Response and Binding Property of Bemisia tabaci Chemosensory Proteins: Role of CSP in Insect Defense (United States)

    Liu, Guoxia; Ma, Hongmei; Xie, Hongyan; Xuan, Ning; Guo, Xia; Fan, Zhongxue; Rajashekar, Balaji; Arnaud, Philippe; Offmann, Bernard; Picimbon, Jean-François


    Chemosensory proteins (CSPs) are believed to play a key role in the chemosensory process in insects. Sequencing genomic DNA and RNA encoding CSP1, CSP2 and CSP3 in the sweet potato whitefly Bemisia tabaci showed strong variation between B and Q biotypes. Analyzing CSP-RNA levels showed not only biotype, but also age and developmental stage-specific expression. Interestingly, applying neonicotinoid thiamethoxam insecticide using twenty-five different dose/time treatments in B and Q young adults showed that Bemisia CSP1, CSP2 and CSP3 were also differentially regulated over insecticide exposure. In our study one of the adult-specific gene (CSP1) was shown to be significantly up-regulated by the insecticide in Q, the most highly resistant form of B. tabaci. Correlatively, competitive binding assays using tryptophan fluorescence spectroscopy and molecular docking demonstrated that CSP1 protein preferentially bound to linoleic acid, while CSP2 and CSP3 proteins rather associated to another completely different type of chemical, i.e. α-pentyl-cinnamaldehyde (jasminaldehyde). This might indicate that some CSPs in whiteflies are crucial to facilitate the transport of fatty acids thus regulating some metabolic pathways of the insect immune response, while some others are tuned to much more volatile chemicals known not only for their pleasant odor scent, but also for their potent toxic insecticide activity. PMID:27167733

  9. Aptamer Binding Studies Using MicroScale Thermophoresis. (United States)

    Breitsprecher, Dennis; Schlinck, Nina; Witte, David; Duhr, Stefan; Baaske, Philipp; Schubert, Thomas


    The characterization and development of highly specific aptamers requires the analysis of the interaction strength between aptamer and target. MicroScale Thermophoresis (MST) is a rapid and precise method to quantify biomolecular interactions in solution at microliter scale. The basis of this technology is a physical effect referred to as thermophoresis, which describes the directed movement of molecules through temperature gradients. The thermophoretic properties of a molecule depend on its size, charge, and hydration shell. Since at least one of these parameters is altered upon binding of a ligand, this method can be used to analyze virtually any biomolecular interaction in any buffer or complex bioliquid. This section provides a detailed protocol describing how MST is used to obtain quantitative binding parameters for aptamer-target interactions. The two DNA-aptamers HD1 and HD22, which are targeted against human thrombin, are used as model systems to demonstrate a rapid and straightforward screening approach to determine optimal buffer conditions.

  10. Studies of Reversible Hydrogen Binding in Nano- Sized Materials


    Lesničenoks, Pēteris; Zemītis, Jānis; Kleperis, Jānis; Čikvaidze, Georgijs; Ignatāns, Reinis


    Experimental review of materials suitable for reversible hydrogen binding in nanoporous and nanosized structures of materials, based on natural zeolite (clinoptilolite) and graphene (exfoliated electrochemically from raw graphite), were analyzed. Characterization of materials with SEM, XRD, EDS and Raman spectroscopy methods and aspects of synthesis of a nanostructured zeolite and a few-layer graphite material was done in this work. It was established from gas analyzer results that hydrogen m...

  11. Studies of Single Biomolecules, DNA Conformational Dynamics, and Protein Binding (United States)


    cars on a parking lot designed for small vehicles. Apart from the binding size λ of the SSBs, two additional physical parameters come into play: the...full denaturation in the right plot of figure 14. Similar finite size effects were investigated for biopolymer translocation in references [74, 75...for example regarding diffusive processes. It appears that subdiffusion of biopolymers occurs in condi- tions of molecular crowding [83–85] this

  12. Approving job profiles for curriculum profiles in health care programs : a study on process and product quality

    NARCIS (Netherlands)

    Mulder, Martin; Engels, Otto


    A study evaluated the approach used for validation of job profiles for curriculum development in three health care programs in the Netherlands: dietetics, podotherapy, and activity therapy. It also evaluated the quality of these job profiles and the relation between process and product quality. The

  13. Comparative study of Passiflora taxa leaves: II. A chromatographic profile

    Directory of Open Access Journals (Sweden)

    Luma Wosch

    Full Text Available ABSTRACT Popularly known as passion fruit, some species of the genus Passiflora are widely used in folk medicines, such as sedatives and tranquilizers in many countries. Although these plants are employed for the same purposes, research with different species of Passiflora has indicated their heterogeneous chemical compositions. Since different chemical compositions can result in varying degrees of therapeutic efficiency, quality control based on the chemical constituents of each species is essential. To that end, the aim of this study was to compare pharmacognostically species of Passiflora in order to establish a chromatographic profile for the quality control of drugs in herbal medicines containing passion fruit. The study was conducted by collecting samples of leaves from twelve Passiflora taxa (i.e., ten species and two forms of P. edulis – P. actinia, P. alata, P. amethystina, P. capsularis, P. cincinnata, P. edulis f. flavicarpa, P. edulis f. edulis, P. incarnata, P. morifolia, P. urnifolia, P. coccinea, and P. setacea – from different locations and obtaining their chromatographic profiles via thin-layer chromatography and high-performance liquid chromatography. Both methods used the flavonoid C-glycosides isoorientin, orientin, vitexin, and isovitexin as reference compounds and could ultimately establish specific profiles for each species. The chromatographic analyses discussed here can be used to assist in determining the quality and authenticity of herbal drugs derived from Passiflora species.

  14. RUNX1/core binding factor A2 regulates platelet 12-lipoxygenase gene (ALOX12): studies in human RUNX1 haplodeficiency (United States)

    Kaur, Gurpreet; Jalagadugula, Gauthami; Mao, Guangfen


    Haploinsufficiency of RUNX1 (also known as CBFA2/AML1) is associated with familial thrombocytopenia, platelet dysfunction, and predisposition to acute leukemia. We have reported on a patient with thrombocytopenia and impaired agonist-induced aggregation, secretion, and protein phosphorylation associated with a RUNX1 mutation. Expression profiling of platelets revealed approximately 5-fold decreased expression of 12-lipoxygenase (12-LO, gene ALOX12), which catalyzes 12-hydroxyeicosatetraenoic acid production from arachidonic acid. We hypothesized that ALOX12 is a direct transcriptional target gene of RUNX1. In present studies, agonist-induced platelet 12-HETE production was decreased in the patient. Four RUNX1 consensus sites were identified in the 2-kb promoter region of ALOX12 (at −1498, −1491, −708, −526 from ATG). In luciferase reporter studies in human erythroleukemia cells, mutation of each site decreased activity; overexpression of RUNX1 up-regulated promoter activity, which was abolished by mutation of RUNX1 sites. Gel shift studies, including with recombinant protein, revealed RUNX1 binding to each site. Chromatin immunoprecipitation revealed in vivo RUNX1 binding in the region of interest. siRNA knockdown of RUNX1 decreased RUNX1 and 12-LO proteins. ALOX12 is a direct transcriptional target of RUNX1. Our studies provide further proof of principle that platelet expression profiling can elucidate novel alterations in platelets with inherited dysfunction. PMID:20181616

  15. Spectroscopic and Docking Studies on the Binding of Liquiritigenin with Hyaluronidase for Antiallergic Mechanism

    Directory of Open Access Journals (Sweden)

    Hua-jin Zeng


    Full Text Available The inhibitory effect of liquiritigenin on hyaluronidase and its binding mechanism were investigated systematically by UV-vis absorption, fluorescence, and molecular modeling approaches. These results indicated that liquiritigenin could interact with hyaluronidase to form a liquiritigenin-hyaluronidase complex. The binding constant, number of binding sites, and thermodynamic parameters were calculated, which indicated that liquiritigenin could spontaneously bind with hyaluronidase mainly through electrostatic and hydrophobic interactions with one binding site. Synchronous fluorescence, three-dimensional fluorescence, and molecular docking results revealed that liquiritigenin bound directly to the enzyme cavity site and this binding influenced the microenvironment of the hyaluronidase activity site, resulting in reduced hyaluronidase activity. The present study provides useful information for clinical applications of liquiritigenin as a hyaluronidase inhibitor.

  16. A screening study of xylitol binding in vitro to activated charcoal. (United States)

    Cope, R B


    Ingestion of foods containing the sweetener xylitol by dogs results in a significant, and often sustained, insulin-mediated hypoglycemic crisis. The efficacy of activated charcoal for gastrointestinal decontamination following xylitol ingestion is unknown. This screening study examined the effect of pH and incubation time on the in vitro binding of xylitol to activated charcoal. The mean percentage activated charcoal binding ranged between 8 and 23%. Mean percentage binding of xylitol at pH 3 was significantly higher (p activated charcoal slurry. These results suggest binding of xylitol to activated charcoal is relatively low; however, activated charcoal administration may still be beneficial in some canine acute oral xylitol exposures.

  17. A computational study of ligand binding affinities in iron(III) porphine and protoporphyrin IX complexes. (United States)

    Durrant, Marcus C


    The search for novel anti-malarial drugs that can disrupt biomineralization of ferriprotoporphyrin IX to haemozoin requires an understanding of the fundamental chemistry of the porphyrin's iron(iii) centre at the water-lipid interface. Towards this end, the binding affinities for a diverse set of 31 small ligands with iron(iii) porphine have been calculated using density functional theory, in the gas phase and also with implicit solvent corrections for both water and n-octanol. In addition, the binding of hydroxide, chloride, acetate, methylamine and water to ferriprotoporphyrin IX has been studied, and very similar trends are observed for the smaller and larger models. Anionic ligands generally give stronger binding than neutral ones; the strongest binding is observed for RO(-) and OH(-) ligands, whilst acetate binds relatively weakly among the anions studied. Electron-rich nitrogen donors tend to bind more strongly than electron-deficient ones, and the weakest binding is found for neutral O and S donors such as oxazole and thiophene. In all cases, ligand binding is stronger in n-octanol than in water, and the differences in binding energies for the two solvents are greater for ionic ligands than for neutrals. Finally, dimerization of ferriprotoporphyrin IX by means of iron(iii)-carboxylate bond formation has been modelled. The results are discussed in terms of haemozoin crystal growth and its disruption by known anti-malarial drugs.

  18. Phenotype-associated lectin-binding profiles of normal and transformed blood cells: a comparative analysis of mannose- and galactose-binding lectins from plants and human serum/placenta. (United States)

    Mann, K K; André, S; Gabius, H J; Sharp, J G


    Surface glycoconjugates of normal and transformed blood cells are commonly characterized by plant lectins. To infer physiological significance of protein-carbohydrate interactions, mammalian lectins are obviously preferable as research tools. So far, human serum lectins have not been used to assess their binding to immunophenotyped human normal or transformed blood cells. Thus, our study combines two groups of lectins with different specificity from plant and human sources. Besides concanavalin A (ConA) we have isolated the mannose-binding protein and serum amyloid P component from human serum. Especially the mannose-binding protein is believed to play a role in host defence against bacteria and yeast cells with unknown impact on normal and tumor cells. These three lectins establish the first group. In addition to the immunomodulatory mistletoe lectin, whose binding can elicit enhanced cytokine secretion from mononuclear blood cells, we included the beta-galactoside-binding lectin (14 kDa) from human placenta in the second group. The initial series of measurements was undertaken using two-color flow cytometry to determine the phenotype-associated binding (based on cluster designation; CD) of the lectins to blood and bone marrow cells from normal donors and the cell line CEM (T-lymphoblastoid), KG1-A (primitive myeloid leukemia) and Croco II (B-lymphoblastoid). Heterogeneity was apparent for each lectin in the CD-defined cell populations. Significant differences in binding were noted between Viscum album agglutinin (VAA) and other lectins for CD4+ cells from blood and between mannose-binding protein (MBP) and VAA versus 14 kDa, ConA and serum amyloid P component (SAP) for CD19+ cells from bone marrow.(ABSTRACT TRUNCATED AT 250 WORDS)

  19. Identification and expression profiling of putative odorant-binding proteins in the malaria mosquitoes, Anopheles gambiae and A.arabiensis

    Institute of Scientific and Technical Information of China (English)

    LI; Zhengxi; Jing-Jiang; ZHOU; SHEN; Zuorui; Lin; FIELD


    Olfaction plays a major role in host-seeking behaviour of mosquitoes. An informatics-based genome-wide analysis of odorant-binding protein (OBP) homologues is undertaken,and 32 putative OBP genes in total in the whole genome sequences of Anopheles gambiae are identified. Tissue-specific expression patterns of all A. gambiae OBP candidates are determined by semi-quantitative Reverse Transcription (RT)-PCR using mosquito actin gene as internal expression control standard. The results showed that 20 OBP candidates had strong expression in mosquito olfactory tissues (female antennae), which indicate that OBPs may play an important role in regulating mosquito olfactory behaviours. Species-specific expression patterns of all putative anopheline OBPs are also studied in two of the most important malaria vectors in A. gambiae complex, i.e.A. gambiae and A. arabiensis, which found 12 of the putative OBP genes examined displayed species-differential expression patterns. The cumulative relative expression intensity of the OBPs in A. arabiensis antennae was higher than that in A. gambiae (the ratio is 1441.45:1314.12), which might be due to their different host preference behaviour. While A.gambiae is a highly anthropophilic mosquito, A. arabiensis is more opportunistic (varying from anthropophilic to zoophilic). So the latter should need more OBPs to support its host selection preference. Identification of mosquito OBPs and verification of their tissue- and species-specific expression patterns represent the first step towards further molecular analysis of mosquito olfactory mechanism, such as recombinant expression and ligand identification.

  20. Spectroscopic and molecular modelling studies of binding mechanism of metformin with bovine serum albumin (United States)

    Sharma, Deepti; Ojha, Himanshu; Pathak, Mallika; Singh, Bhawna; Sharma, Navneet; Singh, Anju; Kakkar, Rita; Sharma, Rakesh K.


    Metformin is a biguanide class of drug used for the treatment of diabetes mellitus. It is well known that serum protein-ligand binding interaction significantly influence the biodistribution of a drug. Current study was performed to characterize the binding mechanism of metformin with serum albumin. The binding interaction of the metformin with bovine serum albumin (BSA) was examined using UV-Vis absorption spectroscopy, fluorescence, circular dichroism, density functional theory and molecular docking studies. Absorption spectra and fluorescence emission spectra pointed out the weak binding of metformin with BSA as was apparent from the slight change in absorbance and fluorescence intensity of BSA in presence of metformin. Circular dichroism study implied the significant change in the conformation of BSA upon binding with metformin. Density functional theory calculations showed that metformin has non-planar geometry and has two energy states. The docking studies evidently signified that metformin could bind significantly to the three binding sites in BSA via hydrophobic, hydrogen bonding and electrostatic interactions. The data suggested the existence of non-covalent specific binding interaction in the complexation of metformin with BSA. The present study will certainly contribute to the development of metformin as a therapeutic molecule.


    NARCIS (Netherlands)



    A cDNA clone encoding the rat metabotropic glutamate receptor mGluR3 was stably transfected into human embryonic kidney 293 cells. Receptor-expressing cell lines were characterized by centrifugation binding assays using [H-3]glutamate as radioligand. The rank order of affinity was L-glutamate>(1S,3R

  2. JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update

    DEFF Research Database (Denmark)

    Bryne, J.C.; Valen, E.; Tang, M.H.E.


    JASPAR is a popular open-access database for matrix models describing DNA-binding preferences for transcription factors and other DNA patterns. With its third major release, JASPAR has been expanded and equipped with additional functions aimed at both casual and power users. The heart of the JASPAR...

  3. Study on Integrated Thermal Cycle and Vibration Profile for HALT

    Institute of Scientific and Technical Information of China (English)

    TAO Jun-yong; CHU Wei-hua; CHEN Xun


    Focusing on electronic products, this paper establishes a finite element model for printed circuit board (PCB) assembling with enhanced ball grid array(EBGA)component under vibration environment. Based on this model, it studies relations between fatigue rate of solder joint and temperature, vibration frequency. Moreover, it analyzes propagation of micro-crack produced by thermal cycle under vibration stress. The results offer a method to optimize the thermal cycle and vibration integrated profile and to combine vibration test and thermal cycling for highly accelerated life test (HALT).

  4. Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus.

    Directory of Open Access Journals (Sweden)

    Evelyn N Kouwenhoven


    Full Text Available Heterozygous mutations in p63 are associated with split hand/foot malformations (SHFM, orofacial clefting, and ectodermal abnormalities. Elucidation of the p63 gene network that includes target genes and regulatory elements may reveal new genes for other malformation disorders. We performed genome-wide DNA-binding profiling by chromatin immunoprecipitation (ChIP, followed by deep sequencing (ChIP-seq in primary human keratinocytes, and identified potential target genes and regulatory elements controlled by p63. We show that p63 binds to an enhancer element in the SHFM1 locus on chromosome 7q and that this element controls expression of DLX6 and possibly DLX5, both of which are important for limb development. A unique micro-deletion including this enhancer element, but not the DLX5/DLX6 genes, was identified in a patient with SHFM. Our study strongly indicates disruption of a non-coding cis-regulatory element located more than 250 kb from the DLX5/DLX6 genes as a novel disease mechanism in SHFM1. These data provide a proof-of-concept that the catalogue of p63 binding sites identified in this study may be of relevance to the studies of SHFM and other congenital malformations that resemble the p63-associated phenotypes.

  5. Cloud profiling radar design study for EarthCARE (United States)

    Kumagai, Hiroshi; Orikasa, Teruaki; Ohno, Yuichi; Horie, Hiroaki; Kimura, Toshiyoshi


    EarthCARE Phase-A study was successfully conducted in collaboration between ESA and Japan (JAXA and NICT). In this study, high sensitivity Cloud Profiling Radar (CPR) design with Doppler capability was studied and demonstrated that the CPR satisfies mission requirements, system resource and launcher constraint. As a result of the study, a nadir looking CPR at 94 GHz with a 2.5 m diameter antenna reflector is designed with sensitivity exceeding -36 dBZ of requirement at TOA with 10 km horizontal integration. The Doppler measurement is a new challenge to attain velocity accuracy less than 1 m/s in vertical direction. In parallel to the CPR system design, algorithm development efforts have been conducted through field campaign. A suite of measured quantities that are very similar combination to the EarthCARE data was collected and applied to the retrieval algorithm test.

  6. Binding of TNT to amplifying fluorescent polymers: an ab initio and molecular dynamics study. (United States)

    Enlow, Mark A


    Molecular modeling techniques were employed to study the interaction of trinitrotoluene with an amplifying fluorescent polymer used in explosive sensor devices. The pentiptycene moiety present in these polymers appears to be the most energetically favorable binding site for trinitrotoluene. Surface features of the polymer suggest that the small cavity feature of the pentiptycene moiety may be more available for binding to analyte compounds due to steric crowding about the large cavity. Binding energies between model binding sites of the polymer and various analyte compounds were more rigorously estimated by semiempirical and ab initio techniques. Binding energies were found to be largest with trinitrotoluene and other nitroaromatic compounds. Electrostatic and π-stacking interactions between trinitrotoluene and the model host were investigated by studying a series of modified host compounds.

  7. Use of surface plasmon resonance in the binding study of vitamin D, metabolites and analogues with vitamin D binding protein. (United States)

    Canoa, Pilar; Rivadulla, Marcos L; Popplewell, Jonathan; van Oosten, René; Gómez, Generosa; Fall, Yagamare


    Vitamin D3 and its metabolites are lipophilic molecules with low aqueous solubility and must be transported bound to plasma carrier proteins, primarily to vitamin D binding protein (DBP). The biological functions of vitamin D3 metabolites are intimately dependent on the protein, hence the importance of determining their affinity for DBP. In this study, we developed a novel procedure for measuring the kinetic and equilibrium constants of human-DBP with vitamin D3 and three metabolites: 1,25-dihydroxyvitamin D3 [1,25(OH)2D3], 25-hydroxyvitamin D3 (25OHD3) and 24,25-dihydroxyvitamin D3 [24,25(OH)2D3] by surface plasmon resonance (SPR). At the same time, five different analogues, synthetized in our laboratory, were evaluated in order to compare the affinity values with the metabolites. Real-time SPR measurements showed that 25OHD3 and 24,25(OH)2D3 had higher affinity (0.3 μM) than 1,25(OH)2D3 (5 μM), with the higher affinity of 25OHD3 and 24,25(OH)2D3 due to dissociation constants 1 order of magnitude slower. In the case of the analogues, the affinity values were lower, with 1-hydroxy-25-nitro-vitamin D3 (NO2-446), structurally closer to 1,25(OH)2D3, showing the highest value with a K D of 50 μM. (24R)-1,25-dihydroxyvitamin-24-buthyl-28-norvitamin D2 (Bu-471) and (24R)-1,25-dihydroxyvitamin-24-phenyl-28-norvitamin D2 (Ph-491), structurally similar, had affinities of 180 and 170 μM, respectively. (22R,23E)-1-hydroxy-22-ethenyl-25-methoxy-23-dehydrovitamin D3 (MeO-455) and 1-hydroxy-20(R)-[5(S)-(2,2-dimethyltetrahydropyran-5-yl)]-22,23-dinor vitamin D3 (Oxan-429) had affinities of 310 and 100 μM, respectively. The binding of the metabolites and analogues was reversible allowing the rapid capture of data for replicates. The kinetic and equilibrium data for both the metabolites and the analogues fitted to the Langmuir model describing a 1:1 interaction. Graphical Abstract Label-free, real time binding study between vitamin D binding protein immmobilized on the

  8. Profile and removal of endocrine disrupting chemicals by using an ER/AR competitive ligand binding assay and chemical analyses

    Institute of Scientific and Technical Information of China (English)

    Ze-hua Liu; Mamoru Ito; Yoshinori Kanjo; Atsushi Yamamoto


    An estrogen receptor (ER)/androgen receptor (AR) ligand competitive binding assay (ER/AR-binding assay) and chemical analyses were used to evaluate the endocrine disrupting chemicals (EDCs) behavior of two municipal wastewater treatment plants (WWTPs) (K and S). In the influents, estrone (El), androsterone (A), androstenedione (AD), BPA (bisphenol A), NP (nonylphenol) and daidzein (DZ) were detected in high amounts with subsequent 24 h-average concentrations of 350, 1000, 29, 1300, 3900, and 5700 ng/L in K-WWTP and of 310, 620, 59, 1600, 2600, and 8400 ng/L in S-WWTP. The estrogenic (androgenic) activity as 17β-estradiol (E2) equivalents (EEQ) or testosterone (Te) equivalents (TEQ) was consequently 620 ng E2/L (570 ng Te/L) and 580 ng E2/L (800 ng Te/L) for the two WWTPs. The removal efficiencies of the above mentioned sole target chemicals were 51%-100% for K-WWTP and 55.6%,100% for S-WWTP. The removal efficiencies of EEQ were about 73% for both WWTPs, while the removal efficiencies of TEQ were 62.1% for K-WWTP and 98.4% for S-WWTP. In addition, chemical-derived EEQ were about 1.2%-52.4% of those by ER-binding assay for K-WWTP and the corresponding ratios were 1.3%-83.3% for S-WWTP, while chemical derived TEQ were less than 3% of values measured by the AR-binding assay for both WWTPs.

  9. Protein profile study of breast cancer tissues using HPLC-LIF: a pilot study (United States)

    Menon, Suraj; Sujatha; Kumar, K. Kalyan; Kurien, Jacob; Krishnanand, B. R.; Mahato, K. K.; George, Sajan D.; Kartha, V. B.; C, Santhosh


    Proteomics based techniques are rapidly emerging as alternative techniques to conventional histo-pathological methods for detection and diagnosis of cancers. Tumor markers are of considerable importance in the study of various cancers. A study of various changes in the protein profile associated with breast cancer will facilitate a better understanding of the various dynamic changes associated with the disease. In our study we have used High Performance Liquid Chromatography coupled with highly sensitive Laser Induced Fluorescence for recording the protein profiles of breast tissue homogenates. The protein profiles were recorded from pathologically certified normal as well as malignant breast tissue samples. The recorded protein profiles were studied by using Principal Component Analysis. Good discrimination of normal, benign and malignant samples was achieved in this pilot study.

  10. Study of Lipid profile in a population of university students

    Directory of Open Access Journals (Sweden)

    Roberto Wagner Junior Freire de Freitas


    Full Text Available OBJECTIVE: to evaluate the lipid profile in a population of university students. METHODS: cross-sectional study with 702 students, of both genders enrolled in various courses at a public university in Fortaleza-CE. The demographic data and data on lifestyle habits were collected through a self-administered questionnaire. The blood collection was performed in a clinical laboratory. RESULTS: showed a predominantly young population, with a mean age of 21.5 years with more females (62.7%. High levels of triglycerides, total cholesterol and cholesterol associated with low density lipoprotein (LDL-c were found in 23.0%, 9.7% and 5.9% of students, respectively. The cholesterol associated with high density lipoprotein (HDL-c was at reduced values in 12.0% of subjects and was significantly associated with smoking (p=0.0231 and physical inactivity (p=0.0357. CONCLUSION: changes in lipid profile are present in the young population and intervention studies should be encouraged in order to reduce the prevalence of cardiovascular disease in adulthood.

  11. Dose profile study in head CT scans using radiochromic films

    Energy Technology Data Exchange (ETDEWEB)

    Ladino G, A. M.; Prata M, A., E-mail: [Universidade Federal de Minas Gerais, Departamento de Engenharia Nuclear, Av. Pte. Antonio Carlos 6627, 31270-901 Belo Horizonte, Minas Gerais (Brazil)


    Diagnostic images of computed tomography generate higher doses than other methods of diagnostic radiology using X-ray beam attenuation. Clinical applications of CT have been increased by technological advances, what leads to a wide variety of scanner in the Brazilian technological pool. It has been difficult to implement dose reduction strategies because of the lack of proper guidance on computed tomography examinations. However, CT scanners allow adjusting acquisition parameter according to the patients physical profile and diagnostic application for which the scan is intended. The knowledge of the dose distribution is important because changes in image acquisition parameters may provide dose reduction. In this study, it was used a cylindrical head phantom in PMMA with 5 openings, what allows dose measurement in 5 regions. In a GE CT scanner, Discovery model of 64 channels, the central slice of the head phantom was irradiated and the absorbed doses were measured using a pencil ionization chamber. Radiochromic film strips were placed in the peripheral and in the central region of the head phantom and was performed a scan of 10 cm in the phantom central region. The scan was performed using the head scanning protocol of the radiobiology service, with a voltage of 120 kV. After scanning, the radiochromic film strips were digitalized and their digital images were used to have the dose longitudinal profiles. The dose values recorded have variation in a range of 18.66 to 23.57 mGy. In the results it was compared the dose index values obtained by the pencil chamber measurement to the dose longitudinal profiles recorded by the film strips. (Author)

  12. ADMET, Docking studies & binding energy calculations of some Novel ACE - inhibitors for the treatment of Diabetic Nephropathy

    Directory of Open Access Journals (Sweden)

    Gade Deepak Reddy


    Full Text Available Diabetic Nephropathy (DN is one of the major complications of diabetes mellitus, representing the leading of cause of chronic renal disease and a major cause of morbidity and mortality in both type 1 and type 2 diabetic patients. The Renin-Angiotensin-Aldosterone System (RAAS has been implicated in the pathophysiology of DN, and suggests a therapeutic target for blocking this system. Therefore, inhibition of RAAS plays a crucial role in the treatment of DN and therapeutic intervention mostly involves administration of angiotensin converting enzyme (ACE inhibitors and angiotensin AT1 receptor blockers. In this current study, we have used computational methods to design 37 novel ACE-inhibitors and evaluated them for the interaction with the enzyme ACE through insilico analysis. The obtained results were compared with the standard drug enalapril to find out the potential inhibitors. Here we report that ligand 4 exhibited strongest inhibitory activity among all. All the analogs are also screened for their ADME & Toxicity profiles using insilico tools and ligand 9 is having better binding affinity next to ligand 4, and also having better ADMET profile when compared to that of ligand 4. Post docking calculations were also performed for the docked complexes in order to identify the individual ligand binding energies by employing Multi-Ligand Bimolecular Association with Energetics (Embrace

  13. A novel method for thermodynamic study on binding of copper ion with Alzheimer's amyliod β peptide

    Institute of Scientific and Technical Information of China (English)

    BEHBEHANI G. Rezaei


    The interaction of Cu2+ with the first 16 residues of the Alzheimer's amyliod β peptide, Afl(1-16), was studied by employing isothermal titration calorimetry at pH 7.2 and 37℃ in aqueous solution. The Gholamreza Rezaei Behbehani (GRB) solvation model was used to reproduce the enthalpies of Cu2++Aβ(1-16) interaction over the whole Cu++concentrations. The binding parameters recovered from the solvation model were attributed to the structural change of Aβ(1-16) due to the metal ion interaction. It was found that there is a set of two identical and non interacting binding sites for Cu2+ ions. The molar enthalpy of binding is △H=27.895 kJ/mol. The association binding constants are 1.895 μM-1 and 1.891 μM-1 for the first and second binding sites respectively.

  14. The complexity of condensed tannin binding to bovine serum albumin--An isothermal titration calorimetry study. (United States)

    Kilmister, Rachel L; Faulkner, Peta; Downey, Mark O; Darby, Samuel J; Falconer, Robert J


    Isothermal titration calorimetry was applied to study the binding of purified proanthocyanidin oligomers to bovine serum albumin (BSA). The molecular weight of the proanthocyanidin oligomer had a major impact on its binding to BSA. The calculated change in enthalpy (ΔH) and association constant (Ka) became greater as the oligomer size increased then plateaued at the heptameric oligomer. These results support a model for precipitation of proteins by proanthocyanidin where increased oligomer size enhanced the opportunity for cross linkages between proteins ultimately forming sediment-able complexes. The authors suggest tannin binding to proteins is opportunistic and involves multiple sites, each with a different Ka and ΔH of binding. The ΔH of binding comprises both an endothermic hydrophobic interaction and exothermic hydrogen bond component. This suggests the calculated entropy value (ΔS) for tannin-protein interactions is subject to a systematic error and should be interpreted with caution.

  15. Comparison of [11C]cocaine binding at tracer and pharmacological doses of baboon brain: A PET study

    Energy Technology Data Exchange (ETDEWEB)

    Volkow, N.D.; Fowler, J.S.; Logan, J. [Brookhaven National Lab., Upton, NY (United States)] [and others


    In vitro studies have shown that cocaine (C) binds to both high and low affinity sites on the dopamine transporter (DAT). We have previously characterized the binding of tracer doses of [{sup 11}C]cocaine (C*)to a high affinity site on the DAT. To assess if in vivo C also binds to low affinity sites we used PET to compare binding of tracer doses (17.8{plus_minus}12.2 {mu}g C) of C* to pharmacological doses (8 mg of C coadministered with C*). Sixteen paired studies were done to assess test/retest variability, specific versus non specific binding and to characterize binding profile. Dynamic scans were started immediately after injection of C* (5-8 mCi) for 50 min on the CTI-931 (6 x 6 x 6.5 mm FWHM). Time activity curves for tissue concentration and for unchanged tracer in plasma were used to calculate the transport constant between plasma and tissue (K1) and to obtain the distribution volume (DV). The ratio of the DV in striatum (ST) to that in cerebellum (CB) (which corresponds to Bmax/Kd-1) was used as model parameter. Peak brain uptake of C* was significantly higher for tracer than for pharmacological doses (0.041 versus 0.033 % dose/cc), as were the values for K1 (1.07{plus_minus}0.21 versus 0.68{plus_minus}0.26 (t=3.0 p<0.01)). Repeated measures were reproducible for tracer ({plus_minus}2%) and pharmacological doses of C* ({plus_minus}4%). Tracer dose C* showed highest binding and slowest clearance in ST which was reduced by C (0.5-2.0 mg/kg iv, -25 to -30%) and by drugs that inhibit DAT (2mg/kg nomifensine - 21%, 0.5 mg/kg methylphenidate -12%) and was increased by serotonin transporter inhibitors (5HT-Ti) (2 mg/kg citalopram +11%, 0.5 mg/kg fluoxetine +6%) and not changed by NE transporter inhibitors (0.5 mg/kg desipramine or 2 mg/kg tomoxetine). The increase with (5HT-Ti) may reflect neurotransmitter interactions or changes in bioavailability. At pharmacological doses C* showed homogeneous distribution and was not changed by C nor by any of the above drugs.

  16. Microdialysis-liquid chromatographic study on competitive binding of drugs to protein

    Institute of Scientific and Technical Information of China (English)

    汪海林; 邹汉法; 张玉奎


    A new method to determine the interaction between drug and protein has been developed by utilizing the technique of microdialysis sampling with the ketoprofen and the human serum albumin (HSA) as the model of drug and protein.Two kinds of binding sites of HSA to ketoprofen have been observed.The binding constants and number of binding sites obtained by the Scatchard equation are 0.799,3.18×106 mol-1 L and 2.15,2.01×105 mol-1 L,respectively The displacement binding of drugs to HSA has also been studied.The strong displacement of competitive binding of ibuprofen with ketoprofen to HSA was observed,which means that the primary binding site of HSA to ketoprofen and that to ibuprofen are the same.However,only a weaker displacement of warfarin for the association of ketoprofen with HSA was observed,which may suggest that the primary binding site of HSA to ketoprofen is different from that to warfarin.Such a displacement effect for competitive binding of drugs to HSA was explained by the displacement model i

  17. Mn(II) binding to human serum albumin: a ¹H-NMR relaxometric study. (United States)

    Fanali, Gabriella; Cao, Yu; Ascenzi, Paolo; Fasano, Mauro


    Human serum albumin (HSA) displays several metal binding sites, participating to essential and toxic metal ions disposal and transport. The major Zn(II) binding site, called Site A, is located at the I/II domain interface, with residues His67, Asn99, His247, and Asp249 contributing with five donor atoms to the metal ion coordination. Additionally, one water molecule takes part of the octahedral coordination geometry. The occurrence of the metal-coordinated water molecule allows the investigation of the metal complex geometry by water (1)H-NMR relaxation, provided that the diamagnetic Zn(II) is replaced by the paramagnetic Mn(II). Here, the (1)H-NMR relaxometric study of Mn(II) binding to HSA is reported. Mn(II) binding to HSA is modulated by Zn(II), pH, and myristate through competitive inhibition and allosteric mechanisms. The body of results indicates that the primary binding site of Zn(II) corresponds to the secondary binding site of Mn(II), i.e. the multimetal binding site A. Excess Zn(II) completely displaces Mn(II) from its primary site suggesting that the primary Mn(II) site corresponds to the secondary Zn(II) site. This uncharacterized site is functionally-linked to FA1; moreover, metal ion binding is modulated by myristate and pH. Noteworthy, water (1)H-NMR relaxometry allowed a detailed analysis of thermodynamic properties of HSA-metal ion complexes.

  18. QM/MM Molecular Dynamics Studies of Metal Binding Proteins

    Directory of Open Access Journals (Sweden)

    Pietro Vidossich


    Full Text Available Mixed quantum-classical (quantum mechanical/molecular mechanical (QM/MM simulations have strongly contributed to providing insights into the understanding of several structural and mechanistic aspects of biological molecules. They played a particularly important role in metal binding proteins, where the electronic effects of transition metals have to be explicitly taken into account for the correct representation of the underlying biochemical process. In this review, after a brief description of the basic concepts of the QM/MM method, we provide an overview of its capabilities using selected examples taken from our work. Specifically, we will focus on heme peroxidases, metallo-β-lactamases, α-synuclein and ligase ribozymes to show how this approach is capable of describing the catalytic and/or structural role played by transition (Fe, Zn or Cu and main group (Mg metals. Applications will reveal how metal ions influence the formation and reduction of high redox intermediates in catalytic cycles and enhance drug metabolism, amyloidogenic aggregate formation and nucleic acid synthesis. In turn, it will become manifest that the protein frame directs and modulates the properties and reactivity of the metal ions.

  19. Fluorescence spectroscopic studies on binding of a flavonoid antioxidant quercetin to serum albumins

    Indian Academy of Sciences (India)

    Beena Mishra; Atanu Barik; K Indira Priyadarsini; Hari Mohan


    Binding of quercetin to human serum albumin (HSA) was studied and the binding constant measured by following the red-shifted absorption spectrum of quercetin in the presence of HSA and the quenching of the intrinsic protein fluorescence in the presence of different concentrations of quercetin. Fluorescence lifetime measurements of HSA showed decrease in the average lifetimes indicating binding at a location, near the tryptophan moiety, and the possibility of fluorescence energy transfer between excited tryptophan and quercetin. Critical transfer distance () was determined, from which the mean distance between tryptophan-214 in HSA and quercetin was calculated. The above studies were also carried out with bovine serum albumin (BSA).

  20. Preferential binding of fisetin to the native state of bovine serum albumin: spectroscopic and docking studies. (United States)

    Singha Roy, Atanu; Pandey, Nitin Kumar; Dasgupta, Swagata


    We have investigated the binding of the biologically important flavonoid fisetin with the carrier protein bovine serum albumin using multi-spectroscopic and molecular docking methods. The binding constants were found to be in the order of 10(4) M(-1) and the number of binding sites was determined as one. MALDI-TOF analyses showed that one fisetin molecule binds to a single bovine serum albumin (BSA) molecule which is also supported by fluorescence quenching studies. The negative Gibbs free energy change (∆G°) values point to a spontaneous binding process which occurs through the presence of electrostatic forces with hydrophobic association that results in a positive entropy change (+51.69 ± 1.18 J mol(-1) K(-1)). The unfolding and refolding of BSA in urea have been studied in absence and presence of fisetin using steady-state fluorescence and lifetime measurements. Urea denaturation studies indicate that fisetin is gradually released from its binding site on the protein. In the absence of urea, an increase in temperature that causes denaturation of the protein results in the release of fisetin from its bound state indicating that fisetin binds only to the native state of the protein. The circular dichroism (CD) and Fourier transform infrared (FTIR) spectroscopic studies showed an increase in % α-helix content of BSA after binding with fisetin. Site marker displacement studies in accordance with the molecular docking results suggested that fisetin binds in close proximity of the hydrophobic cavity in site 1 (subdomain IIA) of the protein. The PEARLS (Program of Energetic Analysis of Receptor Ligand System) has been used to estimate the interaction energy of fisetin with BSA and the results are in good correlation with the experimental findings.

  1. A computational docking study on the pH dependence of peptide binding to HLA-B27 sub-types differentially associated with ankylosing spondylitis (United States)

    Serçinoğlu, Onur; Özcan, Gülin; Kabaş, Zeynep Kutlu; Ozbek, Pemra


    A single amino acid difference (Asp116His), having a key role in a pathogenesis pathway, distinguishes HLA-B*27:05 and HLA-B*27:09 sub-types as associated and non-associated with ankylosing spondylitis, respectively. In this study, molecular docking simulations were carried out with the aim of comprehending the differences in the binding behavior of both alleles at varying pH conditions. A library of modeled peptides was formed upon single point mutations aiming to address the effect of 20 naturally occurring amino acids at the binding core peptide positions. For both alleles, computational docking was applied using Autodock 4.2. Obtained free energies of binding (FEB) were compared within the peptide library and between the alleles at varying pH conditions. The amino acid preferences of each position were studied enlightening the role of each on binding. The preferred amino acids for each position of pVIPR were found to be harmonious with experimental studies. Our results indicate that, as the pH is lowered, the capacity of HLA-B*27:05 to bind peptides in the library is largely lost. Hydrogen bonding analysis suggests that the interaction between the main anchor positions of pVIPR and their respective binding pocket residues are affected from the pH the most, causing an overall shift in the FEB profiles.


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    Full Text Available `INTRODUCTION: Stroke is the third leading cause of death in developed countries after cardiovascular disease and cancer. In India Community Surveys have shown a crude prevalence rate for hemiplegia 200 per 1, 00, 000 population. It accounts for nearly 1.5% of all urban admissions, 4.5 % of all medical and about 20% of neurological cases. AIMS AND OBJECTIVE: Identification of risk factors and evaluation of clinical profile of acute stroke. MATERIAL AND METHOD: INCLUSION CRITERIA: Cases of acute stoke admitted in SGMH hospital were selected for the study. EXCLUSION CRITERIA: Brain injury cases, infective, neoplastic cases producing stroke were excluded. RESULTS: Stroke was more common in male, 58 % patients were male and 42% patients were female. It was more common in 5th and 6th decade. Most common etiology was infarction. Most common risk factor was hypertension followed by smoking. In addition to limb weakness, headache and vomiting were most common presenting symptoms followed by convulsion. These symptoms were more common in hemorrhagic stroke. Right sided hemiplegia was more common than left sided. Middle cerebral artery was involved in majority of cases in atherothrombotic stroke whereas basal ganglion was most common site of bleed in hemorrhagic stroke. Coma and mortality were more in hemorrhagic stroke. CONCLUSION: The risk factors and clinical profile of acute stroke in India are similar to that of Western countries. Common risk factors are hypertension, smoking, diabetes mellitus and hyperlipidemia

  3. Mother and child T cell receptor repertoires: deep profiling study

    Directory of Open Access Journals (Sweden)

    Ekaterina V Putintseva


    Full Text Available The relationship between maternal and child immunity has been actively studied in the context of complications during pregnancy, autoimmune diseases, and haploidentical transplantation of hematopoietic stem cells (HSC and solid organs. Here, we have for the first time used high-throughput Illumina HiSeq sequencing to perform deep quantitative profiling of T-cell receptor (TCR repertoires for peripheral blood samples of three mothers and their six children. Advanced technology allowed accurate identification of 5х105–2х106 TCR beta clonotypes per individual. We performed comparative analysis of these TCR repertoires with the aim of revealing characteristic features that distinguish related mother-child pairs, such as relative TRBV segment usage frequency and relative overlap of TCR beta CDR3 repertoires. We show that thymic selection essentially and similarly shapes the initial output of the TCR recombination machinery in both related and unrelated pairs, with minor effect from inherited differences. The achieved depth of TCR profiling also allowed us to test the hypothesis that mature T cells transferred across the placenta during pregnancy can expand and persist as functional microchimeric clones in their new host, using characteristic TCR beta CDR3 variants as clonal identifiers.

  4. iDNA-Prot|dis: identifying DNA-binding proteins by incorporating amino acid distance-pairs and reduced alphabet profile into the general pseudo amino acid composition.

    Directory of Open Access Journals (Sweden)

    Bin Liu

    Full Text Available Playing crucial roles in various cellular processes, such as recognition of specific nucleotide sequences, regulation of transcription, and regulation of gene expression, DNA-binding proteins are essential ingredients for both eukaryotic and prokaryotic proteomes. With the avalanche of protein sequences generated in the postgenomic age, it is a critical challenge to develop automated methods for accurate and rapidly identifying DNA-binding proteins based on their sequence information alone. Here, a novel predictor, called "iDNA-Prot|dis", was established by incorporating the amino acid distance-pair coupling information and the amino acid reduced alphabet profile into the general pseudo amino acid composition (PseAAC vector. The former can capture the characteristics of DNA-binding proteins so as to enhance its prediction quality, while the latter can reduce the dimension of PseAAC vector so as to speed up its prediction process. It was observed by the rigorous jackknife and independent dataset tests that the new predictor outperformed the existing predictors for the same purpose. As a user-friendly web-server, iDNA-Prot|dis is accessible to the public at Moreover, for the convenience of the vast majority of experimental scientists, a step-by-step protocol guide is provided on how to use the web-server to get their desired results without the need to follow the complicated mathematic equations that are presented in this paper just for the integrity of its developing process. It is anticipated that the iDNA-Prot|dis predictor may become a useful high throughput tool for large-scale analysis of DNA-binding proteins, or at the very least, play a complementary role to the existing predictors in this regard.

  5. Riyadh Mother and Baby Multicenter Cohort Study: The Cohort Profile.

    Directory of Open Access Journals (Sweden)

    Hayfaa Wahabi

    Full Text Available To assess the effects of non-communicable diseases, such as diabetes, hypertension and obesity, on the mother and the infant.A multicentre cohort study was conducted in three hospitals in the city of Riyadh in Saudi Arabia. All Saudi women and their babies who delivered in participating hospitals were eligible for recruitment. Data on socio-demographic characteristics in addition to the maternal and neonatal outcomes of pregnancy were collected. The cohort demographic profile was recorded and the prevalence of maternal conditions including gestational diabetes, pre-gestational diabetes, hypertensive disorders in pregnancy and obesity were estimated.The total number of women who delivered in participating hospitals during the study period was 16,012 of which 14,568 women participated in the study. The mean age of the participants was 29 ± 5.9 years and over 40% were university graduates. Most of the participants were housewives, 70% were high or middle income and 22% were exposed to secondhand smoke. Of the total cohort, 24% were married to a first cousin. More than 68% of the participants were either overweight or obese. The preterm delivery rate was 9%, while 1.5% of the deliveries were postdate. The stillbirth rate was 13/1000 live birth. The prevalence of gestational diabetes was 24% and that of pre-gestational diabetes was 4.3%. The preeclampsia prevalence was 1.1%. The labour induction rate was 15.5% and the cesarean section rate was 25%.Pregnant women in Saudi Arabia have a unique demographic profile. The prevalence of obesity and diabetes in pregnancy are among the highest in the world.

  6. Calorimetric and thermal analysis studies on the binding of phenothiazinium dye thionine with DNA polynucleotides

    Energy Technology Data Exchange (ETDEWEB)

    Paul, Puja; Hossain, Maidul [Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, CSIR, Kolkata 700 032 (India); Suresh Kumar, Gopinatha, E-mail: [Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, CSIR, Kolkata 700 032 (India)


    Research highlights: > Thionine binds to DNA exhibiting alternating guanine-cytosine sequence selectivity. > Exothermic bindings were favoured by negative enthalpy and positive entropy changes. > The binding was characterized by strong thermal stabilization of the polynucleotides. > Complete energetics revealed from the salt and temperature dependent data. - Abstract: Binding of the phenothaizinium dye thionine with four sequence specific deoxyribopolynucleotides, poly(dG-dC).poly(dG-dC), poly(dG).poly(dC), poly(dA-dT).poly(dA-dT), and poly(dA).poly(dT) has been investigated by means of thermal helix melting, isothermal titration calorimetry, and differential scanning calorimetry experiments. The binding affinity values evaluated from isothermal titration calorimetry suggests that thionine exhibits the highest binding affinity to poly(dG-dC).poly(dG-dC). The binding to poly(dG-dC).poly(dG-dC), poly(dA-dT).poly(dA-dT), and poly(dG).poly(dC) is exothermic and favoured by negative enthalpy changes while binding to poly(dA).poly(dT) is endothermic and anomalous. The values of heat capacity changes of the interaction are negative and in the range (-0.4 to -0.5) kJ . K{sup -1} . mol{sup -1}. The binding is characterized by strong stabilization of the polynucleotides against thermal strand separation. The binding affinity values derived from thermal melting data are in excellent agreement with those obtained from isothermal titration calorimetry data. Insights into the energetic aspects and guanine-cytosine selectivity of the DNA interaction of thionine have been obtained from these studies.

  7. Study on the binding mode of Mg(Sal2trien) with DNA

    Institute of Scientific and Technical Information of China (English)

    XI Xiaoli; YANG Manman; ZHOU Chengyong; ZHAO Jing; YANG Pin


    In this study the complex Mg(Sal2trien) was synthesized for the first time, the binding mode of which with CT DNA was studied by the methods of UV spectra, fluorescence spectra, viscosity and CV (cyclic voltammetry). It was found that after the complex acted with CT DNA, the Abs of UV spectra rose obviously; the fluorescence intensity of EB-DNA was almost not changed; viscosity decreased. Determination of cyclic voltammetry showed that DNA made the MgL's formal potential negatively shift. Scatchard plot showed that the addition of the binding mode of the complex to EB was uncompetitive inhibition compared with EB to DNA. So the binding mode of the complex with CT DNA was stable-electricity binding. Then the interaction of the complex with pBR322 was studied by the method of gel electrophoresis. The result showed that the complex could cleave pBR322 DNA effectively.

  8. NMR studies of DNA oligomers and their interactions with minor groove binding ligands

    Energy Technology Data Exchange (ETDEWEB)

    Fagan, Patricia A. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry


    The cationic peptide ligands distamycin and netropsin bind noncovalently to the minor groove of DNA. The binding site, orientation, stoichiometry, and qualitative affinity of distamycin binding to several short DNA oligomers were investigated by NMR spectroscopy. The oligomers studied contain A,T-rich or I,C-rich binding sites, where I = 2-desaminodeoxyguanosine. I•C base pairs are functional analogs of A•T base pairs in the minor groove. The different behaviors exhibited by distamycin and netropsin binding to various DNA sequences suggested that these ligands are sensitive probes of DNA structure. For sites of five or more base pairs, distamycin can form 1:1 or 2:1 ligand:DNA complexes. Cooperativity in distamycin binding is low in sites such as AAAAA which has narrow minor grooves, and is higher in sites with wider minor grooves such as ATATAT. The distamycin binding and base pair opening lifetimes of I,C-containing DNA oligomers suggest that the I,C minor groove is structurally different from the A,T minor groove. Molecules which direct chemistry to a specific DNA sequence could be used as antiviral compounds, diagnostic probes, or molecular biology tools. The author studied two ligands in which reactive groups were tethered to a distamycin to increase the sequence specificity of the reactive agent.

  9. Trends in the Binding of Cell Penetrating Peptides to siRNA: A Molecular Docking Study (United States)

    Gunathunge, B. G. C. M.; Wimalasiri, P. N.; Karunaratne, D. N.


    The use of gene therapeutics, including short interfering RNA (siRNA), is limited by the lack of efficient delivery systems. An appealing approach to deliver gene therapeutics involves noncovalent complexation with cell penetrating peptides (CPPs) which are able to penetrate the cell membranes of mammals. Although a number of CPPs have been discovered, our understanding of their complexation and translocation of siRNA is as yet insufficient. Here, we report on computational studies comparing the binding affinities of CPPs with siRNA, considering a variety of CPPs. Specifically, seventeen CPPs from three different categories, cationic, amphipathic, and hydrophobic CPPs, were studied. Molecular mechanics were used to minimize structures, while molecular docking calculations were used to predict the orientation and favorability of sequentially binding multiple peptides to siRNA. Binding scores from docking calculations were highest for amphipathic peptides over cationic and hydrophobic peptides. Results indicate that initial complexation of peptides will likely occur along the major groove of the siRNA, driven by electrostatic interactions. Subsequent binding of CPPs is likely to occur in the minor groove and later on bind randomly, to siRNA or previously bound CPPs, through hydrophobic interactions. However, hydrophobic CPPs do not show this binding pattern. Ultimately binding yields a positively charged nanoparticle capable of noninvasive cellular import of therapeutic molecules.

  10. Methyl-triclosan binding to human serum albumin: multi-spectroscopic study and visualized molecular simulation. (United States)

    Lv, Wenjuan; Chen, Yonglei; Li, Dayong; Chen, Xingguo; Leszczynski, Jerzy


    Methyl-triclosan (MTCS), a transformation product and metabolite of triclosan, has been widely spread in environment through the daily use of triclosan which is a commonly used anti-bacterial and anti-fungal substance in consumer products. Once entering human body, MTCS could affect the conformation of human serum albumin (HSA) by forming MTCS-HSA complex and alter function of protein and endocrine in human body. To evaluate the potential toxicity of MTCS, the binding mechanism of HSA with MTCS was investigated by UV-vis absorption, circular dichroism and Fourier transform infrared spectroscopy. Binding constants, thermodynamic parameters, the binding forces and the specific binding site were studied in detail. Binding constant at room tempreture (T = 298K) is 6.32 × 10(3)L mol(-1); ΔH(0), ΔS(0) and ΔG(0) were 22.48 kJ mol(-1), 148.16 J mol(-1)K(-1) and -21.68 kJ mol(-1), respectively. The results showed that the interactions between MTCS and HSA are mainly hydrophobic forces. The effects of MTCS on HSA conformation were also discussed. The binding distance (r = 1.2 nm) for MTCS-HSA system was calculated by the efficiency of fluorescence resonance energy transfer. The visualized binding details were also exhibited by molecular modeling method and the results could agree well with that from the experimental study.

  11. Receptor binding profiles and quantitative structure-affinity relationships of some 5-substituted-N,N-diallyltryptamines. (United States)

    Cozzi, Nicholas V; Daley, Paul F


    N,N-Diallyltryptamine (DALT) and 5-methoxy-N,N-diallyltryptamine (5-MeO-DALT) are two tryptamines synthesized and tested by Alexander Shulgin. In self-experiments, 5-MeO-DALT was reported to be psychoactive in the 12-20mg range, while the unsubstituted compound DALT had few discernible effects in the 42-80 mg range. Recently, 5-MeO-DALT has been used in nonmedical settings for its psychoactive effects, but these effects have been poorly characterized and little is known of its pharmacological properties. We extended the work of Shulgin by synthesizing additional 5-substituted-DALTs. We then compared them to DALT and 5-MeO-DALT for their binding affinities at 45 cloned receptors and transporter proteins. Based on in vitro binding affinity, we identified 27 potential receptor targets for the 5-substituted-DALT compounds. Five of the DALT compounds had affinity in the 10-80 nM range for serotonin 5-HT1A and 5-HT2B receptors, while the affinity of DALT itself at 5-HT1A receptors was slightly lower at 100 nM. Among the 5-HT2 subtypes, the weakest affinity was at 5-HT2A receptors, spanning 250-730 nM. Five of the DALT compounds had affinity in the 50-400 nM range for serotonin 5-HT1D, 5-HT6, and 5-HT7 receptors; again, it was the unsubstituted DALT that had the weakest affinity at all three subtypes. The test drugs had even weaker affinity for 5-HT1B, 5-HT1E, and 5-HT5A subtypes and little or no affinity for the 5-HT3 subtype. These compounds also had generally nanomolar affinities for adrenergic α2A, α2B, and α2C receptors, sigma receptors σ1 and σ2, histamine H1 receptors, and norepinephrine and serotonin uptake transporters. They also bound to other targets in the nanomolar-to-low micromolar range. Based on these binding results, it is likely that multiple serotonin receptors, as well as several nonserotonergic sites are important for the psychoactive effects of DALT drugs. To learn whether any quantitative structure-affinity relationships existed, we evaluated

  12. Study Of Clinical Profile of Allergic Contact Dermatitis In Pune

    Directory of Open Access Journals (Sweden)

    Sayal S K


    Full Text Available One hundred and twenty five cases of clinically diagnosed allergic contact dermatitis were studied. All patients were subjected to patch test with standard test allergens and also with suspected test allergens based on history and clinical profile. Allergic contact dermatitis due to Parthenium hysterophorus was commonest and found in 64% cases, followed by wearing apparel and jewellery in 16.8%, topical medicaments in 8% and cosmetics and occupational contactants in 5.6% cases each. The common individual allergens other than parthenium, were nickel in 8.8%, leather, hair dye and cement in 3.2% each, nitrofurazone and petrol, oil, lubricant (POL in 2.4% each. Patch test with suspected allergens was positive in 72% of cases.

  13. NMR Studies of a New Binding Mode of the Amino Acid Esters by Porphyrinatozinc(Ⅱ)

    Institute of Scientific and Technical Information of China (English)


    The binding mode of the amino acid ethyl esters(guest) by 5-(2-carboxylphenyl)-10,15,20-triphenylporphyrinatozinc(Ⅱ)(host 1) was studied by means of 1H NMR spectra. The binding mode is the hydrogen-bonding between the amino group of the guest and the carboxyl group of host 1 plus the coordination between the zinc atom of porphyrinatozinc(Ⅱ) and the carbonyl group of the guest. This is a novel binding mode of the metalloporphyrin to amino acid derivatives.

  14. Multispectroscopic and calorimetric studies on the binding of the food colorant tartrazine with human hemoglobin. (United States)

    Basu, Anirban; Suresh Kumar, Gopinatha


    Interaction of the food colorant tartrazine with human hemoglobin was studied using multispectroscopic and microcalorimetric techniques to gain insights into the binding mechanism and thereby the toxicity aspects. Hemoglobin spectrum showed hypochromic changes in the presence of tartrazine. Quenching of the fluorescence of hemoglobin occurred and the quenching mechanism was through a static mode as revealed from temperature dependent and time-resolved fluorescence studies. According to the FRET theory the distance between β-Trp37 of hemoglobin and bound tartrazine was evaluated to be 3.44nm. Synchronous fluorescence studies showed that tartrazine binding led to alteration of the microenvironment around the tryptophans more in comparison to tyrosines. 3D fluorescence and FTIR data provided evidence for conformational changes in the protein on binding. Circular dichroism studies revealed that the binding led to significant loss in the helicity of hemoglobin. The esterase activity assay further complemented the circular dichroism data. Microcalorimetric study using isothermal titration calorimetry revealed the binding to be exothermic and driven largely by positive entropic contribution. Dissection of the Gibbs energy change proposed the protein-dye complexation to be dominated by non-polyelectrolytic forces. Negative heat capacity change also corroborated the involvement of hydrophobic forces in the binding process.

  15. DNA binding, DNA cleavage, and cytotoxicity studies of two new copper (II) complexes. (United States)

    Kashanian, Soheila; Khodaei, Mohammad Mehdi; Roshanfekr, Hamideh; Shahabadi, Nahid; Rezvani, Alireza; Mansouri, Ghobad


    The DNA binding behavior of [Cu(phen)(phen-dione)Cl]Cl (1) and [Cu(bpy)(phen-dione)Cl]Cl (2) was studied with a series of techniques including UV-vis absorption, circular dichroism spectroscopy, and viscometric methods. Cytotoxicity effect and DNA unwinding properties were also investigated. The results indicate that the Cu(II) complexes interact with calf-thymus DNA by both partially intercalative and hydrogen binding. These findings have been further substantiated by the determination of intrinsic binding constants spectrophotometrically, 12.5 × 10(5) and 5 × 10(5) for 1 and 2, respectively. Our findings suggest that the type of ligands and structure of complexes have marked effect on the binding affinity of complexes involving CT-DNA. Circular dichroism results show that complex 1 causes considerable increase in base stacking of DNA, whereas 2 decreases the base stacking, which is related to more extended aromatic area of 1,10-phenanthroline in 1 rather than bipyridine in 2. Slow decrease in DNA viscosity indicates partially intercalative binding in addition to hydrogen binding on the surface of DNA. The second binding mode was also confirmed by additional tests: interaction in denaturation condition and acidic pH. Also, these new complexes induced cleavage in pUC18 plasmid DNA as indicated in gel electrophoresis and showed excellent antitumor activity against K562 (human chronic myeloid leukemia) cells.

  16. Binding of phenazinium dye safranin T to polyriboadenylic acid: spectroscopic and thermodynamic study. (United States)

    Pradhan, Ankur Bikash; Haque, Lucy; Roy, Snigdha; Das, Suman


    Here, we report results from experiments designed to explore the association of the phenazinium dye safranin T (ST, 3,7-diamino-2,8-dimethyl-5-phenylphenazinium chloride) with single and double stranded form of polyriboadenylic acid (hereafter poly-A) using several spectroscopic techniques. We demonstrate that the dye binds to single stranded polyriboadenylic acid (hereafter ss poly-A) with high affinity while it does not interact at all with the double stranded (ds) form of the polynucleotide. Fluorescence and absorption spectral studies reveal the molecular aspects of binding of ST to single stranded form of the polynucleotide. This observation is also supported by the circular dichroism study. Thermodynamic data obtained from temperature dependence of binding constant reveals that association is driven by negative enthalpy change and opposed by negative entropy change. Ferrocyanide quenching studies have shown intercalative binding of ST to ss poly-A. Experiments on viscosity measurements confirm the binding mode of the dye to be intercalative. The effect of [Na⁺] ion concentration on the binding process suggests the role of electrostatic forces in the complexation. Present studies reveal the utility of the dye in probing nucleic acid structure.

  17. Binding of phenazinium dye safranin T to polyriboadenylic acid: spectroscopic and thermodynamic study.

    Directory of Open Access Journals (Sweden)

    Ankur Bikash Pradhan

    Full Text Available Here, we report results from experiments designed to explore the association of the phenazinium dye safranin T (ST, 3,7-diamino-2,8-dimethyl-5-phenylphenazinium chloride with single and double stranded form of polyriboadenylic acid (hereafter poly-A using several spectroscopic techniques. We demonstrate that the dye binds to single stranded polyriboadenylic acid (hereafter ss poly-A with high affinity while it does not interact at all with the double stranded (ds form of the polynucleotide. Fluorescence and absorption spectral studies reveal the molecular aspects of binding of ST to single stranded form of the polynucleotide. This observation is also supported by the circular dichroism study. Thermodynamic data obtained from temperature dependence of binding constant reveals that association is driven by negative enthalpy change and opposed by negative entropy change. Ferrocyanide quenching studies have shown intercalative binding of ST to ss poly-A. Experiments on viscosity measurements confirm the binding mode of the dye to be intercalative. The effect of [Na⁺] ion concentration on the binding process suggests the role of electrostatic forces in the complexation. Present studies reveal the utility of the dye in probing nucleic acid structure.

  18. The Dynamic Pollen Tube Cytoskeleton: Live Cell Studies Using Actin-Binding and Microtubule-Binding Reporter Proteins

    Institute of Scientific and Technical Information of China (English)

    Alice Y. Cheung; Qiao-hong Duan; Silvia Santos Costa; Barend Graaf; Veronica S.Di Stilio; Jose Feijo; Hen-Ming Wu


    Pollen tubes elongate within the pistil to transport sperm cells to the embryo sac for fertilization.Growth occurs exclusively at the tube apex,rendering pollen tube elongation a most dramatic polar cell growth process.A hall-mark pollen tube feature is its cytoskeleton,which comprises elaborately organized and dynamic actin microfilaments and microtubules.Pollen tube growth is dependent on the actin cytoskeleton;its organization and regulation have been exalined extensively by various approaches.including fluorescent protein labeled actin-binding proteins in live cell studies.Using the previously described GFP-NtADF1 and GFP-LIADF1, and a new actin reporter protein NtPLIM2b-GFP,we re-affirm that the predominant actin structures in elongating tobacco and lily pollen tubes are long,streaming actin cables along the pollen tube shank,and a subapical structure comprising shorter actin cables.The subapical collection of actin microfilaments undergoes dynamic changes,giving rise to the appearance of structures that range from basket-or funnel-shaped,mesh-like to a subtle ring.NtPLIM2b-GFP is used in combination with a guanine nucleotide exchange factor for the Rho GTPases,AtROP-GEF1,to illustrate the use of these actin reporter proteins to explore the linkage between the polar cell growth process and its actin cytoskeleton.Contrary to the actin cytoskeleton,microtubules appear not to play a direct role in supporting the polar cell growth process in angiosperm pollen tubes.Using a microtubule reporter protein based on the microtubule end-binding protein from Arabidopsis AtEB1,GFP-AtEB1,we show that the extensive microtubule network in elongating pollen tubes displays varying degrees of dynamics.These reporter proteins provide versatile tools to explore the functional connection between major structural and signaling components of the polar pollen tube growth process.

  19. Atomic force microscopy study of cellulose surface interaction controlled by cellulose binding domains


    Nigmatullin, R.; Lovitt, R.; Wright, C; Linder, M.; Nakari-Setälä, T; Gama, F. M.


    Colloidal probe microscopy has been used to study the interaction between model cellulose surfaces and the role of cellulose binding domain (CBD), peptides specifically binding to cellulose, in interfacial interaction of cellulose surfaces modified with CBDs. The interaction between pure cellulose surfaces in aqueous electrolyte solution is dominated by double layer repulsive forces with the range and magnitude of the net force dependent on electrolyte concentration. AFM imaging reve...

  20. Didanosine Prodrugs : Synthesis, protein binding, bioanalytical method development and pharmacokinetic studies


    Høyem, Sverre


    A series of prodrugs of 2´, 3´-dideoxyinosine (didanosine, ddI) were synthesized in an effort to alter different pharmacokinetic properties. The 5`OH function of ddI was esterified with three different carboxylic diacids. The diacids used was adipic acid, azelaic acid, dodecanedioic acid. The synthesis was optimized in order to develop a high yielding and regioselective synthesis. Protein binding studies, using ultrafiltration, showed an increased protein binding compared to ddI itself....

  1. Kinome-wide Selectivity Profiling of ATP-competitive Mammalian Target of Rapamycin (mTOR) Inhibitors and Characterization of Their Binding Kinetics* (United States)

    Liu, Qingsong; Kirubakaran, Sivapriya; Hur, Wooyoung; Niepel, Mario; Westover, Kenneth; Thoreen, Carson C.; Wang, Jinhua; Ni, Jing; Patricelli, Matthew P.; Vogel, Kurt; Riddle, Steve; Waller, David L.; Traynor, Ryan; Sanda, Takaomi; Zhao, Zheng; Kang, Seong A.; Zhao, Jean; Look, A. Thomas; Sorger, Peter K.; Sabatini, David M.; Gray, Nathanael S.


    An intensive recent effort to develop ATP-competitive mTOR inhibitors has resulted in several potent and selective molecules such as Torin1, PP242, KU63794, and WYE354. These inhibitors are being widely used as pharmacological probes of mTOR-dependent biology. To determine the potency and specificity of these agents, we have undertaken a systematic kinome-wide effort to profile their selectivity and potency using chemical proteomics and assays for enzymatic activity, protein binding, and disruption of cellular signaling. Enzymatic and cellular assays revealed that all four compounds are potent inhibitors of mTORC1 and mTORC2, with Torin1 exhibiting ∼20-fold greater potency for inhibition of Thr-389 phosphorylation on S6 kinases (EC50 = 2 nm) relative to other inhibitors. In vitro biochemical profiling at 10 μm revealed binding of PP242 to numerous kinases, although WYE354 and KU63794 bound only to p38 kinases and PI3K isoforms and Torin1 to ataxia telangiectasia mutated, ATM and Rad3-related protein, and DNA-PK. Analysis of these protein targets in cellular assays did not reveal any off-target activities for Torin1, WYE354, and KU63794 at concentrations below 1 μm but did show that PP242 efficiently inhibited the RET receptor (EC50, 42 nm) and JAK1/2/3 kinases (EC50, 780 nm). In addition, Torin1 displayed unusually slow kinetics for inhibition of the mTORC1/2 complex, a property likely to contribute to the pharmacology of this inhibitor. Our results demonstrated that, with the exception of PP242, available ATP-competitive compounds are highly selective mTOR inhibitors when applied to cells at concentrations below 1 μm and that the compounds may represent a starting point for medicinal chemistry efforts aimed at developing inhibitors of other PI3K kinase-related kinases. PMID:22223645

  2. Molecular dynamics study of DNA binding by INT-DBD under a polarized force field. (United States)

    Yao, Xue X; Ji, Chang G; Xie, Dai Q; Zhang, John Z H


    The DNA binding domain of transposon Tn916 integrase (INT-DBD) binds to DNA target site by positioning the face of a three-stranded antiparallel β-sheet within the major groove. As the negatively charged DNA directly interacts with the positively charged residues (such as Arg and Lys) of INT-DBD, the electrostatic interaction is expected to play an important role in the dynamical stability of the protein-DNA binding complex. In the current work, the combined use of quantum-based polarized protein-specific charge (PPC) for protein and polarized nucleic acid-specific charge (PNC) for DNA were employed in molecular dynamics simulation to study the interaction dynamics between INT-DBD and DNA. Our study shows that the protein-DNA structure is stabilized by polarization and the calculated protein-DNA binding free energy is in good agreement with the experimental data. Furthermore, our study revealed a positive correlation between the measured binding energy difference in alanine mutation and the occupancy of the corresponding residue's hydrogen bond. This correlation relation directly relates the contribution of a specific residue to protein-DNA binding energy to the strength of the hydrogen bond formed between the specific residue and DNA.

  3. Study of caffeine binding to human serum albumin using optical spectroscopic methods

    Institute of Scientific and Technical Information of China (English)


    The binding of caffeine to human serum albumin (HSA) under physiological conditions has been stud-ied by the methods of fluorescence,UV-vis absorbance and circular dichroism (CD) spectroscopy. The mechanism of quenching of HSA fluorescence by caffeine was shown to involve a dynamic quenching procedure. The number of binding sites n and apparent binding constant Kb were measured by the fluorescence quenching method and the thermodynamic parameters △H,△G,△S were calculated. The results indicate that the binding is mainly enthalpy-driven,with van der Waals interactions and hydrogen bonding playing major roles in the reaction. The distance r between donor (HSA) and acceptor (caffeine) was obtained according to the Frster theory of non-radiative energy transfer. Synchronous fluorescence,CD and three-dimensional fluorescence spectroscopy showed that the microenvironment and conformation of HSA were altered during the reaction.

  4. Mutual positional preference of IPMDH proteins for binding studied by coarse-grained molecular dynamics simulation (United States)

    Ishioka, T.; Yamada, H.; Miyakawa, T.; Morikawa, R.; Akanuma, S.; Yamagishi, A.; Takasu, M.


    Proteins, which incorporate charged and hydrophobic amino acid residues, are useful as a material of nanotechnology. Among these proteins, IPMDH (3-isopropylmalate dehydrogenase), which has thermal stability, has potential as a material of nanofiber. In this study, we performed coarse-grained molecular dynamics simulation of IPMDH using MARTINI force fields, and we investigated the orientation for the binding of IPMDH. In simulation, we analyzed wild type of IPMDH and the mutated IPMDH proteins, where 13, 20, 27, 332, 335 and 338th amino acid residues are replaced by lysine residues which have positive charge and by glutamic acid residues which have negative charge. Since the binding of mutated IPMDH is advantageous compared with the binding of wild type for one orientation, we suggest that the Coulomb interaction for the binding of IPMDH is important.

  5. Experimental and theoretical study on the binding of 2-mercaptothiazoline to bovine serum albumin

    Energy Technology Data Exchange (ETDEWEB)

    Teng, Yue, E-mail:; Wang, Xiang; Zou, Luyi; Huang, Ming; Du, Xianzheng


    2-Mercaptothiazoline (MTZ) is widely utilized as a brightening and stabilization agent, corrosion inhibitor and antifungal reagent. The residue of MTZ in the environment is potentially hazardous to human health. In this study, the binding mode of MTZ with bovine serum albumin (BSA) was investigated using spectroscopic and molecular docking methods under physiological conditions. MTZ could spontaneously bind with BSA through hydrogen bond and van der Waals interactions with one binding site. The site marker displacement experiments and the molecular docking revealed that MTZ bound into site II (subdomain IIIA) of BSA, which further resulted in some backbone structures and microenvironmental changes of BSA. This work is helpful for understanding the transportation, distribution and toxicity effects of MTZ in blood. - Highlights: • The mechanism was explored by multiple spectroscopic and molecular docking methods. • MTZ can spontaneously bind with BSA at subdomain IIIA (site II). • MTZ can lead to some conformational changes of BSA.

  6. Studies on the binding of vinpocetine to human serum albumin by molecular spectroscopy and modeling

    Institute of Scientific and Technical Information of China (English)

    Hua Jiang; Rong Rong Chen; Hong Cui Wang; Han Lin Pu


    The interaction between vinpocetine (VPC) and human serum albumin (HSA) in physiological buffer (pH 7.40) was investigated by fluorescence,FT-IR,UV-vis absorption and molecular modeling.VPC effectively quenched the intrinsic fluorescence of HSA via static quenching.The binding site number n and apparent binding constant Ka,corresponding thermodynamic parameters △G,△H and △S at different temperatures were calculated.The synchronous fluorescence and FT-IR spectra were used to investigate the structural change of HSA molecules with addition of VPC.Molecular modeling indicated that VPC could bind to the site I of HSA and hydrophobic interaction was the major acting force,which was in agreement with the binding mode study.

  7. [Electron paramagnetic resonance study of the interactions between steroid hormones and binding proteins]. (United States)

    Basset, M; Chambaz, E M; Defaye, G; Metz, B


    Interaction of a spin labeled corticosteroid (desoxycorticosterone nitroxyde: DOC -NO) with three purified proteins (albumin, transcortin, progesterone binding protein: PBG) was studied by electron spin resonance (ESR) spectroscopy. DOC-NO was competitive with natural corticosteroids and therefore bound at the same site to specific binding proteins. ESR spectra in the presence of each of the proteins showed an immobilized (bound) form of the spin labeled steroid and allowed the calculation of the corresponding association constant (Ka) at equilibrium. The three binding proteins could be characterized by the ESR parameters of the DOC-NO bound form. The thermodynamic parameters (deltaH, deltaS) of the steroid-protein interactions were calculated from the ESR data obtained within a wide temperature range (3--40 degrees C). The ESR spectra width (2T) was used to evaluate the polarity of the spin label environment within the steroid binding site: a hydrophobic character was observed for transcortin whereas PBG exhibited a more hydrophilic steroid binding sits. The rotational correlation time of the three protein DOC-NO complexes at equilibrium were calculated from ESR data; the results were correlated with the protein molecular size and suggested a non spherical shape for the binding macromolecule in solution. Spin labelling of biologically active steroids thus provides a novel approach for the study of the interaction of these hormones with their binding protein. Providing a suitable spin label, the ESR parameters may allow the characterization of several types of binding sites of different biological significance for the same hormone, in biological fluids as well as in target tissues.

  8. Study on design of the regular concave surface profiles

    Institute of Scientific and Technical Information of China (English)


    Regular concave surface profiles are adopted in many friction surfaces. But up to now,this is seldom tutored by the theory of lubrication. To design them, a model of the regular depthoptimization was provided. To determine the other size, two propositions are given. At same time,two main effect factors on lubrication were discussed in detail. A lubrication test for different regu-lar concave surface profiles was performed on a pin and ring tester. On the basis of theory analy-sis and experiment, a principle to design regular concave surface profiles is provided.

  9. Correlation study between sperm concentration, hyaluronic acid-binding capacity and sperm aneuploidy in Hungarian patients. (United States)

    Mokánszki, Attila; Molnár, Zsuzsanna; Ujfalusi, Anikó; Balogh, Erzsébet; Bazsáné, Zsuzsa Kassai; Varga, Attila; Jakab, Attila; Oláh, Éva


    Infertile men with low sperm concentration and/or less motile spermatozoa have an increased risk of producing aneuploid spermatozoa. Selecting spermatozoa by hyaluronic acid (HA) binding may reduce genetic risks such as chromosomal rearrangements and numerical aberrations. Fluorescence in-situ hybridization (FISH) has been used to evaluate the presence of aneuploidies. This study examined spermatozoa of 10 oligozoospermic, 9 asthenozoospermic, 9 oligoasthenozoospermic and 17 normozoospermic men by HA binding and FISH. Mean percentage of HA-bound spermatozoa in the normozoospermic group was 81%, which was significantly higher than in the oligozoospermic (Psex chromosomes (P=0.014) and chromosome 17 (P=0.0019), diploidy (P=0.03) and estimated numerical chromosome aberrations (P=0.004) were significantly higher in the oligoasthenozoospermic group compared with the other groups. There were statistically significant relationships (Pchromosome aberrations (r=-0.668) and between HA binding and estimated numerical chromosome aberrations (r=-0.682). HA binding and aneuploidy studies of spermatozoa in individual cases allow prediction of reproductive prognosis and provision of appropriate genetic counselling. Infertile men with normal karyotypes and low sperm concentrations and/or less motile spermatozoa have significantly increased risks of producing aneuploid (diminished mature) spermatozoa. Selecting spermatozoa by hyaluronic acid (HA) binding, based on a binding between sperm receptors for zona pellucida and HA, may reduce the potential genetic risks such as chromosomal rearrangements and numerical aberrations. In the present study we examined sperm samples of 45 men with different sperm parameters by HA-binding assay and fluorescence in-situ hybridization (FISH). Mean percentage of HA-bound spermatozoa in the normozoospermic group was significantly higher than the oligozoospermic, the asthenozoospermic and the oligoasthenozoospermic groups. Using FISH, disomy of sex

  10. Development of an autonomous vertical profiler for oceanographic studies

    Digital Repository Service at National Institute of Oceanography (India)

    Dabholkar, N.; Desa, E.; Afzulpurkar, S.; Madhan, R.; Mascarenhas, A.A.M.Q.; Navelkar, G.; Maurya, P.K.; Prabhudesai, S.; Nagvekar, S.; Martins, H.; Sawkar, G.; Fernandes, P.; Manoj, K.K.

    groups. This paper is based on a concept patent on a thruster driven Autonomous Vertical profiler [AVP], and describes the developmental steps being taken on the integration of sensors, control electronics, communications and a Graphical User interface...

  11. Preparation of isolated bovine adipocytes: validation of use for studies characterizing insulin sensitivity and binding. (United States)

    Vasilatos, R; Etherton, T D; Wangsness, P J


    The present study was undertaken to develop techniques to isolate bovine adipocytes, to compare their rates of glucose metabolism and insulin sensitivity with adipocytes in adipose tissue, and to determine if isolated bovine adipocytes specifically bind insulin. Cell size and diameter distributions were the same for adipocytes fixed with OsO4 after isolation with collagenase and adipocytes liberated from OsO4-fixed adipose tissue slices. On a per cell basis, lipogenic rates were greater for isolated adipocytes compared with intact adipose tissue. Similar differences were found for glucose oxidation. In short term incubations, glucose oxidation and lipid synthesis were not stimulated by insulin (0-100 ng/ml) in either isolated adipocytes or tissue. Specific binding of [125I]iodoinsulin at 30 C was low (0.8%) in the first group of six beef cattle sampled, but increased with increasing cell concentration. Insulin degradation after 90 min was less than 5%. The specificity of [125I]iodoinsulin binding was studied in a second group of six animals. There was no specific binding of insulin in this group. In summary, bovine adipocytes can be isolated which are metabolically active and provide a valid system for studying hormone binding and action. In the present study, glucose metabolism in bovine adipocytes was not stimulated by insulin in vitro. This insensitivity to insulin was associated with a negligible capacity for insulin binding. These findings suggest that the lack of insulin sensitivity in bovine adipose tissue may be due to an inability to specifically bind insulin. This may be related to the unique metabolism of ruminant adipose tissue, which is less dependent upon glucose for fatty acid synthesis than is adipose tissue from nonruminant species.

  12. Kinetic studies show that Ca2+ and Tb3+ have different binding preferences toward the four Ca2+-binding sites of calmodulin. (United States)

    Wang, C L; Leavis, P C; Gergely, J


    The stepwise addition of Tb3+ to calmodulin yields a large tyrosine-sensitized Tb3+ luminescence enhancement as the third and fourth ions bind to the protein [Wang, C.-L. A., Aquaron, R. R., Leavis, P. C., & Gergely, J. (1982) Eur. J. Biochem. 124, 7-12]. Since the only tyrosine residues in calmodulin are located within binding sites III and IV, these results suggest that Tb3+ binds first to sites I and II. Recent NMR studies have provided evidence that Ca2+, on the other hand, binds preferentially to sites III and IV. Kinetic studies using a stopped-flow apparatus also show that the preferential binding of Ca2+ and lanthanide ions is different. Upon rapid mixing of 2Ca-calmodulin with two Tb3+ ions, there was a small and rapid tyrosine fluorescence change, but no Tb3+ luminescence was observed, indicating that Tb3+ binds to sites I and II but not sites III and IV. When two Tb3+ ions are mixed with 2Dy-calmodulin, Tb3+ luminescence rises rapidly as Tb3+ binds to the empty sites III and IV, followed by a more gradual decrease (k = 0.4 s-1 as the ions redistribute themselves over the four sites. These results indicate that (i) both Tb3+ and Dy3+ prefer binding to sites I and II of calmodulin and (ii) the binding of Tb3+ to calmodulin is not impeded by the presence of two Ca2+ ions initially bound to the protein. Thus, the Ca2+ and lanthanide ions must exhibit opposite preferences for the four sites of calmodulin: sites III and IV are the high-affinity sites for Ca2+, whereas Tb3+ and Dy3+ prefer sites I and II.

  13. Chick intestinal cytosol binding protein for 1,25-dihydroxyvitamin D/sub 3/: a study of analog binding

    Energy Technology Data Exchange (ETDEWEB)

    Kream, B.E.; Jose, M.J.L.; DeLuca, H.F.


    The structural features of 1,25-dihydroxyvitamin D/sub 3/ that permit its high affinity binding to a 3.7 S protein from chick intestinal cytosol were determined in a series of binding and competition experiments analyzed by sucrose density gradient centrifugation. Optimal binding to the 3.7 S protein was achieved when both 1..cap alpha..- and 25-hydroxyls were present in the vitamin D/sub 3/ molecule. Modification of the side chain by the introduction of a methyl on C-24 and a double bond on C-22,23 (1,25-dihydroxyvitamin D/sub 2/) did not alter the binding of 1,25-dihydroxyvitamin D/sub 3/, but significantly diminished the binding of 25-hydroxyvitamin D/sub 3/. However, introduction of a hydroxyl on C-24 decreased the ability of either 1,25-dihydroxyvitamin D/sub 3/ or 25-hydroxyvitamin D/sub 3/ to compete, especially when the 24-hydroxyl was in the S configuration. These results reveal that the 3.7 S protein requires specific ligand structural features for binding and suggest that metabolite discrimination by the chick intestinal receptor system is likely located in the 3.7 S cytosol protein.

  14. Combinatorial Synthesis, Screening, and Binding Studies of Highly Functionalized Polyamino-amido Oligomers for Binding to Folded RNA

    Directory of Open Access Journals (Sweden)

    Jonathan K. Pokorski


    Full Text Available Folded RNA molecules have recently emerged as critical regulatory elements in biological pathways, serving not just as carriers of genetic information but also as key components in enzymatic assemblies. In particular, the transactivation response element (TAR of the HIV genome regulates transcriptional elongation by interacting specifically with the Tat protein, initiating the recruitment of the elongation complex. Preventing this interaction from occurring in vivo halts HIV replication, thus making RNA-binding molecules an intriguing pharmaceutical target. Using α-amino acids as starting materials, we have designed and synthesized a new class of polyamino-amido oligomers, called PAAs, specifically for binding to folded RNA structures. The PAA monomers were readily incorporated into a 125-member combinatorial library of PAA trimers. In order to rapidly assess RNA binding, a quantum dot-based fluorescent screen was developed to visualize RNA binding on-resin. The binding affinities of hits were quantified using a terbium footprinting assay, allowing us to identify a ligand (SFF with low micromolar affinity (kd=14 μM for TAR RNA. The work presented herein represents the development of a flexible scaffold that can be easily synthesized, screened, and subsequently modified to provide ligands specific for binding to folded RNAs.

  15. Study of MMLV RT- Binding with DNA using Surface Plasmon Resonance Biosensor

    Institute of Scientific and Technical Information of China (English)

    Lei WU; Ming-Hui HUANG; Jian-Long ZHAO; Meng-Su YANG


    Surface plasmon resonance biosensor technique was used to study the binding of Moloney murine leukemia virus reverse transcriptase without RNase H domain (MMLV RT-) with DNA in the absence and in the presence of inhibitors. Different DNA substrates, including single-stranded DNA (ssDNA),DNA template-primer (T-P) duplex and gapped DNA, were immobilized on the biosensor chip surface using streptavidin-biotin, and MMLV RT--DNA binding kinetics were analyzed by different models. MMLV RT-could bind with ssDNA and the binding was involved in conformation change. MMLV RT- binding DNA T-P duplex and gapped DNA could be analyzed using the simple 1:1 Langmuir model. The lack of RNase H domain reduced the affinity between MMLV RT- and T-P duplex. The effects of RT inhibitors, including efavirenz, nevirapine and quercetin, on the interaction between MMLV RT- and gapped DNA were analyzed according to recovered kinetics parameters. Efavirenz slightly interfered with the binding between RT and DNA and the affinity constant in the presence of the inhibitor (KA=1.21× 106 M-1) was lower than in the absence of the inhibitor (KA=4.61× 106 M-1). Nevirapine induced relatively tight binding between RT and DNA and the affinity constant in the presence of the inhibsitor (KA=l.47×107 M-1) was approximately three folds higher than without nevirapine, mainly due to rapid association and slow dissociation. Quercetin, a flavonoid originating from plant which has previously shown strong inhibition of the activity of RT, was found to have minimal effect on the RT-DNA binding.

  16. Mechanism of Auxin Interaction with Auxin Binding Protein (ABP1): A Molecular Dynamics Simulation Study (United States)

    Bertoša, Branimir; Kojić-Prodić, Biserka; Wade, Rebecca C.; Tomić, Sanja


    Auxin Binding Protein 1 (ABP1) is ubiquitous in green plants. It binds the phytohormone auxin with high specificity and affinity, but its role in auxin-induced processes is unknown. To understand the proposed receptor function of ABP1 we carried out a detailed molecular modeling study. Molecular dynamics simulations showed that ABP1 can adopt two conformations differing primarily in the position of the C-terminus and that one of them is stabilized by auxin binding. This is in agreement with experimental evidence that auxin induces changes at the ABP1 C-terminus. Simulations of ligand egress from ABP1 revealed three main routes by which an auxin molecule can enter or leave the ABP1 binding site. Assuming the previously proposed orientation of ABP1 to plant cell membranes, one of the routes leads to the membrane and the other two to ABP1's aqueous surroundings. A network of hydrogen-bonded water molecules leading from the bulk water to the zinc-coordinated ligands in the ABP1 binding site was formed in all simulations. Water entrance into the zinc coordination sphere occurred simultaneously with auxin egress. These results suggest that the hydrogen-bonded water molecules may assist in protonation and deprotonation of auxin molecules and their egress from the ABP1 binding site. PMID:17766341

  17. Electricity Profile Study for Domestic and Commercial Sectors

    Directory of Open Access Journals (Sweden)

    Asmarashid Ponniran


    Full Text Available As Malaysia move towards as a developed country, it is expected that the electricity consumption in domestic and commercial sectors will increase as well as more industrials and households need. This study is to investigate the electricity profile in domestic and commercial sectors by monitoring some appropriate appliances that contribute high electricity consumption. The characteristics for every major loads are examined and the potential energy saving is compared to an efficient electrical appliances in order to obtain the effective energy consumption. Questionnaires have been used to collect respondents, appliances and equipments information. For appliances and equipments measurement data, power quality equipment has been. Samples for domestic sector involved 150 respondents from three residential classes which are high, middle and rural. While for commercial sector, 100 respondents are involved which are restaurant, hotel, workshop, and store/office. It shows, in domestic sector, refrigerator appliance consumed high electricity meanwhile in commercial sector; compressor equipment contributed high consumption in electricity. It is also indicated that by using efficient electrical appliances it can reduce the amount of electricity consumption. However, instead of using high efficient appliances, human factor also contribute significant impact on reducing electricity consumption. By integrating between human factor, high efficient appliances/equipment and government policy, the electricity consumption can be used and managed wisely. Therefore the strategies to build energy efficient society have been proposed in order to achieve efficient electricity consumption.

  18. Binding studies of the antidiabetic drug, metformin to calf thymus DNA using multispectroscopic methods (United States)

    Shahabadi, Nahid; Heidari, Leila


    Interaction between antidiabetic drug, Metformin and calf thymus DNA (CT-DNA) in (50 mM Tris-HCl) buffer were studied by UV-Visible absorption, fluorescence, CD spectroscopy and viscosity measurements. In fluorimetric studies, the enthalpy and entropy of the reaction between the drug and CT-DNA showed that the reaction is exothermic (ΔH = -35.4522 kJ mol-1; ΔS = -49.9523 J mol-1 K-1). The competitive binding studies showed that the drug could release Hoechst 33258 completely. The complex showed absorption hyperchromism in its UV-Vis spectrum with DNA. The calculated binding constant, Kb, obtained from UV-Vis absorption studies was 8.3 × 104 M-1. Moreover, the changes in the CD spectra in the presence of the drug show stabilization of the right-handed B form of CT-DNA. Finally, viscosity measurements revealed that the binding of the complex with CT-DNA could be surface binding, mainly due to groove binding.

  19. Raman, IR and DFT studies of mechanism of sodium binding to urea catalyst (United States)

    Kundu, Partha P.; Kumari, Gayatri; Chittoory, Arjun K.; Rajaram, Sridhar; Narayana, Chandrabhas


    Bis-camphorsulfonyl urea, a newly developed hydrogen bonding catalyst, was evaluated in an enantioselective Friedel-Crafts reaction. We observed that complexation of the sulfonyl urea with a sodium cation enhanced the selectivity of reactions in comparison to reactions performed with urea alone. To understand the role of sodium cation, we performed Infrared and Raman spectroscopic studies. The detailed band assignment of the molecule was made by calculating spectra using Density Functional theory. Our studies suggest that the binding of the cation takes place through the oxygen atoms of carbonyl and sulfonyl groups. Natural Bond Orbital (NBO) analysis shows the expected charge distribution after sodium binding. The changes in the geometrical parameter and charge distribution are in line with the experimentally observed spectral changes. Based on these studies, we conclude that binding of the sodium cation changes the conformation of the sulfonyl urea to bring the chiral camphor groups closer to the incipient chiral center.

  20. Binding of an anticancer Rutaceae plant flavonoid glycoside with calf thymus DNA: Biophysical and electrochemical studies

    Energy Technology Data Exchange (ETDEWEB)

    Balakrishnan, Sandhya; Jaldappagari, Seetharamappa, E-mail:


    In the present work, we report the interaction of a bioactive Rutaceae plant flavonoid glycoside, diosmin (DIO) with calf thymus DNA employing ethidium bromide as a fluorescence probe. The mode of binding between DIO and DNA was investigated by UV absorption, fluorescence, 3D-fluorescence, fluorescence polarization, FT-IR, circular dichroism, melting temperature (T{sub m}) measurements and differential pulse voltammogram studies. The results revealed the intercalative mode of binding between DIO and DNA. Further, the values of thermodynamic parameters, ∆H° (−388.32 kJ mol{sup −1}) and ∆S° (−1.22 kJ mol{sup −1} K{sup −1}) indicated that the van der Waals forces and hydrogen bond played a major role in the binding of DIO to DNA. The observed negative ∆G° values revealed the spontaneity of interaction process. The binding of DIO to DNA–EB was found to be stronger in the presence of coexisting substances. -- Highlights: • Mechanism of interaction of diosmin with DNA was studied by spectroscopic methods. • Ethidium bromide was used as a fluorescence probe in the present study. • The van der Waals forces and hydrogen bond played a significant role in the interaction. • Intercalative mode of binding was proposed between DIO and DNA.

  1. Binding interaction of cationic phenazinium dyes with calf thymus DNA: a comparative study. (United States)

    Sarkar, Deboleena; Das, Paramita; Basak, Soumen; Chattopadhyay, Nitin


    Absorption, steady-state fluorescence, steady-state fluorescence anisotropy, and intrinsic and induced circular dichroism (CD) have been exploited to explore the binding of calf thymus DNA (ctDNA) with three cationic phenazinium dyes, viz., phenosafranin (PSF), safranin-T (ST), and safranin-O (SO). The absorption and fluorescence spectra of all the three dyes reflect significant modifications upon interaction with the DNA. A comparative study of the dyes with respect to modification of fluorescence and fluorescence anisotropy upon binding, effect of urea, iodide-induced fluorescence quenching, and CD measurements reveal that the dyes bind to the ctDNA principally in an intercalative fashion. The effect of ionic strength indicates that electrostatic attraction between the cationic dyes and ctDNA is also an important component of the dye-DNA interaction. Intrinsic and induced CD studies help to assess the structural effects of dyes binding to DNA and confirm the intercalative mode of binding as suggested by fluorescence and other studies. Finally it is proposed that dyes with bulkier substitutions are intercalated into the DNA to a lesser extent.

  2. Personality and intentional binding: an exploratory study using the narcissistic personality inventory. (United States)

    Hascalovitz, Ann Chen; Obhi, Sukhvinder S


    When an individual estimates the temporal interval between a voluntary action and a consequent effect, their estimates are shorter than the real duration. This perceived shortening has been termed "intentional binding", and is often due to a shift in the perception of a voluntary action forward towards the effect and a shift in the perception of the effect back towards the action. Despite much work on binding, there is virtually no consideration of individual/personality differences and how they affect it. Narcissism is a psychological trait associated with an inflated sense of self, and individuals higher in levels of subclinical narcissism tend to see themselves as highly effective agents. Conversely, lower levels of narcissism may be associated with a reduced sense of agency. In this exploratory study, to assess whether individuals with different scores on a narcissism scale are associated with differences in intentional binding, we compared perceived times of actions and effects (tones) between participants with high, middle, and low scores on the narcissistic personality inventory (NPI). We hypothesized that participants with higher scores would show increased binding compared to participants with lower scores. We found that participants in our middle and high groups showed a similar degree of binding, which was significantly greater than the level of binding shown by participants with the lowest scores. To our knowledge, these results are the first to demonstrate that different scores on a personality scale are associated with changes in the phenomenological experience of action, and therefore underscore the importance of considering individual/personality differences in the study of volition. Our results also reinforce the notion that intentional binding is related to agency experience.

  3. Study of V2 vasopressin receptor hormone binding site using in silico methods. (United States)

    Sebti, Yeganeh; Sardari, Soroush; Sadeghi, Hamid Mir Mohammad; Ghahremani, Mohammad Hossein; Innamorati, Giulio


    The antidiuretic effect of arginine vasopressin (AVP) is mediated by the vasopressin V2 receptor. The docking study of AVP as a ligand to V2 receptor helps in identifying important amino acid residues that might be involved in AVP binding for predicting the lowest free energy state of the protein complex. Whereas previous researchers were not able to detect the exact site of the ligand-receptor binding, we designed the current study to identify the vasopressin V2 receptor hormone binding site using bioinformatic methods. The 3D structure of nonapeptide hormone vasopressin was extracted from Protein Data Bank. Since no suitable template resembling V2 receptor was found, an ab initio approach was chosen to model the protein receptor. Using protein docking methods such as Hex protein-protein docking, the model of V2 receptor was docked to the peptide ligand AVP to identify possible binding sites. The residues that involved in binding site are W293, W296, D297, A300, and P301. The lowest free energy state of the protein complex was predicted after mutation in the above residues. The amount of gained energies permits us to compare the mutant forms with native forms and help to asses critical changes such as positive and negative mutations followed by ranking the best mutations. Based on the mutation/docking predictions, we found some mutants such as W293D and A300E possess positively inducing effect in ligand binding and some of them such as A300R present negatively inducing effect in ligand binding.

  4. DNA-binding study of anticancer drug cytarabine by spectroscopic and molecular docking techniques. (United States)

    Shahabadi, Nahid; Falsafi, Monireh; Maghsudi, Maryam


    The interaction of anticancer drug cytarabine with calf thymus DNA (CT-DNA) was investigated in vitro under simulated physiological conditions by multispectroscopic techniques and molecular modeling study. The fluorescence spectroscopy and UV absorption spectroscopy indicated drug interacted with CT-DNA in a groove-binding mode, while the binding constant of UV-vis and the number of binding sites were 4.0 ± 0.2 × 10(4) L mol(-1) and 1.39, respectively. The fluorimetric studies showed that the reaction between the drugs with CT-DNA is exothermic. Circular dichroism spectroscopy was employed to measure the conformational change of DNA in the presence of cytarabine. Furthermore, the drug induces detectable changes in its viscosity for DNA interaction. The molecular modeling results illustrated that cytarabine strongly binds to groove of DNA by relative binding energy of docked structure -20.61 KJ mol(-1). This combination of multiple spectroscopic techniques and molecular modeling methods can be widely used in the investigation on the interaction of small molecular pollutants and drugs with biomacromolecules for clarifying the molecular mechanism of toxicity or side effect in vivo.

  5. Thermodynamic aspects of calcium binding by poly({alpha}-L-guluronate) chains. A molecular simulation study

    Energy Technology Data Exchange (ETDEWEB)

    Plazinski, Wojciech, E-mail: [Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Cracow (Poland); Drach, Mateusz [Department of Theoretical Chemistry, Faculty of Chemistry, UMCS, pl. M. Curie-Sklodowskiej 3, 20-031 Lublin (Poland)


    Highlights: Black-Right-Pointing-Pointer The molecular dynamics studies on binding of calcium ions by poly({alpha}-L-guluronate) chains were carried out. Black-Right-Pointing-Pointer The Gibbs free energy landscapes corresponding to the process of calcium binding were calculated. Black-Right-Pointing-Pointer The Effective coordination number parameter was introduced in order to describe the dynamic changes in the arrangement of water molecules coordinating calcium ions. - Abstract: The theoretical studies on binding of calcium ions by poly({alpha}-L-guluronate) chains were carried out to provide the insight into the molecular basis of this process. The three local minima of the Gibbs free energy (corresponding to the two distinct stable states and to the one short living, meta-stable state) were distinguished. The results emphasize the important role of water molecules. The ECN (effective coordination number) parameter was introduced in order to describe the dynamic changes in the arrangement of solvent molecules coordinating calcium ion.

  6. A study on springback of bending linear flow split profiles (United States)

    Mahajan, P.; Taplick, C.; Özel, M.; Groche, P.


    The bending of linear flow split profiles made up of high strength materials involves high bending loads leading to high springback and geometrical defects. In addition, the linear flow split profiles are made stronger due to the high plastic deformation applied by the process itself. The bending method proposed in this paper combines the linear flow splitting process with a movable bending tool. The aim of the research was to investigate the effect of superimposed stresses exerted by the linear flow splitting process on bending load and springback of the profile by using a finite element model. The latter was validated by means of experimental results. The results show that the bending loads and the springback were reduced by increasing the superposition of stress applied by the linear flow splitting process. The reduction in the bending loads leads to a reduction in the cross-sectional distortion. Furthermore, the springback was compensated by controlling the amount of superimposed stress.

  7. On-line study of flavonoids of Trollius chinensis Bunge binding to DNA with ethidium bromide using a novel combination of chromatographic, mass spectrometric and fluorescence techniques. (United States)

    Song, Zhiling; Wang, Hong; Ren, Biao; Zhang, Baobao; Hashi, Yuki; Chen, Shizhong


    The study of the interaction between drugs and DNA is an important way to understand the role of drug molecules. A novel online analytical method for this purpose combining high-performance liquid chromatography-diode array detector-electrospray ionization-ion-trap time-of-flight mass spectrometry (HPLC-DAD-ESI-IT-TOF-MS(n)) and DNA-ethidium bromide detection with a fluorescence detector (DNA-EB-FLD) was firstly developed, which could rapidly identify the chemical constituents and obtain the profile related to DNA binding activity. This method has been applied for a precise or probable identification of the chemical constituents by ultraviolet (UV) absorption and MS(n) data analysis, while the DNA binding profile has been characterized by directly measuring the fluorescence intensity of compound-DNA-EB. Using this method, Trollius chinensis Bunge was studied and 18 constituents were identified by MS(n) data; six of them (4'-methoxy-2″-O-(2‴-methylbutyryl)vitexin,2″-O-(3‴-methoxycaffeoyl)vitexin) and 4'-methoxy-2″-O-(2‴-methylbutyryl)orientin,acacetin-7-O-rutinoside,quercetin-3-O-xylosylglucoside,quercetin-3-O-arabinosylglucoside) were identified for the first time in T. chinensis Bunge, and 16 constituents accounted for its activity of binding to DNA. The established (HPLC-DAD-ESI-IT-TOF-MS(n) DNA-EB-FLD) system has proved to offer a useful strategy for correlating the chemical profile with the binding to DNA activities of the components without their isolation and purification, and may be used for multicomponent analysis of active substances in other herbs.

  8. Targeting the Cryptococcus neoformans var. grubii Cell Wall Using Lectins: Study of the Carbohydrate-Binding Domain

    Directory of Open Access Journals (Sweden)

    Pamella de Brito Ximenes


    Full Text Available Cryptococcus neoformans var. grubii is considered to be the major cause of cryptococcosis in immunosuppressed patients. Understanding cell wall glycoproteins using lectins is of medical interest and can contribute to specific therapy. The aim of this study was to evaluate the carbohydrates on the cell wall of Cryptococcus neoformans var. grubii clinical isolates, using a fluorescein isothiocyanate-lectin binding protocol. Thirty yeast strains stocked in the culture collection were cultivated for 2 days at 30 °C with shaking. Cells were obtained by centrifugation, washed in phosphate-buffered saline, and a suspension of 107 cells/mL was obtained. To determine the binding profile of lectins, concanavalin A (Con A, wheat germ agglutinin (WGA, Ulex europaeus agglutinin I (UEA-I, and peanut agglutinin (PNA conjugated to fluorescein were used. All the tested clinical isolates of Cryptococcus neoformans var. grubii were intensely stained by WGA, moderately stained by Con A, and weakly stained by PNA and UEA-I. Thus, Cryptococcus can be detected in clinical specimens such as blood and cerebrospinal fluid using the fluorescent lectin WGA, which may be considered as an option for detection in cases of suspected cryptococcosis with low laboratory sensitivity. Future applications may be developed using this basic tool.

  9. Electronic structure of hafnium: A Compton profile study

    Indian Academy of Sciences (India)

    S Khera; S Mathur; B L Ahuja


    In this paper, we report the first-ever isotropic Compton profile of hafnium measured at an intermediate resolution, with 661.65 keV -radiation. To compare our experimental data, the theoretical computations have also been carried out within the framework of pseudopotential using CRYSTAL03 code and the renormalized-free-atom (RFA) model. It is found that the present experimental profile is in better agreement with the RFA calculations if the outer electronic configuration is chosen as 5d3.26s0.8. The cohesive energy of Hf is also deduced from the experimental data and is compared with the available data.

  10. Functional heterologous expression and purification of a mammalian methyl-CpG binding domain in suitable yield for DNA methylation profiling assays. (United States)

    Boyd, Mary E; Heimer, Brandon W; Sikes, Hadley D


    DNA methylation is a major epigenetic modification in mammalian cells, and patterns involving methylation of cytosine bases, known as CpG methylation, have been implicated in the development of many types of cancer. Methyl binding domains (MBDs) excised from larger mammalian methyl-CpG-binding proteins specifically recognize methyl-cytosine bases of CpG dinucleotides in duplex DNA. Previous molecular diagnostic studies involving MBDs have employed Escherichia coli for protein expression with either low soluble yields or the use of time-consuming denaturation-renaturation purification procedures to improve yields. Efficient MBD-based diagnostics require expression and purification methods that maximize protein yield and minimize time and resource expenditure. This study is a systematic optimization analysis of MBD expression using both SDS-PAGE and microscopy and it provides a comparison of protein yield from published procedures to that from the conditions found to be optimal in these experiments. Protein binding activity and specificity were verified using a DNA electrophoretic mobility shift assay, and final protein yield was improved from the starting conditions by a factor of 65 with a simple, single-step purification.

  11. Synthesis and spectroscopic studies of the aminoglycoside (neomycin)--perylene conjugate binding to human telomeric DNA. (United States)

    Xue, Liang; Ranjan, Nihar; Arya, Dev P


    Synthesis of a novel perylene-neomycin conjugate (3) and the properties of its binding to human telomeric G-quadruplex DNA, 5'-d[AG3(T2AG3)3] (4), are reported. Various spectroscopic techniques were employed to characterize the binding of conjugate 3 to 4. A competition dialysis assay revealed that 3 preferentially binds to 4, in the presence of other nucleic acids, including DNA, RNA, DNA-RNA hybrids, and other higher-order structures (single strands, duplexes, triplexes, other G-quadruplexes, and the i-motif). UV thermal denaturation studies showed that thermal stabilization of 4 increases as a function of the increasing concentration of 3. The fluorescence intercalator displacement (FID) assay displayed a significantly tighter binding of 3 with 4 as compared to its parent constituents [220-fold stronger than neomycin (1) and 4.5-fold stronger than perylene diamine (2), respectively]. The binding of 3 with 4 resulted in pronounced changes in the molar ellipticity of the DNA absorption region as confirmed by circular dichroism. The UV-vis absorption studies of the binding of 3 to 4 resulted in a red shift in the spectrum of 3 as well as a marked hypochromic change in the perylene absorption region, suggesting that the ligand-quadruplex interaction involves stacking of the perylene moiety. Docking studies suggest that the perylene moiety serves as a bridge that end stacks on 4, making contacts with two thymine bases in the loop, while the two neomycin moieties branch into the grooves of 4.

  12. Profiling dizziness in older primary care patients: an empirical study.

    NARCIS (Netherlands)

    Dros, J.; Maarsingh, O.R.; Windt, D.A.W.M. van der; Oort, F.J.; Riet, G. ter; Rooij, S.E.J.A. de; Schellevis, F.G.; Horst, H.E. van der; Weert, H.C.P.M. van


    BACKGROUND: The diagnostic approach to dizzy, older patients is not straightforward as many organ systems can be involved and evidence for diagnostic strategies is lacking. A first differentiation in diagnostic subtypes or profiles may guide the diagnostic process of dizziness and can serve as a cla

  13. Profiling dizziness in older primary care patients: an empirical study

    NARCIS (Netherlands)

    Dros, J.; Maarsingh, O.R.; van der Windt, D.A.W.M.; Oort, F.J.; ter Riet, G.; de Rooij, S.E.J.A.; Schellevis, F.G.; van der Horst, H.E.; van Weert, H.C.P.M.


    Background: The diagnostic approach to dizzy, older patients is not straightforward as many organ systems can be involved and evidence for diagnostic strategies is lacking. A first differentiation in diagnostic subtypes or profiles may guide the diagnostic process of dizziness and can serve as a cla

  14. Synthesis and receptor binding studies of (+/-)1-iodo-MK-801

    Energy Technology Data Exchange (ETDEWEB)

    Yang, D.J.; Ciliax, B.J.; Van Dort, M.E.; Gildersleeve, D.; Pirat, J.L.; Young, A.B.; Wieland, D.M. (Univ. of Michigan Medical School, Ann Arbor (USA))


    The glutamate analogue N-methyl-D-aspartate (NMDA) binds to a subset of glutamate receptors that are coupled to a voltage-sensitive cation channel. This NMDA-linked channel is the likely binding locus of the potent anticonvulsant MK-801. To develop single-photon emission computed tomography (SPECT) probes of this brain channel, we synthesized (+/)1-iodo-MK-801 and (+/-)1-({sup 125}I)iodo-MK-801. The effect of (+/-)1-iodo-MK-801 on ligand binding to the NMDA-linked glutamate receptor site was assessed using a rat brain homogenate assay. (+/-)1-Iodo-MK-801 displaced the dissociative anesthetic ligand ({sup 3}H)N-(1-(2-thienyl)cyclohexyl)piperidine (({sup 3}H)TCP) binding with an IC50 of 1 microM, which is a 10-fold lower binding affinity than that of (+/-)MK-801. In in vivo autoradiographic studies, (+/-)MK-801 failed to block selective uptake of (+/-)1-iodo-MK-801 in rat brain. These results suggest that (+/-)1-iodo-MK-801 may not be a suitable ligand for mapping NMDA-linked glutamate receptor channels.

  15. Proton and iodine-127 nuclear magnetic resonance studies on the binding of iodide by lactoperoxidase

    Energy Technology Data Exchange (ETDEWEB)

    Sakurada, J.; Takahashi, S.; Shimizu, T.; Hatano, M.; Nakamura, S.; Hosoya, T.


    Interaction of an iodide ion with lactoperoxidase was studied by the use of /sup 1/H NMR, /sup 127/I NMR, and optical difference spectrum techniques. /sup 1/H NMR spectra demonstrated that a major broad hyperfine-shifted signal at about 60 ppm, which is ascribed to the heme peripheral methyl protons, was shifted toward high field by adding KI, indicating the binding of iodide to the active site of the enzyme; the dissociation constant was estimated to be 38 mM at pH 6.1. The binding was further detected by /sup 127/I NMR, showing no competition with cyanide. Both /sup 1/H NMR and /sup 127/I NMR revealed that the binding of iodide to the enzyme is facilitated by the protonation of an ionizable group with a pK/sup a/ value of 6.0-6.8, which is presumably the distal histidyl residue. Optical difference spectra showed that the binding of an aromatic donor molecule to the enzyme is slightly but distinctly affected by adding KI. On the basis of these results, it was suggested that an iodide ion binds to lactoperoxidase outside the heme crevice but at the position close enough to interact with the distal histidyl residue which possibly mediates electron transport in the iodide oxidation reaction.

  16. Seeking for Non-Zinc-Binding MMP-2 Inhibitors: Synthesis, Biological Evaluation and Molecular Modelling Studies (United States)

    Ammazzalorso, Alessandra; De Filippis, Barbara; Campestre, Cristina; Laghezza, Antonio; Marrone, Alessandro; Amoroso, Rosa; Tortorella, Paolo; Agamennone, Mariangela


    Matrix metalloproteinases (MMPs) are an important family of zinc-containing enzymes with a central role in many physiological and pathological processes. Although several MMP inhibitors have been synthesized over the years, none reached the market because of off-target effects, due to the presence of a zinc binding group in the inhibitor structure. To overcome this problem non-zinc-binding inhibitors (NZIs) have been recently designed. In a previous article, a virtual screening campaign identified some hydroxynaphtyridine and hydroxyquinoline as MMP-2 non-zinc-binding inhibitors. In the present work, simplified analogues of previously-identified hits have been synthesized and tested in enzyme inhibition assays. Docking and molecular dynamics studies were carried out to rationalize the activity data. PMID:27782083

  17. Seeking for Non-Zinc-Binding MMP-2 Inhibitors: Synthesis, Biological Evaluation and Molecular Modelling Studies

    Directory of Open Access Journals (Sweden)

    Alessandra Ammazzalorso


    Full Text Available Matrix metalloproteinases (MMPs are an important family of zinc-containing enzymes with a central role in many physiological and pathological processes. Although several MMP inhibitors have been synthesized over the years, none reached the market because of off-target effects, due to the presence of a zinc binding group in the inhibitor structure. To overcome this problem non-zinc-binding inhibitors (NZIs have been recently designed. In a previous article, a virtual screening campaign identified some hydroxynaphtyridine and hydroxyquinoline as MMP-2 non-zinc-binding inhibitors. In the present work, simplified analogues of previously-identified hits have been synthesized and tested in enzyme inhibition assays. Docking and molecular dynamics studies were carried out to rationalize the activity data.

  18. Protein binding studies with radiolabeled compounds containing radiochemical impurities. Equilibrium dialysis versus dialysis rate determination

    DEFF Research Database (Denmark)

    Honoré, B


    The influence of radiochemical impurities in dialysis experiments with high-affinity ligands is investigated. Albumin binding of labeled decanoate (97% pure) is studied by two dialysis techniques. It is shown that equilibrium dialysis is very sensitive to the presence of impurities resulting...

  19. Equilibrium binding studies of mono, di and triisocyanide ligands on Au powder surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Ontko, Alyn [Iowa State Univ., Ames, IA (United States)


    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 13C-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.

  20. Equilibrium binding studies of mono, di and triisocyanide ligands on Au powder surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Ontko, A.


    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.

  1. Interaction of coumarin with calf thymus DNA: deciphering the mode of binding by in vitro studies. (United States)

    Sarwar, Tarique; Rehman, Sayeed Ur; Husain, Mohammed Amir; Ishqi, Hassan Mubarak; Tabish, Mohammad


    DNA is the major target for a wide range of therapeutic substances. Thus, there has been considerable interest in the binding studies of small molecules with DNA. Interaction between small molecules and DNA provides a structural guideline in rational drug designing and in the synthesis of new and improved drugs with enhanced selective activity and greater clinical efficacy. Plant derived polyphenolic compounds have a large number of biological and pharmacological properties. Coumarin is a polyphenolic compound which has been extensively studied for its diverse pharmacological properties. However, its mode of interaction with DNA has not been elucidated. In the present study, we have attempted to ascertain the mode of binding of coumarin with calf thymus DNA (Ct-DNA) through various biophysical techniques. Analysis of UV-visible absorbance spectra and fluorescence spectra indicates the formation of complex between coumarin and Ct-DNA. Several other experiments such as effect of ionic strength, iodide induced quenching, competitive binding assay with ethidium bromide, acridine orange and Hoechst 33258 reflected that coumarin possibly binds to the minor groove of the Ct-DNA. These observations were further supported by CD spectral analysis, viscosity measurements, DNA melting studies and in silico molecular docking.

  2. Evidence of DNA-Ligand Binding with Different Modes Studied by Spectroscopy

    Institute of Scientific and Technical Information of China (English)


    The binding behavior of several fluorescence dyes to calf thymus DNA has been studied by absorption, fluorescence and atomic force microscopy (AFM), which could provide direct evidence of formation modes and the corresponding nanostructural features of the ligand-DNA complexes.

  3. Self consistent tight binding molecular dynamics study of Ti02 nanoclusters in water.

    Energy Technology Data Exchange (ETDEWEB)

    Erdin, S.; Lin, Y.; Halley, J. W.; Zapol, P.; Redfern, P.; Curtiss, L.; Northern Illinois Univ.; Univ. of Minnesota


    Self-consistent tight binding molecular dynamics studies of TiO{sub 2}2 anatase and rutile nanoclusters in dissociable water are reported. It is found that the structure of the particle expands as a result of interaction between the particle's surface and water. Water molecules dissociate at the nanoparticle surface during simulation.

  4. Personality and Intentional Binding: An exploratory study using scores on the narcissistic personality inventory

    Directory of Open Access Journals (Sweden)

    Ann eHascalovitz


    Full Text Available When an individual estimates the temporal interval between a voluntary action and a consequent effect, their estimates are shorter than the real duration. This perceived shortening has been termed ‘intentional binding’, and is often due to a shift in the perception of a voluntary action forward towards the effect and a shift in the perception of the effect back towards the action. Despite much work on binding, there is virtually no consideration of individual/personality differences and how they affect it. Narcissism is a psychological trait associated with an inflated sense of self, and individuals higher in levels of subclinical narcissism tend to see themselves as highly effective agents. Conversely, lower levels of narcissism may be associated with a reduced sense of agency. In this exploratory study, to assess whether individuals with different scores on a narcissism scale are associated with differences in intentional binding, we compared perceived times of actions and effects (tones between participants with high, middle, and low scores on the Narcissistic Personality Inventory (NPI. We hypothesized that participants with higher scores would show increased binding compared to participants with lower scores. We found that participants in our middle and high groups showed a similar degree of binding, which was significantly greater than the level of binding shown by participants with the lowest scores. To our knowledge, these results are the first to demonstrate that different scores on a personality scale are associated with changes in the phenomenological experience of action, and therefore underscore the importance of considering individual/personality differences in the study of volition. Our results also reinforce the notion that intentional binding is related to agency experience.

  5. Molecular determinants of epidermal growth factor binding: a molecular dynamics study.

    Directory of Open Access Journals (Sweden)

    Jeffrey M Sanders

    Full Text Available The epidermal growth factor receptor (EGFR is a member of the receptor tyrosine kinase family that plays a role in multiple cellular processes. Activation of EGFR requires binding of a ligand on the extracellular domain to promote conformational changes leading to dimerization and transphosphorylation of intracellular kinase domains. Seven ligands are known to bind EGFR with affinities ranging from sub-nanomolar to near micromolar dissociation constants. In the case of EGFR, distinct conformational states assumed upon binding a ligand is thought to be a determining factor in activation of a downstream signaling network. Previous biochemical studies suggest the existence of both low affinity and high affinity EGFR ligands. While these studies have identified functional effects of ligand binding, high-resolution structural data are lacking. To gain a better understanding of the molecular basis of EGFR binding affinities, we docked each EGFR ligand to the putative active state extracellular domain dimer and 25.0 ns molecular dynamics simulations were performed. MM-PBSA/GBSA are efficient computational approaches to approximate free energies of protein-protein interactions and decompose the free energy at the amino acid level. We applied these methods to the last 6.0 ns of each ligand-receptor simulation. MM-PBSA calculations were able to successfully rank all seven of the EGFR ligands based on the two affinity classes: EGF>HB-EGF>TGF-α>BTC>EPR>EPG>AR. Results from energy decomposition identified several interactions that are common among binding ligands. These findings reveal that while several residues are conserved among the EGFR ligand family, no single set of residues determines the affinity class. Instead we found heterogeneous sets of interactions that were driven primarily by electrostatic and Van der Waals forces. These results not only illustrate the complexity of EGFR dynamics but also pave the way for structure-based design of

  6. Mode of binding of the tuberculosis prodrug isoniazid to heme peroxidases: binding studies and crystal structure of bovine lactoperoxidase with isoniazid at 2.7 A resolution. (United States)

    Singh, Amit K; Kumar, Ramasamy P; Pandey, Nisha; Singh, Nagendra; Sinha, Mau; Bhushan, Asha; Kaur, Punit; Sharma, Sujata; Singh, Tej P


    Isoniazid (INH) is an anti-tuberculosis prodrug that is activated by mammalian lactoperoxidase and Mycobacterium tuberculosis catalase peroxidase (MtCP). We report here binding studies, an enzyme assay involving INH, and the crystal structure of the complex of bovine lactoperoxidase (LPO) with INH to illuminate binding properties and INH activation as well as the mode of diffusion and interactions together with a detailed structural and functional comparison with MtCP. The structure determination shows that isoniazid binds to LPO at the substrate binding site on the distal heme side. The substrate binding site is connected to the protein surface through a long hydrophobic channel. The acyl hydrazide moiety of isoniazid interacts with Phe(422) O, Gln(423) O(epsilon1), and Phe(254) O. In this arrangement, pyridinyl nitrogen forms a hydrogen bond with a water molecule, W-1, which in turn forms three hydrogen bonds with Fe(3+), His(109) N(epsilon2), and Gln(105) N(epsilon2). The remaining two sides of isoniazid form hydrophobic interactions with the atoms of heme pyrrole ring A, C(beta) and C(gamma) atoms of Glu(258), and C(gamma) and C(delta) atoms of Arg(255). The binding studies indicate that INH binds to LPO with a value of 0.9 x 10(-6) m for the dissociation constant. The nitro blue tetrazolium reduction assay shows that INH is activated by the reaction of LPO-H(2)O(2) with INH. This suggests that LPO can be used for INH activation. It also indicates that the conversion of INH into isonicotinoyl radical by LPO may be the cause of INH toxicity.

  7. Calcium Binding Ability of Recombinant Buffalo Regucalcin: A Study Using Circular Dichroism Spectroscopy. (United States)

    Harikrishna, P; Thomas, Jobin; Shende, A M; Bhure, S K


    Regucalcin is a calcium regulating multifunctional protein reported to have many important functions like calcium homeostasis, anti-oxidative, anti-apoptotic and anti-cancerous functions. Although it is demonstrated as a calcium regulating protein, the calcium binding ability of regucalcin is still a controversy. The main reason for the controversy is that it lacks a typical EF hand motif which is common to most of the calcium binding proteins. Even though many studies reported regucalcin as a calcium binding protein, there are some studies reporting regucalcin as non-calcium binding also. In the present study, we investigated the calcium binding ability of recombinant buffalo regucalcin by assessing the secondary structural changes of the protein using circular dichroism spectroscopy after adding Ca(2+) to the protein solution. Two types of calcium binding studies were done, one with different concentration of calcium chloride (0.5 mM CaCl2, 1 mM CaCl2, 2 mM CaCl2) and other at different time interval (no incubation and 10 min incubation) after addition of calcium chloride. Significant structural changes were observed in both studies which prove the calcium binding ability of recombinant regucalcin. A constant increase in the α-helix (1.1% with 0.5 mM CaCl2, 1.4% with 1 mM CaCl2, 3.5% with 2 mM CaCl2) and a decrease in β-sheets (78.5% with 0.5 mM CaCl2, 77.4% with 1 mM CaCl2, 75.7% with 2 mM CaCl2) were observed with the increase in calcium chloride concentration. There was a rapid increase in α-helix and decrease in β-sheets immediately after addition of calcium chloride, which subsides after 10 min incubation.


    Directory of Open Access Journals (Sweden)



    Full Text Available ABSTRACT: BACKGROUND: Smoking is one of the environmental factors which can alter normal lipid profile. It is one of the major risk fa ctors in the genesis of coronary atherosclerosis and development of coronary heart disease. AIMS: To evaluate and compare the lipid profile in both groups and to evaluate the existence of dose de pendent relationship and durational significance between smoking and lipid profile among smokers. SETTINGS AND DESIGN: Out of 100 apparently healthy male subjects of age group 21-4 0yrs, 50 were smokers and 50 were non smokers. All the subjects were non alcoholic, non – obese, normotensives and from same socioeconomic status. Subjects who smoke more than equal 10 cigarettes for more than 2 years were considered as smokers group. METHODS AND MATERIAL: The subjects were asked to fast overnight and early morning blood samples colle cted and analyzed for lipid profile by appropriate methods. STATISTICAL ANALYSIS USED: The student’s unpaired “t” test was used for statistical analysis. P-value of < 0.05 or P va lue <0.01 was considered statistically significant. RESULTS: In our study we found serum TC, TG, LDL and VLDL w ere higher in smokers as compared to non smokers and the serum HDL level was significantly decreased in smokers compared to non smokers showing greater risk of thes e persons to atherosclerosis and coronary heart disease. Conclusions: - We conclude our study with the obser vation that smoking causes alteration in lipid profile. Increased amount and duration of smok ing causes more dyslipidaemia .This alteration in serum lipid levels increases risk for coronary artery disease.

  9. Reference tissue modeling with parameter coupling: application to a study of SERT binding in HIV (United States)

    Endres, Christopher J.; Hammoud, Dima A.; Pomper, Martin G.


    When applicable, it is generally preferred to evaluate positron emission tomography (PET) studies using a reference tissue-based approach as that avoids the need for invasive arterial blood sampling. However, most reference tissue methods have been shown to have a bias that is dependent on the level of tracer binding, and the variability of parameter estimates may be substantially affected by noise level. In a study of serotonin transporter (SERT) binding in HIV dementia, it was determined that applying parameter coupling to the simplified reference tissue model (SRTM) reduced the variability of parameter estimates and yielded the strongest between-group significant differences in SERT binding. The use of parameter coupling makes the application of SRTM more consistent with conventional blood input models and reduces the total number of fitted parameters, thus should yield more robust parameter estimates. Here, we provide a detailed evaluation of the application of parameter constraint and parameter coupling to [11C]DASB PET studies. Five quantitative methods, including three methods that constrain the reference tissue clearance (kr2) to a common value across regions were applied to the clinical and simulated data to compare measurement of the tracer binding potential (BPND). Compared with standard SRTM, either coupling of kr2 across regions or constraining kr2 to a first-pass estimate improved the sensitivity of SRTM to measuring a significant difference in BPND between patients and controls. Parameter coupling was particularly effective in reducing the variance of parameter estimates, which was less than 50% of the variance obtained with standard SRTM. A linear approach was also improved when constraining kr2 to a first-pass estimate, although the SRTM-based methods yielded stronger significant differences when applied to the clinical study. This work shows that parameter coupling reduces the variance of parameter estimates and may better discriminate between

  10. Autolytic Activity and Plasma Binding Study of Aap, a Novel Minor Autolysin of Streptococcus pneumoniae

    Directory of Open Access Journals (Sweden)

    Ramina Mahboobi


    Full Text Available Pneumococcal autolysins are enzymes involved in cell wall turnover and cellular division physiologically. They have been found to be involved in the pneumococcus pathogenesis. The aim of this study was to identify the autolytic activity of Spr1754 as a novel protein of Streptococcus pneumoniae. Moreover, the binding of the recombinant protein to plasma proteins was also determined. The spr1754 gene was amplified by PCR and cloned into the pET21a(+ prokaryotic expression vector. The constructed pET21a(+/spr1754 recombinant plasmid was transformed into E. coli Origami (DE3 and induced using IPTG. The recombinant protein of Spr1754 was purified by Ni-NTA affinity chromatography and confirmed by SDS-PAGE and Western blot analysis using anti-His tag monoclonal antibody. Autolytic activity and the ability of the recombinant protein in binding to plasma proteins were performed using zymogram analysis and western blot, respectively. The spr1754 with expected size was cloned and overexpressed in Escherichia coli Origami (DE3, successfully. After purification of the Spr1754 recombinant protein, the autolytic activity was observed by zymography. Of the four plasma proteins used in this study, binding of lactoferrin to Spr1754 recombinant protein was shown. The Spr1754 recombinant protein has a bifunctional activity, i.e., as being autolysin and lactoferrin binding and designated as Aap (autolytic/ adhesion/ pneumococcus. Nevertheless, characterization of the Aap needs to be followed using gene inactivation and cell wall localization.

  11. Terverticillate penicillia studied by direct electrospray mass spectrometric profiling of crude extracts II. Database and identification

    DEFF Research Database (Denmark)

    Smedsgaard, Jørn


    A mass spectral database was built using standard instrument software from 678 electrospray mass spectra (mass profiles) from crude fungal extracts of terverticillate taxa within the genus Penicillium. The match factors calculated from searching all the mass profiles stored in the database were u...... of the isolates stored according to classical taxonomic criteria. Mass profiles collected in previous studies could be identified by a search in the database. (C) 1997 Elsevier Science Ltd....

  12. Heterogeneous behavior of metalloproteins toward metal ion binding and selectivity: insights from molecular dynamics studies. (United States)

    Gogoi, Prerana; Chandravanshi, Monika; Mandal, Suraj Kumar; Srivastava, Ambuj; Kanaujia, Shankar Prasad


    About one-third of the existing proteins require metal ions as cofactors for their catalytic activities and structural complexities. While many of them bind only to a specific metal, others bind to multiple (different) metal ions. However, the exact mechanism of their metal preference has not been deduced to clarity. In this study, we used molecular dynamics (MD) simulations to investigate whether a cognate metal (bound to the structure) can be replaced with other similar metal ions. We have chosen seven different proteins (phospholipase A2, sucrose phosphatase, pyrazinamidase, cysteine dioxygenase (CDO), plastocyanin, monoclonal anti-CD4 antibody Q425, and synaptotagmin 1 C2B domain) bound to seven different divalent metal ions (Ca(2+), Mg(2+), Zn(2+), Fe(2+), Cu(2+), Ba(2+), and Sr(2+), respectively). In total, 49 MD simulations each of 50 ns were performed and each trajectory was analyzed independently. Results demonstrate that in some cases, cognate metal ions can be exchanged with similar metal ions. On the contrary, some proteins show binding affinity specifically to their cognate metal ions. Surprisingly, two proteins CDO and plastocyanin which are known to bind Fe(2+) and Cu(2+), respectively, do not exhibit binding affinity to any metal ion. Furthermore, the study reveals that in some cases, the active site topology remains rigid even without cognate metals, whereas, some require them for their active site stability. Thus, it will be interesting to experimentally verify the accuracy of these observations obtained computationally. Moreover, the study can help in designing novel active sites for proteins to sequester metal ions particularly of toxic nature.

  13. Synthesis, Characterization, and Saccharide Binding Studies of Bile Acid − Porphyrin Conjugates

    Directory of Open Access Journals (Sweden)

    Vladimír Král


    Full Text Available Synthesis and characterization of bile acid-porphyrin conjugates (BAPs are reported. Binding of saccharides with BAPs in aqueous methanol was studied by monitoring changes in the visible absorption spectral of the porphyrin-moieties. Although these studies clearly showed absorbance changes, suggesting quite high if non-selective binding, the mass spectral studies do not unambiguously support these results.

  14. A numerical study of ionospheric profiles for mid-latitudes

    Directory of Open Access Journals (Sweden)

    S.-R. Zhang

    Full Text Available This paper presents a numerical model and results for the mid-latitude ionospheric profile below the peak of the F2-layer. The basis of the model is the solving of equations for four ionic species O+, NO+, O+2 and N+2, as well as the meta-stable O+(2D and O+(2P. Diffusion and wind-induced drifts and 21 photo-chemical reactions are also taken into account. Neutral atmospheric density and temperature are derived from the MSIS86 model and solar extreme ultraviolate irradiance from the EUV91 model. In an effort to obtain a more realistic ionospheric profile, the key point at foF2 and hmF2 is fitted from the simulation to observations. The model also utilizes the vertical drifts derived from ionosonde data with the help of the Servo model. It is shown that the ionospheric height of peak can be reproduced more accurately under the derived vertical drifts from the Servo theory than with the HWM90 model. Results from the simulation are given for Wuchang (30.5°N, 114.4°E and Wakkanai (45.6°N, 141.7°E, showing the profile changes with season and solar activity, and the E-F valley structure (the depth and the width. This simulation also reveals the importance of meta-stable ions and dynamical transport processes on the formation of the F1-ledge and F1-F2 valley.

  15. Thermodynamic Study of Interactions Between ZnO and ZnO Binding Peptides Using Isothermal Titration Calorimetry. (United States)

    Limo, Marion J; Perry, Carole C


    While material-specific peptide binding sequences have been identified using a combination of combinatorial methods and computational modeling tools, a deep molecular level understanding of the fundamental principles through which these interactions occur and in some instances modify the morphology of inorganic materials is far from being fully realized. Understanding the thermodynamic changes that occur during peptide-inorganic interactions and correlating these to structural modifications of the inorganic materials could be the key to achieving and mastering control over material formation processes. This study is a detailed investigation applying isothermal titration calorimetry (ITC) to directly probe thermodynamic changes that occur during interaction of ZnO binding peptides (ZnO-BPs) and ZnO. The ZnO-BPs used are reported sequences G-12 (GLHVMHKVAPPR), GT-16 (GLHVMHKVAPPR-GGGC), and alanine mutants of G-12 (G-12A6, G-12A11, and G-12A12) whose interaction with ZnO during solution synthesis studies have been extensively investigated. The interactions of the ZnO-BPs with ZnO yielded biphasic isotherms comprising both an endothermic and an exothermic event. Qualitative differences were observed in the isothermal profiles of the different peptides and ZnO particles studied. Measured ΔG values were between -6 and -8.5 kcal/mol, and high adsorption affinity values indicated the occurrence of favorable ZnO-BP-ZnO interactions. ITC has great potential in its use to understand peptide-inorganic interactions, and with continued development, the knowledge gained may be instrumental for simplification of selection processes of organic molecules for the advancement of material synthesis and design.

  16. Analytical methods to determine the comparative DNA binding studies of curcumin-Cu(II) complexes. (United States)

    Rajesh, Jegathalaprathaban; Rajasekaran, Marichamy; Rajagopal, Gurusamy; Athappan, Periakaruppan


    DNA interaction studies of two mononuclear [1:1(1); 1:2(2)] copper(II) complexes of curcumin have been studied. The interaction of these complexes with CT-DNA has been explored by physical methods to propose modes of DNA binding of the complexes. Absorption spectral titrations of complex 1 with CT-DNA shows a red-shift of 3 nm with the DNA binding affinity of K(b), 5.21×10(4)M(-1) that are higher than that obtained for 2 (red-shift, 2 nm; K(b), 1.73×10(4)M(-1)) reveal that the binding occurs in grooves as a result of the interaction is via exterior phosphates. The CD spectra of these Cu(II) complexes show a red shift of 3-10nm in the positive band with increase in intensities. This spectral change of induced CD due to the hydrophobic interaction of copper complexes with DNA is the characteristic of B to A conformational change. The EB displacement assay also reveals the same trend as observed in UV-Vis spectral titration. The addition of complexes 1 and 2 to the DNA bound ethidium bromide (EB) solutions causes an obvious reduction in emission intensities indicating that these complexes competitively bind to DNA with EB. The positive shift of both the E(pc) and E(0)' accompanied by reduction of peak currents in differential pulse voltammogram (DPV), upon adding different concentrations of DNA to the metal complexes, are obviously in favor of strong binding to DNA. The super coiled plasmid pUC18 DNA cleavage ability of Cu(II) complexes in the presence of reducing agent reveals the single strand DNA cleavage (ssDNA) is observed. The hydroxyl radical (HO()) and the singlet oxygen are believed to be the reactive species responsible for the cleavage.

  17. Studies on binding mechanism between carotenoids from sea buckthorn and thermally treated α-lactalbumin (United States)

    Dumitraşcu, Loredana; Ursache, Florentina Mihaela; Stănciuc, Nicoleta; Aprodu, Iuliana


    Sea buckthorn is a natural food ingredient rich in bioactive compounds such as carotenoids, tocopherols, sterols, flavonoids, lipids, vitamins, tannins and minerals. Herein, fluorescence and UV-vis techniques were used to study the interaction of heat treated α-lactalbumin (α-LA) with carotenoids from sea buckthorn berries extract (CSB) and β-carotene. Further atomic level details on the interaction between α-LA and β-carotene were obtained by means of molecular modelling techniques. The quenching rate constants, binding constants, and number of binding sites were calculated in the presence of CSB. The emission spectral studies revealed that, CSB have the ability to bind α-LA and form a ground state complex via static quenching process. Maximum degree of quenching was reached at 100 °C, where β-carotene and CSB quenched the Trp fluorescence of α-LA by 56% and 47%, respectively. In order to reveal the interaction between CSB and α-LA, the thermodynamic parameters were determined from the van't Hoff plot based on the temperature dependence of the binding constant. In agreement with the in silico observations, the thermodynamic parameters enabled us to consider that the association between α-LA and β-carotene is a spontaneous process driven by enthalpy, dominated mainly by the van der Waals interaction, but hydrophobic interactions might also be considered. The interaction between CSB and α-LA was further confirmed by UV-vis absorption spectra, where a blue shift of position was noticed at higher temperature suggesting the complex formation. The results provided here supply a better understanding of the binding of CSB to α-LA, which can be further exploited in designing new healthy food applications.

  18. Synthesis of trimethoprim metal complexes: Spectral, electrochemical, thermal, DNA-binding and surface morphology studies. (United States)

    Demirezen, Nihat; Tarınç, Derya; Polat, Duygu; Ceşme, Mustafa; Gölcü, Ayşegül; Tümer, Mehmet


    Complexes of trimethoprim (TMP), with Cu(II), Zn(II), Pt(II), Ru(III) and Fe(III) have been synthesized. Then, these complexes have been characterized by spectroscopic techniques involving UV-vis, IR, mass and (1)H NMR. CHN elemental analysis, electrochemical and thermal behavior of complexes have also been investigated. The electrochemical properties of all complexes have been investigated by cyclic voltammetry (CV) using glassy carbon electrode. The biological activity of the complexes has been evaluated by examining their ability to bind to calf-thymus DNA (CT DNA) with UV spectroscopy and cyclic voltammetry. UV studies of the interaction of the complexes with DNA have shown that these compounds can bind to CT DNA. The binding constants of the complexes with CT DNA have also been calculated. The cyclic voltammograms of the complexes in the presence of CT DNA have shown that the complexes can bind to CT DNA by both the intercalative and the electrostatic binding mode. The antimicrobial activity of these complexes has been evaluated against three Gram-positive and four Gram-negative bacteria. Antifungal activity against two different fungi has been evaluated and compared with the reference drug TMP. Almost all types of complexes show excellent activity against all type of bacteria and fungi. The morphology of the CT DNA, TMP, metal ions and metal complexes has been investigated by scanning electron microscopy (SEM). To get the SEM images, the interaction of compounds with CT DNA has been studied by means of differential pulse voltammetry (DPV) at CT DNA modified pencil graphite electrode (PGE). The decrease in intensity of the guanine oxidation signals has been used as an indicator for the interaction mechanism.

  19. Human Islet Amyloid Polypeptide Fibril Binding to Catalase: A Transmission Electron Microscopy and Microplate Study

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    Nathaniel G. N. Milton


    Full Text Available The diabetes-associated human islet amyloid polypeptide (IAPP is a 37-amino-acid peptide that forms fibrils in vitro and in vivo. Human IAPP fibrils are toxic in a similar manner to Alzheimer's amyloid-β (Aβ and prion protein (PrP fibrils. Previous studies have shown that catalase binds to Aβ fibrils and appears to recognize a region containing the Gly-Ala-Ile-Ile sequence that is similar to the Gly-Ala-Ile-Leu sequence found in human IAPP residues 24-27. This study presents a transmission electron microscopy (TEM—based analysis of fibril formation and the binding of human erythrocyte catalase to IAPP fibrils. The results show that human IAPP 1-37, 8-37, and 20-29 peptides form fibrils with diverse and polymorphic structures. All three forms of IAPP bound catalase, and complexes of IAPP 1-37 or 8-37 with catalase were identified by immunoassay. The binding of biotinylated IAPP to catalase was high affinity with a KD of 0.77nM, and could be inhibited by either human or rat IAPP 1-37 and 8-37 forms. Fibrils formed by the PrP 118-135 peptide with a Gly-Ala-Val-Val sequence also bound catalase. These results suggest that catalase recognizes a Gly-Ala-Ile-Leu—like sequence in amyloid fibril-forming peptides. For IAPP 1-37 and 8-37, the catalase binding was primarily directed towards fibrillar rather than ribbon-like structures, suggesting differences in the accessibility of the human IAPP 24-27 Gly-Ala-Ile-Leu region. This suggests that catalase may be able to discriminate between different structural forms of IAPP fibrils. The ability of catalase to bind IAPP, Aβ, and PrP fibrils demonstrates the presence of similar accessible structural motifs that may be targets for antiamyloid therapeutic development.

  20. The power stroke driven by ATP binding in CFTR as studied by molecular dynamics simulations. (United States)

    Furukawa-Hagiya, Tomoka; Furuta, Tadaomi; Chiba, Shuntaro; Sohma, Yoshiro; Sakurai, Minoru


    Cystic fibrosis transmembrane conductance regulator (CFTR) is a chloride channel belonging to the ATP binding cassette (ABC) protein superfamily. Currently, it remains unclear how ATP binding causes the opening of the channel gate at the molecular level. To clarify this mechanism, we first constructed an atomic model of the inward-facing CFTR using the X-ray structures of other ABC proteins. Molecular dynamics (MD) simulations were then performed to explore the structure and dynamics of the inward-facing CFTR in a membrane environment. In the MgATP-bound state, two nucleotide-binding domains (NBDs) formed a head-to-tail type of dimer, in which the ATP molecules were sandwiched between the Walker A and signature motifs. Alternatively, one of the final MD structures in the apo state was similar to that of a "closed-apo" conformation found in the X-ray analysis of ATP-free MsbA. Principal component analysis for the MD trajectory indicated that NBD dimerization causes significant structural and dynamical changes in the transmembrane domains (TMDs), which is likely indicative of the formation of a chloride ion access path. This study suggests that the free energy gain from ATP binding acts as a driving force not only for NBD dimerization but also for NBD-TMD concerted motions.

  1. Study on the drug resistance and the binding mode of HIV-1 integrase with LCA inhibitor

    Institute of Scientific and Technical Information of China (English)

    HU; JianPing; CHANG; Shan; CHEN; WeiZu; WANG; CunXin


    Human immunodeficiency virus type 1 (HIV-1) integrase (IN) is an essential enzyme in the lifecycle of this virus and also an important target for the study of anti-HIV drugs. The binding mode of the wild type IN core domain and its G140S mutant with L-Chicoric acid (LCA) inhibitor were investigated by using multiple conformation molecular docking and molecular dynamics (MD) simulation. Based on the binding modes, the drug resistance mechanism was explored for the G140S mutant of IN with LCA. The results indicate that the binding site of the G140S mutant of IN core domain with LCA is different from that of the core domain of the wild type IN, which leads to the partial loss of inhibition potency of LCA. The flexibility of the IN functional loop region and the interactions between Mg2+ ion and the three key residues (i.e., D64, D116, E152) stimulate the biological operation of IN. The drug resistance also lies in several other important effects, such as the repulsion between LCA and E152 in the G140S mutant core domain, the weakening of K159 binding with LCA and Y143 pointing to the pocket of the G140S mutant. All of the above simulation results agree well with experimental data, which provide us with some helpful information for designing the drug of anti-HIV based on the structure of IN.

  2. Use of computational modeling approaches in studying the binding interactions of compounds with human estrogen receptors. (United States)

    Wang, Pan; Dang, Li; Zhu, Bao-Ting


    Estrogens have a whole host of physiological functions in many human organs and systems, including the reproductive, cardiovascular, and central nervous systems. Many naturally-occurring compounds with estrogenic or antiestrogenic activity are present in our environment and food sources. Synthetic estrogens and antiestrogens are also important therapeutic agents. At the molecular level, estrogen receptors (ERs) mediate most of the well-known actions of estrogens. Given recent advances in computational modeling tools, it is now highly practical to use these tools to study the interaction of human ERs with various types of ligands. There are two common categories of modeling techniques: one is the quantitative structure activity relationship (QSAR) analysis, which uses the structural information of the interacting ligands to predict the binding site properties of a macromolecule, and the other one is molecular docking-based computational analysis, which uses the 3-dimensional structural information of both the ligands and the receptor to predict the binding interaction. In this review, we discuss recent results that employed these and other related computational modeling approaches to characterize the binding interaction of various estrogens and antiestrogens with the human ERs. These examples clearly demonstrate that the computational modeling approaches, when used in combination with other experimental methods, are powerful tools that can precisely predict the binding interaction of various estrogenic ligands and their derivatives with the human ERs.


    Directory of Open Access Journals (Sweden)



    Full Text Available BACKGROUND: Study aims to determine correlation of the cytological pattern of t hyr oid lesions in ad di t ion to the ut i l it y a nd accu r ac y o f F N A C a s in i t ia l dia g nostic me thod a lo n g with t hy roid h o rmone p ro f i l e ( T 3, T4 a nd TSH whi c h p r ovides info r mation a t p hy sio log i ca l a nd p a tho l o g ic a l lev e ls a nd thus ca n e nh a n c e the l i k e l i hood o f ea r l y de te c t i on of a mb ig uous t hyr oid dy sfu nc t i on with m i ni ma l clin ica l findin gs. OBJECTIVES: To obtain role of thyroid hormone profile (T3, T4 and TSH aimed at defining prognostic parameters and correlating it with cytology r e sul t s, dia g nosis of dif f use n o n t o xi c g oi te r, dia g nos i s of sol i ta ry /do m inant t hy roid nodule, c onfi r mation of c l i nic a l l y obvious t hyr oid ma l ig n anc y . MATERIALS AND METHODS: 150 patients with thyroid sw ellings underwent FNAC along with c omp le te t hy roid ho r mone p r o f i l e in Central Diagnostic Lab o f A JI MS Man ga lor e . P r oce d u re w a s p e r f o r med without L .A with the he lp of a spir a t i ng t ec hnique usi n g 23G nee dle a t tache d to 10 ml di s posa b le sy ri nge . An avera ge of one a t te mpt p e r nodule w a s p e r fo rm e d usual l y re sul t ing in 4 dir ec t sme a rs. B oth a ir d r ied a nd w e t fi xe d sme a rs fi xe d in 95% a l c ohol for a bout 30 m i n ute s a nd stain e d with Le ish ma n ’ s stain a nd Pa p stain e x a m i n e d und e r l ig ht m icr osco pe . T hy roid p ro file is a lso p e r f o r med in a ll the a bo v e p a t ie nts. RESULTS: One hund re d a nd fi ft y a spir a t i ons of p a t ie nts (both f e m a les a nd mal e s w er e analyse d. T 3, T4 a nd TSH w a s analy z e d f o r a ll 150 p a t ie nts . The me a n ag e of p a t ie nts in t his stu d y w a s 39.66 year s a nd ag e rang e w a s 1 - 76 yea rs. The r e w er e 142 femal e s (94. 6 6% a nd 8 mal e s (5.3 3% . M ax i m um nu m b e r of

  4. A comparative study on river hydrokinetic turbines blade profiles

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    Kamal A.R.Ismail


    Full Text Available Diesel based electricity supply is the common practice in rural and isolated areas in the North of Brazil. The diesel fuel is usually transported from a nearby city as Manaus by river to these isolated communities. During wet seasons and inundations this means of transport is very risky and not usually safe. The hydrokinetic technology is among the promising technologies for most of the Amazon areas because of the large hydraulic capacity and low density population settlements. In this paper the authors propose a cheap hydrokinetic turbine system whose blades are easy to design, manufacture, replace when necessary and its operation is independent of flow direction. In this work CFD, RANS (Reynolds Average Navier Stokes equations are used to characterize and develop a methodology of numerical simulation of a vertical axis hydrokinetic turbine. In the simulations, four blade profiles were investigated. The effects of the number of blades, blade profile and water flow velocity on the turbine torque and power coefficients were presented and discussed.

  5. Compton profile study and electronic properties of tantalum diboride. (United States)

    Raykar, Veera; Bhamu, K C; Ahuja, B L


    We have reported the first-ever experimental Compton profile (CP) of TaB2 using 20 Ci(137)Cs Compton spectrometer. To compare the experimental data, we have also computed the theoretical CPs using density functional theory (DFT) and hybridization of DFT and Hartree-Fock (HF) within linear combination of the atomic orbitals (LCAO) method. In addition, we have reported energy bands and density of states of TaB2 using LCAO and full potential-linearized augmented plane wave (FP-LAPW) methods. A real space analysis of CP of TaB2 confirms its metallic character which is in tune with the cross-overs of Fermi level by energy bands and Fermi surface topology. A comparison of equal-valence-electron-density (EVED) experimental profiles of isoelectronic TaB2 and NbB2 show more covalent (or less ionic) character of TaB2 than that of NbB2 which is in agreement with available ionicity data.

  6. Studies and research concerning BNFP pilot-scale pulsed columns: column profile and holdup studies

    Energy Technology Data Exchange (ETDEWEB)

    Cermak, A. F.


    Experimental studies were conducted on pilot-scaled pulsed columns for the purpose of obtaining data for verification of contactor computer programs. This work is in support of safeguards programs related to determination of near real-time inventories in pulsed columns. Holdup tests were performed resulting in the derivation of an empirical equation for estimation of the dispersed phase holdup in a column. Uranium solvent extraction mass-transfer tests were conducted in which all four process cycles were simulated under coprocessing flowsheet conditions. Extensive data were obtained during these tests on uranium profiles and inventories within the columns. Transient profile data were also determined between selected runs under the tested operating conditions. No concentration peaks could be observed during the transient period. Based on the extensive inventory data taken, empirical equations were developed for relating uranium inventory in a column to the test parameters. These equations were found useful for predicting and estimating the column inventory under the known run conditions.

  7. Adverse drug reaction profile of nanoparticle versus conventional formulation of paclitaxel: An observational study

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    Ballari Brahmachari


    Conclusions : Despite its ADR profile being statistically comparable to conventional paclitaxel, this observational study suggests that Nanoxel tolerability could be better, considering that a significantly higher dose was employed. This hypothesis needs confirmation through an interventional study.

  8. Terverticillate Penicillia studied by direct electrospray mass spectrometric profiling of crude extracts: I. Chemosystematics

    DEFF Research Database (Denmark)

    Smedsgaard, Jørn; Frisvad, Jens Christian


    A chemosystematic study of 339 isolates from all known terverticillate Penicillium taxa was performed using electrospray mass spectrometric analysis of extractable metabolites. The mass profiles were made by injecting crude plug extracts made from cultures grown on Czapek Yeast Autolysate agar (C...... to known secondary metabolites were, however, found in all mass profiles. (C) 1997 Elsevier Science Ltd....

  9. A comparative study of recombinant and native frutalin binding to human prostate tissues

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    Domingues Lucília


    Full Text Available Abstract Background Numerous studies indicate that cancer cells present an aberrant glycosylation pattern that can be detected by lectin histochemistry. Lectins have shown the ability to recognise these modifications in several carcinomas, namely in the prostate carcinoma, one of the most lethal diseases in man. Thus, the aim of this work was to investigate if the α-D-galactose-binding plant lectin frutalin is able to detect such changes in the referred carcinoma. Frutalin was obtained from different sources namely, its natural source (plant origin and a recombinant source (Pichia expression system. Finally, the results obtained with the two lectins were compared and their potential use as prostate tumour biomarkers was discussed. Results The binding of recombinant and native frutalin to specific glycoconjugates expressed in human prostate tissues was assessed by using an immuhistochemical technique. A total of 20 cases of prostate carcinoma and 25 cases of benign prostate hyperplasia were studied. Lectins bound directly to the tissues and anti-frutalin polyclonal antibody was used as the bridge to react with the complex biotinilated anti-rabbit IgG plus streptavidin-conjugated peroxidase. DAB was used as visual indicator to specifically localise the binding of the lectins to the tissues. Both lectins bound to the cells cytoplasm of the prostate carcinoma glands. The binding intensity of native frutalin was stronger in the neoplasic cells than in hyperplasic cells; however no significant statistical correlation could be found (P = 0.051. On the other hand, recombinant frutalin bound exclusively to the neoplasic cells and a significant positive statistical correlation was obtained (P Conclusion Native and recombinant frutalin yielded different binding responses in the prostate tissues due to their differences in carbohydrate-binding affinities. Also, this study shows that both lectins may be used as histochemical biomarkers for the prostate

  10. Synthesis, characterization, anti-microbial, DNA binding and cleavage studies of Schiff base metal complexes

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    Poomalai Jayaseelan


    Full Text Available A novel Schiff base ligand has been prepared by the condensation between butanedione monoxime with 3,3′-diaminobenzidine. The ligand and metal complexes have been characterized by elemental analysis, UV, IR, 1H NMR, conductivity measurements, EPR and magnetic studies. The molar conductance studies of Cu(II, Ni(II, Co(II and Mn(II complexes showed non-electrolyte in nature. The ligand acts as dibasic with two N4-tetradentate sites and can coordinate with two metal ions to form binuclear complexes. The spectroscopic data of metal complexes indicated that the metal ions are complexed with azomethine nitrogen and oxyimino nitrogen atoms. The binuclear metal complexes exhibit octahedral arrangements. DNA binding properties of copper(II metal complex have been investigated by electronic absorption spectroscopy. Results suggest that the copper(II complex bind to DNA via an intercalation binding mode. The nucleolytic cleavage activities of the ligand and their complexes were assayed on CT-DNA using gel electrophoresis in the presence and absence of H2O2. The ligand showed increased nuclease activity when administered as copper complex and copper(II complex behave as efficient chemical nucleases with hydrogen peroxide activation. The anti-microbial activities and thermal studies have also been studied. In anti-microbial activity all complexes showed good anti-microbial activity higher than ligand against gram positive, gram negative bacteria and fungi.

  11. Vertical profile of fog microphysics : a case study (United States)

    Burnet, Frédéric; Brilouet, Pierre-Etienne; Mazoyer, Marie; Bourrianne, Thierry; Etcheberry, Jean-Michel; Gaillard, Brigitte; Legain, Dominique; Tzanos, Diane; Barrié, Joel; Barrau, Sébastien; Defoy, Stephan


    The occurrence and development of fogs result from the non-linear interaction of competing radiative, thermodynamic, microphysical and dynamical processes and the forecasting of their life cycle still remains a challenging issue. Several field campaigns have been carried out at the SIRTA observatory in the Paris suburb area (France). These experiments have shown that fog events exhibit large differences of the microphysical properties and various evolutions during their life cycle. To better understand relationships between the different processes and to validate numerical simulations it is necessary however to document the vertical profile of the fog microphysics. A CDP (Cloud Droplet Spectrometer) from DMT (Droplet Measurement Technology, Boulder, CO) has been modified to allow measurements of the droplet size distribution in fog layers with a tethered balloon. This instrumental set-up has been used during a field campaign during the winter 2013-214 in the Landes area in the South West of France. To validate the vertical profiles provided by the modified CDP, a mast was equipped with microphysical instruments at 2 altitude levels with an another CDP at 24 m and a Fog Monitor FM100 at 42 m. The instrumental set-up deployed during this campaign is presented. Data collected during a fog event that occurred during the night of 5-6 March 2014 are analysed. We show that microphysical properties such as droplet number concentration, LWC and mean droplet size, exhibit different time evolution during the fog life cycle depending on the altitude level. Droplet size distribution measurements are also investigated. They reveal sharp variations along the vertical close to the top of the fog layer. In addition it is shown that the shape of the size distributions at the top follows a time evolution typical of a quasi-adiabatic droplet growth.

  12. Raman and surface-enhanced Raman scattering (SERS) studies of the thrombin-binding aptamer. (United States)

    Wu, Tsai-Chin; Vasudev, Milana; Dutta, Mitra; Stroscio, Michael A


    Surface-enhanced Raman scattering is used to study the Raman spectra and peak shifts the thrombin-binding aptamer (TBA) on substrates having two different geometries; one with a single stranded sequence and one with double stranded sequence. The Raman signals of the deoxyribonucleic acids on both substrates are enhanced and specific peaks of bases are identified. These results are highly reproducible and have promising applications in low cost nucleic acid detection.

  13. Chemical integrity of ( sup 3 H)GABA used in binding studies

    Energy Technology Data Exchange (ETDEWEB)

    Balcar, V.J. (Univ. of Sydney, N.S.W. (Australia))


    A method which is claimed to be able to determine the proportion of true GABA within radiolabeled GABA used in binding studies was tested using (3H)GABA. The method was found to be unsuitable for {sup 3}H-labeled GABA and, furthermore, both theoretical considerations and the present experimental data indicated that it could also produce misleading results with ({sup 14}C)GABA.

  14. A practical platform for blood biomarker study by using global gene expression profiling of peripheral whole blood.

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    Ze Tian

    Full Text Available BACKGROUND: Although microarray technology has become the most common method for studying global gene expression, a plethora of technical factors across the experiment contribute to the variable of genome gene expression profiling using peripheral whole blood. A practical platform needs to be established in order to obtain reliable and reproducible data to meet clinical requirements for biomarker study. METHODS AND FINDINGS: We applied peripheral whole blood samples with globin reduction and performed genome-wide transcriptome analysis using Illumina BeadChips. Real-time PCR was subsequently used to evaluate the quality of array data and elucidate the mode in which hemoglobin interferes in gene expression profiling. We demonstrated that, when applied in the context of standard microarray processing procedures, globin reduction results in a consistent and significant increase in the quality of beadarray data. When compared to their pre-globin reduction counterparts, post-globin reduction samples show improved detection statistics, lowered variance and increased sensitivity. More importantly, gender gene separation is remarkably clearer in post-globin reduction samples than in pre-globin reduction samples. Our study suggests that the poor data obtained from pre-globin reduction samples is the result of the high concentration of hemoglobin derived from red blood cells either interfering with target mRNA binding or giving the pseudo binding background signal. CONCLUSION: We therefore recommend the combination of performing globin mRNA reduction in peripheral whole blood samples and hybridizing on Illumina BeadChips as the practical approach for biomarker study.

  15. Adeno-associated virus type 2 binding study on model heparan sulfate surface (United States)

    Negishi, Atsuko; Liu, Jian; McCarty, Douglas; Samulski, Jude; Superfine, Richard


    Understanding the mechanisms involved in virus infections is useful in its application in areas such as gene therapy, drug development and delivery, and biosensors. In collaboration with UNC Gene Therapy Center and School of Pharmacy, we are specifically looking at the interaction between human parvovirus adeno-associated virus type 2 (AAV2), a potential viral vector, and heparan sulfate proteoglycan (HSPG), a known cell surface receptor for AAV2. Recent development in glycobiology has shown that some protein-polysaccharide binding is sugar sequence dependent. Heparan sulfate (HS) is a polysaccharide chain of sulfated iduronic/glucuronic and sulfate glucosamine residues and can be differentiated into sequence specific structures by enzymes. These enzymatic modifications, known as heparan sulfate sulfotransferase modified modifications, have been shown to change the biological nature of heparan sulfate such as specific binding to proteins and viruses. For understanding HS-assisted viral infection mechanisms, we are interested in investigating the binding affinity and stability of AAV to different HS structures. We have developed a model heparan sulfate surface in which AAV adsorption studies are done and analyzed using the atomic force microscope (AFM). In addition, a miniArray assay has been created to facilitate to this study. Adsorption studies are done in 4 white LED wells with approximately 3 mm2 reaction areas which minimize sample use and waste.

  16. Design, synthesis and DNA-binding study of some novel morpholine linked thiazolidinone derivatives (United States)

    War, Javeed Ahmad; Srivastava, Santosh Kumar; Srivastava, Savitri Devi


    The emergence of multiple drug resistance amongst bacterial strains resulted in many clinical drugs to be ineffective. Being vulnerable to bacterial infections any lack in the development of new antimicrobial drugs could pose a serious threat to public health. Here we report design and synthesis of a novel class of morpholine linked thiazolidinone hybrid molecules. The compounds were characterized by FT-IR, NMR and HRMS techniques. Susceptibility tests showed that most of the synthesized molecules were highly active against multiple bacterial strains. Compound 3f displayed MIC values which were better than the standard drug for most of the tested strains. DNA being a well defined target for many antimicrobial drugs was probed as possible target for these synthetic molecules. DNA-binding study of 3f with sm-DNA was probed through UV-vis absorption, fluorescence quenching, gel electrophoresis and molecular docking techniques. The studies revealed that compound 3f has strong affinity towards DNA and binds at the minor groove. The docking studies revealed that the compound 3f shows preferential binding towards A/T residues.

  17. Probing the recognition surface of a DNA triplex: binding studies with intercalator-neomycin conjugates. (United States)

    Xue, Liang; Xi, Hongjuan; Kumar, Sunil; Gray, David; Davis, Erik; Hamilton, Paris; Skriba, Michael; Arya, Dev P


    Thermodynamic studies on the interactions between intercalator-neomycin conjugates and a DNA polynucleotide triplex [poly(dA).2poly(dT)] were conducted. To draw a complete picture of such interactions, naphthalene diimide-neomycin (3) and anthraquinone-neomycin (4) conjugates were synthesized and used together with two other analogues, previously synthesized pyrene-neomycin (1) and BQQ-neomycin (2) conjugates, in our investigations. A combination of experiments, including UV denaturation, circular dichroism (CD) titration, differential scanning calorimetry (DSC), and isothermal titration calorimetry (ITC), revealed that all four conjugates (1-4) stabilized poly(dA).2poly(dT) much more than its parent compound, neomycin. UV melting experiments clearly showed that the temperature (T(m3-->2)) at which poly(dA).2poly(dT) dissociated into poly(dA).poly(dT) and poly(dT) increased dramatically (>12 degrees C) in the presence of intercalator-neomycin conjugates (1-4) even at a very low concentration (2 muM). In contrast to intercalator-neomycin conjugates, the increment of T(m3-->2) of poly(dA).2poly(dT) induced by neomycin was negligible under the same conditions. The binding preference of intercalator-neomycin conjugates (1-4) to poly(dA).2poly(dT) was also confirmed by competition dialysis and a fluorescent intercalator displacement assay. Circular dichroism titration studies revealed that compounds 1-4 had slightly larger binding site size ( approximately 7-7.5) with poly(dA).2poly(dT) as compared to neomycin ( approximately 6.5). The thermodynamic parameters of these intercalator-neomycin conjugates with poly(dA).2poly(dT) were derived from an integrated van't Hoff equation using the T(m3-->2) values, the binding site size numbers, and other parameters obtained from DSC and ITC. The binding affinity of all tested ligands with poly(dA).2poly(dT) increased in the following order: neomycin neomycin. The binding of compounds 1-4 with poly(dA).2poly(dT) was mostly enthalpy

  18. The Binding of Roxarsone at the Silica/Water Interface Studied with Second Harmonic Generation (United States)

    Konek, Christopher; Ostrowski, David; Geiger, Franz


    Arsenic is a carcinogen that can also cause chronic poisoning when ingested via drinking water in quantities as low as 10 micrograms/L. In the US, organic arsenicals such as Roxarsone are commonly used as feed additives in the poultry industry. The use of poultry litter as fertilizer results in environmental arsenic deposition rates of up to 50 metric tons per year; the subsequent environmental fate of Roxarsone is unknown. We use second harmonic generation (SHG) to study the thermodynamics and kinetics of Roxarsone binding to environmentally relevant mineral oxide/water interfaces. Roxarsone binding to water/SiO2 interfaces is fully reversible, consistent with high Roxarsone mobility. Results from Langmuir isotherm measurements and surface SHG spectra are presented as well.

  19. EO-199, a specific antagonist of antiarrhythmic drugs: Assessment by binding experiments and in vivo studies

    Energy Technology Data Exchange (ETDEWEB)

    Oppenheimer, E.; Harel, G.; Lipinsky, D.; Sarne, Y. (Tel-Aviv Univ. (Israel))


    EO-199, a demethylated analog of the novel class I antiarrhythmic drug EO-122 was found to antagonize the antiarrhythmic activity of EO-122 and that of procainamide (Class I{sub A}). EO-199 did not block significantly the activity of a class I{sub B} antiarrhythmic agent, lidocaine. EO-199 also displaced the specific binding of ({sup 3}H)EO-122 to rate heart membranes similarly to procainamide whereas lidocaine did not. The correlation between binding experiments and pharmacological effects points to a possible subclassification of these drugs; the two chemical analogs EO-199 and EO-122, as well as procainamide (I{sub A}) but not lidocaine (I{sub B}), compete at the same site or the same state of the sodium channel. The availability of a specific antagonist might be useful for studying the mechanism of action of antiarrhythmic drugs as well as an antidote in cases of antiarrhythmics overdose intoxication.

  20. Spectroscopic Studies on the Binding of Bacteriophage Mequindox with Bovine Serum Albumin

    Institute of Scientific and Technical Information of China (English)

    ZENG,Zhouhua; LIU,Yi; HU,Xianming; XU,Zhenqiang; ZENG,Kun


    Fluorescence spectra and UV-Vis absorption spectra have been used to study the binding of bacteriophage mequindox (MEQ) with bovine serum albumin (BSA),which performed a dynamic quenching process.The quenching constants and thermodynamic parameters at different temperatures were calculated.The binding was primarily driven by entropy,and hydrophobic forces also played a significant role.The distance between BSA and MEQ was estimated to be 4.5 nm based on the theory of F(o)rster's non-radioactive energy transfer.Furthermore,synchronous fluorescence spectra and 3-dimensional fluorescence spectra were used to figure out the configuration of BSA in the presence or absence of MEQ,which indicated that it was basically the same.

  1. Cytotoxic, DNA binding, DNA cleavage and antibacterial studies of ruthenium-fluoroquinolone complexes

    Indian Academy of Sciences (India)

    Mohan N Patel; Hardik N Joshi; Chintan R Patel


    Six new Ru(II) and Ru(III) complexes have been synthesized and characterized by elemental analysis, LC-MS, electronic spectra, IR spectra and magnetic moment measurements. DNA-binding properties of Ru complexes have been studied by means of absorption spectrophotometry and viscosity measurements as well as their HS DNA cleavage properties by means of agarose gel electrophoresis. The experimental results show that all the complexes can bind to DNA via partial intercalative mode. The b values of complexes were found in the range 2.14 × 104 to 2.70 × 105 M-1. All the complexes show excellent efficiency of cleaving DNA than respective fluoroquinolones. Brine shrimp lethality bioassay has been performed to check the cytotoxic activity. The IC50 values of the complexes are in the range of 6.27 to 16.05 g mL-1.

  2. A longitudinal study of serum cobalamins and its binding proteins in lactating women

    DEFF Research Database (Denmark)

    Mørkbak, A L; Ramlau-Hansen, C H; Møller, U K;


    were analysed. RESULTS: No significant differences were observed in serum cobalamins or its binding proteins related to supplementation with vitamin B12 or the duration of lactation. Serum cobalamins remained unchanged from 3 weeks to 9 months post-partum. Total TC (holoTC) (median+/-s.e. pmol...... in HC during a 9-month period post-partum. No differences were observed between the vitamin B12-supplemented and the unsupplemented groups. Thus, supplementation with vitamin B12 has no impact on the circulating level of serum cobalamins or its binding proteins in a Danish population of lactating......OBJECTIVE: To examine longitudinal changes in serum cobalamins, transcobalamin (TC) and haptocorrin (HC) during lactation and to investigate the influence of vitamin B12 supplementation on these parameters. DESIGN: A 9-month follow-up study. SUBJECTS AND METHODS: Lactating mothers (N=89) including...

  3. Studies on binding interactions between clenbuterol hydrochloride and two serum albumins by multispectroscopic approaches in vitro. (United States)

    Wang, Qin; Zhang, Shengrui


    In this study, binding properties of clenbuterol hydrochloride (CL) with human serum albumin (HSA) and bovine serum albumin (BSA) were examined using constant protein concentrations and various CL contents under physiological conditions. The binding parameters were confirmed using fluorescence quenching spectroscopy at various temperatures. The experimental results confirmed that the quenching mechanisms of CL and HSA/BSA were both static quenching processes. The thermodynamic parameters, namely, enthalpy change (ΔH) and entropy change (ΔS), were calculated according to the van't Hoff equation, which suggested that the electrostatic interactions were the predominant intermolecular forces in stabilizing the CL-HSA complex, and hydrogen bonds and van der Waals force were the predominant intermolecular forces in stabilizing the CL-BSA complex. Furthermore, the conformational changes of HSA/BSA in the presence of CL were determined using the data obtained from three-dimensional fluorescence spectroscopy, ultraviolet-visible absorption spectroscopy and circular dichroism spectroscopy.

  4. Characterization and DNA binding studies of unexplored imidazolidines by electronic absorption spectroscopy and cyclic voltammetry. (United States)

    Shah, Afzal; Nosheen, Erum; Munir, Shamsa; Badshah, Amin; Qureshi, Rumana; Rehman, Zia-Ur-; Muhammad, Niaz; Hussain, Hidayat


    UV-Vis spectroscopic behavior of four imidazolidine derivatives i.e., [5-benzylideneimidazolidine-2,4-dione (NBI), 5-(2-hydroxybenzylidene)imidazolidine-2,4-dione (HBI), 5-(4-methoxybenzylidene)imidazolidine-2,4-dione (MBI) and 5-(3,4-di-methoxybenzylidene)imidazolidine-2,4-dione (DBI)] was studied in a wide pH range. Spectroscopic response of the studied compounds was found sensitive to pH and the attached substituents. Incited by anti-tumor activity, structural miscellany and biological applications of imidazolidines, the DNA binding affinity of some novel derivatives of this class of compounds was examined by cyclic voltammetry (CV) and UV-Vis spectroscopy at pH values of blood (7.4) and lysosomes (4.5). The CV results showed the following order of binding strength: KNBI (6.40×10(6)M(-1))>KHBI (1.77×10(5)M(-1))>KMBI (2.06×10(4)M(-1))>KDBI (1.01×10(4)M(-1)) at pH 7.4. The same order was also obtained from UV-Vis spectroscopy. The greater affinity of NBI justified its preferred candidature as an effective anti-cancer drug. The DNA binding propensity of these compounds was found comparable or greater than most of the clinically used anticancer drugs.

  5. Studies of the binding mode of TXNHCH2COOH with calf thymus DNA by spectroscopic methods (United States)

    Ataci, Nese; Arsu, Nergis


    In this study, a thioxanthone derivative named 2-(9-oxo-9H-thioxanthen-2ylamino) acetic acid (TX-NHCH2COOH) was used to investigate small molecule and DNA binding interactions. Absorption and fluorescence emission spectroscopy were used and melting studies were used to explain the binding mode of TXNHCH2COOH-DNA. Intrinsic binding constant Kb TXNHCH2COOH was found 6 × 105 M- 1from UV-Vis absorption spectroscopy. Fluorescence emmision intensity increased by adding ct-DNA to the TXNHCH2COOH and KI quenching experiments resulted with low Ksv value. Additionally, 3.7 °C increase for Tm was observed. The observed quenching of EB and ct-DNA complex and increase viscosity values of ct-DNA by addition of TXNHCH2COOH was determined. All those results indicate that TXNHCH2COOH can intercalate into DNA base pairs. Fluorescence microscopy helped to display imaging of the TXNHCH2COOH-DNA solution.

  6. Molecular docking and NMR binding studies to identify novel inhibitors of human phosphomevalonate kinase

    Energy Technology Data Exchange (ETDEWEB)

    Boonsri, Pornthip [Chemical Proteomics Facility at Marquette, Department of Chemistry, Marquette University, Milwaukee, WI 53201 (United States); Department of Chemistry, NANOTEC Center of Nanotechnology, National Nanotechnology Center, Faculty of Science, Kasetsart University, Bangkok 10900 (Thailand); Neumann, Terrence S.; Olson, Andrew L.; Cai, Sheng [Chemical Proteomics Facility at Marquette, Department of Chemistry, Marquette University, Milwaukee, WI 53201 (United States); Herdendorf, Timothy J.; Miziorko, Henry M. [Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, MO 64110 (United States); Hannongbua, Supa [Department of Chemistry, NANOTEC Center of Nanotechnology, National Nanotechnology Center, Faculty of Science, Kasetsart University, Bangkok 10900 (Thailand); Sem, Daniel S., E-mail: [Chemical Proteomics Facility at Marquette, Department of Chemistry, Marquette University, Milwaukee, WI 53201 (United States)


    Highlights: Black-Right-Pointing-Pointer Natural and synthetic inhibitors of human phosphomevalonate kinase identified. Black-Right-Pointing-Pointer Virtual screening yielded a hit rate of 15%, with inhibitor K{sub d}'s of 10-60 {mu}M. Black-Right-Pointing-Pointer NMR studies indicate significant protein conformational changes upon binding. -- Abstract: Phosphomevalonate kinase (PMK) phosphorylates mevalonate-5-phosphate (M5P) in the mevalonate pathway, which is the sole source of isoprenoids and steroids in humans. We have identified new PMK inhibitors with virtual screening, using autodock. Promising hits were verified and their affinity measured using NMR-based {sup 1}H-{sup 15}N heteronuclear single quantum coherence (HSQC) chemical shift perturbation and fluorescence titrations. Chemical shift changes were monitored, plotted, and fitted to obtain dissociation constants (K{sub d}). Tight binding compounds with K{sub d}'s ranging from 6-60 {mu}M were identified. These compounds tended to have significant polarity and negative charge, similar to the natural substrates (M5P and ATP). HSQC cross peak changes suggest that binding induces a global conformational change, such as domain closure. Compounds identified in this study serve as chemical genetic probes of human PMK, to explore pharmacology of the mevalonate pathway, as well as starting points for further drug development.

  7. Structural studies on dinuclear ruthenium(II) complexes that bind diastereoselectively to an antiparallel folded human telomere sequence. (United States)

    Wilson, Tom; Costa, Paulo J; Félix, Vítor; Williamson, Mike P; Thomas, Jim A


    We report DNA binding studies of the dinuclear ruthenium ligand [{Ru(phen)2}2tpphz](4+) in enantiomerically pure forms. As expected from previous studies of related complexes, both isomers bind with similar affinity to B-DNA and have enhanced luminescence. However, when tested against the G-quadruplex from human telomeres (which we show to form an antiparallel basket structure with a diagonal loop across one end), the ΛΛ isomer binds approximately 40 times more tightly than the ΔΔ, with a stronger luminescence. NMR studies show that the complex binds at both ends of the quadruplex. Modeling studies, based on experimentally derived restraints obtained for the closely related [{Ru(bipy)2}2tpphz](4+), show that the ΛΛ isomer fits neatly under the diagonal loop, whereas the ΔΔ isomer is unable to bind here and binds at the lateral loop end. Molecular dynamics simulations show that the ΔΔ isomer is prevented from binding under the diagonal loop by the rigidity of the loop. We thus present a novel enantioselective binding substrate for antiparallel basket G-quadruplexes, with features that make it a useful tool for quadruplex studies.

  8. Spectroscopic and Docking Studies on the Binding of Liquiritigenin with Hyaluronidase for Antiallergic Mechanism


    Hua-jin Zeng; Ran Yang; Jing You; Ling-bo Qu; Yan-jun Sun


    The inhibitory effect of liquiritigenin on hyaluronidase and its binding mechanism were investigated systematically by UV-vis absorption, fluorescence, and molecular modeling approaches. These results indicated that liquiritigenin could interact with hyaluronidase to form a liquiritigenin-hyaluronidase complex. The binding constant, number of binding sites, and thermodynamic parameters were calculated, which indicated that liquiritigenin could spontaneously bind with hyaluronidase mainly thro...

  9. Studies of phosphorus Gaussian profile emitter silicon solar cells

    Directory of Open Access Journals (Sweden)

    N. Stem


    Full Text Available Considering recent modifications on n-type highly doped silicon parameters, an emitter optimization was made based on one-dimensional models with analytical solutions. In order to get good accuracy, a fifth order approximation has been considered. Two kinds of emitters, homogeneous and non-homogeneous, with phosphorus Gaussian profile emitter solar cells were optimized. According to our results: homogeneous emitter solar cells show their maximum efficiencies (h @ 21.60-21.74%with doping levelsnus = 1x10(19 - 5x10(18 (cm-3 and (1.2-2.0 mum emitter thickness range. Non-homogeneous emitter solar cells provide a slightly higher efficiency (eta = 21.82-21.92%, with Ns = 1x10(20 (cm-3 with 2.0 mum thickness under metal-contacted surface and Ns = 1x10(19 - 5x10(18 (cm-3 with (1.2-2.0 mum thickness range, (sheet resistance range 90-100 W/ under passivated surface. Although non-homogeneous emitter solar cells have a higher efficiency than homogeneous emitter ones, the required technology is more complex and their overall interest for practical applications is questionable.

  10. Experimental - theoretical study of axially compressed cold formed steel profiles

    Directory of Open Access Journals (Sweden)

    Bešević Miroslav


    Full Text Available Analysis of axially compressed steel members made of cold formed profiles presented in this paper was conducted through both experimental and numerical methods. Numerical analysis was conducted by means of "PAK" finite element software designed for nonlinear static and dynamic analysis of structures. Results of numerical analysis included ultimate bearing capacity with corresponding middle section force-deflection graphs and buckling curves. Extensive experimental investigation were also concentrated on determination of bearing capacity and buckling curves. Experiments were conducted on five series with six specimens each for slenderness values of 50, 70, 90, 110 and 120. Compressed simply supported members were analyzed on Amsler Spherical pin support with unique electronical equipment and software. Besides determination of forcedeflection curves, strains were measured in 18 or 12 cross sections along the height of the members. Analysis included comparisons with results obtained by different authors in this field recently published in international journals. Special attention was dedicated to experiments conducted on high strength and stainless steel members.

  11. Structural and thermodynamic study on aldose reductase: nitro-substituted inhibitors with strong enthalpic binding contribution. (United States)

    Steuber, Holger; Heine, Andreas; Klebe, Gerhard


    strongly favourable contribution to binding enthalpy in case the inhibitor is equipped with a nitro group at the corresponding position. To further investigate this phenomenon, we determined crystal structures and thermodynamic data of two similarly constituted IDD-type inhibitors addressing the specificity pocket with either a nitro or halogen-substituted aromatic moiety. As these data suggest, the nitro group provokes the enthalpic contribution, in addition to the H-bond mentioned above, by accepting two "non-classical" H-bonds donated by the aromatic tyrosine side-chain. In summary, this study provides the platform for further structure-guided design hypotheses of novel drug candidates with higher affinity and selectivity.

  12. Reference tissue modeling with parameter coupling: application to a study of SERT binding in HIV

    Energy Technology Data Exchange (ETDEWEB)

    Endres, Christopher J; Pomper, Martin G [Russell H Morgan Department of Radiology and Radiological Science, Johns Hopkins Medical Institutions, Baltimore, MD 21231 (United States); Hammoud, Dima A, E-mail: [Radiology and Imaging Sciences, National Institutes of Health/Clinical Center, Bethesda, MD (United States)


    When applicable, it is generally preferred to evaluate positron emission tomography (PET) studies using a reference tissue-based approach as that avoids the need for invasive arterial blood sampling. However, most reference tissue methods have been shown to have a bias that is dependent on the level of tracer binding, and the variability of parameter estimates may be substantially affected by noise level. In a study of serotonin transporter (SERT) binding in HIV dementia, it was determined that applying parameter coupling to the simplified reference tissue model (SRTM) reduced the variability of parameter estimates and yielded the strongest between-group significant differences in SERT binding. The use of parameter coupling makes the application of SRTM more consistent with conventional blood input models and reduces the total number of fitted parameters, thus should yield more robust parameter estimates. Here, we provide a detailed evaluation of the application of parameter constraint and parameter coupling to [{sup 11}C]DASB PET studies. Five quantitative methods, including three methods that constrain the reference tissue clearance (k{sup r}{sub 2}) to a common value across regions were applied to the clinical and simulated data to compare measurement of the tracer binding potential (BP{sub ND}). Compared with standard SRTM, either coupling of k{sup r}{sub 2} across regions or constraining k{sup r}{sub 2} to a first-pass estimate improved the sensitivity of SRTM to measuring a significant difference in BP{sub ND} between patients and controls. Parameter coupling was particularly effective in reducing the variance of parameter estimates, which was less than 50% of the variance obtained with standard SRTM. A linear approach was also improved when constraining k{sup r}{sub 2} to a first-pass estimate, although the SRTM-based methods yielded stronger significant differences when applied to the clinical study. This work shows that parameter coupling reduces the

  13. Iron profile in children with behavioural disorders: a prospective study in a tertiary care hospital in north India. (United States)

    Mahajan, Garima; Sikka, Meera; Rusia, Usha; Bhatia, M S


    Iron deficiency anemia is the most frequent micronutrient deficiency in the developing countries like India especially affecting pregnant women and young children. Iron is an essential element involved in myelin formation, neurotransmitter synthesis and neuro-metabolism. Several behavioural disturbances have been reported in iron deficient children. In the present study, we determined the prevalence of iron deficiency anemia in children with behavioural disorders and assessed the improvement in terms of symptoms (by child behaviour check list), haematological parameters and iron status after treatment with oral iron. In this prospective study, 44 children in the age group of 3-12 years who were diagnosed with behavioural disorders were evaluated. Complete blood counts using automated hematology analyzer and iron parameters (serum iron, total iron binding capacity, % transferrin saturation and serum ferritin) were measured in all the patients to assess the prevalence of iron deficiency in these children. Thirty age matched controls were also studied. Iron deficiency was found in 32 (73%) children, as assessed by transferrin saturation <16% and/or serum ferritin <16 μg/l. Following treatment with iron for 100 ± 10 days, there was a statistically (P ≤ 0.05) significant improvement in the clinical features, haematological profile and iron status. The presence of iron deficiency in children with behavioural disorders and subsequent improvement in clinical features, haematological profile and iron status suggests a possible causal relationship between iron deficiency and behavioural disorders.

  14. Label-Free LC-MS Profiling of Skeletal Muscle Reveals Heart-Type Fatty Acid Binding Protein as a Candidate Biomarker of Aerobic Capacity. (United States)

    Malik, Zulezwan Ab; Cobley, James N; Morton, James P; Close, Graeme L; Edwards, Ben J; Koch, Lauren G; Britton, Steven L; Burniston, Jatin G


    Two-dimensional gel electrophoresis provides robust comparative analysis of skeletal muscle, but this technique is laborious and limited by its inability to resolve all proteins. In contrast, orthogonal separation by SDS-PAGE and reverse-phase liquid chromatography (RPLC) coupled to mass spectrometry (MS) affords deep mining of the muscle proteome, but differential analysis between samples is challenging due to the greater level of fractionation and the complexities of quantifying proteins based on the abundances of their tryptic peptides. Here we report simple, semi-automated and time efficient (i.e., 3 h per sample) proteome profiling of skeletal muscle by 1-dimensional RPLC electrospray ionisation tandem MS. Solei were analysed from rats (n = 5, in each group) bred as either high- or low-capacity runners (HCR and LCR, respectively) that exhibited a 6.4-fold difference (1,625 ± 112 m vs. 252 ± 43 m, p ions, which spanned three orders of magnitude. In total, 207 proteins were analysed, which encompassed almost all enzymes of the major metabolic pathways in skeletal muscle. The most abundant protein detected was type I myosin heavy chain (RA = 5,843 ± 897) and the least abundant protein detected was heat shock 70 kDa protein (RA = 2 ± 0.5). Sixteen proteins were significantly (p ion (551.21 m/z) of the doubly-charged peptide SLGVGFATR (454.19 m/z) of residues 23-31 of FABPH. SRM was conducted on technical replicates of each biological sample and exhibited a coefficient of variation of 20%. The abundance of FABPH measured by SRM was 2.84-fold greater (p = 0.0095) in HCR muscle. In addition, SRM of FABPH was performed in vastus lateralis samples of young and elderly humans with different habitual activity levels (collected during a previous study) finding FABPH abundance was 2.23-fold greater (p = 0.0396) in endurance-trained individuals regardless of differences in age. In summary, our findings in HCR/LCR rats provide protein-level confirmation for earlier

  15. Magnetic core/shell Fe3O4/Au nanoparticles for studies of quinolones binding to protein by fluorescence spectroscopy. (United States)

    Jin, Rui; Song, Daqian; Xiong, Huixia; Ai, Lisha; Ma, Pinyi; Sun, Ying


    Magnetic core/shell Fe3O4/Au nanoparticles were used in the determination of drug binding to bovine serum albumin (BSA) using a fluorescence spectroscopic method. The binding constants and number of binding sites for protein with drugs were calculated using the Scatchard equation. Because of their superparamagnetic and biocompatible characteristics, magnetic core/shell Fe3O4/Au nanoparticles served as carrier proteins for fixing proteins. After binding of the protein to a drug, the magnetic core/shell Fe3O4/Au nanoparticles-protein-drug complex was separated from the free drug using an applied magnetic field. The free drug concentration was obtained directly by fluorescence spectrometry and the proteins did not influence the drug determination. So, the achieved number of binding sites should be reliable. The binding constant and site number for ciprofloxacin (CPFX) binding to BSA were 2.055 × 10(5) L/mol and 31.7, and the corresponding values for norfloxacin (NOR) binding to BSA were 1.383 × 10(5) L/mol and 38.8. Based on the achieved results, a suitable method was proposed for the determination of binding constants and the site number for molecular interactions. The method was especially suitable for studies on the interactions of serum albumin with the active ingredients of Chinese medicine.

  16. Isothermal titration calorimetric and computational studies on the binding of chitooligosaccharides to pumpkin (Cucurbita maxima) phloem exudate lectin. (United States)

    Narahari, Akkaladevi; Singla, Hitesh; Nareddy, Pavan Kumar; Bulusu, Gopalakrishnan; Surolia, Avadhesha; Swamy, Musti J


    The interaction of chitooligosaccharides [(GlcNAc)(2-6)] with pumpkin phloem exudate lectin (PPL) was investigated by isothermal titration calorimetry and computational methods. The dimeric PPL binds to (GlcNAc)(3-5) with binding constants of 1.26-1.53 × 10(5) M(-1) at 25 °C, whereas chitobiose exhibits approximately 66-fold lower affinity. Interestingly, chitohexaose shows nearly 40-fold higher affinity than chitopentaose with a binding constant of 6.16 × 10(6) M(-1). The binding stoichiometry decreases with an increase in the oligosaccharide size from 2.26 for chitobiose to 1.08 for chitohexaose. The binding reaction was essentially enthalpy driven with negative entropic contribution, suggesting that hydrogen bonds and van der Waals' interactions are the main factors that stabilize PPL-saccharide association. The three-dimensional structure of PPL was predicted by homology modeling, and binding of chitooligosaccharides was investigated by molecular docking and molecular dynamics simulations, which showed that the protein binding pocket can accommodate up to three GlcNAc residues, whereas additional residues in chitotetraose and chitopentaose did not exhibit any interactions with the binding pocket. Docking studies with chitohexaose indicated that the two triose units of the molecule could interact with different protein binding sites, suggesting formation of higher order complexes by the higher oligomers of GlcNAc by their simultaneous interaction with two protein molecules.

  17. Binding of benzodiazepine drugs to bovine serum albumin: A second derivative spectrophotometric study (United States)

    Omran, Ahmed A.; El-Sayed, Abdel-Aziz; Shehata, Ahmed


    The binding constants ( K values) of three benzodiazepine drugs to bovine serum albumin were determined by a second derivative spectrophotometric method. Despite the sample and reference samples were prepared in the same way to maintain the same albumin content in each sample and reference pair, the absorption spectra show that the baseline compensation was incomplete because of the strong background signals caused by bovine serum albumin. Accordingly, further quantitative spectral information could not be obtained from these absorption spectra. On the other hand, the calculated second derivative spectra clearly show isosbestic points indicating the complete removal of the residual background signal effects. Using the derivative intensity differences (Δ D values) of the studied benzodiazepine drugs before and after the addition of albumin, the binding constants were calculated and obtained with R.S.D. of less than 8%. The interactions of drugs with bovine serum albumin were investigated using Scatchard's plot. In addition, the consistency between the fractions of bound benzodiazepine calculated from the obtained K values and the experimental values were established. The results indicate that the second derivative method can be advantageously applicable to the determination of binding constants of drugs to serum albumin without prior separation. Moreover, the validity of the proposed method was confirmed.

  18. Dual binding mode in cohesin-dockerin complexes as assessed through stretching studies (United States)

    Wojciechowski, Michał; Cieplak, Marek


    A recent experimental study by Jobst et al. of stretching of a wild-type (WT) cohesin-dockerin complex has identified two kinds of the force-displacement patterns, with a single or double-peaked final rupture, which are termed "short" and "long" here. This duality has been interpreted as arising from the existence of two kinds of binding. Here, we analyze the separation of two cohesin-dockerin complexes of C. thermocellum theoretically. We use a coarse-grained structure-based model and the values of the pulling speeds are nearly experimental. In their native states, the two systems differ in the mutual binding orientations of the molecules in the complex. We demonstrate that the WT complex (PDB:1OHZ) unravels along two possible pathways that are qualitatively consistent with the presence of the short and long patterns observed experimentally. On the other hand, the mutated complex (PDB:2CCL) leads only to short trajectories. The short and long stretching pathways also appear in the cohesin-dockerin-Xmodule complex (PDB:4IU3, WT) of R. flavefaciens. Thus the duality in the stretching patterns need not be necessarily due to the duality in binding.

  19. Synthesis and microarray-assisted binding studies of core xylose and fucose containing N-glycans. (United States)

    Brzezicka, Katarzyna; Echeverria, Begoña; Serna, Sonia; van Diepen, Angela; Hokke, Cornelis H; Reichardt, Niels-Christian


    The synthesis of a collection of 33 xylosylated and core-fucosylated N-glycans found only in nonmammalian organisms such as plants and parasitic helminths has been achieved by employing a highly convergent chemo-enzymatic approach. The influence of these core modifications on the interaction with plant lectins, with the human lectin DC-SIGN (Dendritic Cell-Specific Intercellular adhesion molecule-3-Grabbing Nonintegrin), and with serum antibodies from schistosome-infected individuals was studied. Core xylosylation markedly reduced or completely abolished binding to several mannose-binding plant lectins and to DC-SIGN, a C-type lectin receptor present on antigen presenting cells. Employing the synthetic collection of core-fucosylated and core-xylosylated N-glycans in the context of a larger glycan array including structures lacking these core modifications, we were able to dissect core xylose and core fucose specific antiglycan antibody responses in S. mansoni infection sera, and we observed clear and immunologically relevant differences between children and adult groups infected with this parasite. The work presented here suggests that, quite similar to bisecting N-acetylglucosamine, core xylose distorts the conformation of the unsubstituted glycan, with important implications for the immunogenicity and protein binding properties of complex N-glycans.

  20. Studies of the binding of ethidium bromide to cells before and after enzyme treatment. (United States)

    Eisenhut, M; Choné, B


    Binding of ethidium bromide (EB) to cells before and after HCl, pepsin and RNase treatment was investiaged by spectophotometric and fluorimetric methods. Binding isotherms, calculated with the McGheevon Hippel equation, taking EB as a non-interacting ligand, revealed the influcence of these treatments on the fluorescence characteristics of the cells which were measured by flow-through cytofluorimetry. Thus pepsin- and RNase-treated cells have a reduced intercalation capacity due to the loss of cytoplasmic RNA and RNA hydrolysis, respectively. HCl alone, or in association with pepsin, increased the equilibrium constant K considerably. Thus at low free EB concentrations the enchanced EB affinity of acid-pretreated cells generates a high fluorescence intensity, by comparison with treatments at neutral pH. This result contradicts the interpretation of high EB binding to acid pretreated cells which is commonly believed to be due to hydrolytic histone removal from potential intercalation sites. With increasing free EB concentrations the fluorescence intensities of RNase- and pepsin-treated cells culminate at the same level due to their amost identical intercalation capacities. Consequently, quantitative DNA analysis of pretreated cell suspensions with EB can only be performed if the alteration, induced by the pretreatment, has previously been studied.

  1. Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies

    Directory of Open Access Journals (Sweden)

    Keskin Ozlem


    Full Text Available Abstract Background How antibodies recognize and bind to antigens can not be totally explained by rigid shape and electrostatic complimentarity models. Alternatively, pre-existing equilibrium hypothesis states that the native state of an antibody is not defined by a single rigid conformation but instead with an ensemble of similar conformations that co-exist at equilibrium. Antigens bind to one of the preferred conformations making this conformation more abundant shifting the equilibrium. Results Here, two antibodies, a germline antibody of 36–65 Fab and a monoclonal antibody, SPE7 are studied in detail to elucidate the mechanism of antibody-antigen recognition and to understand how a single antibody recognizes different antigens. An elastic network model, Anisotropic Network Model (ANM is used in the calculations. Pre-existing equilibrium is not restricted to apply to antibodies. Intrinsic fluctuations of eight proteins, from different classes of proteins, such as enzymes, binding and transport proteins are investigated to test the suitability of the method. The intrinsic fluctuations are compared with the experimentally observed ligand induced conformational changes of these proteins. The results show that the intrinsic fluctuations obtained by theoretical methods correlate with structural changes observed when a ligand is bound to the protein. The decomposition of the total fluctuations serves to identify the different individual modes of motion, ranging from the most cooperative ones involving the overall structure, to the most localized ones. Conclusion Results suggest that the pre-equilibrium concept holds for antibodies and the promiscuity of antibodies can also be explained this hypothesis: a limited number of conformational states driven by intrinsic motions of an antibody might be adequate to bind to different antigens.

  2. Binding of several anti-tumor drugs to bovine serum albumin: Fluorescence study

    Energy Technology Data Exchange (ETDEWEB)

    Bi Shuyun [College of Chemistry, Changchun Normal University, Changchun 130032 (China)], E-mail:; Sun Yantao [College of Chemistry, Jilin University, Changchun 130023 (China); College of Chemistry, Jilin Normal University, Siping 136000 (China); Qiao Chunyu; Zhang Hanqi [College of Chemistry, Jilin University, Changchun 130023 (China); Liu Chunming [College of Chemistry, Changchun Normal University, Changchun 130032 (China)


    The interactions of mitomycin C (MMC), fluorouracil (FU), mercaptopurine (MP) and doxorubicin hydrochloride (DXR) with bovine serum albumin (BSA) were studied by spectroscopic method. Quenching of fluorescence of serum albumin by these drugs was found to be a static quenching process. The binding constants (K{sub A}) were 9.66x10{sup 3}, 2.08x10{sup 3}, 8.20x10{sup 2} and 7.50x10{sup 3} L mol{sup -1} for MMC-, FU-, MP- and DXR-BSA, respectively, at pH 7.4 Britton-Robinson buffer at 28 deg. C. The thermodynamic functions such as enthalpy change ({delta}H), entropy change ({delta}S) and Gibbs free-energy change ({delta}G) for the reactions were also calculated according to the thermodynamic equations. The main forces in the interactions of these drugs with BSA were evaluated. It was found that the interactions of MMC and FU with BSA were exothermic processes and those of MP and DXR with BSA were endothermic. In addition, the binding sites on BSA for the four drugs were probed by the changes of binding properties of these drugs with BSA in the presence of two important site markers such as ibuprofen and indomethacin. Based on the Foester theory of non-radiation energy transfer, the binding distances between the drugs and tryptophane were calculated and they were 3.00, 1.14, 2.85, and 2.79 nm for MMC, FU, MP and DXR, respectively.

  3. Resonance Raman study on indoleamine 2,3-dioxygenase: Control of reactivity by substrate-binding

    Energy Technology Data Exchange (ETDEWEB)

    Yanagisawa, Sachiko; Hara, Masayuki [Graduate School of Life Science and Picobiology Institute, University of Hyogo, Koto 3-2-1, Kamigori-cho, Ako-gun, Hyogo 678-1297 (Japan); Sugimoto, Hiroshi; Shiro, Yoshitsugu [Biometal Science Laboratory, RIKEN SPring-8 Center, Harima Institute, Koto 1-1-1, Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan); Ogura, Takashi, E-mail: [Graduate School of Life Science and Picobiology Institute, University of Hyogo, Koto 3-2-1, Kamigori-cho, Ako-gun, Hyogo 678-1297 (Japan)


    Highlights: • Indoleamine 2,3-dioygenase has been studied by resonance Raman spectroscopy. • Trp-binding to the enzyme induces high frequency shift of the Fe–His stretching mode. • Increased imidazolate character of histidine promotes the O–O bond cleavage step. • A fine-tuning of the reactivity of the O–O bond cleavage reaction is identified. • The results are consistent with the sequential oxygen-atom-transfer mechanism. - Abstract: Resonance Raman spectra of ligand-bound complexes including the 4-phenylimidazole complex and of free and L-Trp-bound forms of indoleamine 2, 3-dioxygenase in the ferric state were examined. Effects on the vinyl and propionate substituent groups of the heme were detected in a ligand-dependent fashion. The effects of phenyl group of 4-phenylimidazole on the vinyl and propionate Raman bands were evident when compared with the case of imidazole ligand. Substrate binding to the ferrous protein caused an upshift of the iron–histidine stretching mode by 3 cm{sup −1}, indicating an increase in negativity of the imidazole ring, which favors the O–O bond cleavage. The substrate binding event is likely to be communicated from the heme distal side to the iron–histidine bond through heme substituent groups and the hydrogen-bond network which includes water molecules, as identified in an X-ray structure of a 4-phenylimidazole complex. The results provide evidence for fine-tuning of the reactivity of O–O bond cleavage by the oxygenated heme upon binding of L-Trp.

  4. Spectroscopic studies of the binding of Cu(II) complexes of oxicam NSAIDs to alternating G-C and homopolymeric G-C sequences. (United States)

    Chakraborty, Sreeja; Bose, Madhuparna; Sarkar, Munna


    Drugs belonging to the Non-steroidal anti-inflammatory (NSAID) group are not only used as anti-inflammatory, analgesic and anti-pyretic agents, but also show anti-cancer effects. Complexing them with a bioactive metal like copper, show an enhancement in their anti-cancer effects compared to the bare drugs, whose exact mechanism of action is not yet fully understood. For the first time, it was shown by our group that Cu(II)-NSAIDs can directly bind to the DNA backbone. The ability of the copper complexes of NSAIDs namely meloxicam and piroxicam to bind to the DNA backbone could be a possible molecular mechanism behind their enhanced anticancer effects. Elucidating base sequence specific interaction of Cu(II)-NSAIDs to the DNA will provide information on their possible binding sites in the genome sequence. In this work, we present how these complexes respond to differences in structure and hydration pattern of GC rich sequences. For this, binding studies of Cu(II) complexes of piroxicam [Cu(II)-(Px)2 (L)2] and meloxicam [Cu(II)-(Mx)2 (L)] with alternating GC (polydG-dC) and homopolymeric GC (polydG-polydC) sequences were carried out using a combination of spectroscopic techniques that include UV-Vis absorption, fluorescence and circular dichroism (CD) spectroscopy. The Cu(II)-NSAIDs show strong binding affinity to both polydG-dC and polydG-polydC. The role reversal of Cu(II)-meloxicam from a strong binder of polydG-dC (Kb=11.5×10(3) M(-1)) to a weak binder of polydG-polydC (Kb=5.02×10(3) M(-1)), while Cu(II)-piroxicam changes from a strong binder of polydG-polydC (Kb=8.18×10(3) M(-1)) to a weak one of polydG-dC (Kb=2.18×10(3) M(-1)), point to the sensitivity of these complexes to changes in the backbone structures/hydration. Changes in the profiles of UV absorption band and CD difference spectra, upon complex binding to polynucleotides and the results of competitive binding assay using ethidium bromide (EtBr) fluorescence indicate different binding modes in each

  5. Spectroscopic studies of the binding of Cu(II) complexes of oxicam NSAIDs to alternating G-C and homopolymeric G-C sequences (United States)

    Chakraborty, Sreeja; Bose, Madhuparna; Sarkar, Munna


    Drugs belonging to the Non-steroidal anti-inflammatory (NSAID) group are not only used as anti-inflammatory, analgesic and anti-pyretic agents, but also show anti-cancer effects. Complexing them with a bioactive metal like copper, show an enhancement in their anti-cancer effects compared to the bare drugs, whose exact mechanism of action is not yet fully understood. For the first time, it was shown by our group that Cu(II)-NSAIDs can directly bind to the DNA backbone. The ability of the copper complexes of NSAIDs namely meloxicam and piroxicam to bind to the DNA backbone could be a possible molecular mechanism behind their enhanced anticancer effects. Elucidating base sequence specific interaction of Cu(II)-NSAIDs to the DNA will provide information on their possible binding sites in the genome sequence. In this work, we present how these complexes respond to differences in structure and hydration pattern of GC rich sequences. For this, binding studies of Cu(II) complexes of piroxicam [Cu(II)-(Px)2 (L)2] and meloxicam [Cu(II)-(Mx)2 (L)] with alternating GC (polydG-dC) and homopolymeric GC (polydG-polydC) sequences were carried out using a combination of spectroscopic techniques that include UV-Vis absorption, fluorescence and circular dichroism (CD) spectroscopy. The Cu(II)-NSAIDs show strong binding affinity to both polydG-dC and polydG-polydC. The role reversal of Cu(II)-meloxicam from a strong binder of polydG-dC (Kb = 11.5 × 103 M-1) to a weak binder of polydG-polydC (Kb = 5.02 × 103 M-1), while Cu(II)-piroxicam changes from a strong binder of polydG-polydC (Kb = 8.18 × 103 M-1) to a weak one of polydG-dC (Kb = 2.18 × 103 M-1), point to the sensitivity of these complexes to changes in the backbone structures/hydration. Changes in the profiles of UV absorption band and CD difference spectra, upon complex binding to polynucleotides and the results of competitive binding assay using ethidium bromide (EtBr) fluorescence indicate different binding modes in each

  6. Binding and conformational changes of human serum albumin upon interaction with 4-aminoantipyrine studied by spectroscopic methods and cyclic voltammetry. (United States)

    Gowda, Jayant I; Nandibewoor, Sharanappa T


    The interactions of 4-aminoantipyrine (AAP) with human serum albumin (HSA) have been studied by UV-visible spectroscopy, fluorescence spectroscopy and cyclic voltammetry. The binding of 4-aminoantipyrine quenches the HSA fluorescence, revealing a 1:1 interaction with a binding constant of about 10(5) M(-1). The experimental results showed that AAP effectively quenched the intrinsic fluorescence of HSA via dynamic type of quenching. In addition, according to the synchronous fluorescence spectra of HSA in presence of 4-aminoantipyrine, the tryptophan residue of the proteins are most perturbed by the binding process. The number of binding sites, the binding constant, site probe study, some common metal ions effect and the thermodynamic parameters were calculated.

  7. Comparative thermodynamic studies on substrate and product binding of O-Acetylserine Sulfhydrylase reveals two different ligand recognition modes†

    Directory of Open Access Journals (Sweden)

    Kumaran Sangaralingam


    Full Text Available Abstract Background The importance of understanding the detailed mechanism of cysteine biosynthesis in bacteria is underscored by the fact that cysteine is the only sulfur donor for all cellular components containing reduced sulfur. O-acetylserine sulfhydrylase (OASS catalyzes this crucial last step in the cysteine biosynthesis and has been recognized as an important gene for the survival and virulence of pathogenic bacteria. Structural and kinetic studies have contributed to the understanding of mechanistic aspects of OASS, but details of ligand recognition features of OASS are not available. In the absence of any detailed study on the energetics of ligand binding, we have studied the thermodynamics of OASS from Salmonella typhimurium (StOASS, Haemophilus influenzae (HiOASS, and Mycobacterium tuberculosis (MtOASS binding to their substrate O-acetylserine (OAS, substrate analogue (methionine, and product (cysteine. Results Ligand binding properties of three OASS enzymes are studied under defined solution conditions. Both substrate and product binding is an exothermic reaction, but their thermodynamic signatures are very different. Cysteine binding to OASS shows that both enthalpy and entropy contribute significantly to the binding free energy at all temperatures (10-30°C examined. The analyses of interaction between OASS with OAS (substrate or methionine (substrate analogue revealed a completely different mode of binding. Binding of both OAS and methionine to OASS is dominated by a favorable entropy change, with minor contribution from enthalpy change (ΔHSt-Met = -1.5 ± 0.1 kJ/mol; TΔSSt-Met = 8.2 kJ/mol at 20°C. Our salt dependent ligand binding studies indicate that methionine binding affinity is more sensitive to [NaCl] as compared to cysteine affinity. Conclusions We show that OASS from three different pathogenic bacteria bind substrate and product through two different mechanisms. Results indicate that predominantly entropy driven

  8. Calorimetric and spectroscopic studies of aminoglycoside binding to AT-rich DNA triple helices (United States)

    Xi, Hongjuan; Kumar, Sunil; Dosen-Micovic, Ljiljana; Arya, Dev P.


    Calorimetric and fluorescence techniques were used to characterize the binding of aminoglycosides-neomycin, paromomycin, and ribostamycin, with 5′-dA12-x-dT12-x-dT12-3′ intramolecular DNA triplex (x = hexaethylene glycol) and poly(dA).2poly(dT) triplex. Our results demonstrate the following features: (1) UV thermal analysis reveals that the Tm for triplex decreases with increasing pH value in the presence of neomycin, while the Tm for the duplex remains unchanged. (2) The binding affinity of neomycin decreases with increased pH, although there is an increase in observed binding enthalpy. (3) ITC studies conducted in two buffers (sodium cacodylate and MOPS) yield the number of protonated drug amino groups (Δn) as 0.29 and 0.40 for neomycin and paromomycin interaction with 5′-dA12-x-dT12-x-dT12-3′, respectively. (4) The specific heat capacity change (ΔCp) determined by ITC studies is negative, with more negative values at lower salt concentrations. From 100 mM to 250 mM KCl, the ΔCp ranges from −402 to −60 cal/(mol K) for neomycin. At pH 5.5, a more positive ΔCp is observed, with a value of −98 cal/(mol K) at 100 mM KCl. ΔCp is not significantly affected by ionic strength. (5) Salt dependence studies reveal that there are at least three amino groups of neomycin participating in the electrostatic interactions with the triplex. (6) FID studies using thiazole orange were used to derive the AC50 (aminoglycoside concentration needed to displace 50% of the dye from the triplex) values. Neomycin shows a seven fold higher affinity than paromomycin and eleven fold higher affinity than ribostamycin at pH 6.8. (7) Modeling studies, consistent with UV and ITC results, show the importance of an additional positive charge in triplex recognition by neomycin. The modeling and thermodynamic studies indicate that neomycin binding to the DNA triplex depends upon significant contributions from charge as well as shape complementarity of the drug to the DNA triplex

  9. Beach Profiles Characteristics Along Giao Thuy and Hai Hau Coasts,Vietnam: A Field Study

    Institute of Scientific and Technical Information of China (English)

    NGUYEN Viet Thanh; ZHENG Jin-hai; ZHANG Chi


    Giao Thuy and Hai Hau coasts are located in Nam Dinh province,Vietnam,with a total coastline of 54.42 km in length.The sea-dike system has been seriously damaged and there have been many dike breaches which caused floods and losses.This situation is considered of a general representative for coastal area in the northern part of Vietnam.A variety of studies have shown that the gradient in the longshore sediment transport rate and the offshore fine sediment lost are the main mechanisms causing the beach erosion.This study presents a field investigation of the beach profiles at Giao Thuy and Hai Hau beaches.Three types of empirical functions for the equilibrium beach profile are applied and compared with the observations.Results show that all observed beach profiles can be described by a single function.However,one specific equilibrium profile equation is not sufficient to assess all beach profiles.In Section 1 of Giao Thuy and Section 3 of Hai Thinh beaches,beach profiles are consistent with the logarithmic function,while the exponential function fits well in Section 2.This difference is explained with respect to coastal morphology,sediment characteristics and hydrodynamic conditions which vary in site.An analysis of the validity of the beach profile functions is recommended for the numerical modeling and engineering designs in this area.

  10. Construction and analysis of antennal cDNA library from rice striped stem borer, Chilo suppressalis (Walker) (Lepidoptera: Pyralidae), and expression profiles of putative odorant-binding protein and chemosensory protein genes. (United States)

    Gong, Zhong-Jun; Liu, Su; Jiang, Yan-Dong; Zhou, Wen-Wu; Liang, Qing-Mei; Cheng, Jiaan; Zhang, Chuan-Xi; Zhu, Zeng-Rong; Gurr, Geoff M


    In this study, we constructed a high-quality cDNA library from the antennae of the Chilo suppressalis (Walker) (Lepidoptera: Pyralidae). A total of 1,235 colonies with inserts greater than 0.7 kb were sequenced and analyzed. Homology searching coupled with bioinformatics analysis identified 15 and 7 cDNA sequences, respectively, encoding putative odorant-binding proteins (OBPs) and chemosensory proteins (CSPs). A phylogenetic tree of CsupCSPs showed that each CsupCSP has orthologs in Manduca sexta and Bombyx mori with strong bootstrapping support. One CSP was either very specific or more related to the CSPs of another species than to conspecific CSP. The expression profiles of the OBPs and CSPs in different tissues were measured by real-time quantitative PCR. The results revealed that of the 11 OBP genes, the transcript levels of CsupOBP1, CsupOBP5, and CsupOBP7 were higher in both male and female antennae than those in other tissues. And CsupCSP7 was highly expressed in both male and female antennae. Based on these results, the possible physiological functions of CsupOBPs and CsupCSPs were discussed.

  11. The screening and functional study of proteins binding with the BmNPV polyhedrin promoter

    Directory of Open Access Journals (Sweden)

    Yu Wei


    Full Text Available Abstract Background The polyhedrin gene promoter has an essential role in regulating foreign gene expression in baculovirus expression vector systems (BEVS; however, the high-level transcription mechanism is still unknown. One-hybrid screening in yeast is a powerful way of identifying rapidly heterologous transcription factors that can interact with the polyhedrin promoter DNA sequence. In the current study, total RNA was extracted from the fat bodies of fifth-instar silkworm larvae that had been infected with Bombyx mori nuclear polyhedrosis virus (BmNPV for 5 days; complementary DNA (cDNA was then generated using reverse-transcription (RT-PCR to construct a silkworm gene expression library. Key polyhedrin promoter bait sequences were synthesized to generate a bait yeast strain, which was used to screen the one-hybrid cDNA library. Results In total, 12 positive yeast colonies were obtained from the SD/-Leu/AbA plates; sequencing analysis showed that they belong to two different protein cDNA colonies. Positive colonies underwent bioinformatics analysis, which revealed one colony to be ribosomal proteins [B. mori ribosomal protein SA (BmRPSA] and the other to be NPV DNA-binding proteins (DBP. To further verify the regulatory function of these two protein groups, transient expression vectors (pSK-IE-dbp and pSK-IE-BmRPSA were constructed. The recombinant plasmids were then transfected into cultured B. mori N (BmN cells, which had been infected with a recombinant bacmid containing the gene encoding luciferase (luc. The results showed that overexpression of either dbp or BmRPSA upregulated the polh promoter-driven transcription of luc in BmN cells. In addition, dbp or BmRPSA RNA interference (RNAi resulted in the downregulation of luciferase reporter expression in BmN cells, demonstrating that DBP and BmRPSA are important for luc transcription. EMSA results further confirmed that DBP could directly bind to the conserved single-stranded polh

  12. Study on the bindings of dichlorprop and diquat dibromide herbicides to human serum albumin by spectroscopic methods

    Energy Technology Data Exchange (ETDEWEB)

    Tunç, Sibel, E-mail:; Duman, Osman, E-mail:; Soylu, İnanç; Kancı Bozoğlan, Bahar


    Highlights: • The affinity of DCP to HSA is higher than DQ. • DCP and DQ have quenched the fluorescence emission spectrum of HSA by static quenching mechanism. • Electrostatic interactions are very important in HSA-DCP and HSA-DQ complexes. • Binding constants, numbers of binding sites and thermodynamic parameters have been calculated. • The binding of DQ changes the conformation of protein, on the contrary to DCP. - Abstract: The interactions of dichlorprop (DCP) and diquat dibromide (DQ) herbicides with human serum albumin (HSA) protein were studied by UV absorption, fluorescence, synchronous fluorescence and circular dichroism (CD) spectroscopy. Both DCP and DQ quenched the fluorescence emission spectrum of HSA through the static quenching mechanism. The Stern–Volmer quenching constant, binding constant, the number of binding sites and thermodynamic parameters were determined at 288 K, 298 K, 310 K and 318 K. In HSA-DCP and HSA-DQ systems, an increase in temperature led to a decrease in the Stern–Volmer quenching constant and binding constant. One binding site was obtained for DCP and DQ on HSA. It was found that DCP can bind to HSA with higher affinity than DQ. Negative ΔH and positive ΔS values were obtained for the binding processes between protein and herbicide molecules. This result displayed that electrostatic interactions play a major role in the formation of HSA-DCP and HSA-DQ complexes. The binding processes were exothermic reactions and spontaneous. In addition, synchronous fluorescence and CD spectra of HSA revealed that the binding of DCP to HSA did not cause a significant conformational change in protein, but the interaction of DQ with HSA led to an alteration in the protein structure.

  13. Structural Studies of the Alzheimer's Amyloid Precursor Protein Copper-Binding Domain Reveal How It Binds Copper Ions

    Energy Technology Data Exchange (ETDEWEB)

    Kong, G.K.-W.; Adams, J.J.; Harris, H.H.; Boas, J.F.; Curtain, C.C.; Galatis, D.; Master, C.L.; Barnham, K.J.; McKinstry, W.J.; Cappai, R.; Parker, M.W.; /Sydney U.


    Alzheimer's disease (AD) is the major cause of dementia. Amyloid {beta} peptide (A {beta}), generated by proteolytic cleavage of the amyloid precursor protein (APP), is central to AD pathogenesis. APP can function as a metalloprotein and modulate copper (Cu) transport, presumably via its extracellular Cu-binding domain (CuBD). Cu binding to the CuBD reduces A{beta} levels, suggesting that a Cu mimetic may have therapeutic potential. We describe here the atomic structures of apo CuBD from three crystal forms and found they have identical Cu-binding sites despite the different crystal lattices. The structure of Cu[2+]-bound CuBD reveals that the metal ligands are His147, His151, Tyrl68 and two water molecules, which are arranged in a square pyramidal geometry. The site resembles a Type 2 non-blue Cu center and is supported by electron paramagnetic resonance and extended X-ray absorption fine structure studies. A previous study suggested that Met170 might be a ligand but we suggest that this residue plays a critical role as an electron donor in CuBDs ability to reduce Cu ions. The structure of Cu[+]-bound CuBD is almost identical to the Cu[2+]-bound structure except for the loss of one of the water ligands. The geometry of the site is unfavorable for Cu[+], thus providing a mechanism by which CuBD could readily transfer Cu ions to other proteins.

  14. Mechanistic studies of metal ion binding to water-soluble polymers using potentiometry. (United States)

    Jarvis, N V; Wagener, J M


    A method for elucidating metal ion binding mechanisms with water-soluble polymers has been developed in which the polymer is treated as a collection of monomeric units. Data obtained from potentiometric titrations are analysed by the ESTA library of programs and apparent formation constants may be calculated. From this information, predictions may be made as to metal ion separation using complexation-ultrafiltration techniques. The polymer used in this study was Polymin Water-Free and its complexation with Hg(II), Cd(II), Pb(II), Co(II) and Ni(II) was successfully modelled.

  15. Molecular modelling studies on the binding of some protides to the putative human phosphoramidase Hint1. (United States)

    Congiatu, C; Brancale, A; McGuigan, C


    The aim of the present work is to investigate through molecular modelling the possible role of the human enzyme Hint1 in the final P-N bond cleavage of phosphoramidate ProTides, which would lead to the intracellular delivery of unmasked nucleoside analogue monophosphates. Herein, we report our preliminary analysis based on docking studies of (E)-5-(2-bromovinyl)-2'-deoxyuridine (BVdU) related aminoacyl phosphates with Hint1 and the effect of the amino acid moiety on the enzyme-substrate binding affinity.

  16. Metal binding affinity and selectivity in metalloproteins: insights from computational studies. (United States)

    Dudev, Todor; Lim, Carmay


    This review highlights insights gained from computational studies on protein-metal recognition. We systematically dissect the various factors governing metal binding affinity and selectivity in proteins starting from (a) the intrinsic properties of the metal and neighboring metal cations (if present), to (b) the primary coordination sphere, (c) the second coordination shell, (d) the protein matrix, (e) the bulk solvent, and (f) competing non-protein ligands from the surrounding biological environment. The results herein reveal the fundamental principles and the molecular bases underlying protein-metal recognition, which serve as a guide to engineer novel metalloproteins with programmed properties.


    Vijayakirubha, T; Ramprasath, D; Karunambigai, K; Nagavalli, D; Hemalatha, S


    The macroscopic characters of the whole plant, physical constant values, extractive values, preliminary phyto-chemical tests, fluorescence characters under ultra-violet light after treatment with different reagents of the powdered leaves form the tree of Adansonia digitata linn., [Bombacaceae] were studied to fix some pharmacognostical parameters. Preliminary phytochemical screening on the methanolic extract of the plant was also performed. These studies will help in identification of this plant for further research.

  18. Clinical Profile of Extraocular Muscle Palsy: A Retrospective Study

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    Suman Adhikari, BOptom


    Full Text Available Background: The sixth cranial nerve has been found to be the most commonly affected in previous studies of cranial nerve palsies. This study was carried out to determine the most common nerve involved in extraocular muscle (EOM palsies and the most common cause of EOM palsy in Nepal.Methods: The diagnosed cases of third, fourth, or sixth nerve palsy for 10 years (2000-2010 at the B.P. Koirala Lions Center for Ophthalmic Studies outpatient department were included in the study. A retrospective review of patients’ records was performed, and the causes of EOM palsy were grouped as: vascular, trauma, tumor,aneurysm, undetermined, and others. Recovery of the palsy was evaluated by reviewing the records of the patients who were followed up one month after the initial visit.Results: A total of 838 patients was included in the study. The average patient age was 37 years. The sixth nerve was most commonly affected (n=458, 54.65%, and the most common etiology was undetermined (n=408, 48.68%. Among the cases where the cause of palsy was known, the largest number of patients had trauma (n=188, 16.46%.Conclusion: It was concluded that in Nepal, the most commonly affected cranial nerve is the sixth nerve, in accordance with the other studies done in the past in different parts of the world. Most of the cases of cranial nerve palsy were found to have no specific cause and were not associated with diagnosed systemic disease.

  19. Cohort profile: the Quebec Longitudinal Study of Kindergarten Children (QLSKC). (United States)

    Rouquette, Alexandra; Côté, Sylvana M; Pryor, Laura E; Carbonneau, René; Vitaro, Frank; Tremblay, Richard E


    The Quebec Longitudinal Study of Kindergarten Children (QLSKC) is an ongoing population-based prospective longitudinal study presently spanning ages 6-29 years, designed to study the prevalence, risk factors, development and consequences of behavioural and emotional problems during elementary school. Kindergarten boys and girls attending French-speaking public schools in the Canadian province of Quebec during the 1986-87 and 1987-88 school years were included in the cohort: 2000 children representative of the population and 1017 children exhibiting disruptive behaviour problems. To date, 12 waves of data have been collected, and three generations of participants have been involved in the study (i.e. the study child, his parents and the first child of the study child). Information on demographics, psycho-social and lifestyle factors, child and family member characteristics (physical and mental health), and outcomes such as psychiatric diagnoses, delinquency or school diploma were assessed during three important developmental stages (childhood, adolescence and early adulthood). Blood samples were also collected in early adulthood for genetic analyses. Information on publications, available data and access to data can be found on the following website (

  20. The Mode of Inhibitor Binding to Peptidyl-tRNA Hydrolase: Binding Studies and Structure Determination of Unbound and Bound Peptidyl-tRNA Hydrolase from Acinetobacter baumannii (United States)

    Kaushik, Sanket; Singh, Nagendra; Yamini, Shavait; Singh, Avinash; Sinha, Mau; Arora, Ashish; Kaur, Punit; Sharma, Sujata; Singh, Tej P.


    The incidences of infections caused by an aerobic Gram-negative bacterium, Acinetobacter baumannii are very common in hospital environments. It usually causes soft tissue infections including urinary tract infections and pneumonia. It is difficult to treat due to acquired resistance to available antibiotics is well known. In order to design specific inhibitors against one of the important enzymes, peptidyl-tRNA hydrolase from Acinetobacter baumannii, we have determined its three-dimensional structure. Peptidyl-tRNA hydrolase (AbPth) is involved in recycling of peptidyl-tRNAs which are produced in the cell as a result of premature termination of translation process. We have also determined the structures of two complexes of AbPth with cytidine and uridine. AbPth was cloned, expressed and crystallized in unbound and in two bound states with cytidine and uridine. The binding studies carried out using fluorescence spectroscopic and surface plasmon resonance techniques revealed that both cytidine and uridine bound to AbPth at nanomolar concentrations. The structure determinations of the complexes revealed that both ligands were located in the active site cleft of AbPth. The introduction of ligands to AbPth caused a significant widening of the entrance gate to the active site region and in the process of binding, it expelled several water molecules from the active site. As a result of interactions with protein atoms, the ligands caused conformational changes in several residues to attain the induced tight fittings. Such a binding capability of this protein makes it a versatile molecule for hydrolysis of peptidyl-tRNAs having variable peptide sequences. These are the first studies that revealed the mode of inhibitor binding in Peptidyl-tRNA hydrolases which will facilitate the structure based ligand design. PMID:23844024

  1. The mode of inhibitor binding to peptidyl-tRNA hydrolase: binding studies and structure determination of unbound and bound peptidyl-tRNA hydrolase from Acinetobacter baumannii.

    Directory of Open Access Journals (Sweden)

    Sanket Kaushik

    Full Text Available The incidences of infections caused by an aerobic Gram-negative bacterium, Acinetobacter baumannii are very common in hospital environments. It usually causes soft tissue infections including urinary tract infections and pneumonia. It is difficult to treat due to acquired resistance to available antibiotics is well known. In order to design specific inhibitors against one of the important enzymes, peptidyl-tRNA hydrolase from Acinetobacter baumannii, we have determined its three-dimensional structure. Peptidyl-tRNA hydrolase (AbPth is involved in recycling of peptidyl-tRNAs which are produced in the cell as a result of premature termination of translation process. We have also determined the structures of two complexes of AbPth with cytidine and uridine. AbPth was cloned, expressed and crystallized in unbound and in two bound states with cytidine and uridine. The binding studies carried out using fluorescence spectroscopic and surface plasmon resonance techniques revealed that both cytidine and uridine bound to AbPth at nanomolar concentrations. The structure determinations of the complexes revealed that both ligands were located in the active site cleft of AbPth. The introduction of ligands to AbPth caused a significant widening of the entrance gate to the active site region and in the process of binding, it expelled several water molecules from the active site. As a result of interactions with protein atoms, the ligands caused conformational changes in several residues to attain the induced tight fittings. Such a binding capability of this protein makes it a versatile molecule for hydrolysis of peptidyl-tRNAs having variable peptide sequences. These are the first studies that revealed the mode of inhibitor binding in Peptidyl-tRNA hydrolases which will facilitate the structure based ligand design.

  2. Study on measurement of refractive index profile of GI-POF by light scattering (United States)

    Huifen, Jiang; Xiang'e, Han


    This paper is devoted to the study on measurement of refractive index profile of graded-index polymer optical fiber (GI-POF) by light scattering. Using Generalized Airy theory and Debye series of an inhomogeneous cylinder, the scattering intensity distributions are obtained of Airy structure of rainbows for different refractive index profile. The results show that positions of Airy peaks depend closely on refractive index profile of GI-POF. Since each order of rainbow penetrates it to different depths, such methods could be used to provide information of the refractive index profile of GI-POF. For GI-POF with given diameter, positions of Airy peaks of rainbows are simulated as a function of refractive index profile, which can be used to inverse unknown parameters of refractive index profile. The least square method is used in inversion of refractive index profile with the given refractive index of the cladding. The results obtained agree with theoretical values with high precision. The method has the advantages of non-instructive and on-line measurement, and can be used for the measurement of other inhomogeneous droplets.

  3. Profile and Perceptions of Biogas as Automobile Fuel : A Study of Svensk Biogas


    Larsson, Anneli


    From an environmental- and health perspective, biogas and other biomass-based fuels have several advantages; nevertheless the majority of motorists fill their cars with petroleum-based fuels. This thesis is designed to explore the profile of biogas in relation to its perceptions. It is a study concerning the communication between the biogas producing company Svensk Biogas and their biogas users and non biogas users. To obtain a thorough understanding of the profile and perceptions of biogas a...

  4. Selectivity in ligand binding to uranyl compounds: A synthetic, structural, thermodynamic and computational study

    Energy Technology Data Exchange (ETDEWEB)

    Arnold, John [Univ. of California, Berkeley, CA (United States)


    The uranyl cation (UO₂²⁺) is the most abundant form of uranium on the planet. It is estimated that 4.5 billion tons of uranium in this form exist in sea water. The ability to bind and extract the uranyl cation from aqueous solution while separating it from other elements would provide a limitless source of nuclear fuel. A large body of research concerns the selective recognition and extraction of uranyl. A stable molecule, the cation has a linear O=U=O geometry. The short U-O bonds (1.78 Å) arise from the combination of uranium 5f/6d and oxygen 2p orbitals. Due to the oxygen moieties being multiply bonded, these sites were not thought to be basic enough for Lewis acidic coordination to be a viable approach to sequestration. The goal of this research is thus to broaden the coordination chemistry of the uranyl ion by studying new ligand systems via synthetic, structural, thermodynamic and computational methods. It is anticipated that this fundamental science will find use beyond actinide separation technologies in areas such as nuclear waste remediation and nuclear materials. The focus of this study is to synthesize uranyl complexes incorporating amidinate and guanidinate ligands. Both synthetic and computational methods are used to investigate novel equatorial ligand coordination and how this affects the basicity of the oxo ligands. Such an understanding will later apply to designing ligands incorporating functionalities that can bind uranyl both equatorially and axially for highly selective sequestration. Efficient and durable chromatography supports for lanthanide separation will be generated by (1) identifying robust peptoid-based ligands capable of binding different lanthanides with variable affinities, and (2) developing practical synthetic methods for the attachment of these ligands to Dowex ion exchange resins.

  5. Study of the cavitating instability on a grooved Venturi profile

    CERN Document Server

    Danlos, Amélie; Ravelet, Florent; Coutier-Delgosha, Olivier; Bakir, Farid


    Cavitation is a limiting phenomenon in many domains of fluid mechanics. Instabilities of a partial cavity developed on an hydrofoil, a converging-diverging step or in an inter-blade channel in turbomachinery, have already been investigated and described in many previous works. The aim of this study is to evaluate a passive control method of the sheet cavity. According to operating conditions, cavitation can be described by two different regimes: an unstable regime with a cloud cavitation shedding and a stable regime with only a pulsating sheet cavity. Avoiding cloud cavitation can limit structure damages since a pulsating sheet cavity is less agressive. The surface condition of a converging-diverging step, like a Venturi-type obstacle, is here studied as a solution for a passive control of the cavitation. This study discusses the effect of an organized roughness, in the shape of longitudinal grooves, on the developed sheet cavity. Analyzes conducted with Laser Doppler Velocimetry, visualisations and pressure ...

  6. Endo-S-c-di-GMP Analogues-Polymorphism and Binding Studies with Class I Riboswitch

    Directory of Open Access Journals (Sweden)

    Herman O. Sintim


    Full Text Available C-di-GMP, a cyclic guanine dinucleotide, has been shown to regulate biofilm formation as well as virulence gene expression in a variety of bacteria. Analogues of c-di-GMP have the potential to be used as chemical probes to study c-di-GMP signaling and could even become drug leads for the development of anti-biofilm compounds. Herein we report the synthesis and biophysical studies of a series of c-di-GMP analogues, which have both phosphate and sugar moieties simultaneously modified (called endo-S-c-di-GMP analogues. We used computational methods to predict the relative orientation of the guanine nucleobases in c-di-GMP and analogues. DOSY NMR of the endo-S-c-di-GMP series showed that the polymorphism of c-di-GMP can be tuned with conservative modifications to the phosphate and sugar moieties (conformational steering. Binding studies with Vc2 RNA (a class I c-di-GMP riboswitch revealed that conservative modifications to the phosphate and 2'-positions of c-di-GMP dramatically affected binding to class I riboswitch.

  7. Mineralocorticoid specificity of renal type I receptors: in vivo binding studies

    Energy Technology Data Exchange (ETDEWEB)

    Sheppard, K.; Funder, J.W.


    The authors have injected rats with (TH)aldosterone or (TH) corticosterone, plus 100-fold excess of the highly specific glucocorticoid RU 28362, with or without excess unlabeled aldosterone or corticosterone and compared type I receptor occupancy in kidney and hippocampus. Thirty minutes after subcutaneous injection (TH)aldosterone was well retained in renal papilla-inner medulla, renal cortex-outer medulla, and hippocampus; in contrast, (TH)corticosterone was well retained only in hippocampus. Competition studies for (TH)aldosterone binding sites showed corticosterone to be a poor competitor in the kidney compared with hippocampus. Time-course studies, with rats killed 10-180 min after tracer administration, showed very low uptake/retention of (TH)corticosterone by kidney; in hippocampus (TH)corticosterone retention was similar to that of (TH)aldosterone in kidney, and retention of (TH)aldosterone by hippocampus was much more prolonged than of either tracer in any other tissue. Studies in 10-day-old rats, with very low levels of corticosteroid binding globulin (CBG), showed a high degree of aldosterone selectivity in both zones of the kidney, whereas 9TH)aldosterone and (TH)corticosterone were equivalently bound in hippocampus. They interpret these data as evidenced for a mechanism unrelated to extravascular CBG conferring mineralocorticoid specificity on renal type I receptors and propose two models derived from their findings consistent with such differential selectivity.

  8. Development and Application of an HPLC Method for Erlotinib Protein Binding Studies

    Directory of Open Access Journals (Sweden)

    Soheila Bolandnazar


    Full Text Available Purpose: The aim of the present study was to develop a simple and rapid reversed-phase high performance liquid chromatographic method with UV detection for erlotinib hydrochloride quantification, which is applicable for protein binding studies. Methods: Ultrafilteration method was used for protein binding study of erlotinib hydrochloride. For sample analysis a simple and rapid reversed-phase high performance liquid chromatographic method with UV detection at 332 nm was developed. The mobile phase was a mixture of methanol, acetonitril and potassium dihydrogen phosphate buffer (15:45:40 %v/v set at flow rate of 1.3 ml/min. Results: The run time for erlotinib hydrochloride was approximately 6 minutes. The calibration curve was linear over the range of 320-20000 ng/ml with acceptable intra- and inter-day precision and accuracy. The intra-day and inter-day precisions were less than 10% and the accuracies of intra and inter-day assays were within the range of 97.20-104.83% and 98.8-102.2% respectively. Conclusion: Based on the obtained results, a simple, accurate and precise reversed-phase isocratic HPLC method with UV detection has been optimized and validated for the determination of erlotinib hydrochloride in biological samples.

  9. Cohort profile: Epidemiological Clinicopathological studies in Europe (EClipSE). (United States)


    Epidemiological Clinicopathological Studies in Europe (EClipSE) is the harmonization of neuropathological and longitudinal clinical data from three population-based prospective longitudinal studies of aging. The EClipSE database (Version 1.0) comprises data from the first 970 people who donated their brain at death and this number will increase. EClipSE enables sociodemographic, health, cognitive, and genetic measures collected during life to be related to neuropathology at death, testing hypotheses which require more power than has been previously possible. EClipSE aims to help throw light on relationships between biological, health and psychological factors underlying ageing and the manifestation of clinical dementia.

  10. Cohort Profile: The Nicotine Dependence in Teens (NDIT) Study


    O'Loughlin, Jennifer; Brunet, Jennifer; Difranza, Joseph; Gervais, Andre; Gray-Donald, Katherine; Karp, Igor; Sabiston, Catherine; Sylvestre, Marie-Pierre; Dugas, Erika N.; Engert, James C.; Low, Nancy C.; Tyndale, Rachel F.


    The Nicotine Dependence in Teens (NDIT) study is a prospective cohort investigation of 1294 students recruited in 1999–2000 from all grade 7 classes in a convenience sample of 10 high schools in Montreal, Canada. Its primary objectives were to study the natural course and determinants of cigarette smoking and nicotine dependence in novice smokers. The main source of data was self-report questionnaires administered in class at school every 3 months from grade 7 to grade 11 (1999–2005), for a t...

  11. Thermodynamic study of 5-(/sup 3/H)hydroxytryptamine binding to human cortex membranes

    Energy Technology Data Exchange (ETDEWEB)

    Todd, R.D.; Babinski, J.


    Kinetic and equilibrium measurements of (/sup 3/H)-serotonin (5-hydroxytryptamine) binding to human frontal cortex membranes have been made between 4 and 30 degrees C. The effects of spiperone and ascorbate on binding have also been determined. Under the conditions used, binding was saturable and reversible. Affinity constants derived from kinetic and equilibrium data were comparable. Serotonin binding to several sites had substantial enthalpic as well as entropic components.

  12. Renal profile in patients with orthopaedic trauma: a prospective study. (United States)

    Paul, Ashish; John, Bobby; Pawar, Basant; Sadiq, Shalinder


    This prospective study was undertaken to determine the incidence of acute renal failure (ARF) and to identify factors contributing to development of ARF in orthopaedic trauma patients. A total of 55 patients who presented over a period of one year with trauma to upper and lower limbs were studied. Patients with renal injury, chest or abdominal injury, isolated fractures of the hands, feet and axial skeleton involvement were excluded. Out of these, five developed acute renal failure, three recovered and two died. The overall incidence of ARF in this study was 9.1%. Patients with lower limb injuries are at higher risk of developing ARF. Mangled Extremity Severity Score (MESS) > or = 7, higher age, patient presenting with shock, increased myoglobin levels in urine and serum have been correlated with a greater risk of patients developing ARF and a higher mortality. This study attempts to determine the magnitude of crush injury causing renal failure and the incidence of renal failure in patients with injuries affecting the appendicular skeleton exclusively.

  13. Profiling families enrolled in food allergy immunotherapy studies.

    LENUS (Irish Health Repository)

    DunnGalvin, Audrey


    Little is known about specific psychological factors that affect parents\\' decisions to take part in clinical studies. We examined factors, related to health-related quality of life (HRQoL), that may influence parents\\' decision to allow their children to participate in research on clinical food allergy.

  14. Students from Australian Universities Studying Abroad: A Demographic Profile (United States)

    Nerlich, Steve


    Australia is one of many countries to encourage its students to study abroad and hence develop a global perspective. Traditionally, students who have pursued this option represented a relatively privileged and demographically narrow group. More recently, governments and other agencies have been offering funding support with the aim of…

  15. Early Cognitive Profiles of Emergent Readers: A Longitudinal Study (United States)

    Brunswick, Nicola; Martin, G. Neil; Rippon, Georgina


    This longitudinal study examined the contribution of phonological awareness, phonological memory, and visuospatial ability to reading development in 142 English-speaking children from the start of kindergarten to the middle of Grade 2. Partial cross-lagged analyses revealed significant relationships between early performance on block design and…

  16. Study on the Credit Risk in Societies with Agricultural Profile

    Directory of Open Access Journals (Sweden)

    Jenica POPESCU


    Full Text Available The credit risk is one of the most important risks the banks face in their daily work and it has a direct impact on bank performance. In the current context, a bank has available a variety of options to determine capital requirements, to decrease the credit risk. This study aims to analyze the correlation of the main indicators of creditworthiness of firms and the credit risk, that a bank will take giving credit to these firms.


    Directory of Open Access Journals (Sweden)



    Full Text Available INTRODUCTION: Malaria is a major health concern across the world and is endemic in our country. It is imperative for us to know the varied manifestations and lab features both classically described and rare features for early detection of this disease and further treatment. This study was undertaken to study the clinical features, lab features and complications of malaria in a tertiary care centre. METHODOLOGY: It is a retrospective study done on 75 cases of confirmed and treated cases of malaria for a period of one year in KIMS hospital, Bangalore. Detailed history examination and lab features of these patients were recorded and analyzed. RESULTS: A total of 75 cases of confirmed malaria were treated during study period of which 57[76%] were males Out of 75 cases 46[61%] had vivax malaria infection, 10[13%] had falciparum infection and 19[26%] had mixed infections of falciparum and vivax. In all 3 groups more number of cases was seen in age group of 18 – 40 years. fever was the major presentation (100% in the patients and Pain abdomen along with fever seen in 15 [20%] patients. Head ache was another predominant complaint in 35[46.6%] On examination Icterus was seen in 11 [14.6%] patients Pallor was seen in 13[17.3%] patients Systolic BP of 2ULN was seen in 9[12%] patients Out of these 6[8%] patients had severe malaria as defined by WHO category of severe malaria. CONCLUSIONS: Being more vigilant and well versed with the varied presentations/lab features of malaria and anticipating complications early, effective treatment can be instituted thus reducing the morbidity and mortality of this endemic disease.

  18. Cohort profile: the Social Inequality in Cancer (SIC) cohort study. (United States)

    Nordahl, Helene; Hvidtfeldt, Ulla Arthur; Diderichsen, Finn; Rod, Naja Hulvej; Osler, Merete; Frederiksen, Birgitte Lidegaard; Prescott, Eva; Tjønneland, Anne; Lange, Theis; Keiding, Niels; Andersen, Per Kragh; Andersen, Ingelise


    The Social Inequality in Cancer (SIC) cohort study was established to determine pathways through which socioeconomic position affects morbidity and mortality, in particular common subtypes of cancer. Data from seven well-established cohort studies from Denmark were pooled. Combining these cohorts provided a unique opportunity to generate a large study population with long follow-up and sufficient statistical power to develop and apply new methods for quantification of the two basic mechanisms underlying social inequalities in cancer-mediation and interaction. The SIC cohort included 83 006 participants aged 20-98 years at baseline. A wide range of behavioural and biological risk factors such as smoking, physical inactivity, alcohol intake, hormone replacement therapy, body mass index, blood pressure and serum cholesterol were assessed by self-administered questionnaires, physical examinations and blood samples. All participants were followed up in nationwide demographic and healthcare registries. For those interested in collaboration, further details can be obtained by contacting the Steering Committee at the Department of Public Health, University of Copenhagen, at

  19. Cohort profile: the Hawai'i Family Study of Cognition. (United States)

    Onoye, Jane M M; Hishinuma, Earl S; McArdle, John J; Zonderman, Alan B; Bumanglag, R Janine; Takeshita, Junji


    Intergenerational longitudinal studies over the lifespan provide valuable information for understanding the contexts and dynamic relations among cognition, family and health in adults and the elderly. The Hawai'i Family Study of Cognition (HFSC), initiated in the early 1970s, included a cohort of over 6500 individuals representing over 1800 families of parents and their offspring. The HFSC gathered data on cognitive, personality, biological and other psychosocial variables, and provided novel information on the nature of cognitive abilities, especially on family issues. Some families were reassessed with short-term retesting in the 1970s. A select sample of offspring and their siblings and spouses were re-measured in the 1980s. Decades later, a 40-year follow-up of the original HFSC cohort was facilitated by the availability of contemporary tracking and tracing methods and internet-based testing. A subgroup of the original HFSC participants was re-contacted and retested on contemporary cognitive as well as socio-demographic and health measures. In this paper, we describe the original HFSC cohort and the design and methodology of the re-contact and retest studies of the HFSC, plans for expanding the re-contact and retesting, as well as directions for future research and collaborations. The Principal Investigator may be contacted for more information regarding the application, review and approval process for data access requests from qualified individuals outside the project.

  20. A Study on Sustainable Innovation Profile of Turkey

    Directory of Open Access Journals (Sweden)

    Pelin Vardarlier


    Full Text Available Innovation is the only way of solution to achieve sustainable growth, social welfare and employment in a country.This study principally focuses on the relationship between growth and innovation in the light of information derived from a general literature review about definition, sources and risks of innovation, and measurement of innovation performance. Then, the contribution of innovative capability on economic growth and employment as well as innovation systems on a country basis have been discussed, and accordingly, actions to be taken, including a shift in paradigm, for a growth-innovation-national innovation system and its sustainability have been addressed. In addition, current innovation performance indicators of Turkey have been discussed in the light of a scope which is outlined in the initial sections of the study, and the change in such performance indicators between 1998 and 2009 has been examined. After analysis of the above mentioned criteria and comparisons against practices in developed countries and communities, suggestions have been made about the activities to be carried out in order to make Turkey’s current innovation system “sustainable”, to support and improve innovation.In the study, a research application has been conducted using the content analysis method on the “President’s Message” letters of 158 state and foundation universities that are located in Turkey and that have a website, and the importance accorded to innovation by the universities has been determined. 

  1. A Study on Sustainable Innovation Profile of Turkey

    Directory of Open Access Journals (Sweden)

    Pelin Vardarlier


    Full Text Available Innovation is the only way of solution to achieve sustainable growth, social welfare and employment in a country. This study principally focuses on the relationship between growth and innovation in the light of information derived from a general literature review about definition, sources and risks of innovation, and measurement of innovation performance. Then, the contributions of innovative capability on economic growth and employment as well as innovation systems on a country basis have been discussed, and accordingly, actions to be taken, including a shift in paradigm, for a growth-innovation-national innovation system and its sustainability have been addressed. In addition, current innovation performance indicators of Turkey have been discussed in the light of a scope which is outlined in the initial sections of the study, and the change in such performance indicators between 1998 and 2009 has been examined. After analysis of the above mentioned criteria and comparisons against practices in developed countries and communities, suggestions have been made about the activities to be carried out in order to make Turkey’s current innovation system “sustainable”, to support and improve innovation. In the study, a research application has been conducted using the content analysis method on the “President’s Message” letters of 158 state and foundation universities that are located in Turkey and that have a website, and the importance accorded to innovation by the universities has been determined.

  2. Cohort Profile: The Nicotine Dependence in Teens (NDIT) Study. (United States)

    O'Loughlin, Jennifer; Dugas, Erika N; Brunet, Jennifer; DiFranza, Joseph; Engert, James C; Gervais, Andre; Gray-Donald, Katherine; Karp, Igor; Low, Nancy C; Sabiston, Catherine; Sylvestre, Marie-Pierre; Tyndale, Rachel F; Auger, Nathalie; Auger, Nathalie; Mathieu, Belanger; Tracie, Barnett; Chaiton, Michael; Chenoweth, Meghan J; Constantin, Evelyn; Contreras, Gisèle; Kakinami, Lisa; Labbe, Aurelie; Maximova, Katerina; McMillan, Elizabeth; O'Loughlin, Erin K; Pabayo, Roman; Roy-Gagnon, Marie-Hélène; Tremblay, Michèle; Wellman, Robert J; Hulst, Andraeavan; Paradis, Gilles


    The Nicotine Dependence in Teens (NDIT) study is a prospective cohort investigation of 1294 students recruited in 1999-2000 from all grade 7 classes in a convenience sample of 10 high schools in Montreal, Canada. Its primary objectives were to study the natural course and determinants of cigarette smoking and nicotine dependence in novice smokers. The main source of data was self-report questionnaires administered in class at school every 3 months from grade 7 to grade 11 (1999-2005), for a total of 20 survey cycles during high school education. Questionnaires were also completed after graduation from high school in 2007-08 and 2011-12 (survey cycles 21 and 22, respectively) when participants were aged 20 and 24 years on average, respectively. In addition to its primary objectives, NDIT has embedded studies on obesity, blood pressure, physical activity, team sports, sedentary behaviour, diet, genetics, alcohol use, use of illicit drugs, second-hand smoke, gambling, sleep and mental health. Results to date are described in 58 publications, 20 manuscripts in preparation, 13 MSc and PhD theses and 111 conference presentations. Access to NDIT data is open to university-appointed or affiliated investigators and to masters, doctoral and postdoctoral students, through their primary supervisor (

  3. Corroborative studies of tritium characterization and depth profiles in concrete

    Energy Technology Data Exchange (ETDEWEB)

    Hochel, R.C.


    This report is the second by the authors on characterizing the tritium content of cement and structural concrete. The first report reviewed the literature and used several new methods to characterize tritium on the surface and through the bulk of contaminated concrete at two facilities at the U.S. Department of Energy Savannah River Site (SRS). In both cases, a relatively constant tritium concentration as a function of depth was observed, which has not been previously reported in the literature. These findings were explained as the relatively rapid transport of tritiated liquid through pores of the hydrated cement, and the exchange of tritium with hydrogen found primarily as free and bound water in the hydrated cement binder. The study reported here extended the measurement of surface and bulk tritium in concrete to three other locations at SRS. The purpose of the current study was to characterize locations whose tritium exposure histories were well documented, and to characterize a location exposed exclusively to gaseous tritium, to confirm and possibly extend the knowledge gained from the earlier study. Results of the current study corroborate the earlier findings, in that the tritium concentration was constant through the bulk when exposed to aqueous tritium, even from a single aqueous tritium exposure. Exposure to gaseous tritium, on the other hand, lead to the well-known diffusion controlled variation of tritium concentration reported in the literature. Sufficient exposure history is available to enable a semi-quantitative explanation of the magnitude and depth dependence of the tritium in both the aqueous- and gas-exposed locations. The penetration of tritium from a liquid can be described by a hydraulic flow model, and gaseous tritium permeates in a diffusive manner. The general correlation of properly measured surface tritium activity to that in the underlying bulk found in the earlier study was confirmed. However, the surface and near surface tritium

  4. A Descriptive Study on the Neonatal Morbidity Profile of Autism Spectrum Disorders, Including a Comparison with Other Neurodevelopmental Disorders (United States)

    Atladóttir, H. Ó.; Schendel, D. E.; Parner, E. T.; Henriksen, T. B.


    The aim of this study was to describe the profile of specific neonatal morbidities in children later diagnosed with autism spectrum disorder (ASD), and to compare this profile with the profile of children with hyperkinetic disorder, cerebral palsy, epilepsy or intellectual disability. This is a Danish population based cohort study, including all…


    Directory of Open Access Journals (Sweden)



    Full Text Available ABSTRACT: BACKGROUND: Onychomycosis refers to fungal infection of nails w ith various etiological agents, involving dermatophytes, yeasts and moulds. It constitutes an important health problem because of its rising prevalence and u nder-diagnosis especially in developing countries. AIMS: To analyse the mycological and cultural characteri stics of onychomycosis with respect to the various etiological agents. SETTINGS AND DESIGN: Nail samples collected from patients attending the dermatology clinic of Dr B.R Ambedkar medical college were processed in the microbiology department of Dr B.R Ambedkar medic al college. MATERIALS AND METHODS: Nail clippings and subungual scrapings of patients wi th onychomycosis were subjected to KOH preparation. Culture was done on Sab ouraud’s dextrose agar medium and Sabouraud’s dextrose agar with 5% chloramphenicol an d cycloheximide. Species identification was done by colony characteristics, pigment productio n, slide culture and LPCB stain. RESULTS: Out of 98 cases, 73 showed the growth of fungus, a mounting to 74.50% positivity. Among those 73 cases, the infective fungal agents pr edominantly were dermatophytes (54.80%, and the rest were due to yeasts (23.30% and moulds(22% . Among the different species, Trichophyton rubrum (43.84% accounted for the majority of dermatophytes; candida albicans (16.44% was the predominant yeast; and as pergillus niger (16.44% the commonest mould. The age group most commonly affected was 16-3 0yrs and males were commonly affected in our study. CONCLUSION: The present study highlights the need for microbiol ogical confirmation in case of onychomycosis for appropriate management of onychomycosis cases and further epidemiological study

  6. Structural, vibrational, NMR, quantum chemical, DNA binding and protein docking studies of two flexible imine oximes

    Indian Academy of Sciences (India)



    Two flexible imine oxime molecules, namely, 3-(pyridin-2-ylmethylimino)-butan-2-one oxime (HL¹) and 3-(pyridin-2-ylmethylimino)-pentan-2-one oxime (HL²) have been synthesized and characterized by elemental analysis, IR and NMR techniques. The conformational behavior was investigated using the density functional theory (DFT) with the B3LYP method combined with the 6-311++G(d,p) basis set. As a result of the conformational studies, three stable molecules and the most stable conformer were determined for the both imine oximes. The spectroscopic properties such as vibrational and NMR were calculated for the most stable conformer of the HL¹ and HL². The calculation results were applied to simulate infrared spectra of the title compounds, which show good agreement with observed spectra. In addition, the stable three molecules of the both imine oximes have been used to carry out DNA binding and protein docking studies with DNA and protein structures (downloaded from Protein Data Bank) using Discovery Studio 3.5 to find the most preferred binding mode of the ligands inside the DNA and protein cavity.

  7. Binding of Cimetidine to Balb/C Mouse Liver Catalase; Kinetics and Conformational Studies. (United States)

    Jahangirvand, Mahboubeh; Minai-Tehrani, Dariush; Yazdi, Fatemeh; Minai-Tehrani, Arash; Razmi, Nematollah


    Catalase is responsible for converting hydrogen peroxide (H2O2) into water and oxygen in cells. This enzyme has high affinity for hydrogen peroxide and can protect the cells from oxidative stress damage. Catalase is a tetramer protein and each monomer contains a heme group. Cimetidine is a histamine H2 receptor blocker which inhibits acid release from stomach and is used for gasterointestinal diseases. In this research, effect of cimetidine on the activity of liver catalase was studied and the kinetic parameters of this enzyme and its conformational changes were investigated. Cell free extract of mouse liver was used for the catalase assay. The activity of the catalase was detected in the absence and presence of cimetidine by monitoring hydrogen peroxide reduction absorbance at 240 nm. The purified enzyme was used for conformational studies by Fluorescence spectrophotometry. The data showed that cimetidine could inhibit the enzyme in a non-competitive manner. Ki and IC50 values of the drug were determined to be about 0.75 and 0.85 uM, respectively. The Arrhenius plot showed that activation energy was 6.68 and 4.77 kJ/mol in the presence and absence of the drug, respectively. Fluorescence spectrophotometry revealed that the binding of cimetidine to the purified enzyme induced hyperchromicity and red shift which determined the conformational change on the enzyme. Cimetidine could non-competitively inhibit the liver catalase with high affinity. Binding of cimetidine to the enzyme induced conformational alteration in the enzyme.

  8. Binding Studies of Natural Product Berberine with DNA G-Quadruplex

    Directory of Open Access Journals (Sweden)

    Nagendra K. Sharma


    Full Text Available Problem statement: The ends of chromosome had highly repetitive short G and C-rich sequences of DNA. These sequences were known to form stable tetraplex type of secondary structures which help to maintain gene integratity after cell divison. Approach: Any reagent which controls the random cell division would be useful to design anticancer drugs. Therefore a many natural and synthesized molecules which stabilized tetraplex structures are targeted as anticancer drug entities. Results: Among them, Berberine hydrochloride natural product and its analogues are well studies as G-quadruplex stabilizing agent. In this report, DNA sequence 5’-G3-C5-G3-3’ has been designed which has probability to form i-motif and G-qua druplex types of secondary structures. Herein we studied the interaction between this DNA strands and Berberine hydrochloride by 1H-NMR techniques and UV in two different PH (4.7 and 7.4 conditions. Conclusion/Recommendations: Our preliminary results showed that Berberine bind with this DNA strand in both pH conditions which is further supported by UV melting experiments. In future this sequence can be used as probe to screen out tetraplex binding natural products which help to generate new anticancer drugs.

  9. Binding of the neuroleptic drug, gabapentin, to bovine serum albumin: Insights from experimental and computational studies

    Energy Technology Data Exchange (ETDEWEB)

    Jalali, Fahimeh, E-mail: [Department of Chemistry, Razi University, 67346 Kermanshah (Iran, Islamic Republic of); Dorraji, Parisa S. [Department of Chemistry, Razi University, 67346 Kermanshah (Iran, Islamic Republic of); Mahdiuni, Hamid [Department of Biology, Razi University, 67346 Kermanshah (Iran, Islamic Republic of)


    The interaction between antiepileptic drug, gabapentin (GP), and bovin serum albumin (BSA) was studied by spectroscopic and computational methods. The native fluorescence of BSA was quenched by GP. Stern–Volmer quenching constant was calculated at different temperatures which suggested a static mechanism. The association constant (K{sub a}) was calculated from fluorescence quenching studies, which increased with temperature rising. GP competed well with warfarine for hydrophobic subdomain IIA (Sudlow's site I) on the protein. Enthalpy and entropy changes during the interaction of GP with BSA were obtained using van't Hoff plot, which showed an entropy-driven process and involvement of hydrophobic forces (ΔH>0 and ΔS>0). Synchronous fluorescence measurements of BSA solution in the presence of GP showed a considerable blue shift when Δλ=15 nm, therefore, GP interacts with tyrosine-rich sites on BSA. Optimized docked model of BSA–GP mixture confirmed the experimental results. -- Highlights: • Interaction of gabapentin and bovine serum albumin (BSA) is investigated by spectroscopic techniques. • Gabapentin can quench the fluorescence of BSA through a static quenching procedure. • The binding of gabapentin to BSA is driven mainly by hydrophobic interactions. • Subdomain IIA (Sudlow's site I) of BSA is found to be the main binding site for gabapentin. • Molecular docking modeling confirmed the experimental results.

  10. Structural and functional studies of conserved nucleotide-binding protein LptB in lipopolysaccharide transport

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Zhongshan [Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, NR4 7TJ (United Kingdom); College of Life Sciences, Sichuan University, Chengdu 610065 (China); Biomedical Sciences Research Complex, School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST (United Kingdom); Xiang, Quanju [College of Life Sciences, Sichuan University, Chengdu 610065 (China); Biomedical Sciences Research Complex, School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST (United Kingdom); Department of Microbiology, College of Resource and Environment Science, Sichuan Agriculture University, Yaan 625000 (China); Zhu, Xiaofeng [College of Life Sciences, Sichuan University, Chengdu 610065 (China); Dong, Haohao [Biomedical Sciences Research Complex, School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST (United Kingdom); He, Chuan [School of Electronics and Information, Wuhan Technical College of Communications, No. 6 Huangjiahu West Road, Hongshan District, Wuhan, Hubei 430065 (China); Wang, Haiyan; Zhang, Yizheng [College of Life Sciences, Sichuan University, Chengdu 610065 (China); Wang, Wenjian, E-mail: [Laboratory of Department of Surgery, The First Affiliated Hospital, Sun Yat-sen University, 58 Zhongshan Road II, Guangzhou, Guangdong 510080 (China); Dong, Changjiang, E-mail: [Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, NR4 7TJ (United Kingdom)


    Highlights: • Determination of the structure of the wild-type LptB in complex with ATP and Mg{sup 2+}. • Demonstrated that ATP binding residues are essential for LptB’s ATPase activity and LPS transport. • Dimerization is required for the LptB’s function and LPS transport. • Revealed relationship between activity of the LptB and the vitality of E. coli cells. - Abstract: Lipopolysaccharide (LPS) is the main component of the outer membrane of Gram-negative bacteria, which plays an essential role in protecting the bacteria from harsh conditions and antibiotics. LPS molecules are transported from the inner membrane to the outer membrane by seven LPS transport proteins. LptB is vital in hydrolyzing ATP to provide energy for LPS transport, however this mechanism is not very clear. Here we report wild-type LptB crystal structure in complex with ATP and Mg{sup 2+}, which reveals that its structure is conserved with other nucleotide-binding proteins (NBD). Structural, functional and electron microscopic studies demonstrated that the ATP binding residues, including K42 and T43, are crucial for LptB’s ATPase activity, LPS transport and the vitality of Escherichia coli cells with the exceptions of H195A and Q85A; the H195A mutation does not lower its ATPase activity but impairs LPS transport, and Q85A does not alter ATPase activity but causes cell death. Our data also suggest that two protomers of LptB have to work together for ATP hydrolysis and LPS transport. These results have significant impacts in understanding the LPS transport mechanism and developing new antibiotics.

  11. Comparative study of random and oriented antibody immobilization techniques on the binding capacity of immunosensor. (United States)

    Kausaite-Minkstimiene, A; Ramanaviciene, A; Kirlyte, J; Ramanavicius, A


    A comparative study of four different antibody immobilization techniques that are suitable for modification of surface plasmon resonance (SPR) chip (SPR-chip) is reported. Antibodies against human growth hormone (anti-HGH) were used as the model system. The evaluated SPR-chip modification techniques were (i) random immobilization of intact anti-HGH (intact-anti-HGH) via self-assembled monolayer (SAM) based on 11-mercaptoundecanoic acid (MUA); (ii) random immobilization of intact-anti-HGH within carboxymethyl dextran (CMD) hydrogel by direct covalent amine coupling technique; (iii) oriented coupling of intact-anti-HGH via Fc-fragment to protein-G layer assembled on SAM consisting of MUA (MUA/pG); (iv) oriented immobilization of fragmented anti-HGH antibodies (frag-anti-HGH) via their native thiol-groups directly coupled to the gold. To liberate these thiol groups, the intact-anti-HGH was chemically "divided" into two frag-anti-HGH fragments by chemical reduction with 2-mercaptoethylamine (2-MEA). Optimal concentration of 2-MEA for preparation of anti-HGH was 15 mM. The surface concentration of immobilized antibodies and the antigen binding capacity for all four differently modified SPR-chips was evaluated and compared. The maximum surface concentration of immobilized intact-anti-HGH was obtained by immobilizing the antibody within CMD-hydrogel. The maximal antigen binding capacity was obtained by SPR-chip based on intact-anti-HGH immobilized via MUA/pG. The immobilization based on application of frag-anti-HGH was found to be the most suitable for design of SPR-immunosensor for HGH detection, due to its sufficient antigen binding capacity, simplicity, and low cost in respect to the currently evaluated techniques.

  12. Immunological properties of prolactin and studies on a gonadotropin binding inhibitor

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Y.S.


    The physiological role of prolactin in horses has not yet been well defined. With the availability of highly purified ePRL for inducing antibody formation in rabbits and for radiolabeling with Na/sup 125/I, a very sensitive (0.4-0.6 ng/ml) and highly specific homologous RIA for ePRL was developed. A heterologous RIA using /sup 125/I-labeled ovine PRL and anti-ePRL antiserum was also developed and compared to the homologous RIA for ePRL. Of the two systems, it is concluded that this homologous RIA system is more suitable and more reliable for measuring prolactin concentration in horse serum samples. Until now, biochemical information on PRL has not been available for reptilian species. Sea turtle (Chelonia mydas) prolactin was purified from pituitary extracts by selective precipitation, DEAE-cellulose chromatography and gel filtration. Similar to other species of PRL, sea turtle PRL is a 22,000-24,000 daltons protein and contains a high content of glutamic acid, aspartic acid, serine and leucine, the N-terminal amino acid residue. Gonadotropin (FSH) binding inhibitor was partially purified from sheep testes by ammonium sulfate fractionation and ion exchange chromatography. The FSH-BI (molecular weight: 50,000 daltons, estimated by gel filtration) contains a protein moiety necessary for binding inhibitory activity. The inhibition of the binding of /sup 125/I-labeled ovine FSH to its receptor by the FSH-BI is not competitive. Both in vivo and in vitro biological studies of FSH-BI preparations in rats indicated various effects on FSH and LH activities at the gonadal level. These findings suggest a physiological role for FSH-BI in the regulation of reproduction.

  13. Fluorescence-quenching study of glucose binding by yeast hexokinase isoenzymes

    Energy Technology Data Exchange (ETDEWEB)

    Feldman, I.; Kramp, D.C.


    A study of the effect of varying ionic strength on the glucose-induced quenching of tryptophan fluorescence of hexokinase isoenzymes A(P-I) and B(P-II) was carried out at pH 8.3 and pH 5.5. At pH 8.3 both isoenzymes gave apparently linear Scatchard-type data plots even with protein concentrations and ionic strengths for which both dimeric and monomeric forms of hexokinase coexist in significant amounts. Taking into account a 1 percent accuracy in the experimental measurements, we concluded that the intrinsic dissociation constants, K/sub M/ and K/sub D/, for the binding of glucose to the monomeric and dimeric forms of HkB, are within a factor of two of each other, i.e., K/sub D//K/sub M/ equal to or less than 2. The values of K/sub M/, estimated from the apparent K, were so greatly influenced by ionic strength that it is clear that it is meaningless to compare K/sub M/ and K/sub D/ values measured at different ionic strengths as has been done in the literature. Curvature in the pH 5.5 fluorescence-quenching plots for relatively low ionic strengths demonstrates cooperativity for glucose-binding to the dimer, positive for HkA but negative for HkB. In contrast, the binding is relatively noncooperative at high ionic strength at this pH. These results were attributed to the well known effect of salt-neutralization of side chain electrical charges on the flexibility and compactness of proteins.

  14. Methyltransferase and demethylase profiling studies during brown adipocyte differentiation. (United States)

    Son, Min Jeong; Kim, Won Kon; Oh, Kyoung-Jin; Park, Anna; Lee, Da Som; Han, Baek Soo; Lee, Sang Chul; Bae, Kwang-Hee


    Although brown adipose tissue is important with regard to energy balance, the molecular mechanism of brown adipocyte differentiation has not been extensively studied. Specifically, regulation factors at the level of protein modification are largely unknown. In this study, we examine the changes in the expression level of enzymes which are involved in protein lysine methylation during brown adipocyte differentiation. Several enzymes, in this case SUV420H2, PRDM9, MLL3 and JHDM1D, were found to be up-regulated. On the other hand, Set7/9 was significantly down-regulated. In the case of SUV420H2, the expression level increased sharply during brown adipocyte differentiation, whereas the expression of SUV420H2 was marginally enhanced during the white adipocyte differentiation. The knock-down of SUV420H2 caused the suppression of brown adipocyte differentiation, as compared to a scrambled control. These results suggest that SUV420H2, a methyltransferase, is involved in brown adipocyte differentiation, and that the methylation of protein lysine is important in brown adipocyte differentiation. [BMB Reports 2016; 49(7): 388-393].

  15. Expression Profiles and DNA-Binding Affinity of Five ERF Genes in Bunches of Vitis vinifera cv. Cardinal Treated with High Levels of CO2 at Low Temperature (United States)

    Romero, Irene; Vazquez-Hernandez, Maria; Escribano, M. I.; Merodio, Carmen; Sanchez-Ballesta, M. T.


    Ethylene response factors (ERFs) play an important role in plants by regulating defense response through interaction with various stress pathways. After harvest, table grapes (Vitis vinifera L.) are subject to a range of problems associated with postharvest storage at 0°C, such as fungal attack, water loss and rachis browning. The application of a 3-day high CO2 treatment maintained fruit quality and activated the induction of transcription factors belonging to different families such as ERF. In this paper, we have isolated five VviERFs from table grapes cv. Cardinal, whose deduced amino acid sequence contained the conserved apetalous (AP2)/ERF domain. The phylogeny and putative conserved motifs in VviERFs were analyzed and compared with those previously reported in Vitis. VviERFs-c gene expression was studied by quantitative real-time RT-PCR in the different tissues of bunches stored at low temperature and treated with high levels of CO2. The results showed that in most of the tissues analyzed, VviERFs-c gene expression was induced by the storage under normal atmosphere although the application of high levels of CO2 caused a greater increase in the VviERFs-c transcript accumulation. The promoter regions of two PRs (pathogenesis related proteins), Vcchit1b and Vcgns1, were obtained and the in silico analysis revealed the presence of a cis-acting ethylene response element (GCC box). In addition, expression of these two PR genes was analyzed in the pulp and rachis of CO2-treated and non-treated table grapes stored at 0°C and results showed significant correlations with VviERF2-c and VviERF6L7-c gene expression in rachis, and between VviERF11-c and Vcchit1b in pulp. Finally by using electro mobility shift assays, we denoted differences in binding of VviERFs to the GCC sequences present in the promoters of both PRs, with VviERF6L7-c being the only member which did not bind to any tested probe. Overall, our results suggest that the beneficial effect of high CO2

  16. Cohort profile: the Finnish Medication and Alzheimer's disease (MEDALZ) study (United States)

    Tolppanen, Anna-Maija; Taipale, Heidi; Koponen, Marjaana; Lavikainen, Piia; Tanskanen, Antti; Tiihonen, Jari; Hartikainen, Sirpa


    Purpose The aim of the Medicine use and Alzheimer's disease (MEDALZ) study is to investigate the changes in medication and healthcare service use among persons with Alzheimer's disease (AD) and to evaluate the safety and effectiveness of medications in this group. This is important, because the number of persons with AD is rapidly growing and even though they are a particularly vulnerable patient group, the number of representative, large-scale studies with adequate follow-up time is limited. Participants MEDALZ contains all residents of Finland who received a clinically verified diagnosis of AD between 2005 and 2011 and were community-dwelling at the time of diagnosis (N=70 719). The diagnosis is based on the National Institute of Neurological and Communicative Disorders and Stroke and the Alzheimer's Disease and Related Disorders Association (NINCS-ADRDA) and Diagnostic and Statistical Manual Fourth Edition (DSM-IV) criteria for Alzheimer's disease. The cohort contains socioeconomic data (education, occupational status and taxable income, 1972–2012) and causes of death (2005–2012), data from the prescription register (1995–2012), the special reimbursement register (1972–2012) and the hospital discharge register (1972–2012). Future updates are planned. The average age was 80.1 years (range 34.5–104.6 years). The majority of cohort (65.2%) was women. Currently, the average length of follow-up after AD diagnosis is 3.1 years and altogether 26 045 (36.8%) persons have died during the follow-up. Findings Altogether 53% of the cohort had used psychotropic drugs within 1 year after AD diagnoses. The initiation rate of for example, benzodiazepines and related drugs and antidepressants began to increase already before AD diagnosis. Future plans We are currently assessing if these, and other commonly used medications are related to adverse events such as death, hip fractures, head injuries and pneumonia. PMID:27412109

  17. L2 motivation profiling and the role of context: A study in exploratory statistical procedures

    Directory of Open Access Journals (Sweden)

    Lousia Vahtrick


    Full Text Available Two studies were carried out in order to create distinct motivational profiles of students, examine the way in which context had an effect on motivational styles, and attempt to collaborate these findings with the L2 Motivational Self-System. The research questions for this study were concerned with ascertaining whether or not it is possible to identify distinct learner types in terms of their motivational profiles; and to what extent different aspects of motivation contribute towards distinguishing different motivational profiles. The participants for the first study were 42 Dutch university students of English; and the participants for the second study were 26 adult learners of English at a language school in Sydney, Australia. In order to construct the motivational profiles, several exploratory statistical procedures were carried out, including principal components analysis and cluster analysis. The results found that the strength of the factors extracted in the principal components stage differed depending on the context of each study. In addition, the motivational profiles that were formed during the cluster analyses revealed distinct subgroups of learners which displayed varying levels of homogeneous characteristics.

  18. Adverse effect profile of trichlormethiazide: a retrospective observational study

    Directory of Open Access Journals (Sweden)

    Nishida Yayoi


    Full Text Available Abstract Background Trichlormethiazide, a thiazide diuretic, was introduced in 1960 and remains one of the most frequently used diuretics for treating hypertension in Japan. While numerous clinical trials have indicated important side effects of thiazides, e.g., adverse effects on electrolytes and uric acid, very few data exist on serum electrolyte levels in patients with trichlormethiazide treatment. We performed a retrospective cohort study to assess the adverse effects of trichlormethiazide, focusing on serum electrolyte and uric acid levels. Methods We used data from the Clinical Data Warehouse of Nihon University School of Medicine obtained between Nov 1, 2004 and July 31, 2010, to identify cohorts of new trichlormethiazide users (n = 99 for 1 mg, n = 61 for 2 mg daily dosage and an equal number of non-users (control. We used propensity-score matching to adjust for differences between users and control for each dosage, and compared serum chemical data including serum sodium, potassium, uric acid, creatinine and urea nitrogen. The mean exposure of trichlormethiazide of 1 mg and 2 mg users was 58 days and 64 days, respectively. Results The mean age was 66 years, and 55% of trichlormethiazide users of the 1 mg dose were female. In trichlormethiazide users of the 2 mg dose, the mean age was 68 years, and 43% of users were female. There were no statistically significant differences in all covariates (age, sex, comorbid diseases, past drugs, and current antihypertensive drugs between trichlormethiazide users and controls for both doses. In trichlormethiazide users of the 2 mg dose, the reduction of serum potassium level and the elevation of serum uric acid level were significant compared with control, whereas changes of mean serum sodium, creatinine and urea nitrogen levels were not significant. In trichlormethiazide users of the 1 mg dose, all tests showed no statistically significant change from baseline to during the exposure period in

  19. Mineralogical and geological study of quaternary deposits and weathering profiles

    Energy Technology Data Exchange (ETDEWEB)

    Jeong, Gi Young; Lee, Bong Ho [Andong National Univ., Andong (Korea, Republic of)


    Movement history of a quaternary reverse fault cutting marine terrace deposit and tertiary bentonite in the Yangnammyon, Gyoungju city was studied by the mineralogical and microtextural analysis of the fault clays and weathered terrace deposits. Two types of fault clays were identified as greenish gray before the deposition of the marine terrace deposits and reddish brown after deposition. Greenish gray fault clay is composed mostly of smectite probably powdered from bentonite showing at least two events of movement from microtextures. After the bentonite was covered by quaternary marine gravel deposits, the reverse fault was reactivated cutting marine gravel deposits to form open spaces along the fault plane which allowed the hydrological infiltration of soil particles and deposition of clays in deep subsurface. The reddish brown 'fault' clays enclosed the fragments of dark brown ultrafine varved clay, proving two events of faulting, and slicken sides bisecting reddish brown clays suggest another faulting event in the final stage. Mineralogical and microtextural analysis of the fault clay show total five events of faulting, which had not been recognized even by thorough conventional paleoseismological investigation using trench, highlighting the importance of microtextural and mineralogical analysis in paleoseismology.

  20. Computer simulation study of the binding of an antiviral agent to a sensitive and a resistant human rhinovirus (United States)

    Lybrand, Terry P.; McCammon, J. Andrew


    Molecular dynamics simulations have been used to study the free energy of binding of an antiviral agent to the human rhinovirus HRV-14 and to a mutant in which a valine residue in the antiviral binding pocket is replaced by leucine. The simulations predict that the antiviral should bind to the two viruses with similar affinity, in apparent disagreement with experimental results. Possible origins of this discrepancy are outlined. Of particular importance is the apparent need for methods to systematically sample all significant conformations of the leucine side chain.

  1. Binding equilibrium study of phosphotungstic acid and HSA or BSA with UV spectrum, fluorescence spectrum and equilibrium dialysis

    Institute of Scientific and Technical Information of China (English)

    HUANG; Jin(黄瑾); YUAN; Yuzhou(袁余洲); LIANG; Hong(梁宏)


    The binding equilibrium between phosphotungstic acid (H7[P(W2O7)6]@XH2O;PTA) and human serum albumin (HSA) or bovine serum albumin (BSA) has been studied by UV-Vis, fluorescence spectroscopies and equilibrium dialysis. It has been observed that UV absorption enhanced and the fluorescence quenched as the PTA binding to HSA or BSA at physiological pH 7.43( ± 0.02). The Scatchard analysis indicated that there exists a strong binding site of PTA in both HSA and BSA, and the successive stability constants of these two systems are obtained by nonlinear least-squares methods fitting Bjerrum formula.

  2. Cadmium binding in mixtures of phytochelatins and their fragments: a voltammetric study assisted by multivariate curve resolution and mass spectrometry. (United States)

    Gusmão, Rui; Ariño, Cristina; Díaz-Cruz, José Manuel; Esteban, Miquel


    Phytochelatins (PC(n), (gamma-Glu-Cys)(n)Gly) are cysteine-rich peptides synthesized by plants which are involved in metal bioregulation and phytoremediation. Multivariate Curve Resolution by Alternating Least Squares (MCR-ALS) is applied to voltammetric data obtained from the analysis of the competitive binding of Cys or Cys-Gly with PC(2) or PC(3) by Cd(2+). The displacements between ligands, the chain length dependence on the competitive binding to PC(n) and the possible existence of mixed ligand metal-complexes are investigated. The shape analysis of the resulting pure voltammograms and concentration profiles of the components resolved by MCR-ALS suggests that ligands containing more thiol groups are able to displace the shorter chain ligands from their metal complexes, whereas the opposite does not happen. Electrochemical results are compared with ESI-MS measurements.

  3. Study of Binding Interaction between Pif80 Protein Fragment and Aragonite (United States)

    Du, Yuan-Peng; Chang, Hsun-Hui; Yang, Sheng-Yu; Huang, Shing-Jong; Tsai, Yu-Ju; Huang, Joseph Jen-Tse; Chan, Jerry Chun Chung


    Pif is a crucial protein for the formation of the nacreous layer in Pinctada fucata. Three non-acidic peptide fragments of the aragonite-binding domain (Pif80) are selected, which contain multiple copies of the repeat sequence DDRK, to study the interaction between non-acidic peptides and aragonite. The polypeptides DDRKDDRKGGK (Pif80-11) and DDRKDDRKGGKDDRKDDRKGGK (Pif80-22) have similar binding affinity to aragonite. Solid-state NMR data indicate that the backbones of Pif80-11 and Pif80-22 peptides bound on aragonite adopt a random-coil conformation. Pif80-11 is a lot more effective than Pif80-22 in promoting the nucleation of aragonite on the substrate of β-chitin. Our results suggest that the structural arrangement at a protein-mineral interface depends on the surface structure of the mineral substrate and the protein sequence. The side chains of the basic residues, which function as anchors to the aragonite surface, have uniform structures. The role of basic residues as anchors in protein-mineral interaction may play an important role in biomineralization.

  4. Binding and NMR structural studies on indoloquinoline-oligonucleotide conjugates targeting duplex DNA. (United States)

    Eick, Andrea; Riechert-Krause, Fanny; Weisz, Klaus


    An 11-phenyl-indolo[3,2-b]quinoline (PIQ) was tethered through an aminoalkyl linker to the 5'-end of four pyrimidine oligonucleotides with T/C scrambled sequences at their two 5'-terminal positions. Binding to different double-helical DNA targets formed parallel triple helices with a PIQ-mediated stabilization that strongly depends on pH and the terminal base triad at the 5'-triplex-duplex junction. The most effective stabilization was observed with a TAT triplet at the 5'-junction under low pH conditions, pointing to a protonated ligand with a high triplex binding affinity and unfavorable charge repulsions in the case of a terminal C(+)GC triplet at the junction. The latter preference of the PIQ ligand for TAT over CGC is alleviated yet still preserved at higher pH. Intercalation of PIQ at the 5'-triplex-duplex junction as suggested by the triplex melting experiments was confirmed by homonuclear and heteronuclear NMR structural studies on a specifically isotope-labeled triplex. The NMR analysis revealed two coexisting species that only differ by a 180° rotation of the indoloquinoline within the intercalation pocket. NOE-derived molecular models indicate extensive stacking interactions of the indoloquinoline moiety with the TAT base triplet and CG base pair at the junction and a phenyl substituent that is positioned in the major groove and oriented almost perpendicular to the plane of the indoloquinoline.

  5. In vitro RNA-binding assay for studying trans-factors for RNA editing in chloroplasts. (United States)

    Shikanai, Toshiharu; Okuda, Kenji


    In plant organelles, specific C residues are modified to U by RNA editing. Short RNA sequences surrounding the target site (i.e., cis-elements) are recognized by trans-factors, which were recently shown to be pentatricopeptide repeat (PPR) proteins. PPR proteins consist of tandem arrays of a highly degenerate unit of 35 (pentatrico) amino acids, and PPR motifs are believed to recognize specific RNA sequences. In Arabidopsis thaliana, more than 450 sites are edited in mitochondria and plastids, and a similar number of PPR proteins are encoded in the nuclear genome. To study how the tandem array of a PPR motif facilitates the recognition of RNA sequences, an efficient biochemical strategy is an in vitro binding assay of recombinant PPR proteins with target RNA. This analysis is especially powerful with a combination of in vivo analyses based on the phenotypes of mutants and transgenic plants. In this chapter, we describe methods for the expression of recombinant PPR proteins in Escherichia coli, preparation of probe RNAs, and RNA gel shift assays. These methods can also be utilized for other RNA-binding proteins.

  6. Interaction of Sodium Hyaluronate with a Biocompatible Cationic Surfactant from Lysine: A Binding Study. (United States)

    Bračič, Matej; Hansson, Per; Pérez, Lourdes; Zemljič, Lidija F; Kogej, Ksenija


    Mixtures of natural and biodegradable surfactants and ionic polysaccharides have attracted considerable research interest in recent years because they prosper as antimicrobial materials for medical applications. In the present work, interactions between the lysine-derived biocompatible cationic surfactant N(ε)-myristoyl-lysine methyl ester, abbreviated as MKM, and the sodium salt of hyaluronic acid (NaHA) are investigated in aqueous media by potentiometric titrations using the surfactant-sensitive electrode and pyrene-based fluorescence spectroscopy. The critical micelle concentration in pure surfactant solutions and the critical association concentration in the presence of NaHA are determined based on their dependence on the added electrolyte (NaCl) concentration. The equilibrium between the protonated (charged) and deprotonated (neutral) forms of MKM is proposed to explain the anomalous binding isotherms observed in the presence of the polyelectrolyte. The explanation is supported by theoretical model calculations of the mixed-micelle equilibrium and the competitive binding of the two MKM forms to the surface of the electrode membrane. It is suggested that the presence of even small amounts of the deprotonated form can strongly influence the measured electrode response. Such ionic-nonionic surfactant mixtures are a special case of mixed surfactant systems where the amount of the nonionic component cannot be varied independently as was the case for some of the earlier studies.

  7. Quantum mechanics/molecular mechanics study of oxygen binding in hemocyanin. (United States)

    Saito, Toru; Thiel, Walter


    We report a combined quantum mechanics/molecular mechanics (QM/MM) study on the mechanism of reversible dioxygen binding in the active site of hemocyanin (Hc). The QM region is treated by broken-symmetry density functional theory (DFT) with spin projection corrections. The X-ray structures of deoxygenated (deoxyHc) and oxygenated (oxyHc) hemocyanin are well reproduced by QM/MM geometry optimizations. The computed relative energies strongly depend on the chosen density functional. They are consistent with the available thermodynamic data for oxygen binding in hemocyanin and in synthetic model complexes when the BH&HLYP hybrid functional with 50% Hartree-Fock exchange is used. According to the QM(BH&HLYP)/MM results, the reaction proceeds stepwise with two sequential electron transfer (ET) processes in the triplet state followed by an intersystem crossing to the singlet product. The first ET step leads to a nonbridged superoxo CuB(II)-O2(•-) intermediate via a low-barrier transition state. The second ET step is even more facile and yields a side-on oxyHc complex with the characteristic Cu2O2 butterfly core, accompanied by triplet-singlet intersystem crossing. The computed barriers are very small so that the two ET processes are expected to very rapid and nearly simultaneous.

  8. The Target of β-Expansin EXPB1 in Maize Cell Walls from Binding and Solid-State NMR Studies. (United States)

    Wang, Tuo; Chen, Yuning; Tabuchi, Akira; Cosgrove, Daniel J; Hong, Mei


    The wall-loosening actions of β-expansins are known primarily from studies of EXPB1 extracted from maize (Zea mays) pollen. EXPB1 selectively loosens cell walls (CWs) of grasses, but its specific binding target is unknown. We characterized EXPB1 binding to sequentially extracted maize CWs, finding that the protein primarily binds glucuronoarabinoxylan (GAX), the major matrix polysaccharide in grass CWs. This binding is strongly reduced by salts, indicating that it is predominantly electrostatic in nature. For direct molecular evidence of EXPB1 binding, we conducted solid-state nuclear magnetic resonance experiments using paramagnetic relaxation enhancement (PRE), which is sensitive to distances between unpaired electrons and nuclei. By mixing (13)C-enriched maize CWs with EXPB1 functionalized with a Mn(2+) tag, we measured Mn(2+)-induced PRE Strong (1)H and (13)C PREs were observed for the carboxyls of GAX, followed by more moderate PREs for carboxyl groups in homogalacturonan and rhamnogalacturonan-I, indicating that EXPB1 preferentially binds GAX In contrast, no PRE was observed for cellulose, indicating very weak interaction of EXPB1 with cellulose. Dynamics experiments show that EXPB1 changes GAX mobility in a complex manner: the rigid fraction of GAX became more rigid upon EXPB1 binding while the dynamic fraction became more mobile. Combining these data with previous results, we propose that EXPB1 loosens grass CWs by disrupting noncovalent junctions between highly substituted GAX and GAX of low substitution, which binds cellulose. This study provides molecular evidence of β-expansin's target in grass CWs and demonstrates a new strategy for investigating ligand binding for proteins that are difficult to express heterologously.


    Directory of Open Access Journals (Sweden)

    Ramanand Prasad


    Full Text Available OBJECTIVES: To study the clinical profile , course of disease and outcome of peripartum cardiomyopathy (PPCM. METHODS: A prospective study was conducted at Mahatma Gandhi Medical College and Hospital , Rajasthan , India from May 2012 to June 2014. 18 cases were included in the study. Data included age distribution , parity , symptoms and risk factors. Medical management and pregnancy outcome were documented. Serial echocardiography was done for a period of one year. RESULTS: In our study 8/18 (44% were primigravidae , 3/18 (16% had pre - eclam p sia and 4/18 (22% had co - existing hypertension , 7 (38.89% patients underwent Caesarean section and no complication happen during delivery in all . The differ ence in Echocardiography parameters observed between recovered and non - recovered patients was significant; Left Ventricular End diastolic dimension (5.0 cm vs 6.0 cm Left ventricular Ejection fraction (28% vs 22% and left ventricular fractional shortenin g (19% vs 12%. 14 out of 18 patients were followed up for a period of one year out of which 64% (9/14 patients recovered completely. There was no mortality and two patients waiting for cardiac transplant due to refractory symptoms. CONCLUSION: Majority w ere young primigravidae presenting postnatally. Pre - eclampsisa and hypertension were risk factors. ECHO parameters were reliable predictors of recovery

  10. Study of Profile, Knowledge and Problems of Anganwadi Workers in ICDS Blocks: A Cross Sectional Study

    Directory of Open Access Journals (Sweden)

    Sandip B. Patil


    Full Text Available Objectives: To study the profile of Anganwadi Workers (AWWs. To assess knowledge of AWWs & problems faced by them while working. Study Design: Cross sectional study. Methods: Anganwadi centres were selected by stratified sampling technique. From each block 10% AWWs were enrolled into study. The functioning of AWWs was assessed by interviewing Anganwadi workers for their literacy status, years of experience, their knowledge about the services rendered by them and problems faced by them. Result: Most of AWWs were from the age group of between 41-50 years; more than half of them were matriculate and 34(69.38% workers had an experience of more than 10 years. Majority (81.63 % of AWWs had a knowledge assessment score of above 50%. They had best knowledge about nutrition and health education (70%. Of the workers 87.7% complained of inadequate honorarium, 28.5% complained of lack of help from community and other problems reported were infrastructure related supply, excessive work overload and record maintenance. Conclusions: Majority of AWWs were beyond 40 years of age, matriculate, experienced, having more than 50% of knowledge related to their job. Complaints mentioned by them were chiefly honorarium related and excessive workload.

  11. Insect γ-aminobutyric acid receptors and isoxazoline insecticides: toxicological profiles relative to the binding sites of [³H]fluralaner, [³H]-4'-ethynyl-4-n-propylbicycloorthobenzoate, and [³H]avermectin. (United States)

    Zhao, Chunqing; Casida, John E


    Isoxazoline insecticides, such as fluralaner (formerly A1443), are noncompetitive γ-aminobutyric acid (GABA) receptor (GABA-R) antagonists with selective toxicity for insects versus mammals. The isoxazoline target in house fly ( Musca domestica ) brain has subnanomolar affinity for [³H]fluralaner and a unique pattern of sensitivity to isoxazolines and avermectin B(1a) (AVE) but not to fipronil and α-endosulfan. Inhibitor specificity profiles for 15 isoxazolines examined with Musca GABA-R and [³H]fluralaner, [³H]-4'-ethynyl-4-n-propylbicycloorthobenzoate ([³H]EBOB), and [³H]AVE binding follow the same structure-activity trends although without high correlation. The 3 most potent of the 15 isoxazolines tested in Musca [³H]fluralaner, [³H]EBOB, and [³H]AVE binding assays and in honeybee (Apis mellifera) brain [³H]fluralaner assays are generally those most toxic to Musca and four agricultural pests. Fluralaner does not inhibit [³H]EBOB binding to the human GABA-R recombinant β₃ homopentamer, which is highly sensitive to all of the commercial GABAergic insecticides. The unique isoxazoline binding site may resurrect the GABA-R as a major insecticide target.

  12. A Study of Multi-frequency Polarization Pulse Profiles of Millisecond Pulsars

    CERN Document Server

    Dai, S; Manchester, R N; Kerr, M; Shannon, R M; van Straten, W; Mata, A; Bailes, M; Bhat, N D R; Burke-Spolaor, S; Coles, W A; Johnston, S; Keith, M J; Levin, Y; Oslowski, S; Reardon, D; Ravi, V; Sarkissian, J M; Tiburzi, C; Toomey, L; Wang, H G; Wang, J -B; Wen, L; Xu, R X; Yan, W M; Zhu, X -J


    We present high signal-to-noise ratio, multi-frequency polarization pulse profiles for 24 millisecond pulsars that are being observed as part of the Parkes Pulsar Timing Array (PPTA) project. The pulsars are observed in three bands, centred close to 730, 1400 and 3100 MHz, using a dual-band 10 cm/50 cm receiver and the central beam of the 20 cm multibeam receiver. Observations spanning approximately six years have been carefully calibrated and summed to produce high S/N profiles. This allows us to study the individual profile components and in particular how they evolve with frequency. We also identify previously undetected profile features. For many pulsars we show that pulsed emission extends across almost the entire pulse profile. The pulse component widths and component separations follow a complex evolution with frequency; in some cases these parameters increase and in other cases they decrease with increasing frequency. The evolution with frequency of the polarization properties of the profile is also n...

  13. A novel dualistic profile of an allosteric AMPA receptor modulator identified through studies on recombinant receptors, mouse hippocampal synapses and crystal structures

    DEFF Research Database (Denmark)

    Bundgaard Christiansen, Gitte; Harbak, Barbara; E. Hede, Susanne;


    -mediated neurotransmission. The aim of this study was to investigate functional and structural aspects of a novel analog of the AMPA receptor PAM cyclothiazide (CTZ) on recombinant and native glutamate receptors. We expressed rat GluA4flip and flop in Xenopus oocytes and characterized NS1376 and CTZ under two...... information through X-ray structures, docking and molecular dynamics, which revealed that NS1376 interacts at the dimer interface of the ligand-binding domain in a manner overall similar to CTZ. NS1376 reveals that minor structural changes in CTZ can result in an altered modulatory profile, both enhancing...

  14. Empirical study of performance of data binding in ASP.NET web applications

    CERN Document Server

    Stojanovski, Toni; Velinov, Ivan


    Most developers use default properties of ASP.NET server controls when developing web applications. ASP.NET web applications typically employ server controls to provide dynamic web pages, and data-bound server controls to display and maintain database data. Though the default properties allow for fast creation of workable applications, creating a high-performance, multi-user, and scalable web application requires careful configuring of server controls and their enhancement using custom-made code. In providing commonly required functionality in data-driven ASP.NET web applications such as paging, sorting and filtering, our empirical study evaluated the impact of various technical approaches: automatic data binding in web server controls; data paging and sorting on web server; paging and sorting on database server; indexed and non-indexed database columns; clustered vs. non-clustered indices. The study observed significant performance differences between various technical approaches.

  15. Tight-binding study of hydrogen adsorption on palladium decorated graphene and carbon nanotubes

    Energy Technology Data Exchange (ETDEWEB)

    Lopez-Corral, I.; German, E.; Brizuela, G.P.; Juan, A. [Departamento de Fisica, Universidad Nacional del Sur, Av. Alem 1253, 8000 Bahia Blanca (Argentina); Volpe, M.A. [Planta Piloto de Ingenieria Quimica, Universidad Nacional del Sur-CONICET, camino de La Carrindanga Km. 7, 8000 Bahia Blanca (Argentina)


    In this work we report a theoretical study on the atomic and molecular hydrogen adsorption onto Pd-decorated graphene monolayer and carbon nanotubes by a semi-empirical tight-binding method. We first investigated the preferential adsorption geometry, considering different adsorption sites on the carbon surface, and then studied the evolution of the chemical bonding by evaluation of the overlap population (OP) and crystal orbital overlap population (COOP). Our results show that strong C-Pd and H-Pd bonds are formed during atomic hydrogen adsorption, with an important role in the bonding of C 2p{sub z} and Pd 5s, 5p{sub z} and 4d{sub z}{sup 2} orbitals. The hydrogen storage mechanism in Pd-doped carbon-based materials seems to involve the dissociation of H{sub 2} molecule on the decoration points and the bonding between resultant atomic hydrogen and the carbon surface. (author)

  16. Designing isothermal titration calorimetry experiments for the study of 1:1 binding: problems with the "standard protocol". (United States)

    Tellinghuisen, Joel


    Literature recommendations for designing isothermal titration calorimetry (ITC) experiments to study 1:1 binding, M+X -->/applicability of the ITC technique. These deficiencies are discussed here along with other misconceptions. Whether a specific binding process can be studied by ITC is determined less by c (the product of binding constant K and titrand concentration [M](0)) than by the total detectable heat q(tot) and the extent to which M can be converted to MX. As guidelines, with 90% conversion to MX, K can be estimated within 5% over the range 10 to 10(8)M(-1) when q(tot)/σ(q)≈700, where σ(q) is the standard deviation for estimation of q. This ratio drops to ~150 when the stoichiometry parameter n is treated as known. A computer application for modeling 1:1 binding yields realistic estimates of parameter standard errors for use in protocol design and feasibility assessment.

  17. Binding studies of lophirone B with bovine serum albumin (BSA): Combination of spectroscopic and molecular docking techniques (United States)

    Chaves, Otávio Augusto; da Silva, Veridiana A.; Sant'Anna, Carlos Maurício R.; Ferreira, Aurélio B. B.; Ribeiro, Tereza Auxiliadora N.; de Carvalho, Mário G.; Cesarin-Sobrinho, Dari; Netto-Ferreira, José Carlos


    The interaction between the transport protein bovine serum albumin (BSA) and the natural product lophirone B, was investigated by spectroscopic techniques combined with a computational method (molecular docking). From the KSV and kq values it was concluded that lophirone B quenches the fluorescence of BSA by dynamic and static mechanisms. The Ka values, of the order of 104 M-1, and the number of binding sites (n ≈ 1), indicate that the binding is moderate and there is just one main binding site in BSA for lophirone B. The negative ΔG° values are in accordance with the spontaneity of the process and the positive ΔH° and ΔS° values indicate that the binding is entropically driven; the main binding forces for the association BSA:lophirone B are probably lipophilic interactions. Circular dichroism (CD) studies show there is not a significant perturbation on the secondary structure of the albumin upon the binding process. In order to better understand the spectroscopic results, a computational method was applied: molecular docking suggests Trp-213 site, as the main binding site for the ligand. Lophirone B seems to be exposed to the aqueous media as well as accommodated inside the protein cavity, resulting in a moderate affinity for the albumin. The Arg-198, His-287, Lys-294 and Lys-439 residues are interacting via hydrogen bonding with lophirone B, whereas the interaction with Trp-213 residue occurs through a lipophilic interaction.

  18. Spectrophotometric study on the binding of two water soluble Schiff base complexes of Mn(III) with ct-DNA. (United States)

    Dehkordi, Maryam Nejat; Bordbar, Abdol-Khlegh; Mehrgardi, Masood Ayatolahi; Mirkhani, Valiolah


    In this work, binding of two water soluble Schiff base complexes: Bis sodium (5-sulfosalicylaldehyde) o-phenylendiiminato) Manganese (III) acetate (Salophen complex) and Bis sodium (5-sulfosalicylaldehyde) 1, 2 ethylendiiminato) Manganese (III) acetate (Salen complex) with calf thymus (ct) DNA were investigated by using different spectroscopic and electrometric techniques including UV-vis, Circular dichroism (CD) and fluorescence spectroscopy, viscommetry and cyclic voltammetry (CV). Both complexes have shown a hyperchromic and a small bathochromic shift in the visible region spectra. A competitive binding study showed that the enhanced emission intensity of ethidium bromide (EB) in the presence of DNA was quenched by the addition of the two Schiff base complexes indicating that they displace EB from its binding site in DNA. Moreover structural changes in the CD spectra and an increase in the CV spectra with addition of DNA were observed. The results show that both complexes bind to DNA. The binding constants have been calculated using fluorescence data for two complexes also K(b) was calculated with fluorescence Scatchard plot for Salophen. Ultimately, the experimental results show that the dominant interactions are electrostatic while binding mode is surface binding then followed by hydrophobic interactions in grooves in high concentration of complexes.

  19. Reproducibility of mass spectrometry based protein profiles for diagnosis of breast cancer across clinical studies

    DEFF Research Database (Denmark)

    Callesen, Anne Kjærgaard; Vach, Werner; Jørgensen, Per E;


    Serum protein profiling by mass spectrometry has achieved attention as a promising technology in oncoproteomics. We performed a systematic review of published reports on protein profiling as a diagnostic tool for breast cancer. The MEDLINE, EMBASE, and COCHRANE databases were searched for original...... studies reporting discriminatory protein peaks for breast cancer as either protein identity or as m/ z values in the period from January 1995 to October 2006. To address the important aspect of reproducibility of mass spectrometry data across different clinical studies, we compared the published lists....... Although the studies revealed a considerable heterogeneity in relation to experimental design, biological variation, preanalytical conditions, methods of computational data analysis, and analytical reproducibility of profiles, we found that 45% of peaks previously reported to correlate with breast cancer...

  20. Circular dichroism study of the interaction between mutagens and bilirubin bound to different binding sites of serum albumins (United States)

    Orlov, Sergey; Goncharova, Iryna; Urbanová, Marie

    Although recent investigations have shown that bilirubin not only has a negative role in the organism but also exhibits significant antimutagenic properties, the mechanisms of interactions between bilirubin and mutagens are not clear. In this study, interaction between bilirubin bound to different binding sites of mammalian serum albumins with structural analogues of the mutagens 2-aminofluorene, 2,7-diaminofluorene and mutagen 2,4,7-trinitrofluorenone were investigated by circular dichroism and absorption spectroscopy. Homological human and bovine serum albumins were used as chiral matrices, which preferentially bind different conformers of bilirubin in the primary binding sites and make it observable by circular dichroism. These molecular systems approximated a real system for the study of mutagens in blood serum. Differences between the interaction of bilirubin bound to primary and to secondary binding sites of serum albumins with mutagens were shown. For bilirubin bound to secondary binding sites with low affinity, partial displacement and the formation of self-associates were observed in all studied mutagens. The associates of bilirubin bound to primary binding sites of serum albumins are formed with 2-aminofluorene and 2,4,7-trinitrofluorenone. It was proposed that 2,7-diaminofluorene does not interact with bilirubin bound to primary sites of human and bovine serum albumins due to the spatial hindrance of the albumins binding domains. The spatial arrangement of the bilirubin bound to serum albumin along with the studied mutagens was modelled using ligand docking, which revealed a possibility of an arrangement of the both bilirubin and 2-aminofluorene and 2,4,7-trinitrofluorenone in the primary binding site of human serum albumin.

  1. Changing Occupational Profiles in the Hotel Industry: Case Studies in France, Italy and Spain. Synthesis Report. (United States)

    Gatti, Mario; Grazia Mereu, Maria; Tagliaferro, Claudio

    Changing occupational profiles in the hotel industry in France, Italy, and Spain were examined in case studies that included interviews with hotel managers, human resource managers, and individuals employed in hotel occupations identified as new or entailing new skills. The study focused on the following topics: (1) changes in the hotel industry…


    NARCIS (Netherlands)



    A pilot-study was done to investigate the applicability of the sickness impact profile (SIP) in ex-ICU patients. For this study 221 consecutively admitted patients were reviewed retrospectively after excluding children, deceased patients and readmissions. SIP was assessed in these patients by either

  3. A study to evaluate cephalometric hard tissue profile of Tamil population for orthognathic surgery. (United States)

    Nachiappan, S; Tharanikumar, S; Chandran, Ajay; Anusudha, P; Nandini, G D; Balasubramaniam, Murali


    The primary aim of this study is to compare, the cephalometric hard tissue profile values and analysis between Tamil and Caucasian population. The study also aims to create a better understanding in the facial proportions of Tamil Nadu population and to have better diagnosis and treatment planning for orthognathic surgery for Tamil population in Tamil Nadu.

  4. Metabolomic Profiling in Relation to New-Onset Atrial Fibrillation (from the Framingham Heart Study)

    NARCIS (Netherlands)

    Ko, Darae; Riles, Eric M.; Marcos, Ernaldo G.; Magnani, Jared W.; Lubitz, Steven A.; Lin, Honghuang; Long, Michelle T.; Schnabel, Renate B.; McManus, David D.; Ellinor, Patrick T.; Ramachandran, Vasan S.; Wang, Thomas J.; Gerszten, Robert E.; Benjamin, Emelia J.; Yin, Xiaoyan; Rienstra, Michiel


    Previous studies have shown several metabolic biomarkers to be associated with prevalent and incident atrial fibrillation (AF), but the results have not been replicated.. We investigated metabolite profiles of 2,458 European ancestry participants from the Framingham Heart Study without AF at the ind

  5. Transcriptome profiling and genome-wide DNA binding define the differential role of fenretinide and all-trans RA in regulating the death and survival of human hepatocellular carcinoma Huh7 cells. (United States)

    Hu, Ying; Liu, Hui-Xin; He, Yuqi; Fang, Yaping; Fang, Jianwen; Wan, Yu-Jui Yvonne


    Fenretinide is significantly more effective in inducing apoptosis in cancer cells than all-trans retinoic acid (ATRA). The current study uses a genome-wide approach to understand the differential role fenretinide and ATRA have in inducing apoptosis in Huh7 cells. Fenretinide and ATRA-induced gene expressions and DNA bindings were profiled using microarray and chromatin immunoprecipitation with anti-RXRα antibody. The data showed that fenretinide was not a strong transcription regulator. Fenretinide only changed the expressions of 1 093 genes, approximately three times less than the number of genes regulated by ATRA (2 811). Biological function annotation demonstrated that both fenretinide and ATRA participated in pathways that determine cell fate and metabolic processes. However, fenretinide specifically induced Fas/TNFα-mediated apoptosis by increasing the expression of pro-apoptotic genes i.e., DEDD2, CASP8, CASP4, and HSPA1A/B; whereas, ATRA induced the expression of BIRC3 and TNFAIP3, which inhibit apoptosis by interacting with TRAF2. In addition, fenretinide inhibited the expression of the genes involved in RAS/RAF/ERK-mediated survival pathway. In contrast, ATRA increased the expression of SOSC2, BRAF, MEK, and ERK genes. Most genes regulated by fenretinide and ATRA were bound by RXRα, suggesting a direct effect. This study revealed that by regulating fewer genes, the effects of fenretinide become more specific and thus has fewer side effects than ATRA. The data also suggested that fenretinide induces apoptosis via death receptor effector and by inhibiting the RAS/RAF/ERK pathway. It provides insight on how retinoid efficacy can be improved and how side effects in cancer therapy can be reduced.

  6. Racial Profiling as Collective Definition

    Directory of Open Access Journals (Sweden)

    Trevor G. Gardner


    Full Text Available Economists and other interested academics have committed significant time and effort to developing a set of circumstances under which an intelligent and circumspect form of racial profiling can serve as an effective tool in crime finding–the specific objective of finding criminal activity afoot. In turn, anti-profiling advocates tend to focus on the immediate efficacy of the practice, the morality of the practice, and/or the legality of the practice. However, the tenor of this opposition invites racial profiling proponents to develop more surgical profiling techniques to employ in crime finding. In the article, I review the literature on group distinction to discern its relevance to the practice and study of racial profiling. I argue that the costs of racial profiling extend beyond inefficient policing and the humiliation of law-abiding minority pedestrians and drivers. Racial profiling is simultaneously a process of perception and articulation of relative human characteristics (both positive and negative; it binds and reifies the concepts of race and criminality, fixing them into the subconscious of the profiled, the profiler, and society at large.

  7. Similarities between the Binding Sites of SB-206553 at Serotonin Type 2 and Alpha7 Acetylcholine Nicotinic Receptors: Rationale for Its Polypharmacological Profile.

    Directory of Open Access Journals (Sweden)

    Patricia Möller-Acuña

    Full Text Available Evidence from systems biology indicates that promiscuous drugs, i.e. those that act simultaneously at various protein targets, are clinically better in terms of efficacy, than those that act in a more selective fashion. This has generated a new trend in drug development called polypharmacology. However, the rational design of promiscuous compounds is a difficult task, particularly when the drugs are aimed to act at receptors with diverse structure, function and endogenous ligand. In the present work, using docking and molecular dynamics methodologies, we established the most probable binding sites of SB-206553, a drug originally described as a competitive antagonist of serotonin type 2B/2C metabotropic receptors (5-HT2B/2CRs and more recently as a positive allosteric modulator of the ionotropic α7 nicotinic acetylcholine receptor (nAChR. To this end, we employed the crystal structures of the 5-HT2BR and acetylcholine binding protein as templates to build homology models of the 5-HT2CR and α7 nAChR, respectively. Then, using a statistical algorithm, the similarity between these binding sites was determined. Our analysis showed that the most plausible binding sites for SB-206553 at 5-HT2Rs and α7 nAChR are remarkably similar, both in size and chemical nature of the amino acid residues lining these pockets, thus providing a rationale to explain its affinity towards both receptor types. Finally, using a computational tool for multiple binding site alignment, we determined a consensus binding site, which should be useful for the rational design of novel compounds acting simultaneously at these two types of highly different protein targets.

  8. Binding of Cu(II) ions to peptides studied by fluorescence spectroscopy and isothermal titration calorimetry. (United States)

    Makowska, Joanna; Żamojć, Krzysztof; Wyrzykowski, Dariusz; Uber, Dorota; Wierzbicka, Małgorzata; Wiczk, Wiesław; Chmurzyński, Lech


    Steady-state and time-resolved fluorescence quenching measurements supported by Isothermal Titration Calorimetry (ITC) were used to study the interactions of Cu(2+) with four peptides. Two of them were taken from the N-terminal part of the FBP28 protein (formin binding protein) WW domain: Tyr-Lys-Thr-Ala-Asp-Gly-Lys-Thr-Tyr-NH2 (D9) and its mutant Tyr-Lys-Thr-Ala-Asn-Gly-Lys-Thr-Tyr-NH2 (D9_M) as well as two mutated peptides from the B3 domain of the immunoglobulin binding protein G derived from Streptococcus: Asp-Val-Ala-Thr-Tyr-Thr-NH2 (J1) and Glu-Val-Ala-Thr-Tyr-Thr-NH2 (J2). The measurements were carried out at 298.15K in 20mM 2-(N-morpholino)ethanesulfonic acid (MES) buffer solution with a pH of 6. The fluorescence of all peptides was quenched by Cu(2+) ions. The stoichiometry, conditional stability constants and thermodynamic parameters for the interactions of the Cu(2+) ions with D9 and D9_M were determined from the calorimetric data. The values of the conditional stability constants were additionally determined from fluorescence quenching measurements and compared with those obtained from calorimetric studies. There was a good correlation between data obtained from the two techniques. On the other hand, the studies revealed that J1 and J2 do not exhibit an affinity towards metal ions. The obtained results prove that fluorescence quenching experiments may be successfully used in order to determine stability constants of complexes with fluorescent ligands. Finally, based on the obtained results, the coordinating properties of the peptides towards the Cu(2+) ions are discussed.

  9. Upregulated GABA inhibitory function in AD/HD children with Child Behavior Checklist–Dysregulation Profile: 123I-iomazenil SPECT study

    Directory of Open Access Journals (Sweden)

    Shinichiro eNagamitsu


    Full Text Available The Child Behavior Checklist–Dysregulation Profile (CBCL-DP refers to a pattern of elevated scores on the Attention Problems, Aggression, and Anxiety/Depression subscales of the Child Behavior Checklist. The aim of the present study was to investigate the potential role of GABA inhibitory neurons in children with attention deficit/hyperactivity disorder (AD/HD and dysregulation assessed with a dimensional measure. Brain single photon emission computed tomography (SPECT was performed in 35 children with AD/HD using 123I-iomazenil, which binds with high affinity to benzodiazepine receptors. Iomazenil binding activities were assessed with respect to the presence or absence of a threshold CBCL-DP (a score ≥210 for the sum of the three subscales Attention Problems, Aggression, and Anxiety/Depression. We then attempted to identify which CBCL-DP subscale explained the most variance with respect to SPECT data, using age, sex, and history of maltreatment as covariates. Significantly higher iomazenil binding activity was seen in the posterior cingulate cortex (PCC of AD/HD children with a significant CBCL-DP. The Anxiety/Depression subscale on the CBCL had significant effects on higher iomazenil binding activity in the left superior frontal, middle frontal, and temporal regions, as well as in the PCC. The present brain SPECT findings suggest that GABAergic inhibitory neurons may play an important role in the neurobiology of the CBCL-DP, in children with ADHD.

  10. Studies on interaction of insect repellent compounds with odorant binding receptor proteins by in silico molecular docking approach. (United States)

    Gopal, J Vinay; Kannabiran, K


    The aim of the study was to identify the interactions between insect repellent compounds and target olfactory proteins. Four compounds, camphor (C10H16O), carvacrol (C10H14O), oleic acid (C18H34O2) and firmotox (C22H28O5) were chosen as ligands. Seven olfactory proteins of insects with PDB IDs: 3K1E, 1QWV, 1TUJ, 1OOF, 2ERB, 3R1O and OBP1 were chosen for docking analysis. Patch dock was used and pymol for visualizing the structures. The interactions of these ligands with few odorant binding proteins showed binding energies. The ligand camphor had showed a binding energy of -136 kcal/mol with OBP1 protein. The ligand carvacrol interacted with 1QWV and 1TUJ proteins with a least binding energy of -117.45 kcal/mol and -21.78 kcal/mol respectively. The ligand oleic acid interacted with 1OOF, 2ERB, 3R1O and OBP1 with least binding energies. Ligand firmotox interacted with OBP1 and showed least binding energies. Three ligands (camphor, oleic acid and firmotox) had one, two, three interactions with a single protein OBP1 of Nilaparvatha lugens (Rice pest). From this in silico study we identified the interaction patterns for insect repellent compounds with the target insect odarant proteins. The results of our study revealed that the chosen ligands showed hydrogen bond interactions with the target olfactory receptor proteins.

  11. Asthma characteristics and biomarkers from the Airways Disease Endotyping for Personalized Therapeutics (ADEPT) longitudinal profiling study

    DEFF Research Database (Denmark)

    Silkoff, P E; Strambu, I; Laviolette, M;


    BACKGROUND: Asthma is a heterogeneous disease and development of novel therapeutics requires an understanding of pathophysiologic phenotypes. The purpose of the ADEPT study was to correlate clinical features and biomarkers with molecular characteristics, by profiling asthma (NCT01274507). This re......BACKGROUND: Asthma is a heterogeneous disease and development of novel therapeutics requires an understanding of pathophysiologic phenotypes. The purpose of the ADEPT study was to correlate clinical features and biomarkers with molecular characteristics, by profiling asthma (NCT01274507......, were stable over 12 months. Use of the ADEPT data should prove useful in defining biological phenotypes to facilitate personalized therapeutic approaches....

  12. TOLNET – A Tropospheric Ozone Lidar Profiling Network for Satellite Continuity and Process Studies

    Directory of Open Access Journals (Sweden)

    Newchurch Michael J.


    Full Text Available Ozone lidars measure continuous, high-resolution ozone profiles critical for process studies and for satellite validation in the lower troposphere. However, the effectiveness of lidar validation by using single-station data is limited. Recently, NASA initiated an interagency ozone lidar observation network under the name TOLNet to promote cooperative multiple-station ozone-lidar observations to provide highly timeresolved (few minutes tropospheric-ozone vertical profiles useful for air-quality studies, model evaluation, and satellite validation. This article briefly describes the concept, stations, major specifications of the TOLNet instruments, and data archiving.

  13. Synthesis of Cyclic Porphyrin Trimers through Alkyne Metathesis Cyclooligomerization and Their Host–Guest Binding Study

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Chao; Long, Hai; Jin, Yinghua; Zhang, Wei


    Cyclic porphyrin trimers were synthesized through one-step cyclooligomerization via alkyne metathesis from diyne monomers. These macrocycles show interesting host-guest binding interactions with fullerenes, selectively binding C70 (6 x 103 M-1) over C60 and C84 (no binding observed). The fullerene-encapsulated host-guest complex can undergo guest or host exchange in the presence of another guest (2,4,6-tri(4-pyridyl)-1,3,5-triazine) or host (cage COP5) molecule with higher binding affinity.

  14. Criminal profiles of violent juvenile sex and violent juvenile non sex offenders: an explorative longitudinal study. (United States)

    van Wijk, Anton Ph; Mali, Bas R F; Bullens, Ruud A R; Vermeiren, Robert R


    Few studies have longitudinally investigated the criminal profiles of violent juvenile sex and violent juvenile non-sex offenders. To make up for this lack, this study used police records of juveniles to determine the nature of the criminal profiles of violent sex offenders (n = 226) and violent non-sex offenders (n = 4,130). All offenders committed their first offense in 1996 and were followed for 7 years. Results showed that violent sex offenders and violent non-sex offenders cannot be considered a homogeneous group because of different background characteristics and criminal profiles. Sex and violent offenses often constitute a small part of a broader criminal pattern. Further research is necessary to reveal in more detail the developmental and criminological patterns of violent and sexual delinquency. Treatment and intervention programs may benefit from this.

  15. A molecular dynamics study of chloride binding by the cryptand SC24 (United States)

    Owenson, B.; MacElroy, R. D.; Pohorille, A.


    The capture of chloride from water by the tetraprotonated form of the spherical macrotricyclic molecule SC24 was studied using molecular dynamics simulation methods. This model ionophore represents a broad class of molecules which remove ions from water. Two binding sites for the chloride were found, one inside and one outside the ligand. These sites are separated by a potential energy barrier of approximately 20 kcal mol-1. The major contribution to this barrier comes from dehydration of the chloride. The large, unfavorable dehydration effect is compensated for by an increase in electrostatic attraction between the oppositely charged chloride and cryptand, and by energetically favorable rearrangements of water structure. Additional assistance in crossing the barrier and completing the dehydration of the ion is provided by the shift of three positively charged hydrogen atoms of the cryptand towards the chloride. This structural rigidity is partially responsible for its selectivity.

  16. Binding of chrysoidine to catalase: spectroscopy, isothermal titration calorimetry and molecular docking studies. (United States)

    Yang, Bingjun; Hao, Fang; Li, Jiarong; Chen, Dongliang; Liu, Rutao


    Chrysoidine is an industrial azo dye and the presence of chrysoidine in water and food has become an environmental concern due to its negative effects on human beings. In this work, the interactions between chrysoidine and bovine liver catalase (BLC) were explored. Obvious loss in catalytic activity was observed after incubation of BLC with chrysoidine, and the inhibition effect of BLC was found to be of the non-competitive type. No profound conformational change of BLC occurs in the presence of chrysoidine as revealed by UV-vis absorption, circular dichroism and fluorescence spectroscopy studies. Isothermal titration calorimetry results indicate that catalase has two sets of binding sites for chrysoidine. Further, molecular docking simulations show that chrysoidine is located within the bottleneck in the main channel of the substrate to the active site of BLC, which explain the activity inhibition of BLC by chrysoidine.

  17. Binding site of ribosomal proteins on prokaryotic 5S ribonucleic acids: a study with ribonucleases

    DEFF Research Database (Denmark)

    Douthwaite, S; Christensen, A; Garrett, R A


    ., & Garrett, R. A. (1981) Biochemistry 20, 7301--7307], reveal an extensive interaction site for protein L18 and a more localized one for L25. Generally comparable results, with a few important differences, were obtained in a study of the binding sites of the two E. coli proteins on Bacillus...... experiments were performed for both RNAs. The effects of the bound proteins on the ribonuclease digestion of the RNAs could generally be correlated with the results obtained with the E. coli proteins L18 and L25, although there was evidence for an additional protein-induced conformational change in the B...... stearothermophilus 5S RNA. Several protein-induced changes in the RNA structures were identified; some are possibly allosteric in nature. The two prokaryotic 5S RNAs were also incubated with total 50S subunit proteins from E. coli and B. stearothermophilus ribosomes. Homologous and heterologous reconstitution...

  18. Radioligand-binding study of noribogaine, a likely metabolite of ibogaine. (United States)

    Pearl, S M; Herrick-Davis, K; Teitler, M; Glick, S D


    Radioligand-binding studies were performed to ascertain the actions of noribogaine, a suspected metabolite of ibogaine, on opioid receptors. Consistent with previous results, ibogaine showed highest affinity for kappa opioid receptors (Ki = 3.77 +/- 0.81 microM), less affinity for mu receptors (Ki = 11.04 +/- 0.66 microM) and no affinity for delta receptors (Ki > 100 microM). Noribogaine showed a higher affinity than ibogaine for all of the opioid receptors: kappa Ki = 0.96 +/- 0.08 microM, mu Ki = 2.66 +/- 0.62 microM and delta Ki = 24.72 +/- 2.26 microM. These data suggest that noribogaine is active in vivo and that it may contribute to ibogaine's pharmacological effects.

  19. Mechanistic studies on the binding of Acid Yellow 99 on coir pith. (United States)

    Khan, Md Motiar R; Ray, Manju; Guha, Arun K


    The interaction of Acid Yellow 99 (AY 99) with coir pith has been investigated in aqueous medium to understand the mechanism of adsorption and explore the potentiality of this biomass towards controlling pollution resulting from textile dyes. The obtained results establish that one gram of coir pith can adsorb 442.13 mg of AY 99. The adsorption process is found to be a function of pH of the solution, the optimum pH value being 2.0. The process follows Langmuir-Freundlich dual isotherm model. Scanning electron microscopic analysis demonstrates that on dye adsorption the biomass develops uneven and irregular surface. X-ray diffraction study indicates incorporation of the dye into the micropores and macropores of the adsorbent and thereby enhancing its degree of crystallinity. The results of Fourier transform infrared (FTIR) spectroscopy and chemical modification of the functional groups establish that binding of AY 99 on coir pith occurs through electrostatic and complexation reaction.

  20. Elevated serotonin transporter binding in depressed patients with Parkinson's disease: a preliminary PET study with [11C]DASB. (United States)

    Boileau, Isabelle; Warsh, Jerry J; Guttman, Mark; Saint-Cyr, Jean A; McCluskey, Tina; Rusjan, Pablo; Houle, Sylvain; Wilson, Alan A; Meyer, Jeffrey H; Kish, Stephen J


    This study investigated whether abnormalities in serotonin transporter binding occur in Parkinson's disease (PD) patients with concurrent depression. We estimated serotonin transporter levels in seven clinically depressed early-stage PD patients and in seven healthy matched-control subjects during a single positron emission tomography (PET) scan with the serotonin transporter radioligand, [(11)C]DASB. Depressed PD patients displayed a wide-spread increase (8-68%) in [(11)C]DASB specific binding outside of the striatum, which was significant in dorsolateral (37%) and prefrontal (68%) cortices. Elevated [(11)C]DASB binding was positively correlated with depressive symptoms but not with disease severity or duration. Compatible with recent PET/[(11)C]DASB findings in major depression, the present preliminary data suggest that increased [(11)C]DASB binding, possibly reflecting greater serotonin transporter density (up-regulation), might be a pathological feature of depression in Parkinson's disease-and possibly a characteristic of depressive illness in general.

  1. Binding between bixin and whey protein at pH 7.4 studied by spectroscopy and isothermal titration calorimetry. (United States)

    Zhang, Yue; Zhong, Qixin


    Bixin is the major coloring component of annatto used in manufacturing colored cheeses, but its presence in liquid whey causes undesirable quality of the recovered whey protein ingredients. The objective of this work was to study molecular binding between bixin and three major whey proteins (β-lactoglobulin, α-lactalbumin, and bovine serum albumin) at pH 7.4 using UV-vis absorption spectroscopy, fluorescence spectroscopy, isothermal titration calorimetry, and circular dichroism. These complementary techniques illustrated that the binding is a spontaneous complexation process mainly driven by hydrophobic interactions. The complexation is favored at a lower temperature and a higher ionic strength. At a lower temperature, the binding is entropy-driven, while it changes to an enthalpy-driven process at higher temperatures. The binding also increases the percentage of unordered secondary structures of proteins. Findings from this work can be used to develop whey protein recovery processes for minimizing residual annatto content in whey protein ingredients.


    Directory of Open Access Journals (Sweden)



    Full Text Available BACKGROUND: To Study Association b etween Lipid Profile i n Vegetarians a nd Non - Vegetarians in t he Local Population . MATERIALS AND METHODS: Descriptive study was conducted in the area Chittur from April 2014 to April 2015. One hundred and fifty (75 vegetarians and 75 non - vegetarians healthy individuals, aged 30 – 60 years we re studied in the central lab o f Karuna Medical College. Overnight fasting venous blood samples were collected for estimating. Fasting Blood Sugar (FBS, Serum Alanine Transaminase (ALT and , Serum lipid profile. RESULTS: The mean age of the study subjects was 38 and 37 of the vegetarians and non - vegetarians respectively with normal serum ALT. The vegetarians subjects had signifi cantly lower mean serum Total Cholesterol (TC [mean difference (95% CI] [ - 0 . 42 ( - 0 . 78, - 0 . 06] and LDL [ - 0 . 45 ( - 0 . 75, - 0 . 15] compared to non - vegetarians . However, triglyceride, HDL, FBS, were identical . In Pearson’s correlation, consumption of vegetable diet significantly correlated with serum TC, LDL. CONCLUSION: I n our study the vegetarian study have a lower lipid profile status as compared to the non - vegetarian subjects. Therefore consumption of a vegetarian diet has to be encouraged . KEYWORDS: Chittu r; Vegetarian; Non Vegetarian Lipid Profile .

  3. Binding of semenogelin I to intact human spermatozoa studied by flow cytometry and surface plasmon resonance. (United States)

    Jonsson, Magnus; Frohm, Birgitta; Malm, Johan


    Approximately 1 in 10 couples is infertile. No definite cause can be found in about 25% of those cases. Studies have indicated that seminal vesicle secretion functions as an optimizer of fertilization. The Zn(2+) binding protein semenogelin I (SgI) represents a major fraction of the proteins present in seminal vesicle fluid, and it serves as a structural component of the coagulum that is formed after ejaculation. Cleavage of SgI by prostate-specific antigen results in liquefaction of the coagulum. Fragmented SgI has antibacterial effects and inhibits spermatozoa mobility. SgI has also been found complexed to eppin on spermatozoa, and this complex has been suggested to be of importance for fertility. Here, we used flow cytometry and surface plasmon resonance to study SgI regarding its association with spermatozoa and the interaction dependency on Zn(2+). The concentration of Zn(2+) in seminal plasma is approximately 100 times higher than in blood plasma, and the metal ion is known to change the structure of SgI. We found that SgI binds to spermatozoa in a concentration-dependent and saturable manner. In solution, SgI bound to spermatozoa in a non-Zn(2+)-dependent way, whereas immobilized SgI interacts with spermatozoa only in the presence of Zn(2+). It indicates that SgI must exhibit a specific structure or free flexibility to be able to interact with that ligand. Our results indicate that the association of SgI to spermatozoa is conformation dependent and specific. These findings could constitute a basis for the development of a male contraceptive.

  4. Studies on the Detection, Expression, Glycosylation, Dimerization, and Ligand Binding Properties of Mouse Siglec-E. (United States)

    Siddiqui, Shoib; Schwarz, Flavio; Springer, Stevan; Khedri, Zahra; Yu, Hai; Deng, Lingquan; Verhagen, Andrea; Naito-Matsui, Yuko; Jiang, Weiping; Kim, Daniel; Zhou, Jie; Ding, Beibei; Chen, Xi; Varki, Nissi; Varki, Ajit


    CD33-related Siglecs are a family of proteins widely expressed on innate immune cells. Binding of sialylated glycans or other ligands triggers signals that inhibit or activate inflammation. Immunomodulation by Siglecs has been extensively studied, but relationships between structure and functions are poorly explored. Here we present new data relating to the structure and function of Siglec-E, the major CD33-related Siglec expressed on mouse neutrophils, monocytes, macrophages, and dendritic cells. We generated nine new rat monoclonal antibodies specific to mouse Siglec-E, with no cross-reactivity to Siglec-F. Although all antibodies detected Siglec-E on transfected human HEK-293T cells, only two reacted with mouse bone marrow neutrophils by flow cytometry and on spleen sections by immunohistochemistry. Moreover, whereas all antibodies recognized Siglec-E-Fc on immunoblots, binding was dependent on intact disulfide bonds and N-glycans, and only two antibodies recognized native Siglec-E within spleen lysates. Thus, we further investigated the impact of Siglec-E homodimerization. Homology-based structural modeling predicted a cysteine residue (Cys-298) in position to form a disulfide bridge between two Siglec-E polypeptides. Mutagenesis of Cys-298 confirmed its role in dimerization. In keeping with the high level of 9-O-acetylation found in mice, sialoglycan array studies indicate that this modification has complex effects on recognition by Siglec-E, in relationship to the underlying structures. However, we found no differences in phosphorylation or SHP-1 recruitment between dimeric and monomeric Siglec-E expressed on HEK293A cells. Phylogenomic analyses predicted that only some human and mouse Siglecs form disulfide-linked dimers. Notably, Siglec-9, the functionally equivalent human paralog of Siglec-E, occurs as a monomer.

  5. Studies of the effect of maltose on the direct binding of porcine pancreatic α-amylase to maize starch. (United States)

    Warren, Frederick J; Butterworth, Peter J; Ellis, Peter R


    For a two phase system comprising an enzyme in solution acting on an insoluble substrate such as starch, adsorption of the enzyme is a key initial step in the reaction but few studies of agents affecting direct binding have been performed. The effect of maltose on the interaction of maize starch with porcine pancreatic α-amylase was studied by using a method in which the direct binding of starch to amylase is measured under conditions of negligible catalytic activity. The dissociation constant for starch binding increased with maltose concentration and analysis of the binding showed that the kinetic action of maltose was entirely competitive. This result accords with results described in the literature in which maltose was shown to be a competitive inhibitor of amylase action. If the maltose concentration is sufficiently high, a second molecule may bind at the active site but the affinity of the second binding step is approximately 6.5-fold weaker. Because of the relatively low affinity for maltose, it seems unlikely that inhibition by maltose of the initial stage of starch-amylase interaction normally plays any role in regulating intestinal digestion of starch.

  6. Fluorescence quenching studies of γ-butyrolactone binding protein (CprB) from Streptomyces coelicolor A3(2). (United States)

    Biswas, Anwesha; Swarnkar, Ravi K; Hussain, Bhukya; Sahoo, Suraj K; Pradeepkumar, P I; Patwari, G Naresh; Anand, Ruchi


    Quorum sensing is a cell density dependent phenomenon that utilizes small molecule inducers like γ-butyrolactones (GBLs) and their receptor proteins for adaptation to the environment. The cognate GBLs that bind to several of this GBL receptor family of proteins remain elusive. Here, using CprB protein from Streptomyces coelicolor A3(2) as a model system, we devise a method suited for ligand screening that would be applicable to the entire family of GBL receptors. Docking studies were performed to confirm the identity of the ligand binding pocket, and it was ascertained that the common γ-butyrolactone moiety interacts with the conserved tryptophan residue (W127) residing in the ligand binding pocket. The presence of W127 in the cavity was exploited to monitor its fluorescence quenching on the addition of two chemically synthesized GBLs. Analysis of the data with both the native and W185L mutant versions of the protein confirmed that the compounds used as quenchers reside in the ligand binding pocket. Furthermore, fluorescence lifetime and potassium iodide (KI) quenching studies established that the quenching is static in nature and that the tryptophan residue is buried and inaccessible to surface quenchers. Additionally, a combination of concentration dependent fluorescence quenching and dynamic light scattering experiments revealed that the binding properties of the protein are concentration dependent and it was concluded that the most efficient binding of the ligand is evoked by working at the lowest concentration of protein, providing a sufficient signal, where the aggregation effects are negligible.

  7. Co(III and Ni(II Complexes Containing Bioactive Ligands: Synthesis, DNA Binding, and Photocleavage Studies

    Directory of Open Access Journals (Sweden)

    M. C. Prabhakara


    Full Text Available DNA binding and photocleavage characteristics of a series of mixed ligand complexes of the type [M(bpy2qbdp](PF6n⋅xH2O (where M=Co(III or Ni(II, bpy=2.2′-bipryidine, qbdp = Quinolino[3,2-b]benzodiazepine, n=3 or 2 and x=5 or 2 have been investigated. The DNA binding property of the complexes with calf thymus DNA has been investigated by using absorption spectra, viscosity measurements, as well as thermal denaturation studies. Intrinsic binding constant (Kb has been estimated under similar set of experimental conditions. Absorption spectral studies indicate that the Co(III and Ni(II complexes intercalate between the base pairs of the CT-DNA tightly with intrinsic DNA binding constant of 1.3×106 and 3.1×105 M-1 in Tris-HCl buffer containing 50 mM NaCl, respectively. The proposed DNA binding mode supports the large enhancement in the relative viscosity of DNA on binding to quinolo[3,2-b]benzodiazepine. The oxidative as well as photo-induced cleavage reactions were monitered by gel electrophoresis for both complexes. The photocleavage experiments showed that the cobalt(III complex can cleave pUC19 DNA effectively in the absence of external additives as an effective inorganic nuclease.

  8. Experimental and molecular docking studies on DNA binding interaction of adefovir dipivoxil: Advances toward treatment of hepatitis B virus infections (United States)

    Shahabadi, Nahid; Falsafi, Monireh

    The toxic interaction of adefovir dipivoxil with calf thymus DNA (CT-DNA) was investigated in vitro under simulated physiological conditions by multi-spectroscopic techniques and molecular modeling study. The fluorescence spectroscopy and UV absorption spectroscopy indicated drug interacted with CT-DNA in a groove binding mode. The binding constant of UV-visible and the number of binding sites were 3.33 ± 0.2 × 104 L mol-1and 0.99, respectively. The fluorimetric studies showed that the reaction between the drug and CT-DNA is exothermic (ΔH = 34.4 kJ mol-1; ΔS = 184.32 J mol-1 K-1). Circular dichroism spectroscopy (CD) was employed to measure the conformational change of CT-DNA in the presence of adefovir dipivoxil, which verified the groove binding mode. Furthermore, the drug induces detectable changes in its viscosity. The molecular modeling results illustrated that adefovir strongly binds to groove of DNA by relative binding energy of docked structure -16.83 kJ mol-1. This combination of multiple spectroscopic techniques and molecular modeling methods can be widely used in the investigation on the toxic interaction of small molecular pollutants and drugs with bio macromolecules, which contributes to clarify the molecular mechanism of toxicity or side effect in vivo.

  9. Effect of tetrahydrocurcumin on insulin receptor status in type 2 diabetic rats: studies on insulin binding to erythrocytes

    Indian Academy of Sciences (India)

    Pidaran Murugan; Leelavinothan Pari; Chippada Appa Rao


    Curcumin is the most active component of turmeric. It is believed that curcumin is a potent antioxidant and anti-inflammatory agent. Tetrahydrocurcumin (THC) is one of the major metabolites of curcumin, and exhibits many of the same physiological and pharmacological activities as curcumin and, in some systems, may exert greater antioxidant activity than curcumin. Using circulating erythrocytes as the cellular mode, the insulin-binding effect of THC and curcumin was investigated. Streptozotocin (STZ)–nicotinamide-induced male Wistar rats were used as the experimental models. THC (80 mg/kg body weight) was administered orally for 45 days. The effect of THC on blood glucose, plasma insulin and insulin binding to its receptor on the cell membrane of erythrocytes were studied. Mean specific binding of insulin was significantly lowered in diabetic rats with a decrease in plasma insulin. This was due to a significant decrease in mean insulin receptors. Erythrocytes from diabetic rats showed a decreased ability for insulin–receptor binding when compared with THC-treated diabetic rats. Scatchard analysis demonstrated that the decrease in insulin binding was accounted for by a decrease in insulin receptor sites per cell, with erythrocytes of diabetic rats having less insulin receptor sites per cell than THC-treated rats. High affinity (Kd1), low affinity (Kd2) and kinetic analyses revealed an increase in the average receptor affinity of erythrocytes from THC-treated rats compared with those of diabetic rats. These results suggest that acute alteration of the insulin receptor on the membranes of erythrocytes occurred in diabetic rats. Treatment with THC significantly improved specific insulin binding to the receptors, with receptor numbers and affinity binding reaching near-normal levels. Our study suggests the mechanism by which THC increases the number of total cellular insulin binding sites resulting in a significant increase in plasma insulin. The effect of THC is

  10. A comparative study of fatty acid profiles of fat in commercial Spanish suckling kids and lambs

    Directory of Open Access Journals (Sweden)

    Alberto Horcada


    Full Text Available Fatty acid profiles are a major contributor to meat quality in small ruminants. Nevertheless, while fatty acid profiles from suckling lambs have been extensively studied they are virtually unknown in suckling kids. Fatty acid profiles of intramuscular and kidney knob fat depots of suckling kids were compared with fatty acid profiles of lambs with a quality label in the Spanish market. Forty suckling kids from Blanca Celtibérica (BC, Moncaína (Mo, Negra Serrana (NS and Murciano Granadina (MG breeds and 20 Churra male suckling lambs labelled with ‘Lechazo de Castilla y León’ Protected Geographic Indication were slaughtered at commercial live weights (12 kg. In both depots differences in the unsaturated fatty acid profile were observed between breeds. The most pronounced differences were observed between meat goat breeds (BC, Mo and NS and lambs, whilst a greater similarity in the fatty acid profile was observed between kids from dairy goat breeds (MG and lambs. The lowest polyunsaturated fatty acid content was observed in meat goat breeds (approximately 21 to 22% of total fatty acids detected in the intramuscular fat. No significant differences in atherogenic index and desirable fatty acid content (range 68 to 70% of total fatty acids detected were observed. However, a more favourable (lower than 8.07 n-6/n-3 ratio was observed in meat goat breeds. The use of fatty acid profiles from intramuscular and kidney knob fat could be proposed as a tool to differentiate goat kids and lambs. The fact that intramuscular fat from suckling kids and lambs shows appropriate lipid nutritional indices and their low carcass fatness indicate that moderate consumption of suckling kid and lamb meat may contribute to an overall balanced diet for humans.

  11. Metabolomic Profiles of Body Mass Index in the Framingham Heart Study Reveal Distinct Cardiometabolic Phenotypes.

    Directory of Open Access Journals (Sweden)

    Jennifer E Ho

    Full Text Available Although obesity and cardiometabolic traits commonly overlap, underlying pathways remain incompletely defined. The association of metabolite profiles across multiple cardiometabolic traits may lend insights into the interaction of obesity and metabolic health. We sought to investigate metabolic signatures of obesity and related cardiometabolic traits in the community using broad-based metabolomic profiling.We evaluated the association of 217 assayed metabolites and cross-sectional as well as longitudinal changes in cardiometabolic traits among 2,383 Framingham Offspring cohort participants. Body mass index (BMI was associated with 69 of 217 metabolites (P<0.00023 for all, including aromatic (tyrosine, phenylalanine and branched chain amino acids (valine, isoleucine, leucine. Additional metabolic pathways associated with BMI included the citric acid cycle (isocitrate, alpha-ketoglutarate, aconitate, the tryptophan pathway (kynurenine, kynurenic acid, and the urea cycle. There was considerable overlap in metabolite profiles between BMI, abdominal adiposity, insulin resistance [IR] and dyslipidemia, modest overlap of metabolite profiles between BMI and hyperglycemia, and little overlap with fasting glucose or elevated blood pressure. Metabolite profiles were associated with longitudinal changes in fasting glucose, but the involved metabolites (ornithine, 5-HIAA, aminoadipic acid, isoleucine, cotinine were distinct from those associated with baseline glucose or other traits. Obesity status appeared to "modify" the association of 9 metabolites with IR. For example, bile acid metabolites were strongly associated with IR among obese but not lean individuals, whereas isoleucine had a stronger association with IR in lean individuals.In this large-scale metabolite profiling study, body mass index was associated with a broad range of metabolic alterations. Metabolite profiling highlighted considerable overlap with abdominal adiposity, insulin resistance

  12. Binding Preferences of Amino Acids for Gold Nanoparticles: A Molecular Simulation Study. (United States)

    Shao, Qing; Hall, Carol K


    A better understanding of the binding preference of amino acids for gold nanoparticles of different diameters could aid in the design of peptides that bind specifically to nanoparticles of a given diameter. Here we identify the binding preference of 19 natural amino acids for three gold nanoparticles with diameters of 1.0, 2.0, and 4.0 nm, and investigate the mechanisms that govern these preferences. We calculate potentials of mean force between 36 entities (19 amino acids and 17 side chains) and the three gold nanoparticles in explicit water using well-tempered metadynamics simulations. Comparing these potentials of mean force determines the amino acids' nanoparticle binding preferences and if these preferences are controlled by the backbone, the side chain, or both. Twelve amino acids prefer to bind to the 4.0 nm gold nanoparticle, and seven prefer to bind to the 2.0 nm one. We also use atomistic molecular dynamics simulations to investigate how water molecules near the nanoparticle influence the binding of the amino acids. The solvation shells of the larger nanoparticles have higher water densities than those of the smaller nanoparticles while the orientation distributions of the water molecules in the shells of all three nanoparticles are similar. The nanoparticle preferences of the amino acids depend on whether their binding free energy is determined mainly by their ability to replace or to reorient water molecules in the nanoparticle solvation shell. The amino acids whose binding free energy depends mainly on the replacement of water molecules are likely to prefer to bind to the largest nanoparticle and tend to have relatively simple side chain structures. Those whose binding free energy depends mainly on their ability to reorient water molecules prefer a smaller nanoparticle and tend to have more complex side chain structures.

  13. Lysine-functionalized nanodiamonds: synthesis, physiochemical characterization, and nucleic acid binding studies

    Directory of Open Access Journals (Sweden)

    Kaur R


    . These modified NDs formed highly stable aqueous dispersions with a zeta potential of 49 mV and particle size of approximately 20 nm. The functionalized NDs were found to be able to bind plasmid DNA and small interfering RNA by forming nanosized "diamoplexes".Conclusion: The lysine-substituted ND particles generated in this study exhibit stable aqueous formulations and show potential for use as carriers for genetic materials.Keywords: disaggregation, spectroscopy, dispersion, electrophoresis, size, zeta potential

  14. Effect of dactyloscopic powders on DNA profiling from enhanced fingerprints: results from an experimental study. (United States)

    Tozzo, Pamela; Giuliodori, Alice; Rodriguez, Daniele; Caenazzo, Luciana


    We conducted a study on the effect of fingerprint enhancement methods on subsequent short tandem repeat profiling. First, we performed a study typing blood traces deposited on 5 different surfaces, treated with 8 types of dactyloscopic powders. Three different DNA extraction methods were used. Subsequently, we analyzed latent fingerprints on the same 5 surfaces enhanced with the 8 different powders used in the first part of the study. This study has demonstrated that DNA profiling can be performed on fingerprints left on different substrates, and the substrate will affect the amount of DNA that can be recovered for DNA typing. In the first phase of the study, a profile was obtained in 92% of the 120 samples analyzed; in the second part, in 55% of the 80 samples analyzed, we obtained a profile complete in 32.5% of the cases. From the results obtained, it seems that the powders used in latent fingerprints enhancement, rather than having a direct inhibitory effect on extraction and amplification of DNA, may cause partial degradation of DNA, reducing the efficiency of amplification reaction. It should not be forgotten that these results were obtained under laboratory conditions, and in real caseworks, there may still be different problems involved.

  15. Ligand binding-dependent functions of the lipocalin NLaz: an in vivo study in Drosophila. (United States)

    Ruiz, Mario; Ganfornina, Maria D; Correnti, Colin; Strong, Roland K; Sanchez, Diego


    Lipocalins are small extracellular proteins mostly described as lipid carriers. The Drosophila lipocalin NLaz (neural Lazarillo) modulates the IIS pathway and regulates longevity, stress resistance, and behavior. Here, we test whether a native hydrophobic pocket structure is required for NLaz to perform its functions. We use a point mutation altering the binding pocket (NLaz(L130R)) and control mutations outside NLaz binding pocket. Tryptophan fluorescence titration reveals that NLaz(L130R) loses its ability to bind ergosterol and the pheromone 7(z)-tricosene but retains retinoic acid binding. Using site-directed transgenesis in Drosophila, we test the functionality of the ligand binding-altered lipocalin at the organism level. NLaz-dependent life span reduction, oxidative stress and starvation sensitivity, aging markers accumulation, and deficient courtship are rescued by overexpression of NLaz(WT), but not of NLaz(L130R). Transcriptional responses to aging and oxidative stress show a large set of age-responsive genes dependent on the integrity of NLaz binding pocket. Inhibition of IIS activity and modulation of oxidative stress and infection-responsive genes are binding pocket-dependent processes. Control of energy metabolites on starvation appears to be, however, insensitive to the modification of the NLaz binding pocket.

  16. A Comparison Study for DNA Motif Modeling on Protein Binding Microarray

    KAUST Repository

    Wong, Ka-Chun


    Transcription Factor Binding Sites (TFBSs) are relatively short (5-15 bp) and degenerate. Identifying them is a computationally challenging task. In particular, Protein Binding Microarray (PBM) is a high-throughput platform that can measure the DNA binding preference of a protein in a comprehensive and unbiased manner; for instance, a typical PBM experiment can measure binding signal intensities of a protein to all possible DNA k-mers (k=810). Since proteins can often bind to DNA with different binding intensities, one of the major challenges is to build motif models which can fully capture the quantitative binding affinity data. To learn DNA motif models from the non-convex objective function landscape, several optimization methods are compared and applied to the PBM motif model building problem. In particular, representative methods from different optimization paradigms have been chosen for modeling performance comparison on hundreds of PBM datasets. The results suggest that the multimodal optimization methods are very effective for capturing the binding preference information from PBM data. In particular, we observe a general performance improvement using di-nucleotide modeling over mono-nucleotide modeling. In addition, the models learned by the best-performing method are applied to two independent applications: PBM probe rotation testing and ChIP-Seq peak sequence prediction, demonstrating its biological applicability.

  17. A Comparison Study for DNA Motif Modeling on Protein Binding Microarray. (United States)

    Wong, Ka-Chun; Li, Yue; Peng, Chengbin; Wong, Hau-San


    Transcription factor binding sites (TFBSs) are relatively short (5-15 bp) and degenerate. Identifying them is a computationally challenging task. In particular, protein binding microarray (PBM) is a high-throughput platform that can measure the DNA binding preference of a protein in a comprehensive and unbiased manner; for instance, a typical PBM experiment can measure binding signal intensities of a protein to all possible DNA k-mers (k = 8∼10). Since proteins can often bind to DNA with different binding intensities, one of the major challenges is to build TFBS (also known as DNA motif) models which can fully capture the quantitative binding affinity data. To learn DNA motif models from the non-convex objective function landscape, several optimization methods are compared and applied to the PBM motif model building problem. In particular, representative methods from different optimization paradigms have been chosen for modeling performance comparison on hundreds of PBM datasets. The results suggest that the multimodal optimization methods are very effective for capturing the binding preference information from PBM data. In particular, we observe a general performance improvement if choosing di-nucleotide modeling over mono-nucleotide modeling. In addition, the models learned by the best-performing method are applied to two independent applications: PBM probe rotation testing and ChIP-Seq peak sequence prediction, demonstrating its biological applicability.

  18. Synthesis, crystal structure and electrochemical and DNA binding studies of oxygen bridged-copper(II) carboxylate (United States)

    Iqbal, Muhammad; Ali, Saqib; Tahir, Muhammad Nawaz; Muhammad, Niaz; Shah, Naseer Ali; Sohail, Manzar; Pandarinathan, Vedapriya


    A new binuclear O-bridged Cu(II) complex with 4-chlorophenyl acetate and 2,2‧-bipyridine has been synthesized and characterized using FT-IR, powder and single crystal XRD and electrochemical solution studies. The results revealed that the two penta-coordinated Cu(II) centers are linked by two carboxylate ligands in end-on bonding fashion. The coordination geometry is slightly distorted square pyramidal (SP) with bridging oxygen atoms occupying the apical position and other ligands lying in the equatorial plane. The striking difference in Cu-O bond distance of the bridging oxygen atom in the complex may be responsible for the SP geometry of Cu(II) ion. The complex gave rise to metal centered irreversible electro-activity where one electron Cu(II)/Cu(III) oxidation process and a single step two electron Cu(II)/Cu(0) reduction process was observed. The redox processes were found predominantly adsorption controlled. The values of diffusion coefficient and heterogeneous rate constant for oxidation process were 6.98 × 10-7 cm2 s-1 and 4.60 × 10-5 cm s-1 while the corresponding values for reduction were 5.30 × 10-8 cm2 s-1 and 5.41 × 10-6 cm s-1, respectively. The formal potential and charge transfer coefficient were also calculated. The DNA-binding ability was explored through cyclic voltammetry and UV-Visible spectroscopy. Diminution in the value of Do for oxidation indicated the binding of the complex with DNA corresponding to Kb = 8.58 × 104 M-1. UV-Visible spectroscopy yielded ε = 49 L mol-1 cm-1 and Kb = 2.96 × 104 M-1. The data of both techniques support each other. The self-induced redox activation of the complex, as indicated by cyclic voltammetry heralds its potential applications in redox catalysis and anticancer activity.

  19. NMr studies of the AMP binding site and mechanism of adenylate kinase

    Energy Technology Data Exchange (ETDEWEB)

    Kuby, S.A.; Fry, D.C.; Mildvan, A.S.


    The authors recently located by NMR the MgATP binding site on adenylate kinase correcting the proposed location for this site based on X-ray studies of the binding of salicylate. To determine the conformation and location of the other substrate, they have determined distances from Cr/sup 3 +/ AMPPCP to 6 protons and to the phosphorus atom of AMP on adenylate kinase using the paramagnetic-probe-T/sub 1/ method. They have also used time-dependent NOEs to measure five interproton distances on AMP, permitting evaluation of the conformation of enzyme-bound AMP and its position with respect to metal-ATP. Enzyme-bound AMP exhibits a high-anti glycosyl torsional angle (X = 110/sup 0/), a 3'-endo sugar pucker (delta = 105/sup 0/), and a gauche-trans orientation about the C/sub 4/'-C/sub 5/' bond (..gamma.. = 180/sup 0/). The distance from Cr/sup 3 +/ to the phosphorus of AMP is 6.4 +/- 0.3 A, indicating a reaction coordinate distance of greater than or equal to A which is consistent with an associative SN2 mechanism for the phosphoryl transfer. Ten intermolecular NOEs, from protons of the enzyme to those of AMP were detected. These constraints, together with the conformation of AMP and the X-ray structure of the enzyme, suggest proximity (less than or equal to A) of AMP to leu 116, arg 171, val 173, gln 185, thr 188, and asp 191.

  20. Studies of beam heating of proton beam profile monitor SEM's

    Energy Technology Data Exchange (ETDEWEB)

    Pavlovich, Zarko; Osiecki, Thomas H.; Kopp, Sacha E.; /Texas U.


    The authors present calculations of the expected temperature rise of proton beam profile monitors due to beam heating. The profile monitors are secondary emission monitors (SEM's) to be made of Titanium foils. The heating is studied to understand whether there is any loss of tension or alignment of such devices. Additionally, calculations of thermally-induced dynamic stress are presented. Ti foil is compared to other materials and also to wire SEM's. The calculations were initially performed for the NuMI beam, where the per-pulse intensity is quite high; for completeness the calculations are also performed for other beam energies and intensities.

  1. Comparison of Profiling Microwave Radiometer, Aircraft, and Radiosonde Measurements From the Alliance Icing Research Study (AIRS) (United States)

    Reehorst, Andrew L.


    Measurements from a profiling microwave radiometer are compared to measurements from a research aircraft and radiosondes. Data compared is temperature, water vapor, and liquid water profiles. Data was gathered at the Alliance Icing Research Study (AIRS) at Mirabel Airport outside Montreal, Canada during December 1999 and January 2000. All radiometer measurements were found to lose accuracy when the radome was wet. When the radome was not wetted, the radiometer was seen to indicate an inverted distribution of liquid water within a cloud. When the radiometer measurements were made at 15 deg. instead of the standard zenith, the measurements were less accurate.

  2. Genome-wide annotation, expression profiling, and protein interaction studies of the core cell-cycle genes in Phalaenopsis aphrodite. (United States)

    Lin, Hsiang-Yin; Chen, Jhun-Chen; Wei, Miao-Ju; Lien, Yi-Chen; Li, Huang-Hsien; Ko, Swee-Suak; Liu, Zin-Huang; Fang, Su-Chiung


    Orchidaceae is one of the most abundant and diverse families in the plant kingdom and its unique developmental patterns have drawn the attention of many evolutionary biologists. Particular areas of interest have included the co-evolution of pollinators and distinct floral structures, and symbiotic relationships with mycorrhizal flora. However, comprehensive studies to decipher the molecular basis of growth and development in orchids remain scarce. Cell proliferation governed by cell-cycle regulation is fundamental to growth and development of the plant body. We took advantage of recently released transcriptome information to systematically isolate and annotate the core cell-cycle regulators in the moth orchid Phalaenopsis aphrodite. Our data verified that Phalaenopsis cyclin-dependent kinase A (CDKA) is an evolutionarily conserved CDK. Expression profiling studies suggested that core cell-cycle genes functioning during the G1/S, S, and G2/M stages were preferentially enriched in the meristematic tissues that have high proliferation activity. In addition, subcellular localization and pairwise interaction analyses of various combinations of CDKs and cyclins, and of E2 promoter-binding factors and dimerization partners confirmed interactions of the functional units. Furthermore, our data showed that expression of the core cell-cycle genes was coordinately regulated during pollination-induced reproductive development. The data obtained establish a fundamental framework for study of the cell-cycle machinery in Phalaenopsis orchids.

  3. Profiling Approaches to Teaching in Higher Education: A Cluster-Analytic Study (United States)

    Stes, Ann; Van Petegem, Peter


    Teaching approaches in higher education have already been the subject of a considerable body of research. An important contribution was Prosser and Trigwell's development of the Approaches to Teaching Inventory (ATI). The present study aims to map out the approaches to teaching profiles of teachers in higher education on the basis of their scores…

  4. Information Security: A Scientometric Study of the Profile, Structure, and Dynamics of an Emerging Scholarly Specialty (United States)

    Olijnyk, Nicholas Victor


    The central aim of the current research is to explore and describe the profile, dynamics, and structure of the information security specialty. This study's objectives are guided by four research questions: 1. What are the salient features of information security as a specialty? 2. How has the information security specialty emerged and evolved from…

  5. A Challenge to Classical Facial Proportionality Studies: Conventional Profile and 3d Photography Versus Silhouettes (United States)


    facial asymmetry in stereophotogrammetry, video and laser scanning. In relating this to the face and the study of orthodontics, Drs. Gross, Trotman and...attractiveness. They used digital profile and cephalometric x-rays of three men and three women and altered them with aid of Dolphin Imaging

  6. Syntactic and Discourse Skills in Chinese Adolescent Readers with Dyslexia: A Profiling Study (United States)

    Chung, Kevin K. H.; Lo, Jason C. M.; Ho, Connie S.-H.; Xiao, Xiaoyun; Chan, David W.


    This study aims to investigate the relation of syntactic and discourse skills to morphological skills, rapid naming, and working memory in Chinese adolescent readers with dyslexia and to examine their cognitive-linguistic profiles. Fifty-two dyslexic readers (mean age, 13;42) from grade 7 to 9 in Hong Kong high schools were compared with 52…

  7. State Profiles of Subcounty Allocation Procedures: Appendix to the Title I, ESEA, Subcounty Allocation Study. (United States)

    Gutmann, Babette; Paller, Alan T.

    In this appendix to the study of subcounty allocation of Title I of the Elementary and Secondary Education Act, state by state profiles of subcounty allocation are provided. The allocation formula and procedures used by each state for fiscal year 1977 are explained. Other data for each state, such as number of school districts and counties which…

  8. In vitro characterization of luseogliflozin, a potent and competitive sodium glucose co-transporter 2 inhibitor: Inhibition kinetics and binding studies. (United States)

    Uchida, Saeko; Mitani, Akiko; Gunji, Emi; Takahashi, Teisuke; Yamamoto, Koji


    In this study, we evaluated an inhibition model of luseogliflozin on sodium glucose co-transporter 2 (SGLT2). We also analyzed the binding kinetics of the drug to SGLT2 protein using [(3)H]-luseogliflozin. Luseogliflozin competitively inhibited human SGLT2 (hSGLT2)-mediated glucose uptake with a Ki value of 1.10 nM. In the absence of glucose, [(3)H]-luseogliflozin exhibited a high affinity for hSGLT2 with a Kd value of 1.3 nM. The dissociation half-time was 7 h, suggesting that luseogliflozin dissociates rather slowly from hSGLT2. These profiles of luseogliflozin might contribute to the long duration of action of this drug.

  9. Spectroscopic and molecular docking studies of binding interaction of gefitinib, lapatinib and sunitinib with bovine serum albumin (BSA). (United States)

    Shen, Guo-Feng; Liu, Ting-Ting; Wang, Qi; Jiang, Min; Shi, Jie-Hua


    The binding interactions of three kinds of tyrosine kinase inhibitors (TKIs), such as gefitinib, lapatinib and sunitinib, with bovine serum albumin (BSA) were studied using ultraviolet spectrophotometry, fluorescence spectroscopy, circular dichroism (CD), Fourier transform infrared spectroscopy (FT-IR) and molecular docking methods. The experimental results showed that the intrinsic fluorescence quenching of BSA induced by the three TKIs resulted from the formation of stable TKIs-BSA complexes through the binding interaction of TKIs with BSA. The stoichiometry of three stable TKIs-BSA complexes was 1:1 and the binding constants (Kb) of the three TKIs-BSA complexes were in the order of 10(4)M(-1) at 310 K, indicating that there was a strong binding interaction of the three TKIs with BSA. Based on the analysis of the signs and magnitudes of the free energy change (ΔG(0)), enthalpic change (ΔH(0)) and entropic change (ΔS(0)) in the binding process, it can be deduced that the binding process of the three TKIs with BSA was spontaneous and enthalpy-driven process, and the main interaction forces between the three TKIs and BSA were van der Waals force and hydrogen bonding interaction. Moreover, from the results of CD, FT-IR and molecular docking, it can be concluded that there was a significant difference between the three TKIs in the binding site on BSA, lapatinib was located on site II (m) of BSA while gefitinib and sunitinib were bound on site I of BSA, and there were some changes in the BSA conformation when binding three TKIs to BSA but BSA still retains its secondary structure α-helicity.

  10. Cu(I) complexes of bis(methyl)(thia/selena) salen ligands: Synthesis, characterization, redox behavior and DNA binding studies (United States)

    Asatkar, Ashish K.; Tripathi, Mamta; Panda, Snigdha; Pande, Rama; Zade, Sanjio S.


    Mononuclear cuprous complexes 1 and 2, [{CH3E(o-C6H4)CH = NCH2}2Cu]ClO4; E = S/Se, have been synthesized by the reaction of bis(methyl)(thia/selena) salen ligands and [Cu(CH3CN)4]ClO4. Both the products were characterized by elemental analysis, ESI-MS, FT-IR, 1H/13C/77Se NMR, and cyclic voltammetry. The complexes possess tetrahedral geometry around metal center with the N2S2/N2Se2 coordination core. Cyclic voltammograms of complexes 1 and 2 displayed reversible anodic waves at E1/2 = + 0.08 V and + 0.10 V, respectively, corresponding to the Cu(I)/Cu(II) redox couple. DNA binding studies of both the complexes were performed applying absorbance, fluorescence and molecular docking techniques. Competitive binding experiment of complexes with ct-DNA against ethidium bromide is performed to predict the mode of binding. The results indicate the groove binding mode of complexes 1 and 2 to DNA. The binding constants revealed the strong binding affinity of complexes towards ct-DNA.

  11. Multispectroscopic studies of paeoniflorin binding to calf thymus DNA in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Guowen, E-mail: [State Key Laboratory of Food Science and Technology, Nanchang University, No. 235, Nanjing East Road, Nanchang, Jiangxi 330047 (China); Fu, Peng; Pan, Junhui [State Key Laboratory of Food Science and Technology, Nanchang University, No. 235, Nanjing East Road, Nanchang, Jiangxi 330047 (China)


    The mechanism of paeoniflorin binding to calf thymus DNA in physiological buffer (pH 7.4) was investigated by multispectroscopic methods including UV-vis absorption, fluorescence, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy, coupled with viscosity measurements and DNA melting techniques. The results suggested that paeoniflorin molecules could bind to DNA via groove binding mode as evidenced by no significant change in iodide quenching effect, increase in single-stranded DNA (ssDNA) quenching effect, and almost unchanged relative viscosity and melting temperature of DNA. The observed changes in CD signals revealed that DNA remains in the B-conformation. Further, the displacement experiments with Hoechst 33258 probe and the results of FT-IR spectra indicated that paeoniflorin mainly binds in the region of rich A-T base pairs of DNA. The thermodynamic parameters, enthalpy change ({Delta}H Degree-Sign ) and entropy change ({Delta}S Degree-Sign ) were calculated to be -30.09{+-}0.18 kJ mol{sup -1} and -14.07{+-}0.61 J mol{sup -1} K{sup -1} by the van't Hoff equation, suggesting that hydrogen bond and van der Waals forces play a predominant role in the binding of paeoniflorin to DNA. - Highlights: Black-Right-Pointing-Pointer The binding mode of paeoniflorin to calf thymus DNA is the minor groove binding. Black-Right-Pointing-Pointer Paeoniflorin mainly binds in the region of rich A-T base pairs of DNA. Black-Right-Pointing-Pointer The binding does not alter the native B-conformation of DNA. Black-Right-Pointing-Pointer The binding is driven mainly by hydrogen bonds and van der Waals forces.

  12. Electrostatic interactions in the binding pathway of a transient protein complex studied by NMR and isothermal titration calorimetry. (United States)

    Meneses, Erick; Mittermaier, Anthony


    Much of our knowledge of protein binding pathways is derived from extremely stable complexes that interact very tightly, with lifetimes of hours to days. Much less is known about weaker interactions and transient complexes because these are challenging to characterize experimentally. Nevertheless, these types of interactions are ubiquitous in living systems. The combination of NMR relaxation dispersion Carr-Purcell-Meiboom-Gill (CPMG) experiments and isothermal titration calorimetry allows the quantification of rapid binding kinetics for complexes with submillisecond lifetimes that are difficult to study using conventional techniques. We have used this approach to investigate the binding pathway of the Src homology 3 (SH3) domain from the Fyn tyrosine kinase, which forms complexes with peptide targets whose lifetimes are on the order of about a millisecond. Long range electrostatic interactions have been shown to play a critical role in the binding pathways of tightly binding complexes. The role of electrostatics in the binding pathways of transient complexes is less well understood. Similarly to previously studied tight complexes, we find that SH3 domain association rates are enhanced by long range electrostatics, whereas short range interactions are formed late in the docking process. However, the extent of electrostatic association rate enhancement is several orders of magnitudes less, whereas the electrostatic-free basal association rate is significantly greater. Thus, the SH3 domain is far less reliant on electrostatic enhancement to achieve rapid association kinetics than are previously studied systems. This suggests that there may be overall differences in the role played by electrostatics in the binding pathways of extremely stable versus transient complexes.

  13. Reproducibility of mass spectrometry based protein profiles for diagnosis of ovarian cancer across clinical studies

    DEFF Research Database (Denmark)

    Øgendahl Callesen, Anne Kjærgaard; Mogensen, Ole; Jensen, Andreas K;


    The focus of this systematic review is to give an overview of the current status of clinical protein profiling studies using MALDI and SELDI MS platforms in the search for ovarian cancer biomarkers. A total of 34 profiling studies were qualified for inclusion in the review. Comparative analysis......, and data analysis. About 47% of the peaks reported to be associated to ovarian cancer were also represented in our experimental study, and 34% of these redetected peaks also showed a significant difference between cases and controls in our study. Thus, despite known problems related to reproducibility...... an overlap in peaks between clinical studies was demonstrated, which indicate convergence toward a set of common discriminating, reproducible peaks for ovarian cancer. The potential of the discriminating protein peaks for clinical use as ovarian cancer biomarkers will be discussed and evaluated. This article...


    Directory of Open Access Journals (Sweden)



    Full Text Available INTRODUCTION: Chronic renal failure (CRF is decrease in glomerular filtration rate (GFR to 3 consecut ive months with multiple etiologies. CRF results in profound lipid disorder which stems largely from dysregulation of high density lipoproteins (HDL & triglyceride - rich lipoprotein metabolism. Many a time CRF patients live on hemodialysis on regular basis . Present study was done to know whether hemodialysis has any impact on the lipid profile of the CRF patients. MATERIALS AND METHODS: Study were divided into 7 groups, Group - 1: healthy controls (40, Group - 2: CRF patients who never undergone hemodialysis (40, Group - 3: CRF patients on hemodialysis (40, Group - 4: Healthy males (28, Group - 5: Healthy females (12, Group - 6: males with chronic renal failure (28, Group - 7: females with chronic renal failure (12. Sample analysed for high density lipoproteins (H DL, low density lipoproteins (LDL & very low density lipoproteins (VLDL. RESULTS: Among the various parameters tested triglyceride and VLDL levels were significantly higher in group - 2 and3 as compared to controls (p<0.0001. HDL levels were significant ly lower in group - 2 compared to Group - 1(p <0.0001. HDL level was found reduced in group - 3 as compare to Group - 2(p=0.0035. There was no significant change (p=0.132 observed in total cholesterol between healthy controls and CRF patients with hemodialysis. There is a significant change (p=0.0309 observed in LDL - c between CRF patients and controls and no significant change observed (P=0.6070 between Group - 2 and Group - 3. CONCLUSION: CRF patients are at risk of cardiovascular diseases due to the elevation of various forms of lipids. Prescribing lipid lowering treatment in CRF patients with dyslipidemias for preventing future episode of cardiovascular events and will a lso preserve renal function.

  15. Radiolabelling of phoneutria nigriventer spider toxin (Tx1): a tool to study its binding site

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Raquel Gouvea dos [Centro de Desenvolvimento da Tecnologia Nuclear (CDTN), Belo Horizonte, MG (Brazil); Diniz, Carlos Roberto; Nascimento, Marta Cordeiro [FUNED, Belo Horizonte, MG (Brazil); Lima, Maria Elena de [Minas Gerais Univ., Belo Horizonte, MG (Brazil). Dept. de Bioquimica e Imunologia


    The neurotoxin Tx1, isolated from the venom of the South American spider Phoneutria nigriventer produces tail elevation and spastic paralysis of posterior limbs after intracerebral ventricular injection in mice. Tx1 also produces ileum contraction in bioassay. We have investigated the binding of radioiodinated-Tx1 ({sup 125} I-Tx1) on the preparation of myenteric plexus-longitudinal muscle membrane from guinea pig ileum (MPLM) as a tool to characterize the interaction of this neurotoxin with its site. The neurotoxin Tx1 was radioiodinated with Na{sup 125} I by the lactoperoxidase method. {sup 125} I-Tx1 specifically binds to a single class of noninteracting binding sites of high affinity (Kd= 3.5 x 10{sup -10} M) and low capacity (1.2 pmol/mg protein). The specific binding increased in parallel with the protein concentration. In competition experiments the ligands of ionic channels used (sodium, potassium and calcium) did not affect the binding of {sup 125} I-Tx1 to MPLM neither did the cholinergic ligands (hemicholinium-3, hexamethonium, d-tubocurarine and atropine). Another neurotoxin (Tx2-6, one of the isoforms of Tx2 pool) decreased toxin with MPLM and showed that toxin has a specific and saturable binding site in guinea pig ileum and this binding site appears to be related to the Tx2 site. (author)

  16. Mobility of TOAC spin-labelled peptides binding to the Src SH3 domain studied by paramagnetic NMR

    Energy Technology Data Exchange (ETDEWEB)

    Lindfors, Hanna E. [Leiden University, Leiden Institute of Chemistry, Gorlaeus Laboratories (Netherlands); Koning, Peter E. de; Wouter Drijfhout, Jan [Leiden University Medical Centre, Department of Immunohematology and Blood Transfusion (Netherlands); Venezia, Brigida; Ubbink, Marcellus [Leiden University, Leiden Institute of Chemistry, Gorlaeus Laboratories (Netherlands)], E-mail:


    Paramagnetic relaxation enhancement provides a tool for studying the dynamics as well as the structure of macromolecular complexes. The application of side-chain coupled spin-labels is limited by the mobility of the free radical. The cyclic, rigid amino acid spin-label TOAC (2,2,6,6-Tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid), which can be incorporated straightforwardly by peptide synthesis, provides an attractive alternative. In this study, TOAC was incorporated into a peptide derived from focal adhesion kinase (FAK), and the interaction of the peptide with the Src homology 3 (SH3) domain of Src kinase was studied, using paramagnetic NMR. Placing TOAC within the binding motif of the peptide has a considerable effect on the peptide-protein binding, lowering the affinity substantially. When the TOAC is positioned just outside the binding motif, the binding constant remains nearly unaffected. Although the SH3 domain binds weakly and transiently to proline-rich peptides from FAK, the interaction is not very dynamic and the relative position of the spin-label to the protein is well-defined. It is concluded that TOAC can be used to generate reliable paramagnetic NMR restraints.

  17. Molecular docking study investigating the possible mode of binding of C.I. Acid Red 73 with DNA. (United States)

    Guo, Yumei; Yue, Qinyan; Gao, Baoyu


    C.I. Acid Red 73 is a reactive azo dye with a variable potential carcinogenicity. The mechanism mediating interactions that occur between the dye and DNA have not been completely understood thus far. In this study, molecular docking techniques were applied to describe the most probable mode of DNA binding as well as the sequence selectivity of the C.I. Acid Red 73 dye. These docking experiments revealed that the dye is capable of interacting with the minor groove of the DNA on the basis of its curved shape, which fits well with the topology of double-stranded DNA. In addition, the dye can bind selectively to the minor groove of the DNA by applying CGT sequence selectivity. Further, the minor groove can be recognized although DNA targets present intercalation gaps. However, intercalative binding can also occur when the DNA target possesses an appropriate intercalation gap. Compared with the other eight DNA sequences that were studied, the DNA dodecamer d(CGCGATATCGCG)(2) (PDB ID: 1DNE) presents a very favorable target for the binding of C.I. Acid Red 73 to the minor groove, with the lowest binding free energy -9.19 kcal/mol. Results reported from this study are expected to provide useful information for research involving further simulations of molecular dynamics and toxicology investigations of the dye.

  18. In vitro DNA binding studies of the sweetening agent saccharin and its copper(II) and zinc(II) complexes. (United States)

    Icsel, Ceyda; Yilmaz, Veysel T


    The interactions of fish sperm DNA (FS-DNA) with the sodium salt of sweetener saccharin (sacH) and its copper and zinc complexes, namely [M(sac)2(H2O)4]·2H2O (M=Cu(II) or Zn(II)) were studied by using UV-Vis titration, fluorometric competition, thermal denaturation, viscosity and gel electrophoresis measurements. The intrinsic binding constants (Kb) obtained from absorption titrations were estimated to be 2.86 (±0.06)×10(4)M(-1) for Na(sac), 6.67 (±0.12)×10(4)M(-1) for Cu-sac and 4.01 (±0.08)×10(4)M(-1) for Zn-sac. The Cu-sac complex binds to FS-DNA via intercalation with a KA value of 50.12 (±0.22)×10(4)M(-1) as evidenced by competitive binding studies with ethidium bromide. Moreover, competition experiments with Hoechst 33258 are indicative of a groove binding mode of Na(sac) and Zn-sac with binding constants of 3.13 (±0.16)×10(4)M(-1) and 5.25 (±0.22)×10(4)M(-1), respectively. The spectroscopic measurements indicate a moderate DNA binding affinity of Na(sac) and its metal complexes. The suggested binding modes are further confirmed by the thermal denaturation and viscosity measurements. In addition, Cu-sac and Zn-sac show weak ability to damage to pBR322 supercoiled plasmid DNA.

  19. Comparing Longitudinal Profile Patterns of Mathematics and Reading in Early Child Longitudinal Study, Kindergarten: The Profile Analysis via Multidimensional Scaling (PAMS) Approach (United States)

    Kim, Se-Kang


    The aim of the study is to compare longitudinal patterns from Mathematics and Reading data from the direct child assessment of Early Child Longitudinal Study, Kindergarten (ECLS-K, US Department of Education, National Center for Education Statistics 2006), utilizing Profile Analysis via Multidimensional Scaling (PAMS). PAMS has been used initially…

  20. Randomized crossover study comparing the phosphate-binding efficacy of calcium ketoglutarate versus calcium carbonate in patients on chronic hemodialysis

    DEFF Research Database (Denmark)

    Bro, S; Rasmussen, R A; Handberg, J


    The objective of the study was to evaluate the phosphate-binding efficacy, side effects, and cost of therapy of calcium ketoglutarate granulate as compared with calcium carbonate tablets in patients on chronic hemodialysis. The study design used was a randomized, crossover open trial, and the main...

  1. Extrapolating psychological insights from Facebook profiles: a study of religion and relationship status. (United States)

    Young, Sean; Dutta, Debo; Dommety, Gopal


    Online social network users may leave creative, subtle cues on their public profiles to communicate their motivations and interests to other network participants. This paper explores whether psychological predictions can be made about the motivations of social network users by identifying and analyzing these cues. Focusing on the domain of relationship seeking, we predicted that people using social networks for dating would reveal that they have a single relationship status as a method of eliciting contact from potential romantic others. Based on results from a pilot study (n = 20) supporting this hypothesis, we predicted that people attempting to attract users of the same religious background would report a religious affiliation along with a single relationship status. Using observational data from 150 Facebook profiles, results from a multivariate logistic regression suggest that people providing a religious affiliation were more likely to list themselves as single (a proxy for their interest in using the network to find romantic partners) than people who do not provide religious information. We discuss the implications for extracting psychological information from Facebook profiles. To our knowledge, this is the first study to suggest that information from publicly available online social networking profiles can be used to predict people's motivations for using social networks.

  2. Study of H-alpha Spicule Profiles with Line Inversion Techniques (United States)

    Tziotziou, K.; Kontogiannis, I.; Tsiropoula, G.; Kotrc, P.


    High resolution optical spectra of chromospheric spicules obtained in the H? line are studied together with slit-jaw filtergrams. The spectra were recorded along a vertical slit parallel to the solar limb with the HSFA2 (Horizontal-Sonnen-Forschungs-Anlage) Solar Spectrograph at Ondrejov Observatory on August 19, 2007 and show H? line profiles taken in spicules - due to the limb curvature - at different heights from the solar limb. A multi-cloud model that considers two or more spicules along the line-of-sight (LOS), together with a statistical approach that takes into account a large set of initial conditions for solving the radiative transfer equation, is used for the fitting of the observed profiles and the derivation of several parameters such as the LOS velocity, the source function, the optical thickness and the Doppler width that describe the respective spicules. The height-dependence of the shape of the observed profiles, as well as their dependence on the values of the derived parameters are studied in detail. The derived results are compared with the statistical theoretical results of a multi-cloud model where the aforementioned physical parameters, as well as a random number of spicules along the LOS were taken into account, in order to define the dependence of several spicule profile characteristics on them. Specific steps of the used procedures, as well as crucial problems are discussed.

  3. A comparative study of density functional and density functional tight binding calculations of defects in graphene

    Energy Technology Data Exchange (ETDEWEB)

    Zobelli, Alberto [Laboratoire de Physique des Solides, Univ. Paris Sud, CNRS UMR, Orsay (France); Ivanovskaya, Viktoria; Wagner, Philipp; Yaya, Abu; Ewels, Chris P. [Institut des Materiaux Jean Rouxel (IMN), CNRS UMR, University of Nantes (France); Suarez-Martinez, Irene [Nanochemistry Research Institute, Curtin University of Technology, Perth, Western Australia (Australia)


    The density functional tight binding approach (DFTB) is well adapted for the study of point and line defects in graphene based systems. After briefly reviewing the use of DFTB in this area, we present a comparative study of defect structures, energies, and dynamics between DFTB results obtained using the dftb+ code, and density functional results using the localized Gaussian orbital code, AIMPRO. DFTB accurately reproduces structures and energies for a range of point defect structures such as vacancies and Stone-Wales defects in graphene, as well as various unfunctionalized and hydroxylated graphene sheet edges. Migration barriers for the vacancy and Stone-Wales defect formation barriers are accurately reproduced using a nudged elastic band approach. Finally we explore the potential for dynamic defect simulations using DFTB, taking as an example electron irradiation damage in graphene. DFTB-MD derived sputtering energy threshold map for a carbon atom in a graphene plane. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  4. DNA-binding studies and biological activities of new nitrosubstituted acyl thioureas (United States)

    Tahir, Shaista; Badshah, Amin; Hussain, Raja Azadar; Tahir, Muhammad Nawaz; Tabassum, Saira; Patujo, Jahangir Ali; Rauf, Muhammad Khawar


    Four new nitrosubstituted acylthioureas i.e. 1-acetyl-3-(4-nitrophenyl)thiourea (TU1), 1-acetyl-3-(2-methyl-4-nitrophenyl)thiourea (TU2), 1-acetyl-3-(2-methoxy-4-nitrophenyl)thiourea (TU3) and 1-acetyl-3-(4-chloro-3-nitrophenyl)thiourea (TU4) have been synthesized and characterized (by C13 and H1 nuclear magnetic resonance, Fourier transform infrared spectroscopy and single crystal X-ray diffraction). As a preliminary investigation of the anti-cancer potencies of the said compounds, DNA interaction studies have been carried out using cyclic voltammetry and UV-vis spectroscopy along with verification from computational studies. The drug-DNA binding constants are found to be in the order, KTU3 9.04 × 106 M-1 > KTU4 8.57 × 106 M-1 > KTU2 6.05 × 106 M-1 > KTU1 1.16 × 106 M-1. Furthermore, the antioxidant, cytotoxic, antibacterial and antifungal activities have been carried out against DPPH (1,1-diphenyl-2-dipicrylhydrazyl), Brine shrimp eggs, gram positive (Micrococcus luteus, Staphylococcus aureus) and gram negative (Bordetella bronchiseptica, Salmonella typhimurium, Enterobacter aerogens) and fungal cultures (Aspergillus fumigatus, Mucor species, Aspergillus niger, Aspergillus flavus) respectively.

  5. 1HNMR study of methotrexate serum albumin (MTX SA) binding in rheumatoid arthritis (United States)

    Sułkowska, A.; Maciążek-Jurczyk, M.; Bojko, B.; Równicka, J.; Sułkowski, W. W.


    Rheumatoid arthritis (RA) is an immunologically depended disease. It is characterized by a chronic, progressive inflammatory process. Methotrexate (4-amino-10-methylfolic acid, MTX) is the modifying drug used to treat RA. The aim of the presented studies is to determine the low affinity binding site of MTX in bovine (BSA) and human (HSA) serum albumin with the use of proton nuclear magnetic resonance ( 1HNMR) spectroscopy. The analysis of 1HNMR spectra of MTX in the presence of serum albumin (SA) allows us to observe the interactions between aromatic rings of the drug and the rings of amino acids located in the hydrophobic subdomains of the protein. On the basis of the chemical shifts σ [ppm] and the relaxation times T1 [s] of drug protons the hydrophobic interaction between MTX-SA and the stoichiometric molar ratio of the complex was evaluated. This work is a part of a spectroscopic study on MTX-SA interactions [A. Sułkowska, M. Maciążek, J. Równicka, B. Bojko, D. Pentak, W.W. Sułkowski, J. Mol. Struct. 834-836 (2007) 162-169].

  6. DNA-binding, cytotoxicity, cellular uptake, apoptosis and photocleavage studies of Ru(II) complexes. (United States)

    N Deepika; C Shobha Devi; Y Praveen Kumar; K Laxma Reddy; P Venkat Reddy; D Anil Kumar; Surya S Singh; S Satyanarayana


    Two Ru(II) complexes [Ru(phen)2bppp](ClO4)2 (1) and [Ru(phen)27-Br-dppz](ClO4)2 (2) [phen=1,10 phenanthroline, 7-Br-dppz=7-fluorodipyrido[3,2-a:2',3'-c]phenazine, bppp=11-bromo-pyrido[2',3':5,6]pyrazino[2,3-f] [1,10]phenanthroline] have been synthesized and characterized by elemental analysis, ES-MS, (1)H-NMR, (13)C-NMR and IR. The in vitro cytotoxicity of the complexes examined against a panel of cancer cell lines (HeLa, Du145 and A549) by MTT method, both complexes show prominent anticancer activity against various cancer cells. Live cell imaging study and flow cytometric analysis demonstrate that both the complexes 1 and 2 could cross the cell membrane accumulating in the nucleus. Further, flow cytometry experiments showed that the cytotoxic Ru(II) complexes 1 and 2 induced apoptosis of HeLa tumor cell lines. Photo induced DNA cleavage studies have been performed and results indicate that both the complexes efficiently photo cleave pBR322 DNA. The binding properties of two complexes toward CT-DNA were investigated by various optical methods and viscosity measurements. The experimental results suggested that both Ru(II) complexes can intercalate into DNA base pairs. The complexes were docked into DNA-base pairs using the GOLD docking program.

  7. Profiling postgraduate workplace-based assessment implementation in Ireland: a retrospective cohort study


    Barrett, Aileen; Galvin, Rose; Steinert, Yvonne; Scherpbier, Albert; O’Shaughnessy, Ann; Walsh, Gillian; Horgan, Mary


    In 2010, workplace-based assessment (WBA) was formally integrated as a method of formative trainee assessment into 29 basic and higher specialist medical training (BST/HST) programmes in six postgraduate training bodies in Ireland. The aim of this study is to explore how WBA is being implemented and to examine if WBA is being used formatively as originally intended. A retrospective cohort study was conducted and approved by the institution’s Research Ethics Committee. A profile of WBA require...

  8. Synthesis, characterization, biological studies (DNA binding, cleavage, antibacterial and topoisomerase I) and molecular docking of copper(II) benzimidazole complexes. (United States)

    Arjmand, Farukh; Parveen, Shazia; Afzal, Mohd; Shahid, Mohd


    To explore the therapeutic potential of copper-based benzimidazole complexes, tetranuclear Cu(II) complex 1 and dinuclear ternary amino acid complexes 2 and 3 {L-trp and L-val, respectively} were synthesized and thoroughly characterized. In vitro DNA binding studies of complexes 1-3 were carried out employing UV-vis titrations, fluorescence, circular dichroic and viscosity measurements which revealed that the complexes 1-3 bind to CT DNA preferably via groove binding. Complex 1 cleaved pBR322 DNA via hydrolytic pathway (validated by T4 DNA ligase assay), accessible to major groove while 2 followed oxidative mechanism, binding to minor groove of DNA double helix; binding events were further validated by molecular docking studies. Additionally, the complexes 1 and 2 exhibit high Topo-I inhibitory activity at different concentrations. The complexes 1-3 were evaluated for antibacterial activity against Escherichia coli and Staphylococcus aureus, and 2 was found to be most effective against Gram-positive bacteria.

  9. Competitive binding of (-)-epigallocatechin-3-gallate and 5-fluorouracil to human serum albumin: A fluorescence and circular dichroism study (United States)

    Yuan, Lixia; Liu, Min; Liu, Guiqin; Li, Dacheng; Wang, Zhengping; Wang, Bingquan; Han, Jun; Zhang, Min


    Combination therapy with more than one therapeutic agent can improve therapeutic efficiency and decrease drug resistance. In this study, the interactions of human serum albumin (HSA) with individual or combined anticancer drugs, (-)-epigallocatechin-3-gallate (EGCG) and 5-fluorouracil (FU), were investigated by fluorescence and circular dichroism (CD) spectroscopy. The results demonstrated that the interaction of EGCG or FU with HSA is a process of static quenching and EGCG formed a more stable complex. The competitive experiments of site markers suggested that both anti-carcinogens mainly bound to site I (subdomain IIA). The interaction forces which play important roles in the binding process were discussed based on enthalpy and entropy changes. Moreover, the competition binding model for a ternary system was proposed so as to precisely calculate the binding parameters. The results demonstrated that one drug decreased the binding affinity of another drug with HSA, resulting in the increasing free drug concentration at the action sites. CD studies indicated that there was an alteration in HSA secondary structure due to the binding of EGCG and FU. It can be concluded that the combination of EGCG with FU may enhance anticancer efficacy. This finding may provide a theoretical basis for clinical treatments.

  10. Experimental and molecular modeling studies on the DNA-binding of diazacyclam-based acrocyclic copper complex. (United States)

    Shahabadi, Nahid; Hakimi, Mohammad; Morovati, Teimoor; Falsafi, Monireh; Fili, Soraya Moradi


    The interaction of a new macrocyclic copper complex, [CuL(NO3)2] in which L is 1,3,6,10,12,15-hexaaza tricyclo[,10)] eicosane was investigated in vitro under simulated physiological conditions by multi-spectroscopic techniques and molecular modeling study. The fluorescence spectroscopy and UV absorption spectroscopy indicated the complex interacted with ct-DNA in a groove binding mode while the binding constant of UV-vis and the number of binding sites were 1.0±0.2×10(4)Lmol(-1) and 1.01, respectively. The fluorometric studies showed that the reaction between the complex with ct-DNA is exothermic (ΔH=14.85kJmol(-1); ΔS=109.54Jmol(-1)K(-1)). Circular dichroism spectroscopy (CD) was employed to measure the conformational change of DNA in the presence of [CuL(NO3)2] complex. Furthermore, the complex induces detectable changes in the viscosity of DNA. The molecular modeling results illustrated that the complex strongly binds to groove of DNA. Experimental and molecular modeling results showed that Cu(II) complex bound to DNA by a groove binding mode.

  11. RNA targeting by small molecule alkaloids: Studies on the binding of berberine and palmatine to polyribonucleotides and comparison to ethidium (United States)

    Islam, Md. Maidul; Suresh Kumar, Gopinatha


    The binding affinity, energetics and conformational aspects of the interaction of isoquinoline alkaloids berberine and palmatine to four single stranded polyribonucleotides polyguanylic acid [poly(G)], polyinosinic acid [poly(I)], polycytidylic acid [poly(C)] and polyuridylic acid [poly(U)] were studied by absorption, fluorescence, isothermal titration calorimetry and circular dichroism spectroscopy and compared with ethidium. Berberine, palmatine and ethidium binds strongly with poly(G) and poly(I) with affinity in the order 10 5 M -1 while their binding to poly(C) and poly(U) were very weak or practically nil. The same conclusions have also emerged from isothermal titration calorimetric studies. The binding of all the three compounds to poly(C) and poly(I) was exothermic and favored by both negative enthalpy change and positive entropy change. Conformational change in the polymer associated with the binding was observed in poly(I) with all the three molecules and poly(U) with ethidium but not in poly(G) and poly(C) revealing differences in the orientation of the bound molecules in the hitherto different helical organization of these polymers. These fundamental results may be useful and serve as database for the development of futuristic RNA based small molecule therapeutics.

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

    DEFF Research Database (Denmark)

    Rehling, M


    [99mTc]DTPA has achieved widespread use for the measurement of glomerular filtration rate (GFR) with the single injection plasma clearance technique and for gamma-camera renography. However, the quality of the commercial preparations varies. The purpose of the present investigation was to study...... 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...

  13. Investigations on Binding Pattern of Kinase Inhibitors with PPARγ: Molecular Docking, Molecular Dynamic Simulations, and Free Energy Calculation Studies (United States)

    Mazumder, Mohit; Das, Umashankar; Gourinath, Samudrala


    Peroxisome proliferator-activated receptor gamma (PPARγ) is a potential target for the treatment of several disorders. In view of several FDA approved kinase inhibitors, in the current study, we have investigated the interaction of selected kinase inhibitors with PPARγ using computational modeling, docking, and molecular dynamics simulations (MDS). The docked conformations and MDS studies suggest that the selected KIs interact with PPARγ in the ligand binding domain (LBD) with high positive predictive values. Hence, we have for the first time shown the plausible binding of KIs in the PPARγ ligand binding site. The results obtained from these in silico investigations warrant further evaluation of kinase inhibitors as PPARγ ligands in vitro and in vivo.

  14. Study on the Binding Mode of a Co(Ⅱ) Complex with DNA

    Institute of Scientific and Technical Information of China (English)

    ZHOU Qing-Hua; YANG Pin


    The mode of binding of CoLCl2, here L=bis(2-benzimidazolylmethyl)amine, with calf thymus DNA has been investigated by fluorescence measurements, equilibrium dialysis, viscosity experiments and gel electrophoresis. The complex was found to bind but weakly to DNA, with binding constant of 1.96× 104 L/mol determind at 20 ℃ in a solution containing 5 mmol/L Tris-HCl (pH 7.1) and 50 mmol/L NaCl. Polyelectrolyte theory was applied to analyse these values. Viscosity experiments show that binding did not alter the relative viscosity of DNA with any complexes to an appreciable extent. Electrophoresis test displayed that the compound could not cleave the DNA.These results show that the complex is essentially electrostatically bound to DNA.

  15. Crystallization and preliminary structural studies of champedak galactose-binding lectin. (United States)

    Gabrielsen, Mads; Riboldi-Tunnicliffe, Alan; Abdul-Rahman, Puteri Shafinaz; Mohamed, Emida; Ibrahim, Wan Izlina Wan; Hashim, Onn Haji; Isaacs, Neil W; Cogdell, Richard J


    Galactose-binding lectin from champedak (Artocarpus integer) consists of two chains: alpha and beta (133 and 21 amino acids, respectively). It has been shown to recognize and bind to carbohydrates involved in IgA and C1 inhibitor molecules. The protein was purified and crystallized at 293 K. Crystals were observed in two space groups, P2(1) and P2(1)2(1)2, and diffracted to 1.65 and 2.6 A, respectively.

  16. Studies on the metabolism of chlorotrianisene to a reactive intermediate and subsequent covalent binding to microsomal proteins

    Energy Technology Data Exchange (ETDEWEB)

    Juedes, M.J.


    The studies on chlorotrianisene were conducted to determine whether metabolism of chlorotrianisene occurs via the cytochrome P450 monooxygenase system and whether a reactive intermediate is being formed that is capable of binding covalently to microsomal proteins. ({sup 3}H)-chlorotrianisene was incubated with liver microsomes supplemented with NADPH. At the termination of the incubation, the protein was trapped on a glass filter and the unbound chlorotrianisene was removed by extensive washing of the protein with organic solvent. A dramatic stimulation of covalent binding was demonstrated in microsomes from rats treated with methylcholanthrene (60 fold increase) versus control or phenobarbital treatment. Verification of covalent binding was achieved by localization of radiolabeled bands following sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) of the macromolecules in the incubation mixture. Further analysis of the radiolabeled macromolecules separated on SDS-PAGE revealed that these macromolecules were degraded by protease degradation indicating that the macromolecules were proteins. Further investigations were done to determine the cause of the dramatic stimulation of covalent binding detected in microsomes from methylcholanthrene treated rats versus control or phenobarbital treated rats. Further evidence for the participation of P-450c was obtained with a reconstituted cytochrome P-450 system. Incubations of chlorotrianisene with reconstituted P-450c and NADPH-cytochrome P-450 reductase exhibited covalent binding characteristics comparable to those seen in microsomal incubations. Investigations into the nature of the binding site and the reactive intermediate are currently being conducted. By analyzing the BSA adduct, the author intends to isolate the specific amino acid binding site(s).

  17. Computational Study of the Binding Mechanism of Actin-Depolymerizing Factor 1 with Actin in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Juan Du

    Full Text Available Actin is a highly conserved protein. It plays important roles in cellular function and exists either in the monomeric (G-actin or polymeric form (F-actin. Members of the actin-depolymerizing factor (ADF/cofilin protein family bind to both G-actin and F-actin and play vital roles in actin dynamics by manipulating the rates of filament polymerization and depolymerization. It has been reported that the S6D and R98A/K100A mutants of actin-depolymerizing factor 1 (ADF1 in Arabidopsis thaliana decreased the binding affinity of ADF for the actin monomer. To investigate the binding mechanism and dynamic behavior of the ADF1-actin complex, we constructed a homology model of the AtADF1-actin complex based on the crystal structure of AtADF1 and the twinfilin C-terminal ADF-H domain in a complex with a mouse actin monomer. The model was then refined for subsequent molecular dynamics simulations. Increased binding energy of the mutated system was observed using the Molecular Mechanics Generalized Born Surface Area and Poisson-Boltzmann Surface Area (MM-GB/PBSA methods. To determine the residues that make decisive contributions to the ADF1 actin-binding affinity, per-residue decomposition and computational alanine scanning analyses were performed, which provided more detailed information on the binding mechanism. Root-mean-square fluctuation and principal component analyses confirmed that the S6D and R98A/K100A mutants induced an increased conformational flexibility. The comprehensive molecular insight gained from this study is of great importance for understanding the binding mechanism of ADF1 and G-actin.

  18. Effects of ligand binding on the mechanical stability of protein GB1 studied by steered molecular dynamics simulation. (United States)

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


    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.

  19. Binding of thiocyanate to lactoperoxidase: 1H and 15N nuclear magnetic resonance studies

    Energy Technology Data Exchange (ETDEWEB)

    Modi, S.; Behere, D.V.; Mitra, S. (Tata Institute of Fundamental Research, Bombay (India))


    The binding of thiocyanate to lactoperoxidase (LPO) has been investigated by 1H and 15N NMR spectroscopy. 1H NMR of LPO shows that the major broad heme methyl proton resonance at about 61 ppm is shifted upfield by addition of the thiocyanate, indicating binding of the thiocyanate to the enzyme. The pH dependence of line width of 15N resonance of SC15N- in the presence of the enzyme has revealed that the binding of the thiocyanate to the enzyme is facilitated by protonation of an ionizable group (with pKa of 6.4), which is presumably distal histidine. Dissociation constants (KD) of SC15N-/LPO, SC15N-/LPO/I-, and SC15N-/LPO/CN- equilibria have been determined by 15N T1 measurements and found to be 90 +/- 5, 173 +/- 20, and 83 +/- 6 mM, respectively. On the basis of these values of KD, it is suggested that the iodide ion inhibits the binding of the thiocyanate but cyanide ion does not. The thiocyanate is shown to bind at the same site of LPO as iodide does, but the binding is considerably weaker and is away from the ferric ion. The distance of 15N of the bound thiocyanate ion from the iron is determined to be 7.2 +/- 0.2 A from the 15N T1 measurements.

  20. Synthesis and crystal structure elucidation of new copper(II)-based chemotherapeutic agent coupled with 1,2-DACH and orthovanillin: Validated by in vitro DNA/HSA binding profile and pBR322 cleavage pathway. (United States)

    Zaki, Mehvash; Afzal, Mohd; Ahmad, Musheer; Tabassum, Sartaj


    New copper(II)-based complex (1) was synthesized and characterized by analytical, spectroscopic and single crystal X-ray diffraction. The in vitro binding studies of complex 1 with CT DNA and HSA have been investigated by employing biophysical techniques to examine the binding propensity of 1 towards DNA and HSA. The results showed that 1 avidly binds to CT DNA via electrostatic mode along with the hydrogen bonding interaction of NH2 and CN groups of Schiff base ligand with the base pairs of DNA helix, leads to partial unwinding and destabilization of the DNA double helix. Moreover, the CD spectral studies revealed that complex 1 binds through groove binding interaction that stabilizes the right-handed B-form of DNA. Complex 1 showed an impressive photoinduced nuclease activity generating single-strand breaks in comparison with the DNA cleavage activity in presence of visible light. The mechanistic investigation revealed the efficiency of 1 to cleave DNA strands by involving the generation of reactive oxygen species. Furthermore, the time dependent DNA cleavage activity showed that there was gradual increase in the amount of NC DNA on increasing the photoexposure time. However, the interaction of 1 and HSA showed that the change of intrinsic fluorescence intensity of HSA was induced by the microenvironment of Trp residue.

  1. A Study of Air/Space-borne Dual-Wavelength Radar for Estimation of Rain Profiles

    Institute of Scientific and Technical Information of China (English)


    In this study, a framework is given by which air/space-borne dual-wavelength radar data can be used to estimate the characteristic parameters of hydrometeors. The focus of the study is on the Global Precipitation Measurement (GPM) precipitation radar, a dual-wavelength radar that will operate in the Ku (13.6 GHz) and Ka (35 GHz) bands. A key aspect of the retrievals is the relationship between the differential frequency ratio (DFR) and the median volume diameter, Do, and its dependence on the phase state of the hydrometeors. It is shown that parametric plots of Do and particle concentration in the plane of the DFR and the radar reflectivity factor in the Ku band can be used to reduce the ambiguities in deriving Do from DFR. A self-consistent iterative algorithm, which does not require the use of an independent pathattenuation constraint, is examined by applying it to the apparent radar reflectivity profiles simulated from a drop size distribution (DSD) model. For light to moderate rain, the self-consistent rain profiling approach converges to the correct solution only if the same shape factor of the Gamma distributions is used both to generate and retrieve the rain profiles. On the other hand, if the shape factors differ, the iteration generally converges but not to the correct solution. To further examine the dual-wavelength techniques, the selfconsistent iterative algorithm, along with forward and backward rain profiling algorithms, are applied to measurements taken from the 2nd generation Precipitation Radar (PR-2) built by the Jet Propulsion Laboratory. Consistent with the model results, it is found that the estimated rain profiles are sensitive to the shape factor of the size distribution when the iterative, self-consistent approach is used but relatively insensitive to this parameter when the forward- and backward-constrained approaches are used.

  2. Profile of Nigerians with diabetes mellitus - Diabcare Nigeria study group (2008: Results of a multicenter study

    Directory of Open Access Journals (Sweden)

    Sunday Chinenye


    Full Text Available Background: Diabetes Mellitus is the commonest endocrine-metabolic disorder in Nigeria similar to the experience in other parts of the world. The aim was to assess the clinical and laboratory profile, and evaluate the quality of care of Nigerian diabetics with a view to planning improved diabetes care. Materials and Methods: In a multicenter study across seven tertiary health centers in Nigeria, the clinical and laboratory parameters of diabetic out-patients were evaluated. Clinical parameters studied include type of diabetes, anthropometry, and blood pressure (BP status, chronic complications of diabetes, and treatment types. Laboratory data assessed included fasting plasma glucose (FPG, 2-h post-prandial (2-HrPP glucose, glycated hemoglobin (HbA1c, urinalysis, serum lipids, electrolytes, urea, and creatinine. Results: A total of 531 patients, 209 (39.4% males and 322 (60.6% females enrolled. The mean age of the patients was 57.1 ± 12.3 years with the mean duration of diabetes of 8.8 ± 6.6 years. Majority (95.4% had type 2 diabetes mellitus (DM compared to type 1 DM (4.6%, with P < 0.001. The mean FPG, 2-HrPP glucose, and HbA1c were 8.1 ± 3.9 mmol/L, 10.6 ± 4.6 mmol/L, and 8.3 ± 2.2%, respectively. Only 170 (32.4% and 100 (20.4% patients achieved the ADA and IDF glycemic targets, respectively. Most patients (72.8% did not practice self-monitoring of blood glucose. Hypertension was found in 322 (60.9%, with mean systolic BP 142.0 ± 23.7 mmHg, and mean diastolic BP 80.7 ± 12.7 mmHg. Diabetic complications found were peripheral neuropathy (59.2%, retinopathy (35.5%, cataracts (25.2%, cerebrovascular disease (4.7%, diabetic foot ulcers (16.0%, and nephropathy (3.2%. Conclusion: Most Nigerian diabetics have suboptimal glycemic control, are hypertensives, and have chronic complications of DM. Improved quality of care and treatment to target is recommended to reduce diabetes-related morbidity and mortality.

  3. DNA-binding specificities of human transcription factors. (United States)

    Jolma, Arttu; Yan, Jian; Whitington, Thomas; Toivonen, Jarkko; Nitta, Kazuhiro R; Rastas, Pasi; Morgunova, Ekaterina; Enge, Martin; Taipale, Mikko; Wei, Gonghong; Palin, Kimmo; Vaquerizas, Juan M; Vincentelli, Renaud; Luscombe, Nicholas M; Hughes, Timothy R; Lemaire, Patrick; Ukkonen, Esko; Kivioja, Teemu; Taipale, Jussi


    Although the proteins that read the gene regulatory code, transcription factors (TFs), have been largely identified, it is not well known which sequences TFs can recognize. We have analyzed the sequence-specific binding of human TFs using high-throughput SELEX and ChIP sequencing. A total of 830 binding profiles were obtained, describing 239 distinctly different binding specificities. The models represent the majority of human TFs, approximately doubling the coverage compared to existing systematic studies. Our results reveal additional specificity determinants for a large number of factors for which a partial specificity was known, including a commonly observed A- or T-rich stretch that flanks the core motifs. Global analysis of the data revealed that homodimer orientation and spacing preferences, and base-stacking interactions, have a larger role in TF-DNA binding than previously appreciated. We further describe a binding model incorporating these features that is required to understand binding of TFs to DNA.

  4. Quercetin-Iron Complex: Synthesis, Characterization, Antioxidant, DNA Binding, DNA Cleavage, and Antibacterial Activity Studies. (United States)

    Raza, Aun; Xu, Xiuquan; Xia, Li; Xia, Changkun; Tang, Jian; Ouyang, Zhen


    Quercetin-iron (II) complex was synthesized and characterized by elemental analysis, ultraviolet-visible spectrophotometry, fourier transform infrared spectroscopy, mass spectrometry, proton nuclear magnetic resonance spectroscopy, thermogravimetry and differential scanning calorimetry, scanning electron micrography and molar conductivity. The low molar conductivity value investigates the non-electrolyte nature of the complex. The elemental analysis and other physical and spectroscopic methods reveal the 1:2 stoichiometric ratio (metal:ligand) of the complex. Antioxidant study of the quercetin and its metal complex against 2, 2-di-phenyl-1-picryl hydrazyl radical showed that the complex has much more radical scavenging activity than free quercetin. The interaction of quercetin-iron (II) complex with DNA was determined using ultraviolet visible spectra, fluorescence spectra and agarose gel electrophoresis. The results showed that quercetin-iron (II) complex can intercalate moderately with DNA, quench a strong intercalator ethidium bromide and compete for the intercalative binding sites. The complex showed significant cleavage of pBR 322 DNA from supercoiled form to nicked circular form and these cleavage effects were dose-dependent. Moreover, the mechanism of DNA cleavage indicated that it was an oxidative cleavage pathway. These results revealed the potential nuclease activity of complex to cleave DNA. In addition, antibacterial activity of complex on E.coli and S. aureus was also investigated. The results showed that complex has higher antibacterial activity than ligand.

  5. Can DNA-binding proteins of replisome tautomerize nucleotide bases? Ab initio model study. (United States)

    Brovarets', Ol'ha O; Yurenko, Yevgen P; Dubey, Igor Ya; Hovorun, Dmytro M


    Ab initio quantum-chemical study of specific point contacts of replisome proteins with DNA modeled by acetic acid with canonical and mutagenic tautomers of DNA bases methylated at the glycosidic nitrogen atoms was performed in vacuo and continuum with a low dielectric constant (ϵ ∼ 4) corresponding to a hydrophobic interface of protein-nucleic acid interaction. All tautomerized complexes were found to be dynamically unstable, because the electronic energies of their back-reaction barriers do not exceed zero-point vibrational energies associated with the vibrational modes whose harmonic vibrational frequencies become imaginary in the transition states of the tautomerization reaction. Additionally, based on the physicochemical arguments, it was demonstrated that the effects of biomolecular environment cannot ensure dynamic stabilization. This result allows suggesting that hypothetically generated by DNA-binding proteins of replisome rare tautomers will have no impact on the total spontaneous mutation due to the low reverse barrier allowing a quick return to the canonical form.

  6. Studies of Fe-binding sites within multiwall carbon nanotubes using Moessbauer spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Luberda-Durnas, Katarzyna; Nieznalska, Magdalena; Matlak, Krzysztof; Korecki, Jozef; Burda, Kvetoslava [Faculty of Physics and Applied Computer Science, AGH - University of Science and Technology, Krakow (Poland); Mazurkiewicz, Marta; Malolepszy, Artur [Faculty of Material Science and Engineering, Warsaw University of Technology, Warsaw (Poland); Khachataryan, Gohar; Khachataryan, Karen; Tomasik, Piotr; Michalski, Oskar [Department of Chemistry, Agricultural University, Krakow (Poland); Stobinski, Leszek [Faculty of Material Science and Engineering, Warsaw University of Technology, Warsaw (Poland); Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw (Poland)


    The potential applications of carbon nanotubes (CNTs) are strongly related to their physical and chemical properties. In this work, results of different methods for the oxidation of crude CNTs are reported. These methods changed Fe binding sites within multiwall carbon nanotubes (MWCNTs). Moessbauer spectroscopy was used to detect the chemical properties of the Fe-phases in MWCNTs. Signals from the iron carbide Fe{sub 3}C were the main components in the Moessbauer spectra of unmodified MWCNTs revealing magnetic ordering even at 300 K. In oxidized MWCNTs, the amount of Fe{sub 3}C decreased and {gamma}-Fe and {alpha}-Fe, ferrihydrates of iron oxides and different forms of goethite appeared. In MWCNTs oxidized with HClO{sub 4}, a significant fraction ({proportional_to}24%) of magnetically ordered Fe{sub 2}O{sub 3} particles was detected. This study showed that traces of iron catalyst embedded in MWCNTs could be used as a sensitive probe to monitor various MWCNT modifications. (Copyright copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  7. Molecular level studies on binding modes of labeling molecules with polyalanine peptides (United States)

    Mao, Xiaobo; Wang, Chenxuan; Ma, Xiaojing; Zhang, Min; Liu, Lei; Zhang, Lan; Niu, Lin; Zeng, Qindao; Yang, Yanlian; Wang, Chen


    In this work, the binding modes of typical labeling molecules (thioflavin T (ThT), Congo red (CR) and copper(ii) phthalocyanine tetrasulfonic acid tetrasodium salt (PcCu(SO3Na)4)) on pentaalanine, which is a model peptide segment of amyloidpeptides, have been resolved at the molecular level by using scanning tunneling microscopy (STM). In the STM images, ThT molecules are predominantly adsorbed parallel to the peptide strands and two binding modes could be identified. It was found that ThT molecules are preferentially binding on top of the peptide strand, and the mode of intercalated between neighboring peptides also exists. The parallel binding mode of CR molecules can be observed with pentaalaninepeptides. Besides the binding modes of labeling molecules, the CR and PcCu(SO3Na)4 display different adsorption affinity with the pentaalaninepeptides. The results could be beneficial for obtaining molecular level insight of the interactions between labeling molecules and peptides.In this work, the binding modes of typical labeling molecules (thioflavin T (ThT), Congo red (CR) and copper(ii) phthalocyanine tetrasulfonic acid tetrasodium salt (PcCu(SO3Na)4)) on pentaalanine, which is a model peptide segment of amyloidpeptides, have been resolved at the molecular level by using scanning tunneling microscopy (STM). In the STM images, ThT molecules are predominantly adsorbed parallel to the peptide strands and two binding modes could be identified. It was found that ThT molecules are preferentially binding on top of the peptide strand, and the mode of intercalated between neighboring peptides also exists. The parallel binding mode of CR molecules can be observed with pentaalaninepeptides. Besides the binding modes of labeling molecules, the CR and PcCu(SO3Na)4 display different adsorption affinity with the pentaalaninepeptides. The results could be beneficial for obtaining molecular level insight of the interactions between labeling molecules and peptides. Electronic

  8. Measurement of serotonin transporter binding with PET and [11C]MADAM: a test-retest reproducibility study. (United States)

    Lundberg, Johan; Halldin, Christer; Farde, Lars


    [(11)C]MADAM, or [(11)C]N,N-dimethyl-2-(2-amino-4-methylphenyl thio)benzylamine, is a radioligand suitable for positron emission tomography (PET) studies of the serotonin transporter (5-HTT) in man. The purpose of this study was to examine the test-retest reproducibility using a design tailored for future applied studies. Nine healthy male subjects were examined with PET and [(11)C]MADAM under baseline conditions at two occasions 4-8 weeks apart. The subjects participated in a Phase 1 trial to which the present study was an addendum. Eight regions of interest were studied, including frontal cortex, hippocampal complex, and the raphe nuclei. All regions, but the raphe nuclei, were defined on MR-images to which the PET-images were coregistered using SPM2. Binding potentials were calculated using the simplified reference tissue model, with cerebellum as reference region. Test-retest data were calculated from the binding potentials, and included binding potential (BP) quotient, BP difference, and the intraclass correlation coefficient. The quotient was about one in all regions, and the mean difference varied between 0 and 11%. The intraclass correlation coefficient varied between 0.96 and 0.51 in the raphe nuclei and averaged bilateral regions. [(11)C]MADAM was shown to have good to excellent reliability in measurements of 5-HTT binding in brain regions of interest in research on psychiatric disorders.

  9. A structure-activity-relationship (SAR) study of somatostatin receptor-binding peptides radiolabeled with Tc-99m

    Energy Technology Data Exchange (ETDEWEB)

    Lister-James, J.; McBride, W.J.; Moyer, B.R. [Diatech, Inc, Londonderry, NH (United States)] [and others


    Somatostatin receptor (SSTR)-expressing tumors can be detected with high accuracy using In-111-[DTPA]octreotide. We sought a high-affinity SSTR-binding peptide labeled with the preferred radioisotope Tc-99m. We have prepared over 120 SSTR-binding peptides each containing a (N{sub 3}S or N{sub 2}S{sub 2}) chelator for Tc-99m in a SAR study in which peptide structure was systematically altered to optimize SSTR-binding affinity, in vivo rumor uptake and favorable biodistribution and pharmacokinetics. The HPLC-purified (>90% purity), chelator-containing peptides were characterized by FAB/ESMS and assayed in vitro for SSTR binding affinity by a competition assay (I-125 somatostatin-14 tracer and AR42J rat pancreatic tumor cell membranes). The oxo-rhenium complexes of the peptides were prepared by ligand exchange, characterized by FAB or ESMS and assayed for SSTR binding affinity as surrogates for the Tc-99m complexes. The Tc-99m complexes of peptides giving high-affinity oxo-rhenium complexes were also prepared by ligand exchange with specific activities of approx 300 mCi/mmol and examined in vivo for biodistribution and tumor uptake characteristics in CA20948 tumor-bearing rats.

  10. Leadership development study :success profile competencies and high-performing leaders at Sandia National Laboratories.

    Energy Technology Data Exchange (ETDEWEB)

    Becker, Katherine M.; Mulligan, Deborah Rae; Szenasi, Gail L.; Crowder, Stephen Vernon


    Sandia is undergoing tremendous change. Sandia's executive management recognized the need for leadership development. About ten years ago the Business, Leadership, and Management Development department in partnership with executive management developed and implemented the organizational leadership Success Profile Competencies to help address some of the changes on the horizon such as workforce losses and lack of a skill set in the area of interpersonal skills. This study addresses the need for the Business, Leadership, and Management Development department to provide statistically sound data in two areas. One is to demonstrate that the organizational 360-degree success profile assessment tool has made a difference for leaders. A second area is to demonstrate the presence of high performing leaders at the Labs. The study utilized two tools to address these two areas. Study participants were made up of individuals who have solid data on Sandia's 360-degree success profile assessment tool. The second assessment tool was comprised of those leaders who participated in the Lockheed Martin Corporation Employee Preferences Survey. Statistical data supports the connection between leader indicators and the 360-degree assessment tool. The study also indicates the presence of high performing leaders at Sandia.

  11. Association of Helicobacter pylori infection with lipid profiles: The Persian Gulf Healthy Heart Study

    Directory of Open Access Journals (Sweden)

    Hussain Darabi


    Full Text Available Background: Helicobacter pylori (H.pylori infection may contribute to the development of extra-gastrointestinal manifestations like cardiovascular diseases. Detection of Helicobacter pylori in Athrosclerotic plaques is a strong evidence for this association which may play a role in pathogenesis of atherosclerosis with classic cardiovascular risk factor such as hypertension and lipid profile. The aim of this study was to explore the influence of H. pylori infection on lipid profiles in a large community- based study. Material and Methods: A total of 1754 (50.8% Female & 49.2% male subjects (age >25 years old were selected randomely from Monica Healthy Heart Study project. H. pylori status was determined by IgG ELISA method. Subjects with titers > 30 Iu/ml were cansidered seropositive. Data were analazed by using statistical software Spss version 18 and probability values 0.05 Conclusion: According to this large – scale population- based study in large northern cities of Persian Gulf, there was no significant association between H.pylori IgG seropositivity and lipid profiles in both men and women.

  12. Species-dependent stereoselective drug binding to albumin: a circular dichroism study. (United States)

    Pistolozzi, Marco; Bertucci, Carlo


    Drug binding to albumins from different mammalian species was investigated to disclose evidence of species-dependent stereoselectivity in drug-binding processes and affinities. This aspect is important for evaluating the reliability of extrapolating distribution data among species. The circular dichroism (CD) signal induced by drug binding to the albumins [human serum albumin (HSA), bovine serum albumin (BSA), rat serum albumin (RSA), and dog serum albumin (DSA)] were measured and analyzed. The binding of selected drugs and metabolites to HSA significantly differed from the binding to the other albumins in terms of affinity and conformation of the bound ligands. In particular, phenylbutazone, a marker of site one on HSA, showed a higher affinity for binding to BSA with respect to RSA, HSA, and DSA, respectively. In the case of diazepam, a marker of site two on HSA, the affinity decreased in order from HSA to DSA, RSA, and BSA. The induced CD spectra were similar in terms of energy and band signs, suggesting almost the same conformation for the bound drug to the different albumins. Stereoselectivity was high for the binding of ketoprofen to HSA and RSA. A different sign was observed for the CD spectra induced by the drug to the two albumins because of the prevalence of a different conformation of the bound drug. Interestingly, the same induced CD spectra were obtained using either the racemic form or the (S)-enantiomer. Finally, significant differences were observed in the affinity of bilirubin, being highest for BSA, then decreasing for RSA, HSA, and DSA. A more complex conformational equilibrium was observed for bound bilirubin.

  13. Docking Studies of Binding of Ethambutol to the C-Terminal Domain of the Arabinosyltransferase from Mycobacterium tuberculosis

    Directory of Open Access Journals (Sweden)

    Guillermo Salgado-Moran


    Full Text Available The binding of ethambutol to the C-terminal domain of the arabinosyltransferase from Mycobacterium tuberculosis was studied. The analysis was performed using an in silico approach in order to find out, by docking calculations and energy descriptors, the conformer of Ethambutol that forms the most stable complex with the C-terminal domain of arabinosyltransferase. The complex shows that location of the Ethambutol coincides with the cocrystallization ligand position and that amino acid residues ASH1051, ASN740, ASP1052, and ARG1055 should be critical in the binding of Ethambutol to C-terminal domain EmbC.

  14. Application of a simple calorimetric data analysis on the binding study of cyanide ions by Jack bean urease

    Institute of Scientific and Technical Information of China (English)

    G.Rezaei; Behbehani; A.A.Saboury; M.Mohebbian; S.Ghammamy


    Cyanide ion was studied as an effector of Jack bean urease(JBU) at 300 K in 30 mmol/LTris buffer,pH 7 by isothermal titration calorimetry(ITC).The simple novel model was used for CN~- + JBU interaction over the whole range of CN~- concentrations.The binding parameters recovered from the simple novel model were attributed to the cyanide ion interaction.It was found that cyanide ion acted as a noncooperative inhibitor of JBU,and there is a set of 12 identical and independent binding sites for CN~- ions.The...

  15. Structural and functional studies of a large winged Z-DNA-binding domain of Danio rerio protein kinase PKZ. (United States)

    Subramani, Vinod Kumar; Kim, Doyoun; Yun, Kyunghee; Kim, Kyeong Kyu


    The Z-DNA-binding domain of PKZ from zebrafish (Danio rerio; drZαPKZ ) contains the largest β-wing among known Z-DNA-binding domains. To elucidate the functional implication of the β-wing, we solved the crystal structure of apo-drZαPKZ . Structural comparison with its Z-DNA-bound form revealed a large conformational change within the β-wing during Z-DNA binding. Biochemical studies of protein mutants revealed that two basic residues in the β-wing are responsible for Z-DNA recognition as well as fast B-Z transition. Therefore, the extra basic residues in the β-wing of drZαPKZ are necessary for the fast B-Z transition activity.

  16. Organometallic B12-DNA conjugate: synthesis, structure analysis, and studies of binding to human B12-transporter proteins. (United States)

    Hunger, Miriam; Mutti, Elena; Rieder, Alexander; Enders, Barbara; Nexo, Ebba; Kräutler, Bernhard


    Design, synthesis, and structural characterization of a B12-octadecanucleotide are presented herein, a new organometallic B12-DNA conjugate. In such covalent conjugates, the natural B12 moiety may be a versatile vector for controlled in vivo delivery of oligonucleotides to cellular targets in humans and animals, through the endogenous B12 transport systems. Binding of the organometallic B12 octadecanucleotide to the three important human proteins of B12 transport was studied, to examine its structural suitability for the task of eventual in vivo oligonucleotide delivery. Binding was efficient with transcobalamin (TC), but not so efficient with the homologous glycoproteins intrinsic factor and haptocorrin. Binding of the B12 octadecanucleotide to TC suggests the capacity of the B12 moiety to serve as a natural vector for specific transport of single stranded, organometallic oligonucleotide loads from the blood stream into cells.

  17. A study to measure the impact of implementation of 5-S on pipe and profile: A case study of a pipe and profile maker

    Directory of Open Access Journals (Sweden)

    Hamidreza Karkehabadi


    Full Text Available Productivity improvement plays essential role on cost reduction and production planning in many organizations. There are literally various methods for measuring productivity and improving systems’ capabilities such as total quality management, 5S, etc. In this paper, we perform an empirical investigation to find out whether implementing 5S could reduce interruptions in production systems in one of pipe and profile manufacturing units located in province of Semnan, Iran. The proposed study compares the mean and standard deviations of waste materials before and after the implementation of 5-S in three different lines and statistical tests indicate that 5-S have made the necessary change on production planning and it could reduce waste materials, significantly.

  18. Molecular modeling study on the allosteric inhibition mechanism of HIV-1 integrase by LEDGF/p75 binding site inhibitors.

    Directory of Open Access Journals (Sweden)

    Weiwei Xue

    Full Text Available HIV-1 integrase (IN is essential for the integration of viral DNA into the host genome and an attractive therapeutic target for developing antiretroviral inhibitors. LEDGINs are a class of allosteric inhibitors targeting LEDGF/p75 binding site of HIV-1 IN. Yet, the detailed binding mode and allosteric inhibition mechanism of LEDGINs to HIV-1 IN is only partially understood, which hinders the structure-based design of more potent anti-HIV agents. A molecular modeling study combining molecular docking, molecular dynamics simulation, and binding free energy calculation were performed to investigate the interaction details of HIV-1 IN catalytic core domain (CCD with two recently discovered LEDGINs BI-1001 and CX14442, as well as the LEDGF/p75 protein. Simulation results demonstrated the hydrophobic domain of BI-1001 and CX14442 engages one subunit of HIV-1 IN CCD dimer through hydrophobic interactions, and the hydrophilic group forms hydrogen bonds with HIV-1 IN CCD residues from other subunit. CX14442 has a larger tert-butyl group than the methyl of BI-1001, and forms better interactions with the highly hydrophobic binding pocket of HIV-1 IN CCD dimer interface, which can explain the stronger affinity of CX14442 than BI-1001. Analysis of the binding mode of LEDGF/p75 with HIV-1 IN CCD reveals that the LEDGF/p75 integrase binding domain residues Ile365, Asp366, Phe406 and Val408 have significant contributions to the binding of the LEDGF/p75 to HIV1-IN. Remarkably, we found that binding of BI-1001 and CX14442 to HIV-1 IN CCD induced the structural rearrangements of the 140 s loop and oration displacements of the side chains of the three conserved catalytic residues Asp64, Asp116, and Glu152 located at the active site. These results we obtained will be valuable not only for understanding the allosteric inhibition mechanism of LEDGINs but also for the rational design of allosteric inhibitors of HIV-1 IN targeting LEDGF/p75 binding site.

  19. Criminal Profiles of Violent Juvenile Sex and Violent Juvenile Non-Sex Offenders: An Explorative Longitudinal Study (United States)

    van Wijk, Anton Ph.; Mali, Bas R. F.; Bullens, Ruud A. R.; Vermeiren, Robert R.


    Few studies have longitudinally investigated the criminal profiles of violent juvenile sex and violent juvenile non-sex offenders. To make up for this lack, this study used police records of juveniles to determine the nature of the criminal profiles of violent sex offenders (n = 226) and violent non-sex offenders (n = 4,130). All offenders…

  20. [[superscript 3]H]-Flunitrazepam-Labeled Benzodiazepine Binding Sites in the Hippocampal Formation in Autism: A Multiple Concentration Autoradiographic Study (United States)

    Guptill, Jeffrey T.; Booker, Anne B.; Gibbs, Terrell T.; Kemper, Thomas L.; Bauman, Margaret L.; Blatt, Gene J.


    Increasing evidence indicates that the GABAergic system in cerebellar and limbic structures is affected in autism. We extended our previous study that found reduced [[superscript 3]H] flunitrazepam-labeled benzodiazepine sites in the autistic hippocampus to determine whether this reduction was due to a decrease in binding site number (B [subscript…

  1. Metal-ligand binding affinity vs reactivity: qualitative studies in Rh(I)-catalyzed asymmetric ring-opening reactions. (United States)

    Tsui, Gavin Chit; Dougan, Patrick; Lautens, Mark


    Rh(I)-catalyzed asymmetric ring opening (ARO) of oxabenzonorbornadiene is used as a model system to qualitatively study reactions involving multiple metal-ligand interactions. The key feature of this approach is the use of product ee as an indicator to quickly gain important information such as the relative ligand binding affinity and relative reactivity of catalysts.

  2. Quantum Monte Carlo study of the cooperative binding of NO2 to fragment models of carbon nanotubes

    NARCIS (Netherlands)

    Lawson, John W.; Bauschlicher Jr., Charles W.; Toulouse, Julien; Filippi, Claudia; Umrigar, C.J.


    Previous calculations on model systems for the cooperative binding of two NO2 molecules to carbon nanotubes using density functional theory and second order Moller–Plesset perturbation theory gave results differing by 30 kcal/mol. Quantum Monte Carlo calculations are performed to study the role of e

  3. Proton magnetic resonance studies on peptide fragments of troponin-C containing single calcium-binding sites. (United States)

    Leavis, P C; Evans, J S; Levine, B A


    Proton magnetic resonance spectroscopy has been employed to study the solution conformation of three cleavage fragments of troponin-C, each containing a single Ca(II)-binding site and corresponding to different regions in the primary sequence; viz. CB8 (residues 46-77), CB9 (residues 85-134) and TH2 (residues 121-159). Although all three peptides lack a well-defined tertiary fold in the absence of metal ions, several spectral features indicate the presence of local conformational constraints in each apo-peptide. Ca(II) binding led to spectral changes consistent with increased restriction of backbone motility and the adoption of a more compact conformation. Studies using paramagnetic ions as conformational probes support current views concerning the nature of the ligands at the metal binding sites. The nature and kinetics of the structural influence of metal binding suggest that the conformational constraints existing in the CB8 apo-peptide provide an adequate Ca(II)-binding configuration. In contrast, the CB9 and TH2 peptides exhibit spectral changes consistent with an increased local structure in the region of helix E (residues 94-102) in the case of CB9 and helix H (residues 148-159) in the case of TH2. In CB9, conformation changes also appear to be transmitted to a portion of the sequence (residues 87-93) preceding helix E, a putative site of interaction between troponin-C and troponin-I. These data are discussed with reference to the contribution of long-range (interdomain) interactions within troponin-C and the modulation of troponin subunit protein-protein interactions by Ca(II) binding.

  4. Spectroscopic study of interaction between osthole and human serum albumin: Identification of possible binding site of the compound

    Energy Technology Data Exchange (ETDEWEB)

    Bijari, Nooshin [Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Shokoohinia, Yalda [Department of Pharmacognosy and Biotechnology, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Ashrafi-Kooshk, Mohammad Reza; Ranjbar, Samira; Parvaneh, Shahram [Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Moieni-Arya, Maryam [Student Research Committee, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Khodarahmi, Reza, E-mail: [Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Department of Pharmacognosy and Biotechnology, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of)


    The studies on the interaction between human serum albumin (HSA) and drugs have been an interesting research field in life science, chemistry and clinical medicine. Osthole possesses a variety of pharmacological activities including anti-tumor, anti-inflammation, anti-seizure, anti-hyperlipidemic and anti-osteoporosis effects. The interaction of osthole with HSA and its binding site in HSA by spectroscopic methods is the subject of this work. By monitoring the intrinsic fluorescence of the single Trp{sub 214} residue and performing site markers displacement measurements, the specific binding of osthole in the vicinity of Sudlow's site I of HSA has been clarified. The changes in the secondary structure of HSA after its complexation with ligand were studied with CD spectroscopy, which indicate that osthole induced only a slight decrease in the helix structural content of the protein. In addition, the mean distance between osthole and HSA fluorophores is estimated to be 4.96 nm using Föster's equation on the basis of the fluorescence energy transfer. Furthermore, the synchronous fluorescence spectra show that the microenvironment of the tryptophan residues does not have obvious changes. Osthole can quench the intrinsic fluorescence of HSA by dynamic quenching, and analysis of the thermodynamic parameters of binding showed that hydrophobic interactions play an important role in the stabilizing of the complex. Increase of protein surface hydrophobicity (PSH) was also observed upon the osthole binding. -- Highlights: • Hydrophobic interactions play an important role in osthole–HSA interaction. • Sudlow's I site is possible binding site of osthole. • Osthole inhibits esterase activity of HSA. • Osthole binding induces no gross protein structural changes.

  5. How different an emotional competence profile can be, when we became slim? – longitudinal case study


    Veiga-Branco, Augusta


    This case study focuses on Emotional Competence (Saarni, 2000; Veiga Branco, 2004, 2007), the concept redefined from the initial Emotional Intelligence (Mayer-Salovey, 1990, 1997, Goleman, 1995), here applied, to perceive the behavioral differences when someone lost 43Kg of body weight, without pathology associated. The longitudinal research compares, the behavior profile, before (obese) and after (non obese) a weight loss, through Self-conscience, Self-motivation, Emotions ...

  6. A study of the Lyman-$\\alpha$ line profile in DBA white dwarfs

    CERN Document Server

    Genest-Beaulieu, C


    The hydrogen abundances in DBA white dwarfs determined from optical or UV spectra have been reported to differ significantly in some studies. We revisit this problem using our own model atmospheres and synthetic spectra, and present a theoretical investigation of the Lyman-$\\alpha$ line profile as a function of effective temperature and hydrogen abundance. We identify one possible solution to this discrepancy and show considerable improvement from a detailed analysis of optical and UV spectra of DBA stars.

  7. Theoretical studies on the binding energy of β-sheet models

    Institute of Scientific and Technical Information of China (English)


    In this paper,B3LYP and MP2 methods are used to investigate the binding energy of seventeen antiparallel and parallel β-sheet models. The results indicate that the binding energy obtained from B3LYP calculations is weaker than that obtained from MP2 calculations but the relative binding energy yielded by B3LYP is almost the same as that by MP2. For the antiparallel β-sheets in which two N―H···O═C hydrogen bonds can form either a large hydrogen-bonded ring or a small hydrogen-bonded ring,the binding energy increases obviously when one large ring unit is added,whereas it only changes slightly when one small ring unit is added because of the secondary electrostatic repulsive interaction existing in the small ring unit which is estimated to be about 20 kJ/mol. For the parallel β-sheet models,the binding energy increases almost exactly linearly with the increase of the chain length.

  8. Binding of Ru(terpyridine)(pyridine)dipyridophenazine to DNA studied with polarized spectroscopy and calorimetry. (United States)

    Mårtensson, Anna K F; Lincoln, Per


    Linear and circular dichroism (LD and CD) spectroscopy as well as isothermal titration calorimetry (ITC) have been used to investigate the interaction of Ru(tpy)(py)dppz(2+) (tpy = 2,2':6',2''-terpyridyl; py = pyridine; dppz = dipyrido[3,2-a:2'3'-c]phenazine) with DNA, providing detailed information about the DNA binding thermodynamics and binding geometry of the metal complex. Flow LD, CD and isotropic absorption indicate that Ru(tpy)(py)dppz(2+) bind to DNA from the minor groove with the dppz ligand intercalated between base pairs, very similar to its chiral structural isomers Δ- and Λ-Ru(bpy)2dppz(2+) (bpy = 2,2'-bipyridine). A simple cooperative binding model with one binding geometry provide an excellent fit for calorimetric and absorption titration data. The values of the neighbor interaction thermodynamic parameters for Ru(tpy)(py)dppz(2+) suggest that complexes bound contiguously prefer to have their tpy ligands oriented towards the same strand.

  9. Decreased benzodiazepine receptor binding in epileptic El mice: A quantitative autoradiographic study

    Energy Technology Data Exchange (ETDEWEB)

    Shirasaka, Y.; Ito, M.; Tsuda, H.; Shiraishi, H.; Oguro, K.; Mutoh, K.; Mikawa, H. (Kyoto Univ. (Japan))


    Benzodiazepine receptors and subtypes were examined in El mice and normal ddY mice with a quantitative autoradiographic technique. Specific (3H)flunitrazepam binding in stimulated El mice, which had experienced repeated convulsions, was significantly lower in the cortex and hippocampus than in ddY mice and unstimulated El mice. In the amygdala, specific ({sup 3}H)flunitrazepam binding in stimulated El mice was lower than in ddY mice. There was a tendency for the ({sup 3}H)flunitrazepam binding in these regions in unstimulated El mice to be intermediate between that in stimulated El mice and that in ddY mice, but there was no significant difference between unstimulated El mice and ddY mice. ({sup 3}H)Flunitrazepam binding displaced by CL218,872 was significantly lower in the cortex of stimulated El mice than in that of the other two groups, and in the hippocampus of stimulated than of unstimulated El mice. These data suggest that the decrease in ({sup 3}H)flunitrazepam binding in stimulated El mice may be due mainly to that of type 1 receptor and may be the result of repeated convulsions.

  10. Curcumin effects on blood lipid profile in a 6-month human study. (United States)

    Baum, Larry; Cheung, Stanley K K; Mok, Vincent C T; Lam, Linda C W; Leung, Vivian P Y; Hui, Elsie; Ng, Chelsia C Y; Chow, Moses; Ho, Ping C; Lam, Sherry; Woo, Jean; Chiu, Helen F K; Goggins, William; Zee, Benny; Wong, Adrian; Mok, Hazel; Cheng, William K F; Fong, Carmen; Lee, Jenny S W; Chan, Ming-Houng; Szeto, Samuel S L; Lui, Victor W C; Tsoh, Joshua; Kwok, Timothy C Y; Chan, Iris H S; Lam, Christopher W K


    Studies in animals and a short-term human study have suggested that curcumin, a polyphenolic compound concentrated in the curry spice turmeric, decreases serum cholesterol concentration. However, no controlled human trials have examined the effect of curcumin on cholesterol. This study investigated the effects of consuming curcumin on the serum lipid profile in men and women. Elderly subjects (n=36) consumed 4 g/d curcumin, 1g/d curcumin, or placebo in a 6-month, randomized, double-blind trial. Plasma curcumin and its metabolites were measured at 1 month, and the serum lipid profile was measured at baseline, 1 month, and 6 months. The plasma curcumin concentration reached a mean of 490 nmol/L. The curcumin concentration was greater after capsule than powder administration. Consumption of either dose of curcumin did not significantly affect triacylglycerols, or total, LDL, and HDL cholesterol over 1 month or 6 months. However, the concentrations of plasma curcumin and serum cholesterol were positively and significantly correlated. Curcumin consumption does not appear to have a significant effect on the serum lipid profile, unless the absorbed concentration of curcumin is considered, in which case curcumin may modestly increase cholesterol.

  11. Vacancy profile in reverse osmosis membranes studied by positron annihilation lifetime measurements and molecular dynamics simulations (United States)

    Shimazu, A.; Goto, H.; Shintani, T.; Hirose, M.; Suzuki, R.; Kobayashi, Y.


    The positron annihilation technique using a slow positron beam can be used for the study of the vacancy profiles in typical reverse osmosis (RO) membranes. In this study, the vacancy profile in the polyamide membrane that exhibits a high permselectivity between ions and water was studied using the positron annihilation technique and molecular dynamics simulations. Ortho-positronium (o-Ps) lifetimes in the surface region of the membranes were evaluated by using a slow positron beam. The diffusion behavior of Na+ and water in the polyamides was simulated by molecular dynamics (MD) methods using the TSUBAME2 supercomputer at the Tokyo Institute of Technology and discussed with the vacancy profile probed by the o-Ps. The results suggested that the large hydration size of Na+ compared to the vacancy size in the polyamides contributes to the increased diffusivity selectivity of water/Na+ that is related to the NaCl desalination performance of the membrane. Both the hydration size of the ions and the vacancy size appeared to be significant parameters to discuss the diffusivity selectivity of water/ions in typical polyamide membranes.

  12. Studies on a Novel Minor-groove Targeting Artificial Nuclease: Synthesis and DNA Binding Behavior

    Institute of Scientific and Technical Information of China (English)


    Nucleases play an important role in molecular biology, for example, in DNA sequencing. Synthetic polyamide conjugates can be considered as a novel tool for the selective inhibition of gene expressions and also as potential drugs in anticancer or antiviral chemotherapy. In this article, the synthesis of a novel minor-groove targeting artificial nuclease, an oligopyrrol-containing compound, has been reported. It was found that this novel compound can bind DNA in AT-rich minor groove with high affinity and site specificity. DNA binding behavior was determined by using UV-Vis and CD. It is indicated that compound 6 can enhance the Tm of DNA from 80. 4 C to 84. 4 ℃ and that it possesses a high binding constant value(Kb = 3.05×104 L/mol).

  13. Comparative study of the binding of pepsin to four alkaloids by spectrofluorimetry (United States)

    Wang, Ruiyong; Xie, Yuanzhe; Zhang, Yuhai; Kang, Xiaohui; Wang, Xiaogai; Ge, Baoyu; Chang, Junbiao


    The interactions between pepsin and four alkaloids, including caffeine (Caf), aminophylline (Ami), acefylline (Ace), diprophylline (Dip), were investigated by fluorescence, UV-visible absorption, resonance light scattering, synchronous fluorescence spectroscopy and 3D spectroscopy under mimic physiological conditions. The results revealed that Caf (Ami/Ace/Dip) caused the fluorescence quenching of pepsin by the formation of Caf (Ami/Ace/Dip)-pepsin complex. The binding constants and thermodynamic parameters at three different temperatures, the binding locality and the binding power were obtained. The hydrophobic and electrostatic interactions were the predominant intermolecular forces to stabilize the complex. Results showed that aminophylline was the stronger quencher and bound to pepsin with higher affinity than other three alkaloids.

  14. Combined spectroscopy and molecular modeling studies on the binding of galbanic acid and MMP9. (United States)

    Kiani, Amir; Almasi, Khadijeh; Shokoohinia, Yalda; Sadrjavadi, Komail; Nowroozi, Amin; Shahlaei, Mohsen


    The molecular mechanism of galbanic acid (GBA) binding to matrix metalloproteinase 9 (MMP9) was investigated by fluorescence quenching, absorption spectroscopy, FT-IR, molecular docking and molecular dynamics (MD) simulation procedures. The fluorescence emission of MMP9 was quenched by GBA. The titration of MMP9 by various amount of GBA was also followed by UV-Vis absorption spectroscopy. The results revealed that GBA, as a biologically active sesquiterpene coumarin derivative, has an ability to bind strongly to MMP9. Molecular docking results indicated that the main active binding site for GBA has been located in a hydrophobic cavity in the vicinity of Zn atom. Moreover, MD simulation results suggested that GBA as a coumarin derivative can interact with MMP9, without affecting the secondary structure of MMP9. MD simulations, molecular docking as computational methods from one hand and experimental data from other hand reciprocally supported each other.

  15. Comparative study of the binding of trypsin to caffeine and theophylline by spectrofluorimetry

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Ruiyong, E-mail: [Department of Chemistry, Zhengzhou University, Zhengzhou 450001 (China); Kang, Xiaohui [Department of Chemistry, Zhengzhou University, Zhengzhou 450001 (China); Wang, Ruiqiang [The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052 (China); Wang, Rui; Dou, Huanjing; Wu, Jing; Song, Chuanjun [Department of Chemistry, Zhengzhou University, Zhengzhou 450001 (China); Chang, Junbiao, E-mail: [Department of Chemistry, Zhengzhou University, Zhengzhou 450001 (China)


    The interactions between trypsin and caffeine/theophylline were investigated by fluorescence spectroscopy, UV–visible absorption spectroscopy, resonance light scattering and synchronous fluorescence spectroscopy under mimic physiological conditions. The results revealed that the fluorescence quenching of trypsin by caffeine and theophylline was the result of the formed complex of caffeine–trypsin and theophylline–trypsin. The binding constants and thermodynamic parameters at three different temperatures were obtained. The hydrophobic interaction was the predominant intermolecular forces to stabilize the complex. Results showed that caffeine was the stronger quencher and bound to trypsin with higher affinity than theophylline. -- Highlights: ► The fluorescence of trypsin can be quenched by caffeine or theophylline via hydrophobic contacts. ► Caffeine binds to trypsin with higher affinity than theophylline. ► The influence of molecular structure on the binding aspects is reported.

  16. A High Performance Theory for Thermodynamic Study on the Binding of Human Serum Albumin with Erbium Chloride

    Institute of Scientific and Technical Information of China (English)



    A thermodynamic study of the interaction between erbium(Ⅲ) chloride (Er3+) and human serum albumin (HAS) was studied at pH=7.0, 27 and 37℃ in phosphate buffer by isothermal titration calorimetry (ITC). The present study reports the thermodynamic parameters that govern HAS-Er3+ interactions. The extended solvation theory was used to reproduce the enthalpies of HAS-Er3+ interactions over the whole range of Er3+ concentrations. The bind-ing parameters recovered from the new model were attributed to the structural change of HAS and its biological ac-tivity. The results obtained indicate that there is a set of two identical binding sites for Er3+ ions with negative co-operativity. The enhancement of complex formation by Er3+ and concomitant increase in △S suggest that the metal ion plays a role in increasing the number of hydrophobic contacts. The binding parameters discovered from the ex-tended solvation model indicate that the stability of HAS molecule is increased as a result of its interaction with Er3+ ions.

  17. DNA interaction studies of a platinum (II) complex containing an antiviral drug, ribavirin: the effect of metal on DNA binding. (United States)

    Shahabadi, Nahid; Mirzaei kalar, Zeinab; Moghadam, Neda Hosseinpour


    The water-soluble Pt (II) complex, [PtCl (DMSO)(N(4)N(7)-ribavirin)]· H(2)O (ribavirin is an antiviral drug) has been synthesized and characterized by physico-chemical and spectroscopic methods. The binding interactions of this complex with calf thymus DNA (CT-DNA) were investigated using fluorimetry, spectrophotometry, circular dichroism and viscosimetry. The complex binds to CT-DNA in an intercalative mode. The calculated binding constant, K(b), was 7.2×10(5) M(-1). In fluorimetric studies, the enthalpy (ΔH0) changes of the reaction between the Pt (II) complex with CT-DNA showed hydrophobic interaction. In addition, CD study showed stabilization of the right-handed B form of CT-DNA. All these results prove that the complex interacts with CT-DNA via intercalative mode of binding. In comparison with the previous study of the DNA interaction with ribavirin, these results show that platinum complex has greater affinity to CT-DNA.

  18. Potential of [{sup 11}C]DASB for measuring endogenous serotonin with PET: binding studies

    Energy Technology Data Exchange (ETDEWEB)

    Lundquist, Pinelopi [Division of Pharmacokinetics and Drug Therapy, Department of Pharmaceutical Biosciences, Uppsala University, SE-751 24 Uppsala (Sweden) and Hospital Pharmacy, University Hospital, SE-751 85 Uppsala (Sweden)]. E-mail:; Wilking, Helena [Uppsala Imanet, SE-751 09 Uppsala (Sweden); Hoeglund, A. Urban [Uppsala Imanet, SE-751 09 Uppsala (Sweden); Sandell, Johan [Uppsala Imanet, SE-751 09 Uppsala (Sweden); Bergstroem, Mats [Uppsala Imanet, SE-751 09 Uppsala (Sweden); Hartvig, Per [Hospital Pharmacy, University Hospital, SE-751 85 Uppsala (Sweden); Langstroem, Bengt [Uppsala Imanet, SE-751 09 Uppsala (Sweden)


    The serotonin transporter radioligand [{sup 11}C]-3-amino-4-(2-dimethylaminomethylphenylsulfanyl)-benzonitrile, or [{sup 11}C]DASB, was examined in order to assess its potential for measuring fluctuations in endogenous serotonin concentrations with positron emission tomography. Binding characteristics of [{sup 11}C]DASB and the propensity for serotonin to displace the tracer were explored in rat brain homogenates. Experiments showed that serotonin displaced [{sup 11}C]DASB in vitro. Ex vivo experiments performed after tranylcypromine injection (3 or 15 mg/kg) showed a dose-dependent trend in radioactivity uptake and suggested that serotonin may compete with [{sup 11}C]DASB for transporter binding.

  19. Impact of metal-alkoxide functionalized linkers on H2 binding: A density functional study (United States)

    Banu, Tahamida; Ghosh, Avik; Das, Abhijit K.


    The effect of metal-alkoxide functionalization of different organic linkers on the H2 binding is investigated employing DFT approach. While analyzing the H2 binding interaction of magnesium-alkoxide modified benzene, naphthalene, anthracene and pyrene linkers, we find their comparable affinity toward H2 molecules. Six-member alkoxide ring containing naphthalene and pyrene systems interact with the H2 molecules in a comparatively better way than their five-member analogues. AIM, NBO and LMO-EDA analyses have been performed to comprehend the bonding nature between Mg center and the H2 molecules. Polarization along with the charge transfer interactions play significant role in stabilizing the systems.

  20. In vitro study: binding of 99mTc-DPD to synthetic amyloid fibrils

    Directory of Open Access Journals (Sweden)

    Buroni Federica E


    Full Text Available This paper is an report of the investigation of the in vitro binding of 99mTc-DPD for synthetic amyloid fibrils used for the diagnosis of cardiac amyloidosis (CA, as compared with the use of 99mTc-HMDP and 99mTc-PPI. It also includes an inquiry into the role played by Ca2+ ions and serum proteins on binding to amyloid like materials, as well as the saturability and specificity of DPD for fibrils versus amorphous precipitates (AP.

  1. Plasticity-related binding of GABA and muscarinic receptor sites in piriform cortex of rat: An autoradiographic study

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, A.P.; Westrum, L.E. (Univ. of Washington, Seattle (USA))


    This study has used the recently developed in vitro quantitative autoradiographic technique to examine the effects of olfactory bulb (OB) removal on receptor-binding sites in the deafferented piriform cortex (PC) of the rat. The gamma-aminobutyric acid-benzodiazepine receptor (GABA-BZR)- and muscarinic cholinergic receptor (MChR)-binding sites in layer I of PC were localized using (3H)flunitrazepam and (3H)quinuclidinyl benzilate as ligands, respectively. From the resultant autoradiograms the optical densities were measured using a Drexel-DUMAS image analysis system. The densities of BZR and MChR-binding sites were markedly increased in the PC ipsilateral to the lesion as compared to the contralateral side in those subjects that were operated in adulthood (Postnatal Day 100, PN 100). Comparisons between the unoperated and PN 100 operated animals also showed significant increases in the deafferented PC. In the animals operated on the day of birth (PN 0) no significant differences were seen between the operated and the contralateral PC. The difference between the PN 0 deafferented PC and the unoperated controls shows a slight decrease in BZR density in the former group; however, in case of the MChR there is a slight increase on the side of the lesion. These results demonstrate that deafferentation of PC by OB removal appears to modulate both the BZR-binding sites that are coupled with the GABA-A receptor complex and the MChR-binding sites. The results also suggest that possibility of a role for these neurotransmitter receptor-binding sites in plasticity following deafferentation.

  2. EPSP synthase: binding studies using isothermal titration microcalorimetry and equilibrium dialysis and their implications for ligand recognition and kinetic mechanism. (United States)

    Ream, J E; Yuen, H K; Frazier, R B; Sikorski, J A


    Isothermal titration calorimetry measurements are reported which give important new binding constant (Kd) information for various substrate and inhibitor complexes of Escherichia coli EPSP synthase (EPSPS). The validity of this technique was first verified by determining Kd's for the known binary complex with the substrate, shikimate 3-phosphate (S3P), as well as the herbicidal ternary complex with S3P and glyphosate (EPSPS.S3P.glyphosate). The observed Kd's agreed very well with those from previous independently determined kinetic and fluorescence binding measurements. Further applications unequivocally demonstrate for the first time a fairly tight interaction between phosphoenolpyruvate (PEP) and free enzyme (Kd = 390 microM) as well as a correspondingly weak affinity for glyphosate (Kd = 12 mM) alone with enzyme. The formation of the EPSPS.PEP binary complex was independently corroborated using equilibrium dialysis. These results strongly suggest that S3P synergizes glyphosate binding much more effectively than it does PEP binding. These observations add important new evidence to support the hypothesis that glyphosate acts as a transition-state analogue of PEP. However, the formation of a catalytically productive PEP binary complex is inconsistent with the previously reported compulsory binding order process required for catalysis and has led to new studies which completely revise the overall EPSPS kinetic mechanism. A previously postulated ternary complex between S3P and inorganic phosphate (EPSPS.S3P.Pi, Kd = 4 mM) was also detected for the first time. Quantitative binding enthalpies and entropies were also determined for each ligand complex from the microcalorimetry data. These values demonstrate a clear difference in thermodynamic parameters for recognition at the S3P site versus those observed for the PEP, Pi, and glyphosate sites.

  3. Molecular dynamics studies of the nucleoprotein of influenza A virus: role of the protein flexibility in RNA binding.

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    Bogdan Tarus

    Full Text Available The influenza viruses contain a segmented, negative stranded RNA genome. Each RNA segment is covered by multiple copies of the nucleoprotein (NP. X-ray structures have shown that NP contains well-structured domains juxtaposed with regions of missing electron densities corresponding to loops. In this study, we tested if these flexible loops gated or promoted RNA binding and RNA-induced oligomerization of NP. We first performed molecular dynamics simulations of wt NP monomer and trimer in comparison with the R361A protein mutated in the RNA binding groove, using the H1N1 NP as the initial structure. Calculation of the root-mean-square fluctuations highlighted the presence of two flexible loops in NP trimer: loop 1 (73-90, loop 2 (200-214. In NP, loops 1 and 2 formed a 10-15 Å-wide pinch giving access to the RNA binding groove. Loop 1 was stabilized by interactions with K113 of the adjacent β-sheet 1 (91-112 that interacted with the RNA grove (linker 360-373 via multiple hydrophobic contacts. In R361A, a salt bridge formed between E80 of loop 1 and R208 of loop 2 driven by hydrophobic contacts between L79 and W207, due to a decreased flexibility of loop 2 and loop 1 unfolding. Thus, RNA could not access its binding groove in R361A; accordingly, R361A had a much lower affinity for RNA than NP. Disruption of the E80-R208 interaction in the triple mutant R361A-E80A-E81A increased its RNA binding affinity and restored its oligomerization back to wt levels in contrast with impaired levels of R361A. Our data suggest that the flexibility of loops 1 and 2 is required for RNA sampling and binding which likely involve conformational change(s of the nucleoprotein.

  4. Serum corticosteroid-binding globulin concentration and insulin resistance syndrome: a population study. (United States)

    Fernandez-Real, José-Manuel; Pugeat, Michel; Grasa, Mar; Broch, Montserrat; Vendrell, Joan; Brun, Jocelyne; Ricart, Wifredo


    It has been suggested that a low grade inflammatory state could predispose for developing insulin resistance and contribute to the development of obesity and type 2 diabetes. Corticosteroid-binding globulin (CBG), the main plasma protein transport for cortisol, has been shown to be negatively regulated by insulin and IL-6, at least in vitro, suggesting that insulin resistance and inflammation may both contribute to decreasing CBG levels. In the present study we measured CBG concentrations in a human healthy population and investigated the relationships of CBG with anthropometric and biochemical markers for inflammation and/or insulin resistance. The data showed that the mean serum CBG level was significantly lower in males (n = 151) than in females (n = 113; 32.5 +/- 9.1 vs. 39.2 +/- 13.9 mg/liter; P fasting cortisol/CBG) was significantly associated with WHR (r = 0.24; P = 0.001), systolic (r = 0.18; P = 0.01) and diastolic (r = 0.19; P = 0.007) blood pressures, and HOMA value (r = 0.20; P = 0.005), but not with BMI or age. BMI (P < 0.0001), free cortisol (P = 0.003), and CBG (P = 0.009), but not WHR and age, contributed to 20%, 6%, and 8%, respectively, of HOMA variance in women in a multiple regression analysis. In this model only BMI (P < 0.0001) independently contributed to HOMA variance in men. These findings support the hypothesis that the CBG level is an interesting indicator for both insulin resistance and low grade inflammation. Whether the decrease in CBG levels is genetic by nature or directly associated to increased insulin and/or IL-6 merits further investigation. Nevertheless, because CBG has been shown to be expressed by the adipose tissue, decreased CBG could create locally increased cortisol disposal, with no change in circulating cortisol, and facilitate fat accumulation, insulin resistance, and type 2 diabetes.

  5. Kinetic study of coniferyl alcohol radical binding to the (+)-pinoresinol forming dirigent protein. (United States)

    Halls, Steven C; Davin, Laurence B; Kramer, David M; Lewis, Norman G


    An essential step in lignan and lignin formation in planta is one electron oxidation of (E)-coniferyl alcohol (CA) to generate the radical intermediate (CA(*)), which can then undergo directed radical-radical couplings in vivo. For lignan formation in vitro and in vivo, stereoselective coupling of CA(*) only occurs to afford (+)-pinoresinol in the additional presence of (+)-pinoresinol forming dirigent protein (DP). Presented herein is a kinetic and thermodynamic study which reveals the central mechanistic details of the coupling process involved in DP-mediated coupling. DP activity was maximal between pH 4.25 and pH 6.0, with activity being maintained at temperatures below 33 degrees C. Equilibrium binding assays revealed that coniferyl alcohol was only weakly bound to the DP, with a K(D) of 370 +/- 65 microM. On the other hand, the enantiomeric excess of (+)-pinoresinol formed was dependent on both DP concentration and rate of CA oxidation and, thus, on apparent steady-state [CA(*)]. The data obtained could best be explained using a kinetic model where radical-radical coupling via DP competes with that occurring in open solution. Using this model, an apparent K(M) of about 10 nM was estimated from the saturation behavior of (+)-pinoresinol formation with respect to apparent steady-state [CA(*)]. These data strongly suggest that CA(*), rather than CA, is the substrate for DP, in agreement with earlier predictions. A mechanism of directed radical-radical coupling, where two coniferyl alcohol radical substrates are bound per protein dimer, is proposed.

  6. Theory of dielectric loss in Graphene-on-substrate: A tight- binding model study (United States)

    Sahu, Sivabrata; Panda, S. K.; Rout, G. C.


    Graphene-on-substrate exhibits interesting dielectric behaviour due to screening of coulomb interaction induced by many body effects. In this communication we attempt to study the dielectric loss property of graphene within tight-binding model approach. The Hamiltonian consisting of electron hopping upto third-nearest-neighbour's with impurities in two in equivalent sub-lattices. The graphene-on-substrate raises the energy +Δ at one sub lattice and reduces energy -Δ at other sub lattice. Further we introduced coulomb interaction between π - electrons at the two sub lattices separately with the same effective coulomb interaction. We calculate polarization function Π(q, ω) which is a two particle Green's function arising due to charge-charge correlation by using Zubarev's Green's function technique. Finally we calculate dielectric function of graphene i.e. ε(q, ω) =1+Π(q,ω) at arbitrary wave vector q and frequency ra. The dielectric loss in graphene calculated from the imaginary part of dielectric function which is a measure of absorption spectrum. Only a few Fragmentary theoretical attempts have been made to utilize the full frequency and wave vector dependent dielectric function. We compute numerically the frequency dependent dielectric loss function for 100x100 momentum grid points. We observe a low energy Plasmon resonance peak and a high energy flat peak arising due to absorption of optical energy at substrate induced gap. With increase of small Plasmon wave vector, both low and high energy peaks approach each other. The dielectric loss at low energies exhibits a parabolic curve, but it exhibit a clear peak on introduction of higher order electron hopping's. The Coulomb interaction suppresses induced gap in graphene and decreases the optical energy absorption spectra. The increase of substrate induced gap shifts the high energy flat peak to higher energies and enhances the dielectric loss throughout the frequency range. Finally the effect of doping on

  7. Shortwave radiative heating rate profiles in hazy and clear atmosphere: a sensitivity study (United States)

    Doppler, Lionel; Fischer, Jürgen; Ravetta, François; Pelon, Jacques; Preusker, René


    Aerosols have an impact on shortwave heating rate profiles (additional heating or cooling). In this survey, we quantify the impact of several key-parameters on the heating rate profiles of the atmosphere with and without aerosols. These key-parameters are: (1) the atmospheric model (tropical, midlatitude summer or winter, US Standard), (2) the integrated water vapor amount (IWV ), (3) the ground surface (flat and rough ocean, isotropic surface albedo for land), (4) the aerosol composition (dusts, soots or maritimes mixtures with respect to the OPAC-database classification), (5) the aerosol optical depth and (6) vertical postion, and (7) the single-scattering albedo (?o) of the aerosol mixture. This study enables us to evaluate which parameters are most important to take into account in a radiative energy budget of the atmosphere and will be useful for a future study: the retrieval of heating rates profiles fro