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Sample records for opc invasin binds

  1. Novel Vinculin Binding Site of the IpaA Invasin of Shigella

    Energy Technology Data Exchange (ETDEWEB)

    Park, HaJeung; Valencia-Gallardo, Cesar; Sharff, Andrew; Van Nhieu, Guy Tran; Izard, Tina (Globel Phasing); (Scripps); (CF)

    2012-10-25

    Internalization of Shigella into host epithelial cells, where the bacteria replicates and spreads to neighboring cells, requires a type 3 secretion system (T3SS) effector coined IpaA. IpaA binds directly to and activates the cytoskeletal protein vinculin after injection in the host cell cytosol, and this was previously thought to be directed by two amphipathic {alpha}-helical vinculin-binding sites (VBS) found in the C-terminal tail domain of IpaA. Here, we report a third VBS, IpaA-VBS3, that is located N-terminal to the other two VBSs of IpaA and show that one IpaA molecule can bind up to three vinculin molecules. Biochemical in vitro Shigella invasion assays and the 1.6 {angstrom} crystal structure of the vinculin {center_dot} IpaA-VBS3 complex showed that IpaA-VBS3 is functionally redundant with the other two IpaA-VBSs in cell invasion and in activating the latent F-actin binding functions of vinculin. Multiple VBSs in IpaA are reminiscent of talin, which harbors 11 VBSs. However, most of the talin VBSs have low affinity and are buried in helix bundles, whereas all three of the VBSs of IpaA are high affinity, readily available, and in close proximity to each other in the IpaA structure. Although deletion of IpaA-VBS3 has no detectable effects on Shigella invasion of epithelial cells, deletion of all three VBSs impaired bacterial invasion to levels found in an ipaA null mutant strain. Thus, IpaA-directed mimicry of talin in activating vinculin occurs through three high affinity VBSs that are essential for Shigella pathogenesis.

  2. Gut proteases target Yersinia invasin in vivo

    Directory of Open Access Journals (Sweden)

    Freund Sandra

    2011-04-01

    Full Text Available Abstract Background Yersinia enterocolitica is a common cause of food borne gastrointestinal disease. After oral uptake, yersiniae invade Peyer's patches of the distal ileum. This is accomplished by the binding of the Yersinia invasin to β1 integrins on the apical surface of M cells which overlie follicle associated lymphoid tissue. The gut represents a barrier that severely limits yersiniae from reaching deeper tissues such as Peyer's patches. We wondered if gut protease attack on invasion factors could contribute to the low number of yersiniae invading Peyer's patches. Findings Here we show that invasin is rapidly degraded in vivo by gut proteases in the mouse infection model. In vivo proteolytic degradation is due to proteolysis by several gut proteases such as trypsin, α-chymotrypsin, pancreatic elastase, and pepsin. Protease treated yersiniae are shown to be less invasive in a cell culture model. YadA, another surface adhesin is cleaved by similar concentrations of gut proteases but Myf was not cleaved, showing that not all surface proteins are equally susceptible to degradation by gut proteases. Conclusions We demonstrate that gut proteases target important Yersinia virulence factors such as invasin and YadA in vivo. Since invasin is completely degraded within 2-3 h after reaching the small intestine of mice, it is no longer available to mediate invasion of Peyer's patches.

  3. Role of the beta1-integrin cytoplasmic tail in mediating invasin-promoted internalization of Yersinia

    DEFF Research Database (Denmark)

    Gustavsson, Anna; Armulik, Annika; Brakebusch, Cord

    2002-01-01

    Invasin of Yersinia pseudotuberculosis binds to beta1-integrins on host cells and triggers internalization of the bacterium. To elucidate the mechanism behind the beta1-integrin-mediated internalization of Yersinia, a beta1-integrin-deficient cell line, GD25, transfected with wild-type beta1A, beta......1B or different mutants of the beta1A subunit was used. Both beta1A and beta1B bound to invasin-expressing bacteria, but only beta1A was able to mediate internalization of the bacteria. The cytoplasmic region of beta1A, differing from beta1B, contains two NPXY motifs surrounding a double threonine...... site. Exchanging the tyrosines of the two NPXYs to phenylalanines did not inhibit the uptake, whereas a marked reduction was seen when the first tyrosine (Y783) was exchanged to alanine. A similar reduction was seen when the two nearby threonines (TT788-9) were exchanged with alanines. It was also...

  4. Two barriers or not? Dynamic force spectroscopy on the integrin α7β1 invasin complex

    DEFF Research Database (Denmark)

    Boye, Kristian; Ligezowska, Agnieszka; Eble, Johannes A.

    2013-01-01

    Dynamic force spectroscopy was used to test force-induced dissociation of the complex between the integrin α7β1 and the bacterial protein invasin. Both proteins were used in truncated forms comprising the respective binding sites. Using the biomembrane force-probe, the bond system was exposed to ...

  5. Oilwell Power Controller (OPC)

    Energy Technology Data Exchange (ETDEWEB)

    1993-08-01

    The Oil Well Power Controller (OPC) prototype units is nearing completion. This device is an oilwell beam pump controller and data logger. Applications for this device have been for an electrical power saving device, pump off control, parafffin detection, demand power load control, chemical treatment data, dynamometer and pump efficiency data. Preliminary results appear vary promising. A total of ten OPC rod pump controllers were assembled and installed on oilwells in several areas of Central and Western United States. Data was analyzed on these wells and forwarded to the participating oil companies. Cost savings on each individual oil well participating in the OPC testing vary considerably, savings on some situations have been outstanding. In situations where the pump efficiency was determined to be low, the cost savings have been considerable. Cost savings due to preventive maintenance are also present, but are difficult to pin point an exact dollar amount at the present time. A break out of actual cost data obtained on some of the oilwells controlled and monitored with the oilwell power controller.

  6. Modular process modeling for OPC

    Science.gov (United States)

    Keck, M. C.; Bodendorf, C.; Schmidtling, T.; Schlief, R.; Wildfeuer, R.; Zumpe, S.; Niehoff, M.

    2007-03-01

    Modular OPC modeling, describing mask, optics, resist and etch processes separately is an approach to keep efforts for OPC manageable. By exchanging single modules of a modular OPC model, a fast response to process changes during process development is possible. At the same time efforts can be reduced, since only single modular process steps have to be re-characterized as input for OPC modeling as the process is adjusted and optimized. Commercially available OPC tools for full chip processing typically make use of semi-empirical models. The goal of our work is to investigate to what extent these OPC tools can be applied for modeling of single process steps as separate modules. For an advanced gate level process we analyze the modeling accuracy over different process conditions (focus and dose) when combining models for each process step - optics, resist and etch - for differing single processes to a model describing the total process.

  7. AUTOMATED TESTING OF OPC SERVERS

    CERN Document Server

    Farnham, B

    2011-01-01

    CERN relies on OPC Server implementations from 3rd party device vendors to provide a software interface to their respective hardware. Each time a vendor releases a new OPC Server version it is regression tested internally to verify that existing functionality has not been inadvertently broken during the process of adding new features. In addition bugs and problems must be communicated to the vendors in a reliable and portable way. This presentation covers the automated test approach used at CERN to cover both cases: Scripts are written in a domain specific language specifically created for describing OPC tests and executed by a custom software engine driving the OPC Server implementation.

  8. Essential domains of Anaplasma phagocytophilum invasins utilized to infect mammalian host cells.

    Directory of Open Access Journals (Sweden)

    David Seidman

    2015-02-01

    Full Text Available Anaplasma phagocytophilum causes granulocytic anaplasmosis, an emerging disease of humans and domestic animals. The obligate intracellular bacterium uses its invasins OmpA, Asp14, and AipA to infect myeloid and non-phagocytic cells. Identifying the domains of these proteins that mediate binding and entry, and determining the molecular basis of their interactions with host cell receptors would significantly advance understanding of A. phagocytophilum infection. Here, we identified the OmpA binding domain as residues 59 to 74. Polyclonal antibody generated against a peptide spanning OmpA residues 59 to 74 inhibited A. phagocytophilum infection of host cells and binding to its receptor, sialyl Lewis x (sLe(x-capped P-selectin glycoprotein ligand 1. Molecular docking analyses predicted that OmpA residues G61 and K64 interact with the two sLe(x sugars that are important for infection, α2,3-sialic acid and α1,3-fucose. Amino acid substitution analyses demonstrated that K64 was necessary, and G61 was contributory, for recombinant OmpA to bind to host cells and competitively inhibit A. phagocytophilum infection. Adherence of OmpA to RF/6A endothelial cells, which express little to no sLe(x but express the structurally similar glycan, 6-sulfo-sLe(x, required α2,3-sialic acid and α1,3-fucose and was antagonized by 6-sulfo-sLe(x antibody. Binding and uptake of OmpA-coated latex beads by myeloid cells was sensitive to sialidase, fucosidase, and sLe(x antibody. The Asp14 binding domain was also defined, as antibody specific for residues 113 to 124 inhibited infection. Because OmpA, Asp14, and AipA each contribute to the infection process, it was rationalized that the most effective blocking approach would target all three. An antibody cocktail targeting the OmpA, Asp14, and AipA binding domains neutralized A. phagocytophilum binding and infection of host cells. This study dissects OmpA-receptor interactions and demonstrates the effectiveness of binding

  9. OPC aware mask and wafer metrology

    Science.gov (United States)

    Maurer, Wilhelm; Wiaux, Vincent; Jonckheere, Rik M.; Philipsen, Vicky; Hoffmann, Thomas; Verhaegen, Staf; Ronse, Kurt G.; England, Jonathan G.; Howard, William B.

    2002-08-01

    Lithography at its limit of resolution is a highly non- linear pattern transfer process. Typically the shapes of printed features deviate considerably from their corresponding features in the layout. This deviation is known as Optical Proximity Effect, and its correction Optical Proximity effect Correction or OPC. Although many other so-called optical enhancement technologies are applied to cope with the issues of lithography at its limit of resolution, almost none of these can re-store the linearity of the pattern transfer. Hence fully functional OPC has become a very basic requirement for current and future lithography processes. In general, proximity effects are two-dimensional (2d) effects. Thus any measurement of proximity effects or any characterization of the effectiveness of OPC has to be two- dimensional. As OPC modifies shapes in the data for mask writing in a way to compensate for the expected proximity effects of the following processing steps, parameters describing the particular OPC-mask quality is a major concern. One-dimensional mask specifications, such as linewidth mean-to-target and uniformity, pattern placement, and maximum size of a tolerable defect, are not sufficient anymore to completely describe the functionality of a given mask for OPC. Two-dimensional mask specifications need to be evaluated. We present in this paper a basic concept for 2d metrology. Examples for 2d measurements to assess the effectiveness of OPC are given by the application of an SEM Image Analysis tool to an advanced 130nm process.

  10. Bayesian inference for OPC modeling

    Science.gov (United States)

    Burbine, Andrew; Sturtevant, John; Fryer, David; Smith, Bruce W.

    2016-03-01

    The use of optical proximity correction (OPC) demands increasingly accurate models of the photolithographic process. Model building and inference techniques in the data science community have seen great strides in the past two decades which make better use of available information. This paper aims to demonstrate the predictive power of Bayesian inference as a method for parameter selection in lithographic models by quantifying the uncertainty associated with model inputs and wafer data. Specifically, the method combines the model builder's prior information about each modelling assumption with the maximization of each observation's likelihood as a Student's t-distributed random variable. Through the use of a Markov chain Monte Carlo (MCMC) algorithm, a model's parameter space is explored to find the most credible parameter values. During parameter exploration, the parameters' posterior distributions are generated by applying Bayes' rule, using a likelihood function and the a priori knowledge supplied. The MCMC algorithm used, an affine invariant ensemble sampler (AIES), is implemented by initializing many walkers which semiindependently explore the space. The convergence of these walkers to global maxima of the likelihood volume determine the parameter values' highest density intervals (HDI) to reveal champion models. We show that this method of parameter selection provides insights into the data that traditional methods do not and outline continued experiments to vet the method.

  11. Improvements in accuracy of dense OPC models

    Science.gov (United States)

    Kallingal, Chidam; Oberschmidt, James; Viswanathan, Ramya; Abdo, Amr; Park, OSeo

    2008-10-01

    Performing model-based optical proximity correction (MBOPC) on layouts has become an integral part of patterning advanced integrated circuits. Earlier technologies used sparse OPC, the run times of which explode when the density of layouts increases. With the move to 45 nm technology node, this increase in run time has resulted in a shift to dense simulation OPC, which is pixel-based. The dense approach becomes more efficient at 45nm technology node and beyond. New OPC model forms can be used with the dense simulation OPC engine, providing the greater accuracy required by smaller technology nodes. Parameters in the optical model have to be optimized to achieve the required accuracy. Dense OPC uses a resist model with a different set of parameters than sparse OPC. The default search ranges used in the optimization of these resist parameters do not always result in the best accuracy. However, it is possible to improve the accuracy of the resist models by understanding the restrictions placed on the search ranges of the physical parameters during optimization. This paper will present results showing the correlation between accuracy of the models and some of these optical and resist parameters. The results will show that better optimization can improve the model fitness of features in both the calibration and verification set.

  12. Intelligent model-based OPC

    Science.gov (United States)

    Huang, W. C.; Lai, C. M.; Luo, B.; Tsai, C. K.; Chih, M. H.; Lai, C. W.; Kuo, C. C.; Liu, R. G.; Lin, H. T.

    2006-03-01

    Optical proximity correction is the technique of pre-distorting mask layouts so that the printed patterns are as close to the desired shapes as possible. For model-based optical proximity correction, a lithographic model to predict the edge position (contour) of patterns on the wafer after lithographic processing is needed. Generally, segmentation of edges is performed prior to the correction. Pattern edges are dissected into several small segments with corresponding target points. During the correction, the edges are moved back and forth from the initial drawn position, assisted by the lithographic model, to finally settle on the proper positions. When the correction converges, the intensity predicted by the model in every target points hits the model-specific threshold value. Several iterations are required to achieve the convergence and the computation time increases with the increase of the required iterations. An artificial neural network is an information-processing paradigm inspired by biological nervous systems, such as how the brain processes information. It is composed of a large number of highly interconnected processing elements (neurons) working in unison to solve specific problems. A neural network can be a powerful data-modeling tool that is able to capture and represent complex input/output relationships. The network can accurately predict the behavior of a system via the learning procedure. A radial basis function network, a variant of artificial neural network, is an efficient function approximator. In this paper, a radial basis function network was used to build a mapping from the segment characteristics to the edge shift from the drawn position. This network can provide a good initial guess for each segment that OPC has carried out. The good initial guess reduces the required iterations. Consequently, cycle time can be shortened effectively. The optimization of the radial basis function network for this system was practiced by genetic algorithm

  13. Integrating OPC Data into GSN Infrastructures

    CERN Document Server

    Passalacqua, Olivier; Huget, Marc-Philippe; Moreaux, Patrice

    2008-01-01

    This paper presents the design and the implementation of an interface software component between OLE for Process Control (OPC) formatted data and the Global Sensor Network (GSN) framework for management of data from sensors. This interface, named wrapper in the GSN context, communicates in Data Access mode with an OPC server and converts the received data to the internal GSN format, according to several temporal modes. This work is realized in the context of a Ph.D. Thesis about the control of distributed information fusion systems. The developed component allows the injection of OPC data, like measurements or industrial processes states information, into a distributed information fusion system deployed in a GSN framework. The component behaves as a client of the OPC server. Developed in Java and based on the Opensaca Utgard, it can be deployed on any computation node supporting a Java virtual machine. The experiments show the component conformity according to the Data Access 2.05a specification of the OPC st...

  14. Enforcement of Mask Rule Compliance in Model-Based OPC'ed Layouts during Data Preparation

    Science.gov (United States)

    Meyer, Dirk H.; Vuletic, Radovan; Seidl, Alexander

    2002-12-01

    Currently available commercial model-based OPC tools do not always generate layouts which are mask rule compliant. Additional processing is required to remove mask rule violations, which are often too numerous for manual patching. Although physical verification tools can be used to remove simple mask rule violations, the results are often unsatisfactory for more complicated geometrical configurations. The subject of this paper is the development and application of a geometrical processing engine that automatically enforces mask rule compliance of the OPC'ed layout. It is designed as an add-on to a physical verification tool. The engine constructs patches, which remove mask rule violations such as notches or width violations. By employing a Mixed Integer Programming (MIP) optimization method, the edges of each patch are placed in a way that avoids secondary violations while modifying the OPC'ed layout as little as possible. A sequence of enforcement steps is applied to the layout to remove all types of mask rule violations. This approach of locally confined minimal layout modifications retains OPC corrections to a maximum amount. This method has been used successfully in production on a variety of DRAM designs for the non-array regions.

  15. A phase 1 study of a meningococcal native outer membrane vesicle vaccine made from a group B strain with deleted lpxL1 and synX, over-expressed factor H binding protein, two PorAs and stabilized OpcA expression.

    Science.gov (United States)

    Keiser, P B; Biggs-Cicatelli, S; Moran, E E; Schmiel, D H; Pinto, V B; Burden, R E; Miller, L B; Moon, J E; Bowden, R A; Cummings, J F; Zollinger, W D

    2011-02-04

    This phase I clinical trial assessed the safety and immunogenicity of a native outer membrane vesicle (NOMV) vaccine prepared from an lpxL1(-) synX(-) mutant of strain 8570(B:4:P1.19,15:L8-5) of Neisseria meningitidis. Additional mutations enhance the expression of factor H binding protein variant 1 (fHbp v.1), stabilize expression of OpcA and introduce a second PorA (P1.22,14). Thirty-six volunteers were assigned to one of four dose groups (10, 25, 50 and 75 mcg, based on protein content) to receive three intramuscular injections at six week intervals with aluminum hydroxide adjuvant. Specific local and systemic adverse events were solicited by diary and at visits on days 2, 7, and 14 after each vaccination. Blood chemistries, complete blood count, and coagulation studies were measured on each vaccination day and again 2 and 14 days later. Blood for ELISA and serum bactericidal assays was drawn two and six weeks after each vaccination. The proportion of volunteers who developed a fourfold or greater increase in bactericidal activity to the wild type parent of the vaccine strain at two weeks after the third dose was 27 out of 34 (0.79, 95% C.I. 0.65-0.93). Against four other group B strains the response rate ranged from 41% to 82% indicating a good cross reactive antibody response. Depletion assays show contributions to bactericidal activity from antibodies to lipooligosaccharide (LOS), fHbp v.1 and OpcA. Published by Elsevier Ltd.

  16. OPC recipe optimization using genetic algorithm

    Science.gov (United States)

    Asthana, Abhishek; Wilkinson, Bill; Power, Dave

    2016-03-01

    Optimization of OPC recipes is not trivial due to multiple parameters that need tuning and their correlation. Usually, no standard methodologies exist for choosing the initial recipe settings, and in the keyword development phase, parameters are chosen either based on previous learning, vendor recommendations, or to resolve specific problems on particular special constructs. Such approaches fail to holistically quantify the effects of parameters on other or possible new designs, and to an extent are based on the keyword developer's intuition. In addition, when a quick fix is needed for a new design, numerous customization statements are added to the recipe, which make it more complex. The present work demonstrates the application of Genetic Algorithm (GA) technique for optimizing OPC recipes. GA is a search technique that mimics Darwinian natural selection and has applications in various science and engineering disciplines. In this case, GA search heuristic is applied to two problems: (a) an overall OPC recipe optimization with respect to selected parameters and, (b) application of GA to improve printing and via coverage at line end geometries. As will be demonstrated, the optimized recipe significantly reduced the number of ORC violations for case (a). For case (b) line end for various features showed significant printing and filling improvement.

  17. Chemically amplified resist modeling in OPC

    Science.gov (United States)

    Zheng, Xin; Huang, Jason; Kuo, Fred; Kazarian, Aram; Chin, Fook; Fan, Yongfa

    2009-03-01

    The mechanism of chemically amplified resist plays a critical role in the modeling of the latent image. To achieve a practical model which can fit into the time frame of OPC, some simplifications and assumptions have to be made. We introduced regression kernels that take into account best exposure focus difference between isotropic pitch, dense, and line end features for the evaluation of image intensity. It compares the image intensity (signal) over small changes above and/or below the regressed "nominal" image position, which in principle corresponds to evaluating the intensity signal at various depths of a fixed resist profile thus can also be regressed for optimization during model development. Our calibration has shown that the model brought a great improvement in prediction for difficult structures such as dense features at or near the optical resolution limit and 2-dimensional features, which are the limiter of the overall model fitting accuracy for 45nm node and below. By replacing other existing techniques, total number of output kernels used for OPC operation is actually reduced with improvement of model accuracy. This model is proven to be a very effective yet accurate addition to the current OPC technology.

  18. OPC care-area feedforwarding to MPC

    Science.gov (United States)

    Dillon, Brian; Peng, Yi-Hsing; Hamaji, Masakazu; Tsunoda, Dai; Muramatsu, Tomoyuki; Ohara, Shuichiro; Zou, Yi; Arnoux, Vincent; Baron, Stanislas; Zhang, Xiaolong

    2016-10-01

    Demand for mask process correction (MPC) is growing for leading-edge process nodes. MPC was originally intended to correct CD linearity for narrow assist features difficult to resolve on a photomask without any correction, but it has been extended to main features as process nodes have been shrinking. As past papers have observed, MPC shows improvements in photomask fidelity. Using advanced shape and dose corrections could give more improvements, especially at line-ends and corners. However, there is a dilemma on using such advanced corrections on full mask level because it increases data volume and run time. In addition, write time on variable shaped beam (VSB) writers also increases as the number of shots increases. Optical proximity correction (OPC) care-area defines circuit design locations that require high mask fidelity under mask writing process variations such as energy fluctuation. It is useful for MPC to switch its correction strategy and permit the use of advanced mask correction techniques in those local care-areas where they provide maximum wafer benefits. The use of mask correction techniques tailored to localized post-OPC design can result in similar desired level of data volume, run time, and write time. ASML Brion and NCS have jointly developed a method to feedforward the care-area information from Tachyon LMC to NDE-MPC to provide real benefit for improving both mask writing and wafer printing quality. This paper explains the detail of OPC care-area feedforwarding to MPC between ASML Brion and NCS, and shows the results. In addition, improvements on mask and wafer simulations are also shown. The results indicate that the worst process variation (PV) bands are reduced up to 37% for a 10nm tech node metal case.

  19. The new OPC method for obtaining the stability of MBAF OPC

    Science.gov (United States)

    Song, Jookyoung; Choi, Jaeseung; Park, Chanha; Yang, Hyunjo; Kang, Daekwon; Oh, Minsu; Park, Manjae; Moon, James; Ye, Jun; Baron, Stanislas

    2017-03-01

    Current patterning technology for manufacturing memory devices is being developed towards enabling high density and high resolution capability. However, as applying high resolution technology results in decreased process margin, OPC has to compensate for such effect. Since the process margin is decreased greatly for contact layers, technologies such as RBAF (Rule-Based Assist Feature), MBAF (Model-Based Assist Feature), and ILT (Inverse Lithography Technology) are considered to maximize the process margin [1, 2, 3]. Although ILT is the best solution in terms of process margin, it has several disadvantages such as long OPC run-time, mask complexity, and unstable mask fidelity. MBAF method is a good compromise for more advanced techniques mitigating those risks (but not eliminating it), which is why it is often used for contact layers. When setting up the rules for RBAF, not all patterns are considered. Thus, applying RBAF for contact layers may result in decreased process margin for certain patterns since the same rule is applied globally. MBAF, on the other hand, can maximize the process margin for various patterns as it generates AF (Assist Feature) to locations that maximize the margin for the patterns considered. However, MBAF method is very sensitive to even a slight change of a target, which influences the locations of the AF. This leads to generating different OPCed CD of the main features, even for those that should not be affected by the changed target. Once the OPCed CD is changed, it is impossible to obtain the same mask CD even when the mask is manufactured with the same method. If this case occurs during mass production, the entire layer needs to be confirmed after each revision which leads to unnecessary time loss. In this paper, we suggest a new OPC method to prevent this issue. With this flow, OPCed shapes of unchanged patterns remain the same while only the changed targets are OPCed and replaced into the corresponding location, while the boundaries

  20. Dynamic mapping of EDDL device descriptions to OPC UA

    Science.gov (United States)

    Atta Nsiah, Kofi; Schappacher, Manuel; Sikora, Axel

    2017-07-01

    OPC UA (Open Platform Communications Unified Architecture) is already a well-known concept used widely in the automation industry. In the area of factory automation, OPC UA models the underlying field devices such as sensors and actuators in an OPC UA server to allow connecting OPC UA clients to access device-specific information via a standardized information model. One of the requirements of the OPC UA server to represent field device data using its information model is to have advanced knowledge about the properties of the field devices in the form of device descriptions. The international standard IEC 61804 specifies EDDL (Electronic Device Description Language) as a generic language for describing the properties of field devices. In this paper, the authors describe a possibility to dynamically map and integrate field device descriptions based on EDDL into OPCUA.

  1. Role of Host Type IA Phosphoinositide 3-Kinase Pathway Components in Invasin-Mediated Internalization of Yersinia enterocolitica.

    Science.gov (United States)

    Dowd, Georgina C; Bhalla, Manmeet; Kean, Bernard; Thomas, Rowan; Ireton, Keith

    2016-06-01

    Many bacterial pathogens subvert mammalian type IA phosphoinositide 3-kinase (PI3K) in order to induce their internalization into host cells. How PI3K promotes internalization is not well understood. Also unclear is whether type IA PI3K affects different pathogens through similar or distinct mechanisms. Here, we performed an RNA interference (RNAi)-based screen to identify components of the type IA PI3K pathway involved in invasin-mediated entry of Yersinia enterocolitica, an enteropathogen that causes enteritis and lymphadenitis. The 69 genes targeted encode known upstream regulators or downstream effectors of PI3K. A similar RNAi screen was previously performed with the food-borne bacterium Listeria monocytogenes The results of the screen with Y. enterocolitica indicate that at least nine members of the PI3K pathway are needed for invasin-mediated entry. Several of these proteins, including centaurin-α1, Dock180, focal adhesion kinase (FAK), Grp1, LL5α, LL5β, and PLD2 (phospholipase D2), were recruited to sites of entry. In addition, centaurin-α1, FAK, PLD2, and mTOR were required for remodeling of the actin cytoskeleton during entry. Six of the human proteins affecting invasin-dependent internalization also promote InlB-mediated entry of L. monocytogenes Our results identify several host proteins that mediate invasin-induced effects on the actin cytoskeleton and indicate that a subset of PI3K pathway components promote internalization of both Y. enterocolitica and L. monocytogenes.

  2. OPC model sampling evaluation and weakpoint "in-situ" improvement

    Science.gov (United States)

    Fu, Nan; Elshafie, Shady; Ning, Guoxiang; Roling, Stefan

    2016-10-01

    One of the major challenges of optical proximity correction (OPC) models is to maximize the coverage of real design features using sampling pattern. Normally, OPC model building is based on 1-D and 2-D test patterns with systematically changing pitches alignment with design rules. However, those features with different optical and geometric properties will generate weak-points where OPC simulation cannot precisely predict resist contours on wafer due to the nature of infinite IC designs and limited number of model test patterns. In this paper, optical property data of real design features were collected from full chips and classified to compare with the same kind of data from OPC test patterns. Therefore sample coverage could be visually mapped according to different optical properties. Design features, which are out of OPC capability, were distinguished by their optical properties and marked as weak-points. New patterns with similar optical properties would be added into model build site-list. Further, an alternative and more efficient method was created in this paper to improve the treatment of issue features and remove weak-points without rebuilding models. Since certain classification of optical properties will generate weak-points, an OPC-integrated repair algorithm was developed and implemented to scan full chip for optical properties, locate those features and then optimize OPC treatment or apply precise sizing on site. This is a named "in-situ" weak-point improvement flow which includes issue feature definition, allocation in full chip and real-time improvement.

  3. Essential role of invasin for colonization and persistence of Yersinia enterocolitica in its natural reservoir host, the pig.

    Science.gov (United States)

    Schaake, Julia; Drees, Anna; Grüning, Petra; Uliczka, Frank; Pisano, Fabio; Thiermann, Tanja; von Altrock, Alexandra; Seehusen, Frauke; Valentin-Weigand, Peter; Dersch, Petra

    2014-03-01

    In this study, an oral minipig infection model was established to investigate the pathogenicity of Yersinia enterocolitica bioserotype 4/O:3. O:3 strains are highly prevalent in pigs, which are usually symptomless carriers, and they represent the most common cause of human yersiniosis. To assess the pathogenic potential of the O:3 serotype, we compared the colonization properties of Y. enterocolitica O:3 with O:8, a highly mouse-virulent Y. enterocolitica serotype, in minipigs and mice. We found that O:3 is a significantly better colonizer of swine than is O:8. Coinfection studies with O:3 mutant strains demonstrated that small variations within the O:3 genome leading to higher amounts of the primary adhesion factor invasin (InvA) improved colonization and/or survival of this serotype in swine but had only a minor effect on the colonization of mice. We further demonstrated that a deletion of the invA gene abolished long-term colonization in the pigs. Our results indicate a primary role for invasin in naturally occurring Y. enterocolitica O:3 infections in pigs and reveal a higher adaptation of O:3 than O:8 strains to their natural pig reservoir host.

  4. Inhibition of TROY promotes OPC differentiation and increases therapeutic efficacy of OPC graft for spinal cord injury

    Institute of Scientific and Technical Information of China (English)

    Sun Liang; Feng Xiaoling; Duan Yongshun; Zhang Yafang; Wu Shuliang; Liu Shengliang; Sun Qi; Li Zhuying; Xu Fengyan; Hou Chunmei; Harada Toshihide; Chu Ming; Xu Kun

    2015-01-01

    Objective:To observe the regulatory effects of TROY on neural myelination in central nervous system ( CNS ) and remyelination in response to spinal cord injury ( SCI ) by oligodendrocyte precursor cell ( OPC) . Results:TROY expression was detected by RT-PCR and Western blotting in OPCs as well as in differen-tiated premature and mature oligodendrocytes of postnatal mice. Pharmacological inhibition or RNAi-induced knockdown of TROY promotes OPC differentiation, whereas overexpression of TROY dampens oligodendrocyte mat-uration. Furthermore, treatment of co-cultures of DRG neurons and OPCs with TROY inhibitors promotes myelina-tion and myelin sheath-like structures. Mechanically, protein kinase C ( PKC) signaling is involved in the regula-tion of the inhibitory effects of TROY. Moreover, in situ transplantation of OPCs with TROY knockdown leads to notably enhanced remyelination as well as augmented recovery of motor function and nervous conduction in rats with SCI. Conclusions:Our results indicate that TROY negatively modulates remyelination in the CNS, and thus may be a suitable target for improving the therapeutic efficacy of cell transplantation for CNS injury.

  5. Mechanically enforced bond dissociation reports synergistic influence of Mn2+ and Mg2+ on the interaction between integrin α7β1 and invasin

    DEFF Research Database (Denmark)

    Ligezowska, Agnieszka; Boye, Kristian; Eble, Johannes A.

    2011-01-01

    Integrins require the divalent ions magnesium and manganese for ligand recognition. Here we mechanically enforced bond dissociation to explore the influence of these ions on the mechanical strength of the specific bond between α7β1 integrin and its pathologically relevant ligand invasin. Upon add...

  6. Suppressing rippling with minimized corner rounding through OPC fragmentation optimization

    Science.gov (United States)

    Wang, Jingyu; Wei, Alexander; Wilkinson, William; Chen, Norman

    2016-10-01

    As technology shrinks, the requirements placed on the post-OPC solution become so exacting that even small residual optical effects are significant. Simultaneously minimizing rippling and corner rounding cannot be accom- plished in parallel in wafer patterning especially when complex asymmetric pixelated sources are used. While either effect can be moderated by accurate application of optical proximity correction, they are both charac- teristic of unfiltered diffraction due to asymmetric illumination or design geometry and will remain inherent. Corrections that over emphasize reduced corner-rounding necessarily sacrifice edge convergence, resulting in a standing wave or unacceptable rippling along an entire edge. OPC can be used to reduce the magnitude of this rippling, but fragment placing is extremely critical. In this paper, we discuss optimized OPC fragmentation that offers balanced consideration to suppressing rippling and minimizing corner rounding. Specifically, we correlate design shapes with simulated post-OPC contours to account for design geometry-dependent rippling signature given existing illumination conditions. In contrast to adaptive fragmentation that relies on multiple iterations of simulation of intensity extrema redistribution, our method predicts the optimum contour as allowed by process and fragments the mask accordingly. The maximum imaging curvature resolvable by process coupled with the rippling signature, gives rise to the exact locations of the inflection points of the wafer contour. From there we achieve the best correction results by segmenting edges at the inflection points.

  7. Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination.

    Directory of Open Access Journals (Sweden)

    Xiaomin Dong

    2015-12-01

    Full Text Available Long non-coding RNAs (lncRNAs (> 200 bp play crucial roles in transcriptional regulation during numerous biological processes. However, it is challenging to comprehensively identify lncRNAs, because they are often expressed at low levels and with more cell-type specificity than are protein-coding genes. In the present study, we performed ab initio transcriptome reconstruction using eight purified cell populations from mouse cortex and detected more than 5000 lncRNAs. Predicting the functions of lncRNAs using cell-type specific data revealed their potential functional roles in Central Nervous System (CNS development. We performed motif searches in ENCODE DNase I digital footprint data and Mouse ENCODE promoters to infer transcription factor (TF occupancy. By integrating TF binding and cell-type specific transcriptomic data, we constructed a novel framework that is useful for systematically identifying lncRNAs that are potentially essential for brain cell fate determination. Based on this integrative analysis, we identified lncRNAs that are regulated during Oligodendrocyte Precursor Cell (OPC differentiation from Neural Stem Cells (NSCs and that are likely to be involved in oligodendrogenesis. The top candidate, lnc-OPC, shows highly specific expression in OPCs and remarkable sequence conservation among placental mammals. Interestingly, lnc-OPC is significantly up-regulated in glial progenitors from experimental autoimmune encephalomyelitis (EAE mouse models compared to wild-type mice. OLIG2-binding sites in the upstream regulatory region of lnc-OPC were identified by ChIP (chromatin immunoprecipitation-Sequencing and validated by luciferase assays. Loss-of-function experiments confirmed that lnc-OPC plays a functional role in OPC genesis. Overall, our results substantiated the role of lncRNA in OPC fate determination and provided an unprecedented data source for future functional investigations in CNS cell types. We present our datasets and

  8. OPC UA技术在冶金设备监测系统中的应用%Application of OPC UA Technology in Monitoring System for Metallurgical Equipment

    Institute of Scientific and Technical Information of China (English)

    姜泽苗; 孔庆奎; 范瑜

    2014-01-01

    OPC UA技术在工业控制方面有着不可替代的优势,主要体现在其跨平台性和实时性上,可以方便地解决工业现场监控过程中各个子系统和底层设备之间互操作以及互通信的难题。结合冶金现场设备监测系统的搭建,对OPC UA技术规范进行了研究,开发了OPC UA客户端和服务器,实现了对冶金设备运行状态的实时监测并及时制定故障应对方案的目的。 OPC UA技术在信息建模与跨平台方面的强大优势预示着基于OPC UA技术的集成系统必将成为今后的开发热点。%The technology of OPC UA has irreplaceable superior in industrial control area, especially its cross platform and real time performance;the difficulties of the interoperability and intercommunication among all the subsystems and bottom layer equipment in industrial field monitoring. The specifications of OPC US technology is researched combining with the establishment of monitoring system for metallurgy field equipment;and client and server of OPC UA are developed for implementing real time monitoring for the operation status of metallurgy equipment and failure timely responded scheme. The outstanding superior of OPC UA in information modeling and cross-platform indicates that the integrated systems based on OPC UA will definitely become the hot spots of development in the future.

  9. Fibronectin-binding protein acts as Staphylococcus aureus invasin via fibronectin bridging to integrin alpha5beta1

    NARCIS (Netherlands)

    Sinha, B; François, P P; Nüsse, O; Foti, M; Hartford, O M; Vaudaux, P; Foster, T J; Lew, D P; Herrmann, M; Krause, K H

    The ability of Staphylococcus aureus to invade mammalian cells may explain its capacity to colonize mucosa and to persist in tissues after bacteraemia. To date, the underlying molecular mechanisms of cellular invasion by S. aureus are unknown, despite its high prevalence and difficulties in

  10. Converting an OPC UA software development kit from Java to Delphi.

    OpenAIRE

    Uimonen, Teppo

    2016-01-01

    OPC UA provides a secure and interoperable standard for communication between devices and information systems, but to use it efectively in a software system, an OPC UA SDK written in the implementation language is needed. To develop one for Delphi programming language, this thesis studies how Prosys OPC UA Java SDK can be converted to Delphi. Three issues are identifed in the conversion. First, Java code should be translated to Delphi. Second, an interface is needed to use a C language OP...

  11. 7nm logic optical lithography with OPC-Lite

    Science.gov (United States)

    Smayling, Michael C.; Tsujita, Koichiro; Yaegashi, Hidetami; Axelrad, Valery; Nakayama, Ryo; Oyama, Kenichi; Yamauchi, Shohei; Ishii, Hiroyuki; Mikami, Koji

    2015-03-01

    The CMOS logic 22nm node was the last one done with single patterning. It used a highly regular layout style with Gridded Design Rules (GDR). Smaller nodes have required the same regular layout style but with multiple patterning for critical layers. A "line/cut" approach is being used to achieve good pattern fidelity and process margin.[1] As shown in Fig. 1, even with "line" patterns, pitch division will eventually be necessary. For the "cut" pattern, Design-Source-Mask Optimization (DSMO) has been demonstrated to be effective at the 20nm node and below.[2,3,4] Single patterning was found to be suitable down to 16nm, while double patterning extended optical lithography for cuts to the 10-12nm nodes. Design optimization avoided the need for triple patterning. Lines can be patterned with 193nm immersion with no complex OPC. The final line dimensions can be achieved by applying pitch division by two or four.[5] In this study, we extend the scaling using simplified OPC to the 7nm node for critical FEOL and BEOL layers. The test block is a reasonably complex logic function with ~100k gates of combinatorial logic and flip-flops, scaled from previous experiments. Simulation results show that for cuts at 7nm logic dimensions, the gate layer can be done with single patterning whose minimum pitch is 53nm, possibly some of the 1x metal layers can be done with double patterning whose minimum pitch is 53nm, and the contact layer will require triple patterning whose minimum pitch is 68nm. These pitches are less than the resolution limit of ArF NA=1.35 (72nm). However these patterns can be separated by a combination of innovative SMO for less than optical resolution limit and a process trick of hole-repair technique. An example of triple patterning coloring is shown in Fig 3. Fin and local interconnect are created by lines and trims. The number of trim patterns are 3 times (min. pitch=90nm) and twice (min. pitch=120nm), respectively. The small number of masks, large pitches, and

  12. Estimates of zooplankton abundance and size distribution with the Optical Plankton Counter (OPC)

    DEFF Research Database (Denmark)

    Wieland, Kai; Petersen, D.; Schnack, D.

    1997-01-01

    The capability of the Optical Plankton Count er (OPC) to examine the abundance and size distribution of zooplankton was tested in Storfjorden, Norway, in June 1993. Selected material obtained from net sampling was measured with a laboratory version of the OPC and compared with microscope analysis...... in order to identify main species in the in situ size frequency distributions obtained by the submersible version of the OPC. Differences in the particle concentration between shallow and deep water layers were clearly resolved by the submersible OPC, but the high diversity of the zooplankton community...... of zooplankton...

  13. SEM-contour-based OPC model calibration through the process window

    Science.gov (United States)

    Vasek, Jim; Menedeva, Ovadya; Levitzky, Dan; Lindman, Ofer; Nemadi, Youval; Bailey, George E.; Sturtevant, John L.

    2007-03-01

    As design rules shrink, there is an unavoidable increase in the complexity of OPC/RET schemes required to enable design printability. These complex OPC/RET schemes have been facilitating unprecedented yield at k I factors previously deemed "unmanufacturable", but they increase the mask complexity and production cost, and can introduce yield-detracting errors. The most common errors are found in OPC design itself, and in the resulting patterning robustness across the process window. Two factors in the OPC design process that contribute to these errors are a) that 2D structures used in the design are not sufficiently well-represented in the OPC model calibration test pattern suite, and b) that the OPC model calibration is done only at the nominal process settings and not across the entire focus-exposure window. This work compares two alternative methods for calibrating OPC models. The first method uses a traditional industry flow for making CD measurements on standard calibration target structures. The second method uses 2D contour profiles extracted automatically by the CD-SEM over varying focus and exposure conditions. OPC models were developed for aggressive quadrupole illumination conditions (k I=0.35) used in 65nm- and 45nm-node logic gate patterning. Model accuracy improvement using 2D contours for calibration through the process window is demonstrated. Additionally this work addresses the issues of automating the contour extraction and calibration process, reducing the data collection burden with improved calibration cycle time.

  14. The comparison of OPC performance and run time for dense versus sparse solutions

    Science.gov (United States)

    Abdo, Amr; Stobert, Ian; Viswanathan, Ramya; Burns, Ryan; Herold, Klaus; Kallingal, Chidam; Meiring, Jason; Oberschmidt, James; Mansfield, Scott

    2008-03-01

    The lithographic processes and resolution enhancement techniques (RET) needed to achieve pattern fidelity are becoming more complicated as the required critical dimensions (CDs) shrink. For technology nodes with smaller devices and tolerances, more complex models and proximity corrections are needed and these significantly increase the computational requirements. New simulation techniques are required to address these computational challenges. The new simulation technique we focus on in this work is dense optical proximity correction (OPC). Sparse OPC tools typically require a laborious, manual and time consuming OPC optimization approach. In contrast, dense OPC uses pixel-based simulation that does not need as much manual setup. Dense OPC was introduced because sparse simulation methodology causes run times to explode as the pattern density increases, since the number of simulation sites in a given optical radius increases. In this work, we completed a comparison of the OPC modeling performance and run time for the dense and the sparse solutions. The analysis found the computational run time to be highly design dependant. The result should lead to the improvement of the quality and performance of the OPC solution and shed light on the pros and cons of using dense versus sparse solution. This will help OPC engineers to decide which solution to apply to their particular situation.

  15. Anaplasma phagocytophilum Asp14 Is an Invasin That Interacts with Mammalian Host Cells via Its C Terminus To Facilitate Infection

    Science.gov (United States)

    Kahlon, Amandeep; Ojogun, Nore; Ragland, Stephanie A.; Seidman, David; Troese, Matthew J.; Ottens, Andrew K.; Mastronunzio, Juliana E.; Truchan, Hilary K.; Walker, Naomi J.; Borjesson, Dori L.; Fikrig, Erol

    2013-01-01

    Anaplasma phagocytophilum, a member of the family Anaplasmataceae, is the tick-transmitted obligate intracellular bacterium that causes human granulocytic anaplasmosis. The life cycle of A. phagocytophilum is biphasic, transitioning between the noninfectious reticulate cell (RC) and infectious dense-cored (DC) forms. We analyzed the bacterium's DC surface proteome by selective biotinylation of surface proteins, NeutrAvidin affinity purification, and mass spectrometry. Transcriptional profiling of selected outer membrane protein candidates over the course of infection revealed that aph_0248 (designated asp14 [14-kDa A. phagocytophilum surface protein]) expression was upregulated the most during A. phagocytophilum cellular invasion. asp14 transcription was induced during transmission feeding of A. phagocytophilum-infected ticks on mice and was upregulated when the bacterium engaged its receptor, P-selectin glycoprotein ligand 1. Asp14 localized to the A. phagocytophilum surface and was expressed during in vivo infection. Treating DC organisms with Asp14 antiserum or preincubating mammalian host cells with glutathione S-transferase (GST)–Asp14 significantly inhibited infection of host cells. Moreover, preincubating host cells with GST-tagged forms of both Asp14 and outer membrane protein A, another A. phagocytophilum invasin, pronouncedly reduced infection relative to treatment with either protein alone. The Asp14 domain that is sufficient for cellular adherence and invasion lies within the C-terminal 12 to 24 amino acids and is conserved among other Anaplasma and Ehrlichia species. These results identify Asp14 as an A. phagocytophilum surface protein that is critical for infection, delineate its invasion domain, and demonstrate the potential of targeting Asp14 in concert with OmpA for protecting against infection by A. phagocytophilum and other Anaplasmataceae pathogens. PMID:23071137

  16. Auto-Mapping and Configuration Method of IEC 61850 Information Model Based on OPC UA

    Directory of Open Access Journals (Sweden)

    In-Jae Shin

    2016-11-01

    Full Text Available The open-platform communication (OPC unified architecture (UA (IEC62541 is introduced as a key technology for realizing a variety of smart grid (SG use cases enabling relevant automation and control tasks. The OPC UA can expand interoperability between power systems. The top-level SG management platform needs independent middleware to transparently manage the power information technology (IT systems, including the IEC 61850. To expand interoperability between the power system for a large number of stakeholders and various standards, this paper focuses on the IEC 61850 for the digital substation. In this paper, we propose the interconnection method to integrate communication with OPC UA and convert OPC UA AddressSpace using system configuration description language (SCL of IEC 61850. We implemented the mapping process for the verification of the interconnection method. The interconnection method in this paper can expand interoperability between power systems for OPC UA integration for various data structures in the smart grid.

  17. Auto-score system to optimize OPC recipe parameters using genetic algorithm

    Science.gov (United States)

    Cao, Liang; Asthana, Abhishek; Ning, Guoxiang; Feng, Jui-Hsuan; Zhang, Jie; Wilkinson, William

    2016-10-01

    The ever increasing pattern densities and design complexities make the tuning of optical proximity correction (OPC) recipes more challenging. There are various recipe tuning methods to meet the challenge, such as genetic algorithm (GA), simulated annealing, and OPC software vendor provided recipe optimizers. However, these methodologies usually only consider edge placement errors (EPEs). Therefore, these techniques may not provide adequate freedom to solve unique problems at special geometries, for example bridge, pinch, and process variation band related violations at complex 2D geometries. This paper introduces a general methodology to fix specific problems identified at the OPC verification stage and demonstrates its successful application to two test-cases. The algorithm and method of the automatic scoring system is introduced in order to identify and prioritize the problems that need to be fixed based on severity, with the POR recipe score used as the baseline reference. A GA optimizer, whose objective function is based on the scoring system, is applied to tune the OPC recipe parameters to optimum condition after generations of selections. The GA optimized recipe would be compared to existing recipe to quantify the amount of improvement. This technique was subsequently applied to eliminate certain chronic OPC verification problems which were encountered in the past. Though the benefits have been demonstrated for limited test cases, employing this technique more universally will enable users to efficiently reduce the number of OPC verification violations and provide robust OPC solutions.

  18. Building block style recipes for productivity improvement in OPC, RET and ILT flows

    Science.gov (United States)

    Wu, Linghui; Kwa, Denny; Wan, Jinyin; Wang, Tom; St. John, Matt; Deeth, Steven; Chen, Xiaohui; Cecil, Tom; Meng, Xiaodong; Lucas, Kevin

    2016-03-01

    Traditional model-based Optical Proximity Correction (OPC) and rule-based Resolution Enhancement Technology (RET) methods have been the workhorse mask synthesis methods in volume production for logic and memory devices for more than 15 years. Rule-based OPC methods have been in standard use for over 20 years now. With continuous technical enhancements, these methods have proven themselves robust, flexible and fast enough to meet many of the technical needs of even the most advanced nodes. Inverse Lithography Technology (ILT) methods are well known to have strong benefits in finding flexible mask pattern solutions to improve process window for the most advanced design locations where traditional methods are not sufficient. However, OPC/RET requirements at each node have changed radically in the last 20 years beyond just technical requirements. The volume of engineering work to be done has also skyrocketed. The number of device layers which need OPC/RET can be 10X higher than in earlier nodes. Additionally, the number of mask layers per device layer is often 2X or more times higher with multiple patterning. Finally, the number of features to correct per mask increases ~2X with each node. These factors led to a large increase in the number of OPC engineers needed to develop the complex new OPC/RET recipes for advanced nodes. In this paper, we describe new developments which significantly improve the productivity of OPC engineers to deploy Rule Based OPC (RBOPC), Model Based OPC (MBOPC), AF, and ILT recipes in modern manufacturing flows. In addition to technical improvements such as novel multiple segment hotspot fixing solvers and ILT hot-spot fixing necessary to support correction needs, we have re-architected the entire flow based on how OPC engineers now develop and maintain OPC/RET recipes. The re-architecture of the flow takes advantages of more recent developments in modular and structured programming methods which are known to benefit ease engineering software

  19. OPC Unified Architecture within the Control System of the ATLAS Experiment

    CERN Document Server

    Nikiel, P P; Franz, S; Schlenker, S; Boterenbrood, H; Filimonov, V

    2014-01-01

    The Detector Control System (DCS) of the ATLAS experiment at the LHC has been using the OPC DA standard as an interface for controlling various standard and custom hardware components and their integration into the SCADA layer.

  20. Synthesis, Characterization, and Photovoltaic Properties of Soluble TiOPc Derivatives

    Directory of Open Access Journals (Sweden)

    Hyo-Jin Kang

    2008-12-01

    Full Text Available We have synthesized soluble TiOPc derivatives containing alkoxy groups for use as additives in dye-sensitized solar cells (DSSCs. The DSSC devices containing these TiOPc derivatives exhibited short-circuit current densities of 8.49~10.04 mA/cm2 and power conversion efficiencies of 2.73~3.62 % under AM 1.5 illumination and 100 mW/cm2 irradiation.

  1. Hybrid OPC modeling with SEM contour technique for 10nm node process

    Science.gov (United States)

    Hitomi, Keiichiro; Halle, Scott; Miller, Marshal; Graur, Ioana; Saulnier, Nicole; Dunn, Derren; Okai, Nobuhiro; Hotta, Shoji; Yamaguchi, Atsuko; Komuro, Hitoshi; Ishimoto, Toru; Koshihara, Shunsuke; Hojo, Yutaka

    2014-03-01

    Hybrid OPC modeling is investigated using both CDs from 1D and simple 2D structures and contours extracted from complex 2D structures, which are obtained by a Critical Dimension-Scanning Electron Microscope (CD-SEM). Recent studies have addressed some of key issues needed for the implementation of contour extraction, including an edge detection algorithm consistent with conventional CD measurements, contour averaging and contour alignment. Firstly, pattern contours obtained from CD-SEM images were used to complement traditional site driven CD metrology for the calibration of OPC models for both metal and contact layers of 10 nm-node logic device, developed in Albany Nano-Tech. The accuracy of hybrid OPC model was compared with that of conventional OPC model, which was created with only CD data. Accuracy of the model, defined as total error root-mean-square (RMS), was improved by 23% with the use of hybrid OPC modeling for contact layer and 18% for metal layer, respectively. Pattern specific benefit of hybrid modeling was also examined. Resist shrink correction was applied to contours extracted from CD-SEM images in order to improve accuracy of the contours, and shrink corrected contours were used for OPC modeling. The accuracy of OPC model with shrink correction was compared with that without shrink correction, and total error RMS was decreased by 0.2nm (12%) with shrink correction technique. Variation of model accuracy among 8 modeling runs with different model calibration patterns was reduced by applying shrink correction. The shrink correction of contours can improve accuracy and stability of OPC model.

  2. Degree of Hydration of OPC and OPC/Fly ash Paste Samples Conditioned at Different Relative Humidity

    Directory of Open Access Journals (Sweden)

    Nasir Shafiq

    2011-05-01

    Full Text Available Degree of hydration of cement paste controls many properties of hardened concrete and/or mortar such as compressive strength. During the drying process, the degree and the rate of hydration of cement paste in concrete/mortar samples are significantly affected by the ambient relative humidity of the exposure conditions. There are various parameters such as the amount of calcium hydroxide, Ca(OH2 in the paste, quantity of the chemically bound water, specific gravity of the paste, fraction of un-hydrated cement, liberated heat of hydration and strength of the hydrated cement may be used to determine the degree of hydration of the cement paste. This paper presents the results of the experimental investigation for the determination of the degree of hydration of 100% cement paste and fly ash blended cement pastes. After 28 days moist curing, the samples were conditioned in 100%, 75%, 65%, 40% and 12% relative humidity. Conditioning of samples in different relative humidity had significant effects on the compressive strength of the mortar samples and the degree of hydration of the paste samples. Conditioning of samples in 100% RH resulted in higher compressive strength and the degree of hydration. Because of the 28 days moist curing and 12 weeks moisture conditioning in different RH, fly ash based samples showed better compressive strength than the OPC samples.

  3. Computational nano OPC DFM for LV Fin-type SRAM

    Science.gov (United States)

    Kadota, Kazuya

    2016-05-01

    Design For Manufacturing (DFM) where the state-of-the-art nano-devices of the sub-20nm node to a subject, for each of the technology has been intricately sophisticated, comprehensive optimization to predict the performance of the device came become very important. [1] To get effective solutions on these subjects, one of the lithographic key is a nano Optical Proximity Correction (OPC) control with SMO technology, and another is TCAD approach using the most advanced computer simulations. And, it is very important to obtain DFM solutions by integrating both. On the other hand, to meet the needs of low-voltage drive and the characteristic variability reduction, in order to obtain a state-of-the-art device performance, the Fin-type transistors are introduced globally as the mainstream because of wider process control margin. This paper, from the point of view of the sub-20nm node DFM, the simulation are conducted on ArF-imm. technology with SMO in SPT, DPT and QPT on TachyonTM [2], and the guideline of design rules are obtained. Furthermore, the simulated transistor pattern shape are directly migrated into TCAD process flow on HyENEXSSTM [3]. Then calculated I-V characteristics on 6 transistors under the various parameters on TCAD, and finally summarized Static Noise Margin (SNM) of SRAMs. Here, various parameters that determine the performance of SRAMs (Fin width, height, angle, dopant concentrations, electric field strength, work function, drive voltage, and operation speed) are intentionally varied and calculated on the TCAD. This computational method is highly sophisticated DFM technology to predict for the leading-edge nano-devices toward for the sub-20nm nodes era [4] [5] [6] [7] .

  4. High accuracy jog CD control on OPC pattern by advanced laser writer Sigma7500

    Science.gov (United States)

    Chin, Tomas; Wu, Wen-Bin; Shih, Chiang-Lin

    2008-10-01

    With the progress of mask writer technology, 50 KV electron beam writers always perform with better pattern fidelity and critical dimension (CD) control than traditional laser raster-scan writers because laser spot size is confined by the laser longer wavelength relative to electron beam. As far as Optical Proximity Correction (OPC) pattern fidelity is concerned, critical masks with OPC process have to choose Variable-Shape-Beam (VSB) electron beam writer presently. However, the over-aggressive OPC fragmentation induces data volume abrupt explosion, longer writing time, higher mask cost and even mask quality degradation 1. Micronic Sigma7500 laser writer introduces a novel imaging system combining partial coherent light and DUV spatial light modulation (SLM) to generate a high-quality pattern image 2. The benefit of raster-scan laser writer is high throughput with consistent writing time regardless of pattern geometry, complexity and data size. However, pattern CD accuracy still needs improvement. This study is to evaluate jog CD control capability of Sigma7500 on OPC typical line-and-space test patterns with different orientations of 0°, 90°, 45° and 135°. In addition, mask CD uniformity and OPC jog height linearity will also be demonstrated.

  5. Electric Signals Regulate the Directional Migration of Oligodendrocyte Progenitor Cells (OPCs) via β1 Integrin.

    Science.gov (United States)

    Zhu, Bangfu; Nicholls, Matthew; Gu, Yu; Zhang, Gaofeng; Zhao, Chao; Franklin, Robin J M; Song, Bing

    2016-11-22

    The guided migration of neural cells is essential for repair in the central nervous system (CNS). Oligodendrocyte progenitor cells (OPCs) will normally migrate towards an injury site to re-sheath demyelinated axons; however the mechanisms underlying this process are not well understood. Endogenous electric fields (EFs) are known to influence cell migration in vivo, and have been utilised in this study to direct the migration of OPCs isolated from neonatal Sprague-Dawley rats. The OPCs were exposed to physiological levels of electrical stimulation, and displayed a marked electrotactic response that was dependent on β1 integrin, one of the key subunits of integrin receptors. We also observed that F-actin, an important component of the cytoskeleton, was re-distributed towards the leading edge of the migrating cells, and that this asymmetric rearrangement was associated with β1 integrin function.

  6. The improvement of OPC accuracy and stability by the model parameters' analysis and optimization

    Science.gov (United States)

    Chung, No-Young; Choi, Woon-Hyuk; Lee, Sung-Ho; Kim, Sung-Il; Lee, Sun-Yong

    2007-10-01

    The OPC model is very critical in the sub 45nm device because the Critical Dimension Uniformity (CDU) is so tight to meet the device performance and the process window latitude for the production level. The OPC model is generally composed of an optical model and a resist model. Each of them has physical terms to be calculated without any wafer data and empirical terms to be fitted with real wafer data to make the optical modeling and the resist modeling. Empirical terms are usually related to the OPC accuracy, but are likely to be overestimated with the wafer data and so those terms can deteriorate OPC stability in case of being overestimated by a small cost function. Several physical terms have been used with ideal value in the optical property and even weren't be considered because those parameters didn't give a critical impact on the OPC accuracy, but these parameters become necessary to be applied to the OPC modeling at the low k1 process. Currently, real optic parameter instead of ideal optical parameter like the laser bandwidth, source map, pupil polarization including the phase and intensity difference start to be measured and those real measured value are used for the OPC modeling. These measured values can improve the model accuracy and stability. In the other hand these parameters can make the OPC model to overcorrect the process proximity errors without careful handling. The laser bandwidth, source map, pupil polarization, and focus centering for the optical modeling are analyzed and the sample data weight scheme and resist model terms are investigated, too. The image blurring by actual laser bandwidth in the exposure system is modeled and the modeling result shows that the extraction of the 2D patterns is necessary to get a reasonable result due to the 2D patterns' measurement noise in the SEM. The source map data from the exposure machine shows lots of horizontal and vertical intensity difference and this phenomenon must come from the measurement noise

  7. OPC UA Information Modeling:A Case Study of Coal Mine Supervisory Control System%OPC UA信息建模:煤矿监控系统集成案例研究

    Institute of Scientific and Technical Information of China (English)

    江城; 张英俊; 谢斌红

    2014-01-01

    In order to solve the traditional OPC technology which is lack of data modeling ability of interoperability problems, OPC foundation releases OPC UA specification, solving the problem in theory, but the specific modeling process is not completed. This paper puts forward operable OPC UA information modeling process, and takes the coal mine integrated monitoring system as a case to verify feasibility of this modeling process, at the same time, promotes the development of OPC UA from theory to practice.%为了传统OPC技术由于数据建模能力不足而导致的互操作性问题,OPC基金会发布了OPC UA规范,从理论上解决了此问题,但缺乏具体的建模流程。提出具有可操作性的OPC UA信息建模流程,并以煤矿监控系统集成作为案例来验证此建模流程具有可行性,同时推动了OPC UA从理论到实践的发展。

  8. Communication Test for ‘MatrikonOPC Server for SCADA DNP 3’ with RTDS

    DEFF Research Database (Denmark)

    Wu, Qiuwei; Cha, Seung-Tae; Saleem, Arshad;

    2010-01-01

    The purpose of the communication test for ‘MatrikonOPC server for SCADA DNP 3’ with RTDS is to verify the data exchange between the ‘MatrikonOPC server for SCADA DNP 3’ and the RTDS using the DNP 3 protocol.The communication test is part of the work for the ‘Wind in Øresund’ project. The objective...... of the ‘Wind in Øresund’ project is to build a demonstration and education system of power system operation and control with a RTDS and a SCADA system....

  9. Research of Integrity and Authentication in OPC UA Communication Using Whirlpool Hash Function

    Directory of Open Access Journals (Sweden)

    Kehe Wu

    2015-08-01

    Full Text Available Currently, the demand for information security of industrial control systems is becoming more and more urgent, but the security model proposed by OPC UA cannot meet the practical requirements of industrial control systems. For this reason, this paper proposes a new security communication model to provide integrity and authentication in OPC UA. This model uses the Whirlpool hash function to check integrity and generates digital signature along with RSA in message transmission. Compared to SHA-1, Whirlpool has a higher calculation speed and lower collision rate. Through this model, terminals in the upper layer can communicate with field devices via a channel with high security and efficiency.

  10. Aplicación cliente-servidor MatLab®-WinCC® empleando comunicación OPC

    National Research Council Canada - National Science Library

    Ana Isabel González Santos; Daniel Sabín

    2011-01-01

    ... de la comunicación OPC con otras aplicaciones específicas de mayor potencial en materia de cálculo numérico como las desarrolladas en el Simulink de MatLab ® . Palabras claves: Comunicación OPC, control, detección de fallos, identificación, MatLab ® , WinCC®

  11. Combining mask and OPC process verification for improved wafer patterning and yield

    Science.gov (United States)

    Hamouda, Ayman; Abdelghany, Hesham

    2016-10-01

    As technology advances into deep submicron nodes, the mask manufacturing process accuracy become more important. Mask Process Correction (MPC) has been transitioning from Rules-Based Mask Process correction to Model-Based Mask Process Correction mode. MPC is a subsequent step to OPC, where additional perturbation is applied to the mask shapes to correct for the mask manufacturing process. Shifting towards full model-based MPC is driven mainly by the accuracy requirements in advanced technology nodes, both for DUV and EUV processes. In the current state-of-the-art MPC process, MPC is completely decoupled from OPC, where each of them assumes that the other is executing perfectly. However, this decoupling is not suitable anymore due to the limited tolerance in the mask CDU budget and the increased wafer CDU requirements required from OPC. It is becoming more important to reduce any systematic mask errors, especially where they matter the most. In this work, we present a new combined-verification methodology that allows testing the combined effect of mask process and lithography process together and judging the final wafer patterning quality. This has the potential to intercept risks due to superposition of OPC and MPC correction residual errors, and capturing and correcting such a previously hidden source of patterning degradation.

  12. Co-expression of the C-terminal domain of Yersinia enterocolitica invasin enhances the efficacy of classical swine-fever-vectored vaccine based on human adenovirus

    Indian Academy of Sciences (India)

    Helin Li; Pengbo Ning; Zhi Lin; Wulong Liang; Kai Kang; Lei He; Yanming Zhang

    2015-03-01

    The use of adenovirus vector-based vaccines is a promising approach for generating antigen-specific immune responses. Improving vaccine potency is necessary in other approaches to address their inadequate protection for the majority of infectious diseases. This study is the first to reconstruct a recombinant replication-defective human adenovirus co-expressing E2 and invasin C-terminal (InvC) glycoproteins (rAd-E2-InvC). rAd-E2-InvC with 2×106 TCID50 was intramuscularly administered two times to CSFV-free pigs at 14 day intervals. No adverse clinical reactions were observed in any of the pigs after the vaccination. The CSFV E2-specific antibody titer was significantly higher in the rAd-E2-InvC group than that in the rAdV-E2 group as measured by NPLA and blocking ELISA. Pigs immunized with rAd-E2-InvC were completely protected against lethal challenge. Neither CSFV RNA nor pathological changes were detected in the tissues after CSFV challenge. These results demonstrate that rAd-E2-InvC could be an alternative to the existing CSF vaccine. Moreover, InvC that acts as an adjuvant could enhance the immunogenicity of rAdV-E2 and induce high CSFV E2-specific antibody titer and protection level.

  13. Integration of Sensors, Controllers and Instruments Using a Novel OPC Architecture

    Science.gov (United States)

    2017-01-01

    The interconnection between sensors, controllers and instruments through a communication network plays a vital role in the performance and effectiveness of a control system. Since its inception in the 90s, the Object Linking and Embedding for Process Control (OPC) protocol has provided open connectivity for monitoring and automation systems. It has been widely used in several environments such as industrial facilities, building and energy automation, engineering education and many others. This paper presents a novel OPC-based architecture to implement automation systems devoted to R&D and educational activities. The proposal is a novel conceptual framework, structured into four functional layers where the diverse components are categorized aiming to foster the systematic design and implementation of automation systems involving OPC communication. Due to the benefits of OPC, the proposed architecture provides features like open connectivity, reliability, scalability, and flexibility. Furthermore, four successful experimental applications of such an architecture, developed at the University of Extremadura (UEX), are reported. These cases are a proof of concept of the ability of this architecture to support interoperability for different domains. Namely, the automation of energy systems like a smart microgrid and photobioreactor facilities, the implementation of a network-accessible industrial laboratory and the development of an educational hardware-in-the-loop platform are described. All cases include a Programmable Logic Controller (PLC) to automate and control the plant behavior, which exchanges operative data (measurements and signals) with a multiplicity of sensors, instruments and supervisory systems under the structure of the novel OPC architecture. Finally, the main conclusions and open research directions are highlighted. PMID:28654002

  14. Oligomeric proanthocyanidin complexes (OPC) exert anti-proliferative and pro-apoptotic effects on prostate cancer cells.

    Science.gov (United States)

    Neuwirt, Hannes; Arias, Mercedes Cedeno; Puhr, Martin; Hobisch, Alfred; Culig, Zoran

    2008-11-01

    Oligomeric proanthocyanidin complexes (OPC) are extracted from grape seeds or maritime pine bark and have been used for enhancement of capillary stability and lymphatic drainage. Since a role for OPC in cancer prevention was postulated, we asked whether they have an effect on prostate cancer cells. Cell proliferation was determined by (3)H-thymidine assay and cell cycle status was analyzed on a flow cytometer. Expression of regulators of proliferation and apoptosis was determined by Western blot. We found that androgen-responsive cells LNCaP are more sensitive to OPC in terms of inhibition of proliferation in comparison to androgen receptor-negative PC3 or DU145 cells. Treatment with OPC resulted in a decrease in the percentage of LNCaP cells in the S phase and an increase in the percentage of cells in sub G1 phase. The anti-proliferative and pro-apoptotic effect of OPC in the LNCaP cell line was associated with down-regulation of expression of the androgen receptor. Interestingly, similar regulatory effects of OPC, such as inhibition of expression of cyclin-dependent kinases and cyclins and stimulation of tumor suppressors p21 and p27, were seen in LNCaP and PC3 cells. Favorable changes in the Bcl-2/Bax ratio were observed in LNCaP and PC3 cells after the treatment with OPC. OPC caused an increase of phosphorylated mitogen-activated protein kinase p44 and p42, thus suggesting induction of cellular differentiation. We conclude that OPC is a candidate that fulfills criteria for chemopreventive strategies in prostate cancer that might be established in following in vivo studies. (c) 2008 Wiley-Liss, Inc.

  15. OPC mask simplification using over-designed timing slack of standard cells

    Science.gov (United States)

    Qu, Yifan; Heng, Chun Huat; Tay, Arthur; Lee, Tong Heng

    2013-05-01

    It is well known that VLSI circuits must be designed to sustain the variations in process, voltage, temperature, etc. As a result, standard cell libraries (collections of the basic circuit components) are usually designed with large margin (also known as "timing slack"). However, in circuit manufacturing, only part of the margin will be utilized. The knowledge of the rest of the margin (over-designed timing slack), armed with models that link between timing domain and shape domain, can help to reduce the complexity of mask patterns and manufacturing cost. This paper proposed a novel methodology to simplify mask patterns in optical proximity correction (OPC) by using extra margin in timing (over-designed timing slack). This methodology can be applied after a conventional OPC, and is compatible with the current application-specific integrated circuit (ASIC) design flow. This iterative method is applied to each occurrence of over-designed timing slack. The actual value of timing slack can be estimated from post-OPC simulation. A timing cost function is developed in this work to map timing slack in timing domain to mask patterns in shape domain. This enables us to adjust mask patterns selectively based on the outcome of the cost function. All related mask patterns with over-designed timing slack will be annotated and simplified using our proposed mask simplification algorithm, which is in fact to merge the nearby edge fragments on the mask patterns. Simulations are conducted on a standard cell library and a full chip design to validate this proposed approach. When compared to existing OPC methods without mask simplification in the literature, our approach achieved a 51% reduction in mask fragment count, and this directly leads to a large saving in lithography manufacturing cost. The result also shows that timing closure is ensured, though part of the timing slack has been sacrificed.

  16. Calibrating OPC model with full CD profile data for 2D and 3D patterns using scatterometry

    Science.gov (United States)

    Dave, Aasutosh D.; Kritsun, Oleg; Deng, Yunfei; Yoshimoto, Kenji; Li, Jie; Hu, Jiangtao

    2009-03-01

    The ability to manage critical dimensions (CDs) of structures on IC devices is vital to improving product yield and performance. It is challenging to achieve accurate metrology data as the geometries shrink beyond 40 nm features. At this technology node CDSEM noise and resist LER are of significant concerns1. This paper examines the extendibility of scatterometry techniques to characterize structures that are close to limits of lithographic printing and to extract full profile information for 2D and 3D features for OPC model calibration2. The resist LER concerns are diminished because of the automatic averaging that scatterometry provides over the measurement pad; this represents a significant added value for proper OPC model calibration and verification. This work develops a comparison matrix to determine the impact of scatterometry data on OPC model calibration with conventional CDSEM measurements. The paper will report test results for the OPC model through process data for accuracy and predictability.

  17. Universal lab on a smartphone: a research of TiOPc thin film as a light dependence electrode

    Science.gov (United States)

    Lin, PoHan; Hsu, Y. H.; Lee, C. K.

    2014-02-01

    In this paper, we study the photoconductivity of a polymer-based TiOPc (Titanium Oxide Phthalocyanine) thin-film for the development of a multi-opto-piezoelectric-valve-array. Using a polymer-based TiOPc thin film to serve as the electrode and a structural layer of a piezoelectric polymer, P(VDF-TrFE) poly[(vinylidenefluoride-co-trifluoroethylene], an optical control valve-array could be developed for manipulating multiple microdroplets for the application of digital microfluidic. In this ongoing project, the dependency of the light intensity, thickness, and composition of spin-coated polymer-based TiOPc thin-film was studied. The experimental finding suggested that a 14 to 55 times resistivity change could be achieved by controlling the film thickness to be between 0.9 μm and 1.5 μm with TiOPc concentration of 20% and 30% w/w compositions.

  18. Optical and electrical properties of TiOPc doped Alq3 thin films

    Science.gov (United States)

    Ramar, M.; Suman, C. K.; Tyagi, Priyanka; Srivastava, R.

    2015-06-01

    The Titanyl phthalocyanine (TiOPc) was doped in Tris (8-hydroxyquinolinato) aluminum (Alq3) with different concentration. The thin film of optimized doping concentration was studied extensively for optical and electrical properties. The optical properties, studied using ellipsometry, absorption and photoluminescence. The absorption peak of Alq3 and TiOPc was observed at 387 nm and 707 nm and the photo-luminescence intensity (PL) peak of doped thin film was observed at 517 nm. The DC and AC electrical properties of the thin film were studied by current density-voltage (J-V) characteristics and impedance over a frequency range of 100 Hz - 1 MHz. The electron mobility calculated from trap-free space-charge limited region (SCLC) is 0.17×10-5 cm2/Vs. The Cole-Cole plots shows that the TiOPc doped Alq3 thin film can be represented by a single parallel resistance RP and capacitance CP network with a series resistance RS (10 Ω). The value of RP and CP at zero bias was 1587 Ω and 2.568 nF respectively. The resistance RP decreases with applied bias whereas the capacitance CP remains almost constant.

  19. Optical and electrical properties of TiOPc doped Alq{sub 3} thin films

    Energy Technology Data Exchange (ETDEWEB)

    Ramar, M.; Suman, C. K., E-mail: sumanck@nplindia.org; Tyagi, Priyanka; Srivastava, R. [CSIR-Network of Institutes for Solar Energy CSIR - National Physical Laboratory, Dr. K. S. Krishnan Marg, New Delhi -110012 (India)

    2015-06-24

    The Titanyl phthalocyanine (TiOPc) was doped in Tris (8-hydroxyquinolinato) aluminum (Alq3) with different concentration. The thin film of optimized doping concentration was studied extensively for optical and electrical properties. The optical properties, studied using ellipsometry, absorption and photoluminescence. The absorption peak of Alq{sub 3} and TiOPc was observed at 387 nm and 707 nm and the photo-luminescence intensity (PL) peak of doped thin film was observed at 517 nm. The DC and AC electrical properties of the thin film were studied by current density-voltage (J-V) characteristics and impedance over a frequency range of 100 Hz - 1 MHz. The electron mobility calculated from trap-free space-charge limited region (SCLC) is 0.17×10{sup −5} cm{sup 2}/Vs. The Cole-Cole plots shows that the TiOPc doped Alq{sub 3} thin film can be represented by a single parallel resistance R{sub P} and capacitance C{sub P} network with a series resistance R{sub S} (10 Ω). The value of R{sub P} and C{sub P} at zero bias was 1587 Ω and 2.568 nF respectively. The resistance R{sub P} decreases with applied bias whereas the capacitance C{sub P} remains almost constant.

  20. OPC Server and BridgeView Application for High Voltage Power Supply Lecroy 1458

    CERN Document Server

    Swoboda, D; CERN. Geneva

    2000-01-01

    Abstract The aim of this project was to develop an OPC server to communicate over an RS232 serial line. This communication media is commonly used with commercial instruments. The development was made for a High Voltage power supply in the context of the Alice [1] experiment. In addition, the structured modular concept will allow changing the transmission media or power supply type with little effort. The high voltage power supply should be accessible remotely through a network. OPC[2] is an acronym for OLE[3] for Process Control. OPC is based on the DCOM [3] communication protocol, which allows communication with any computer running a Windows based OS. This standard is widely used in industry to access device data through Windows applications. The concept is based on the client-server architecture. The hardware and the software architecture are described. Subsequently details of the implemented programs are given with emphasis on the possibility to replace parts of the software in order to use differ...

  1. Skeleton-based OPC application for DSA full chip mask correction

    Science.gov (United States)

    Schneider, L.; Farys, V.; Serret, E.; Fenouillet-Beranger, C.

    2015-09-01

    Recent industrial results around directed self-assembly (DSA) of block copolymers (BCP) have demonstrated the high potential of this technique [1-2]. The main advantage being cost reduction thanks to a reduced number of lithographic steps. Meanwhile, the associated correction for mask creation must account for the introduction of this new technique, maintaining a high level of accuracy and reliability. In order to create VIA (Vertical Interconnect Layer) layer, graphoepitaxy DSA can be used. The technique relies on the creation of a confinement guides where the BCP can separate into distinct regions and resulting patterns are etched in order to obtain an ordered series of VIA contact. The printing of the guiding pattern requires the use of classical lithography. Optical proximity correction (OPC) is applied to obtain the best suited guiding pattern allowing to match a specific design target. In this study, an original approach for DSA full chip mask optical proximity correction based on a skeleton representation of a guiding pattern is proposed. The cost function for an OPC process is based on minimizing the Central Placement Error (CPE), defined as the difference between an ideal skeleton target and a generated skeleton from a guiding contour. The high performance of this approach for DSA OPC full chip correction and its ability to minimize variability error on via placement is demonstrated and reinforced by the comparison with a rigorous model. Finally this Skeleton approach is highlighted as an appropriate tool for Design rules definition.

  2. Halftone biasing OPC technology: an approach for achieving fine bias control on raster-scan systems

    Science.gov (United States)

    Nakagawa, Kent H.; Chen, J. Fung; Socha, Robert J.; Laidig, Thomas L.; Wampler, Kurt E.; Van Den Broeke, Douglas J.; Dusa, Mircea V.; Caldwell, Roger F.

    1999-08-01

    As the semiconductor roadmap continues to require imaging of smaller features on wafers, we continue to explore new approaches in OPC strategies to enhance existing technology. Advanced reticle design, intended for printing sub-wavelength features, requires the support of very fine-increment biases on semi-densely-pitched lines, where the CD correction requires only a fraction of the spot size of an e-beam system. Halftone biasing, a new OPC strategy, has been proposed to support these biases on a raster-scan e-beam system without the need for a reduced address unit and the consequent write time penalty. The manufacturability and inspectability of halftone-biased lines are explored, using an OPC characterization reticle. Pattern fidelity is examined using both optical and SEM tools. Printed DUV resist line edge profiles are compared for both halftone and non-halftone feature edges. Halftone biasing was applied to an SRAM-type simulation reticle, to examine its impact on data volume, write time reduction, and printing performance.

  3. 基于VC的上位机与PLC间的OPC通讯%Implemention of opc communication between PC and plc through VC

    Institute of Scientific and Technical Information of China (English)

    赵芳婷; 陈树亮

    2015-01-01

    This paper mainly introduced how to implement the OPC communication between Industrial PC and S7 300 under Visual C++. It also referred to the function and application of the OPC com component.%主要通过Visual C++实现了上位机与下位机之间的OPC通讯,概述了OPC com组件的功能及其应用。

  4. Cost effective solution using inverse lithography OPC for DRAM random contact layer

    Science.gov (United States)

    Jun, Jinhyuck; Hwang, Jaehee; Choi, Jaeseung; Oh, Seyoung; Park, Chanha; Yang, Hyunjo; Dam, Thuc; Do, Munhoe; Lee, Dong Chan; Xiao, Guangming; Choi, Jung-Hoe; Lucas, Kevin

    2017-04-01

    Many different advanced devices and design layers currently employ double patterning technology (DPT) as a means to overcome lithographic and OPC limitations at low k1 values. Certainly device layers with k1 value below 0.25 require DPT or other pitch splitting methodologies. DPT has also been used to improve patterning of certain device layers with k1 values slightly above 0.25, due to the difficulty of achieving sufficient pattern fidelity with only a single exposure. Unfortunately, this broad adoption of DPT also came with a significant increase in patterning process cost. In this paper, we discuss the development of a single patterning technology process using an integrated Inverse Lithography Technology (ILT) flow for mask synthesis. A single pattering technology flow will reduce the manufacturing cost for a k1 > 0.25 full chip random contact layer in a memory device by replacing the more expensive DPT process with ILT flow, while also maintaining good lithographic production quality and manufacturable OPC/RET production metrics. This new integrated flow consists of applying ILT to the difficult core region and traditional rule-based assist features (RBAFs) with OPC to the peripheral region of a DRAM contact layer. Comparisons of wafer results between the ILT process and the non-ILT process showed the lithographic benefits of ILT and its ability to enable a robust single patterning process for this low-k1 device layer. Advanced modeling with a negative tone develop (NTD) process achieved the accuracy levels needed for ILT to control feature shapes through dose and focus. Details of these afore mentioned results will be described in the paper.

  5. Meningococcal surface fibril (Msf) binds to activated vitronectin and inhibits the terminal complement pathway to increase serum resistance.

    Science.gov (United States)

    Griffiths, Natalie J; Hill, Darryl J; Borodina, Elena; Sessions, Richard B; Devos, Nathalie I; Feron, Christiane M; Poolman, Jan T; Virji, Mumtaz

    2011-12-01

    Complement evasion is an important survival strategy of Neisseria meningitidis (Nm) during colonization and infection. Previously, we have shown that Nm Opc binds to serum vitronectin to inhibit complement-mediated killing. In this study, we demonstrate meningococcal interactions with vitronectin via a novel adhesin, Msf (meningococcal surface fibril, previously NhhA or Hsf). As with Opc, Msf binds preferentially to activated vitronectin (aVn), engaging at its N-terminal region but the C-terminal heparin binding domain may also participate. However, unlike Opc, the latter binding is not heparin-mediated. By binding to aVn, Msf or Opc can impart serum resistance, which is further increased in coexpressers, a phenomenon dependent on serum aVn concentrations. The survival fitness of aVn-binding derivatives was evident from mixed population studies, in which msf/opc mutants were preferentially depleted. In addition, using vitronectin peptides to block Msf-aVn interactions, aVn-induced inhibition of lytic C5b-9 formation and of serum killing could be reversed. As Msf-encoding gene is ubiquitous in the meningococcal strains examined and is expressed in vivo, serum resistance via Msf may be of significance to meningococcal pathogenesis. The data imply that vitronectin binding may be an important strategy for the in vivo survival of Nm for which the bacterium has evolved redundant mechanisms.

  6. RuMBa: a rule-model OPC for low MEEF 130-nm KrF lithography

    Science.gov (United States)

    Hsu, Stephen; Shi, Xuelong; Hsu, Chungwei Michael; Corcoran, Noel P.; Chen, J. Fung; Desai, Sunil; Sherrill, Micheal J.; Tseng, Y. C.; Chang, H. A.; Kao, J. F.; Tseng, Alex; Liu, WeiJyh; Chen, Anseime; Lin, Arthur; Kujten, Jan P.; Jacobs, Eric; Verhappen, Arjan

    2001-09-01

    For cost effective 130nm node manufacturing, it is prefer to use KrF binary chrome mask. To realize a production worth process for making random logic device, we need to effectively control mask error enhancement factor (MEEF) through pitch. In low k1 lithography, process parameters such as focus, lens aberration, linewidth, and line pitch, style of proximity correction (OPC), and resist process conditions, etc., all impact MEEF. We show a powerful RuMBa OPC method that can reduce MEEF to an acceptable level (close to 1(using KrF resist process. We believe that RuMBa OPC method can be further extended for sub 100nm ArF process. In wafer printing experiment, we have designed a new style of LineSweeper reticles for our lithography process optimization. Both simulated and printed wafer CD data were used to calculate the overlapped process window along with respective MEEF. These are the metric we used to assess the 130nm process performance. Using RuMBa OPC, we are able to achieve overlapped process window that is sufficient for 130nm gate mask process. The CD through pitch calibration is critical for an accurate model-based correct at location where OPC rule cannot cover. A high accuracy CD through pitch calibration methodology is developed for model calibration. In this paper, we have compared the 130nm performance using KrF binary mask, KrF 6% attenuated PSM, and ArF binary mask.

  7. DKIST visible tunable filter control software: connecting the DKIST framework to OPC UA

    Science.gov (United States)

    Bell, Alexander; Halbgewachs, Clemens; Kentischer, Thomas J.; Schmidt, Wolfgang; von der Lühe, Oskar; Sigwarth, Michael; Fischer, Andreas

    2014-07-01

    The Visible Tunable Filter (VTF) is a narrowband tunable filter system for imaging spectroscopy and spectropolarimetry based on large-format Fabry Perot interferometers that is currently built by the Kiepenheuer Institut fuer Sonnenphysik for the Daniel K. Inouye Solar Telescope (DKIST). The control software must handle around 30 motorised drives, 3 etalons, a polarizing modulator, a helium neon laser for system calibration, temperature controllers and a multitude of sensors. The VTF is foreseen as one of the DKISTs first-light instruments and should become operational in 2019. In the design of the control software we strongly separate between the high-level part interfacing to the DKIST common services framework (CSF) and the low-level control system software which guarantees real-time performance and synchronization to precision time protocol (PTP) based observatory time. For the latter we chose a programmable logic controller (PLC) from Beckhoff Automation GmbH which supports a wide set of input and output devices as well as distributed clocks for synchronizing signals down to the sub-microsecond level. In this paper we present the design of the required control system software as well as our work on extending the DKIST CSF to use the OPC Unified Architecture (OPC UA) standard which provides a cross-platform communication standard for process control and automation as an interface between the high-level software and the real-time control system.

  8. Vertical Integration in factories using OPC-UA and IEC-61499

    Directory of Open Access Journals (Sweden)

    Marcelo V. García

    2017-02-01

    Full Text Available Nowadays, factory automation systems need to cope with very different challenges, such as big data, IIoT, etc. These challenges lead to a new generation of automation systems based on the so-called Cyber-Physical Production Systems (CPPS globally connected to form a flexible System of Cyber-Physical Production Systems (SoCPPS. CPPSs require acquisition of production system data and smart data processing to extract information to improve the overall system performance. To achieve that it is needed to bridge the gap between the control systems and higher layers. This paper discusses an approach to use the IEC 61499 function block concept to exchange data between plant floor and higher layers using an industrial standard like OPC UA. The OPC UA server offers subscription mechanisms, making possible the integration of several resources residing at plant floor. As it runs on embedded devices, the proposal makes possible to acquire plant information at low cost, enabling at the same time, a component-based design for enterprise plant floor control with independence of the hardware platform used

  9. Considering mask pellicle effect for more accurate OPC model at 45nm technology node

    Science.gov (United States)

    Wang, Ching-Heng; Liu, Qingwei; Zhang, Liguo

    2008-11-01

    Now it comes to the 45nm technology node, which should be the first generation of the immersion micro-lithography. And the brand-new lithography tool makes many optical effects, which can be ignored at 90nm and 65nm nodes, now have significant impact on the pattern transmission process from design to silicon. Among all the effects, one that needs to be pay attention to is the mask pellicle effect's impact on the critical dimension variation. With the implement of hyper-NA lithography tools, light transmits the mask pellicle vertically is not a good approximation now, and the image blurring induced by the mask pellicle should be taken into account in the computational microlithography. In this works, we investigate how the mask pellicle impacts the accuracy of the OPC model. And we will show that considering the extremely tight critical dimension control spec for 45nm generation node, to take the mask pellicle effect into the OPC model now becomes necessary.

  10. Design strategies for future lithography technologies (or: OPC will never die)

    Science.gov (United States)

    Schellenberg, Franklin M.

    2003-06-01

    Resolution Enhancement Technologies (RETs) have extended the life of optical lithography well into the regimes of k1=0.3. Although there are a number of RTEs widely in use now, all involve some degree of optical and process correction (OPC). This puts additional strain on the data handling and management capabilities for process calibration and mask preparation. Alternative lithogrpahic technologies, such as Extreme UV (EUV), electron projection lithography (EPL), direct-write maskless lithography (MLL), and even nanoimprint techniques have been proposed and are under rapid development. All these alternatives create patterns usinga wavelength (or the dimension of the writing tool itself) smaller than the desired feature. Since these should confortably increase k1 back to the values enjoyed many years ago, it is generally assumed that the issues associated with OPC and the data management for RETs will go away. This is not true. Although these will no longer have "optical proximity" effects to compensate, each of these processes introduces its own signature of distortions, which in turn will require compensation and the associated data management. In this paper, we will inventory the state of development for each of these technologies, and outline the expected compensations and requirements palced on data management that are associated with the adoption of the technology. These effects include electron proximity effects and pattern stitching for EPL, Flare induced proximity effects for EUV, gray scale mapping for various maskless techniques, and even local process biasing for various nanoimprint approaches.

  11. Bayesian analysis for OPC modeling with film stack properties and posterior predictive checking

    Science.gov (United States)

    Burbine, Andrew; Fenger, Germain; Sturtevant, John; Fryer, David

    2016-10-01

    The use of optical proximity correction (OPC) demands increasingly accurate models of the photolithographic process. Model building and analysis techniques in the data science community have seen great strides in the past two decades which make better use of available information. This paper expands upon Bayesian analysis methods for parameter selection in lithographic models by increasing the parameter set and employing posterior predictive checks. Work continues with a Markov chain Monte Carlo (MCMC) search algorithm to generate posterior distributions of parameters. Models now include wafer film stack refractive indices, n and k, as parameters, recognizing the uncertainties associated with these values. Posterior predictive checks are employed as a method to validate parameter vectors discovered by the analysis, akin to cross validation.

  12. Chloride Transport in OPC Concrete Subjected to the Freeze and Thaw Damage

    Directory of Open Access Journals (Sweden)

    Ki Yong Ann

    2017-01-01

    Full Text Available To predict the durability of a concrete structure under the coupling degradation consisting of the frosting and chloride attack, microstructural analysis of the concrete pore structure should be accompanied. In this study, the correlation between the pore structure and chloride migration for OPC concrete was evaluated at the different cement content in the concrete mix accounting for 300, 350, and 400 kg/m3 at 0.45 of a free water cement ratio. The influence of frosting damage on the rate of chloride transport was assessed by testing with concrete specimens subjected to a rapid freezing and thawing cyclic environment. As a result, it was found that chloride transport was accelerated by frost damage, which was more influential at the lower cement content. The microscopic examination of the pore structure showed that the freezing environment increased the volume of the large capillary pore in the concrete matrix.

  13. 基于光刻模型的动态自适应切分OPC%Model-Based Dynamic Dissection in OPC

    Institute of Scientific and Technical Information of China (English)

    杨祎巍; 史峥; 严晓浪; 陈晔

    2008-01-01

    光学邻近校正(OPC)技术已经成为纳米级半导体工艺技术中的一个关键.目前在OPC中多边形的切分算法均基于配方(recipe),但随着特征线宽减小及版图越来越复杂,用于切分的配方难以覆盖所有的情况;不完备的配方引发或加剧了芯片上的纹波、断线和桥连等现象.论文提出了一种新的基于光刻模型的动态自适应切分算法,根据不同的光刻模型和几何环境可以给出不同的切分,并且可在校正循环中动态改变切分方式和采样点的放置位置.通过90nm工艺下版图设计的验证,这种切分不仅减少了被切分出的小线段(segment)数量的10%~15%,节省了调试切分规则的时间,而且提高了 OPC的质量,使PRV(post RET verification)错误率降低了35%.

  14. Monte Carlo sensitivity analysis of EUV mask reflectivity and its impact on OPC accuracy

    Science.gov (United States)

    Chen, Yulu; Wood, Obert; Rankin, Jed; Gullikson, Eric; Meyer-Ilse, Julia; Sun, Lei; Qi, Zhengqing John; Goodwin, Francis; Kye, Jongwook

    2017-03-01

    Unlike optical masks which are transmissive optical elements, use of extreme ultraviolet (EUV) radiation requires a reflective mask structure - a multi-layer coating consisting of alternating layers of high-Z (wave impedance) and low-Z materials that provide enhanced reflectivity over a narrow wavelength band peaked at the Bragg wavelength.1 Absorber side wall angle, corner rounding,2 surface roughness,3 and defects4 affect mask performance, but even seemingly simple parameters like bulk reflectivity on mirror and absorber surfaces can have a profound influence on imaging. For instance, using inaccurate reflectivity values at small and large incident angles would diminish the benefits of source mask co-optimization (SMO) and result in larger than expected pattern shifts. The goal of our work is to calculate the variation in mask reflectivity due to various sources of inaccuracies using Monte Carlo simulations. Such calculation is necessary as small changes in the thickness and optical properties of the high-Z and low-Z materials can cause substantial variations in reflectivity. This is further complicated by undesirable intermixing between the two materials used to create the reflector.5 One of the key contributors to mask reflectivity fluctuation is identified to be the intermixing layer thickness. We also investigate the impacts on OPC when the wrong mask information is provided, and evaluate the deterioration of overlapping process window. For a hypothetical N7 via layer, the lack of accurate mask information costs 25% of the depth of focus at 5% exposure latitude. Our work would allow the determination of major contributors to mask reflectivity variation, drive experimental efforts of measuring such contributors, provide strategies to optimize mask reflectivity, and quantize the OPC errors due to imperfect mask modeling.

  15. Factors affecting early compressive strength of alkali activated fly ash (OPC-free concrete

    Directory of Open Access Journals (Sweden)

    Palomo, A.

    2007-08-01

    Full Text Available This paper presents the findings of experimental research into the chief characteristics of a new type of concrete made solely with alkali activated fly ash (AAFA: i.e., free of ordinary Portland cement (OPC. The results of testing to determine specific properties of the fresh concrete and the development of its mechanical strength showed that most of the factors that affect the manufacture and final properties of Portland cement concrete (water/cement ratio, curing conditions, etc. also impact the preparation and final quality of this new material. A number of parameters specific to AAFA concrete (nature and concentration of alkali present in the system were also explored to determine their role in the setting and hardening process.Este trabajo presenta los resultados de una investigación experimental llevada a cabo para evaluar las principales características de un nuevo tipo de hormigón fabricado solamente con ceniza volante activada alcalinamente (AAFA; es decir, sin cemento Portland comercial (OPC. Los resultados de los ensayos realizados para determinar las propiedades específicas del hormigón fresco y el desarrollo de resistencias mecánicas mostraron que la mayoría de los factores que afectan al proceso de fabricación y a las propiedades finales de los hormigones de cemento Portland (relación agua/cemento, condiciones de curado, etc. también afectan a la preparación y calidad final de estos nuevos materiales. También fueron estudiados otros parámetros específicos de los hormigones de AAFA (la naturaleza y concentración del álcali presente en el sistema para determinar su papel en el proceso de fraguado y endurecimiento.

  16. New methodologies for lower-K1 EUV OPC and RET optimization

    Science.gov (United States)

    Hooker, Kevin; Kazarian, Aram; Zhou, Xibin; Tuttle, Josh; Xiao, Guangming; Zhang, Yunqiang; Lucas, Kevin

    2017-03-01

    EUV lithography is viewed as a highly desirable technology for 5nm and 7nm node patterning cost reduction and process simplicity. However, for the 5nm and 7nm nodes EUV not only needs to function in a low-K1 resolution environment but has several new and complex patterning issues which will need accurate compensation by mask synthesis tools and flows. The main new issues are: long-range flare variation across the chip, feature dependent focus offsets due to high mask topography, asymmetry inducing shadowing effects which vary across the lens slit, significantly higher lens aberrations, illumination source changes (across the lens and with time) and new resist exposure mechanisms. These solutions must be successfully deployed at low K1 values and must be integrated together to create OPC/RET flows which have high resolution, high accuracy, and are fast to deploy. Therefore, the combined requirements of low-K1 resolution, full reticle correction accuracy and process window can be even more challenging than in current optical lithography mask synthesis flows. Advanced computational methods such as ILT and model-based SRAF optimization are well known to have considerable benefits in process window and resolution for low-K1 193 lithography. However, these methods have not been well studied to understand their benefits for lower-K1 EUV lithography where fabs must push EUV resolution, 2D accuracy and process window to their limits. In this paper, we investigate where inverse lithography methods can improve EUV patterning weaknesses vs. traditional OPC/RET. We first show how ILT can be used to guide a better understanding of optimal solutions for EUV mask synthesis. We then provide detailed comparisons of ILT and traditional methods on a wide range of mask synthesis applications.

  17. OPC 技术在氯乙烯聚合过程软测量中的应用%Application of OPC Technology in Soft Measurement of Vinyl Chloride Polymerization Process

    Institute of Scientific and Technical Information of China (English)

    朱鹏飞; 夏陆岳; 周猛飞; 潘海天

    2014-01-01

    For the application of soft measurement technology , the OPC technology-based method was de-signed.This method contains a server station and an operator station which operating independently .The serv-er station connecting with control system can read online data , calculate target variables through the soft meas-urement model and can write values into control system before having results fed back to the control system and sent via OPC server .The operator station connecting with server station via the industrial Ethernet can ex-change data with OPC server through OPC client so as to monitor target variables .Applying this method to on-line monitoring reaction rate and conversion of a vinyl chloride polymerization process proves the stability and reliability of this method .%针对软测量技术的应用问题,设计了基于OPC通信技术的解决方案。服务器站与操作站独立运行,服务器站计算机与控制系统连接,进行现场数据采集与软测量模型计算,计算出目标变量,并将结果反馈给控制系统,再由OPC服务器发送。操作站计算机通过工业以太网与服务器站计算机连接,利用OPC客户端与OPC服务器进行数据交换,实现对目标变量的监控。将该方案应用于氯乙烯聚合过程聚合速率与单体转化率的在线检测中,运行结果表明该方案稳定可靠。

  18. Accurate mask model implementation in OPC model for 14nm nodes and beyond

    Science.gov (United States)

    Zine El Abidine, Nacer; Sundermann, Frank; Yesilada, Emek; Farys, Vincent; Huguennet, Frederic; Armeanu, Ana-Maria; Bork, Ingo; Chomat, Michael; Buck, Peter; Schanen, Isabelle

    2015-10-01

    In a previous work [1] we demonstrated that current OPC model assuming the mask pattern to be analogous to the designed data is no longer valid. Indeed as depicted in figure 1, an extreme case of line-end shortening shows a gap up to 10 nm difference (at mask level). For that reason an accurate mask model, for a 14nm logic gate level has been calibrated. A model with a total RMS of 1.38nm at mask level was obtained. 2D structures such as line-end shortening and corner rounding were well predicted using SEM pictures overlaid with simulated contours. The first part of this paper is dedicated to the implementation of our improved model in current flow. The improved model consists of a mask model capturing mask process and writing effects and a standard optical and resist model addressing the litho exposure and development effects at wafer level. The second part will focus on results from the comparison of the two models, the new and the regular, as depicted in figure 2.

  19. U.S. Coast Guard Cutter Procurement Lessons Impacts on the Offshore Patrol Cutter (OPC) Program Affordability

    Science.gov (United States)

    2015-12-01

    Sponsored Report Series U.S. Coast Guard Cutter Procurement Lessons’ Impacts on the Offshore Patrol Cutter (OPC) Program Affordability December 2015...School of Business & Public Policy - i - Naval Postgraduate School ABSTRACT The U.S. Coast Guard’s upcoming acquisition of the Offshore Patrol...School NPS-AM-16-012 Acquisition Research Program Sponsored Report Series U.S. Coast Guard Cutter Procurement Lessons’ Impacts on the Offshore

  20. Therapeutic effect of transplanted human Wharton's jelly stem cell-derived oligodendrocyte progenitor cells (hWJ-MSC-derived OPCs) in an animal model of multiple sclerosis.

    Science.gov (United States)

    Mikaeili Agah, Elmira; Parivar, Kazem; Joghataei, Mohammad Taghi

    2014-04-01

    Multiple sclerosis (MS) is an immune-mediated demyelinating disease of the central nervous system (CNS). A potential new therapeutic approach for MS is cell transplantation which may promote remyelination. We transplanted human Wharton's jelly stem cell-derived oligodendrocyte progenitor cells (hWJ-MSC-derived OPCs) into the brain ventricles of mice induced with experimental autoimmune encephalomyelitis (EAE), the animal model of MS. We studied the effect of the transplanted OPCs on the functional and pathological manifestations of the disease. Transplanted hWJ-MSC-derived OPCs significantly reduced the clinical signs of EAE. Histological examinations showed that remyelination was significantly increased after transplantation. These results suggest that hWJ-MSC-derived OPCs promote the regeneration of myelin sheaths in the brain.

  1. Use of Occupational Performance Coaching for stroke survivors (OPC-Stroke in late rehabilitation: A descriptive case study

    Directory of Open Access Journals (Sweden)

    Danika Belliveau

    2016-04-01

    Full Text Available Background: Stroke is a leading cause of disability in adults. Following stroke, 60% of people report needing help with everyday activities, and 80% report having very few meaningful activities. These restrictions often continue for years. This study explored the efficacy of Occupational Performance Coaching for stroke survivors (OPC-Stroke on the participation level of adults in the later stage of stroke rehabilitation. Method: A descriptive case study design was used. One participant in the later stages of rehabilitation was recruited. Outcome measures for participation, goal performance and satisfaction, and emotional well-being were administered pre and postintervention to observe for direction of change. A semi-structured interview was carried out postintervention to explore the participant’s experiences of the intervention. Results: The participant who took part in the study reported improvement with his goal performance and satisfaction. However, the level of participation did not improve and emotional well-being decreased. Qualitative data revealed an appreciation of the intervention and a recommendation of the intervention for others. Conclusion: OPC-Stroke was valued by the participant and shows promise for improving goal performance and satisfaction. Further research is necessary to determine the potential efficacy of OPC-Stroke in later stages of rehabilitation.

  2. Improvement on post-OPC verification efficiency for contact/via coverage check by final CD biasing of metal lines and considering their location on the metal layout

    Science.gov (United States)

    Kim, Youngmi; Choi, Jae-Young; Choi, Kwangseon; Choi, Jung-Hoe; Lee, Sooryong

    2011-04-01

    As IC design complexity keeps increasing, it is more and more difficult to ensure the pattern transfer after optical proximity correction (OPC) due to the continuous reduction of layout dimensions and lithographic limitation by k1 factor. To guarantee the imaging fidelity, resolution enhancement technologies (RET) such as off-axis illumination (OAI), different types of phase shift masks and OPC technique have been developed. In case of model-based OPC, to cross-confirm the contour image versus target layout, post-OPC verification solutions continuously keep developed - contour generation method and matching it to target structure, method for filtering and sorting the patterns to eliminate false errors and duplicate patterns. The way to detect only real errors by excluding false errors is the most important thing for accurate and fast verification process - to save not only reviewing time and engineer resource, but also whole wafer process time and so on. In general case of post-OPC verification for metal-contact/via coverage (CC) check, verification solution outputs huge of errors due to borderless design, so it is too difficult to review and correct all points of them. It should make OPC engineer to miss the real defect, and may it cause the delay time to market, at least. In this paper, we studied method for increasing efficiency of post-OPC verification, especially for the case of CC check. For metal layers, final CD after etch process shows various CD bias, which depends on distance with neighbor patterns, so it is more reasonable that consider final metal shape to confirm the contact/via coverage. Through the optimization of biasing rule for different pitches and shapes of metal lines, we could get more accurate and efficient verification results and decrease the time for review to find real errors. In this paper, the suggestion in order to increase efficiency of OPC verification process by using simple biasing rule to metal layout instead of etch model

  3. 基才C#和OPC技术实现对矿井环境的检测%Detection of the mine environment based on C# and OPC technology

    Institute of Scientific and Technical Information of China (English)

    赵龙涛; 乔元华; 周胜梅; 魏兰磊; 杨靖

    2012-01-01

    In order to achieve the detection of the mine working environment ,the design is proposed for mine environmental monitoring based on C # and OPC technologies. The design using the SIMATIC NET OPC as a server, making S7-400H and SIMATIC NET OPC server connection configuration, using the advanced programming language C# to achieve the operation of data read and write of OPC client with OPC Server,thereby realizes the purpose of data monitoring, data storage and warning handling on the host computer.%为了实现对矿井工作环境的检测,基于C#和OPC技术提出了一种对矿井环境进行检测的一种设计方案。该设计以SIMATICNETOPC作为服务器,对S7—400H与OPCSERVER进行连接配置,采用高级编程语言C#编程使OPC客户程序与OPCSERVER进行数据读写操作,从而在上位机上达到数据监测、数据存储及预警处理的目的。

  4. OPC服务器开发工具包软件的设计与实现%Design and Implement of OPC Server Development Toolkit Software

    Institute of Scientific and Technical Information of China (English)

    王平; 李大庆; 王颋

    2009-01-01

    This paper proposes OLE for Process Control(OPC) server development toolkit software, aiming at exploitation of source OPC server too complex. Visual C++6.0 as the development platform, it encapsulates OPC data access criterion and COM knowledge to a single DLL to realize the software, and introduces the structure and primary module function of OPC server develop toolkit. Test result proves that the software design enhances reusability of code integer and reduces cycle of software development, the server can realize basal data communication.%针对源码级的用于过程控制的对象链接和嵌入(OPC)服务器开发过于复杂问题,提出OPC服务器开发工具包软件.该软件以Visual C++6.0为开发平台,通过将OPC数据存取规范和COM知识封装成DLL的方式实现.介绍该软件的结构和主要模块的功能,设计OPC服务器.测试结果证明,该软件没计提高程序代码的重用性,缩短软件开发周期,该服务器能实现基本的数据通信.

  5. Communication protocol conversion platform based on OPC technology%基于OPC技术的通信协议转换平台

    Institute of Scientific and Technical Information of China (English)

    2013-01-01

      在通信领域,OPC技术满足了现场设备与操作系统之间的通信要求,把现场的数据转化成统一的、规范的OPC数据,有利于科学集中地管理通信数据。文章在OPC技术的基础上,探究其在通信协议转换平台中的实践应用。%OPC technology has meet the communication demand between site equipment and operating system in the communications field,changing spot data into unitive and normative OPC data is of benefit to administrate communication data intensively.The applica-tion of the OPC technology in the communication protocol conversion platform is discussed in this paper.

  6. Development of the ACS+OPC UA based control system for a CTA medium size telescope prototype

    Science.gov (United States)

    Behera, Bagmeet; Oya, Igor; Birsin, Emrah; Köppel, Hendryk; Melkumyan, David; Schlenstedt, Stefan; Schmidt, Torsten; Schwanke, Ullrich; Wegner, Peter; Wiesand, Stephan; Winde, Michael

    2012-09-01

    The Cherenkov Telescope Array (CTA) is the next generation Very High Energy (VHE, defined as > 50GeV to several 100TeV) telescope facility, currently in the design and prototyping phase, and expected to come on-line around 2016. The array would have both a Northern and Southern hemisphere site, together delivering nearly complete sky coverage. The CTA array is planned to have ~100 telescopes of several different sizes to fulfill the sensitivity and energy coverage needs. Each telescope has a number of subsystems with varied hardware and control mechanisms; a drive system that gets commands and inputs via OPC UA (OPC Unified Architecture), mirror alignment systems based on XBee/ZigBee protocol and/or CAN bus, weather monitor accessed via serial/Ethernet ports, CCD cameras for calibration, Cherenkov camera, and the data read out electronics, etc. Integrating the control and data-acquisitions of such a distributed heterogeneous system calls for a framework that can handle such a multi-platform, multi-protocol scenario. The CORBA based ALMA Common software satisfies these needs very well and is currently being evaluated as the base software for developing the control system for CTA. A prototype for a Medium Size Telescope (MST, ~12m) is being developed and will be deployed in Berlin, by end of 2012. We present the development being carried out to integrate and control the various hardware subsystems of this MST prototype using ACS.

  7. From nightmares to sweet dreams: inspection of aggressive OPC on 14nm reticles (and beyond) using a novel high-NA and low-NA dual method

    Science.gov (United States)

    Badger, Karen D.; Hibbs, Michael; Seki, Kazunori; Broadbent, William; Hutchinson, Trent; Redding, Vincent

    2015-10-01

    To prevent catastrophic failures in wafer manufacturing lines from reticle defects, mask manufacturers employ sophisticated reticle inspection systems to examine every shape on every reticle for defects. The predominant inspection systems in use today compare the reticle directly with the design database using high-NA optics (typically 3x higher resolution at the reticle plane than advanced wafer scanners). High-NA optical inspection with its high signal to noise ratio (SNR) can readily detect small defects before they have lithographic impact, thus ensuring reticle quality. However, when inspecting certain aggressive OPC, high-NA inspection can overload on small OPC defects which do not have lithographic impact and thus, should generally be ignored. Whereas, inspecting a reticle as imaged in the wafer plane (low-NA in the reticle plane) will generally ignore such small OPC defects; however, the SNR is often too low for certain defect types to provide the needed defect detection sensitivity to ensure reticle quality. This paper discusses the design and performance of a novel reticle inspection method using high-NA and low-NA dual optical imaging and processing. This method offers the high defect sensitivity of high-NA inspection with the OPC tolerance of low-NA inspection. These two imaging methods are blended together into a seamless inspection mode suitable for aggressive OPC of the 14nm generation and beyond. The test reticles include 14nm logic designs containing aggressive OPC and native defects, as well as a 14 nm test reticle containing relevant programmed defects. Defect lithographic significance is judged using a Zeiss AIMS™ system.

  8. Application of Wind Power Monitoring System Based on OPC Technology%基于OPC技术在风电监控系统上的应用

    Institute of Scientific and Technical Information of China (English)

    李晓斌; 王迪

    2011-01-01

    Wind power,a kind of green and clean energy is widely emphasized in all of countries. OPC technology is introduced in this article. A wind power monitoring system is applied based on OPC technology at low cost.%风电作为成熟的绿色能源受到各国的重视.在介绍OPC技术的基础上提出并实现了基于OPC技术的低成本的风电监控系统的应用方案.

  9. First Experience with PLC, OPC and BridgeVIEW in the context of the HMPID liquid distribution prototype

    CERN Document Server

    Maatta, E; CERN. Geneva; Swoboda, Detlef; Lecoeur, G

    1999-01-01

    The TESt (Test and Evaluation Station) [3] project consists in the construction of a stand alone unit for a specific sub-system of an ALICE detector in order to gain first experience with commercial products for detector control. Although the control system includes only a small number of devices and is designed for a particular application, it covers nevertheless all layers of a complete system and can be extended or used in different applications. The control system prototype has been implemented for the Perfluorohexane (C6F14) liquid distribution of the ALICE-HMPID (High-Momentum Particle IDentification)[5]. This report presents the experience acquired while developing the control system with off the shelf items: National Instruments BridgeVIEW [6] supervision software, SIEMENS PLC S7-300 [7] and the programming tool STEP 7. The OPC standard (OLE [12] for Process Control) [8] was used for the communication between BridgeVIEW and the PLC.

  10. Relation between speckle decorrelation and optical phase conjugation (OPC)- based turbidity suppression through dynamic scattering media: a study on in vivo mouse skin

    NARCIS (Netherlands)

    Jang, Mooseok; Ruan, Haowen; Vellekoop, Ivo Micha; Judkewitz, Benjamin; Chung, Euiheon; Yang, Changhuei

    2015-01-01

    Light scattering in biological tissue significantly limits the accessible depth for localized optical interrogation and deep-tissue optical imaging. This challenge can be overcome by exploiting the time-reversal property of optical phase conjugation (OPC) to reverse multiple scattering events or

  11. OPC在数据交互系统中的应用%Application of OPC in Data Interaction System

    Institute of Scientific and Technical Information of China (English)

    鲍坤; 孙学华

    2012-01-01

    In accordance with the feature of isolated information between loading platform system and production system, the data interaction system is designed. This system is developed by adopting OPC technology and C# language, and remotely connected to database to read and write the data in the loading platform system via ADO. NET, and the data in production system is operated by using OPC interface. Since the system has been operated, data transmission between two originally separated systems are capable to implement monitoring related data of loading platform system from production control system, thus the problem of data interaction existing in enterprises is resolved effectively, it offers great significance to enhance safety production level.%针对装车台系统与生产系统之间的信息孤立问题,设计了一套数据交互系统.该数据交互系统利用OPC技术和C#语言进行开发,通过ADO.NET远程连接数据库,对装车台系统中的数据进行相应的读写操作,并利用OPC接口实现对生产系统中的数据进行操作.该数据交互系统自投用以来,使得原本独立的两个系统之间能够进行数据传输,实现了在控制生产系统中对装车台系统相关数据的监控,有效地解决了企业数据交互上存在的问题,对提高企业安全生产水平有重大意义.

  12. Aplicación cliente-servidor MatLab®-WinCC® empleando comunicación OPC

    Directory of Open Access Journals (Sweden)

    Ana Isabel González Santos

    2011-01-01

    Full Text Available Normal 0 21 false false false MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Tabla normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman"; mso-ansi-language:#0400; mso-fareast-language:#0400; mso-bidi-language:#0400;} Se presenta una aplicación desarrollada con el sistema SCADA WinCC®. La aplicación permite el control proporcional integral de una red RC de primer orden, la identificación de un motor de corriente continua para la detección de fallos y el análisis de sensibilidad de las condiciones iniciales en un reactor semi-batch. La principal ventaja de la aplicación demostrativa realizada es mostrar las potencialidades que pueden adquirir las aplicaciones SCADAs, implantadas actualmente en la industria, cuando interactúan a través de la comunicación OPC con otras aplicaciones específicas de mayor potencial en materia de cálculo numérico como las desarrolladas en el Simulink de MatLab®. Palabras claves: Comunicación OPC, control, detección de fallos, identificación, MatLab®, WinCC®

  13. Application of OPC technology in the software about PLC virtual simulation%OPC技术在PLC虚拟仿真实验软件中的应用

    Institute of Scientific and Technical Information of China (English)

    周亚军; 曾洋; 俞武嘉

    2011-01-01

    为解决所设计的可编程逻辑控制器(PLC)虚拟仿真实验软件与PLC之间的通信问题,分析研究了OPC客户端与服务器端之间的通信机制,将OPC技术应用到仿真实验软件与PLC的通信交互中.设计了一种通用型OPC数据采集发送客户端,该客户端可连接通信现代工业控制上常用的多种类型的PLC,采用实时反馈的数据传送模式.最后以西门子PC Access服务器和S7-200PLC为平台,使用仿真软件中虚拟电梯实验对OPC客户端进行了测试,运行效果显示OPC技术很好地实现了系统的高效性和实时性.%To solve the problem of the communication between the programmable logic controller(PLC) and the PLC virtual simulation software, the communication mechanism between the OLE for process controll(OPC) client and server was analy ed. The OPC technology was applied in the connecting experimental program with PLC. Besides, a general-purpose data acquisition OPC client was designed, which can connect with many types of PLC used in the modern industrial controlling and which adopts the real-time feedback data transfer mode. Finally, the OPC client was tested by using virtual elevator experiment of simulation software based on the platform of Siemens PC access server and S7-200 PLC. The result of the test show that OPC technology can improve the efficiency and real-time performance of the system.

  14. Ehrlichia chaffeensis uses its surface protein EtpE to bind GPI-anchored protein DNase X and trigger entry into mammalian cells.

    Directory of Open Access Journals (Sweden)

    Dipu Mohan Kumar

    Full Text Available Ehrlichia chaffeensis, an obligatory intracellular rickettsial pathogen, enters and replicates in monocytes/macrophages and several non-phagocytic cells. E. chaffeensis entry into mammalian cells is essential not only for causing the emerging zoonosis, human monocytic ehrlichiosis, but also for its survival. It remains unclear if E. chaffeensis has evolved a specific surface protein that functions as an 'invasin' to mediate its entry. We report a novel entry triggering protein of Ehrlichia, EtpE that functions as an invasin. EtpE is an outer membrane protein and an antibody against EtpE (the C-terminal fragment, EtpE-C greatly inhibited E. chaffeensis binding, entry and infection of both phagocytes and non-phagocytes. EtpE-C-immunization of mice significantly inhibited E. chaffeensis infection. EtpE-C-coated latex beads, used to investigate whether EtpE-C can mediate cell invasion, entered both phagocytes and non-phagocytes and the entry was blocked by compounds that block E. chaffeensis entry. None of these compounds blocked uptake of non-coated beads by phagocytes. Yeast two-hybrid screening revealed that DNase X, a glycosylphosphatidyl inositol-anchored mammalian cell-surface protein binds EtpE-C. This was confirmed by far-Western blotting, affinity pull-down, co-immunoprecipitation, immunofluorescence labeling, and live-cell image analysis. EtpE-C-coated beads entered bone marrow-derived macrophages (BMDMs from wild-type mice, whereas they neither bound nor entered BMDMs from DNase X(-/- mice. Antibody against DNase X or DNase X knock-down by small interfering RNA impaired E. chaffeensis binding, entry, and infection. E. chaffeensis entry and infection rates of BMDMs from DNase X(-/- mice and bacterial load in the peripheral blood in experimentally infected DNase X(-/- mice, were significantly lower than those from wild-type mice. Thus this obligatory intracellular pathogen evolved a unique protein EtpE that binds DNase X to enter and infect

  15. Double-exposure strategy using OPC and simulation and the performance on wafer with sub-0.10-μm design rule in ArF lithography

    Science.gov (United States)

    Oh, Se-Young; Kim, Wan-Ho; Yune, Hyoung-Soon; Kim, Hee-Bom; Kim, Seo-Min; Ahn, Chang-Nam; Shin, Ki-Soo

    2002-07-01

    As the pattern size becomes smaller, double or multi exposure is required unless the epochal solutions for overcoming the limits of present lithography system do appear or are discovered. ArF DET (double exposure technology) strategy based on manual OPC with in-house simulation tool, HOST (Hynix OPC simulation tool), is suggested as a possible exposure method to extend the limitation of current lithography. HOST requires no additional procedures and separate layout optimizations of each region in terms of OPC are enough. Furthermore, it is possible to change illumination condition of each region and the overlap between two regions with ease. The results from the simulation are pattern size and profile of each condition according to the defous and misregistration. 0.63 NA ArF Scanner and Clariant resist is used for wafer process. The resist was coated on Clariant organic BARC using 0.24 um thickness. Dipole illumination for cell region and annular illumination for peripheral region are used. Cell region contains 0.20 um pitch duty pattern and peripheral region 0.24 um pitch duty pattern. The boundary of two regions is investigated in view of validity of stitching itself. The layout of reticles used as the cell and peripheral region are optimized by OPC, respectively and then, additional OPC was treated to the boundary, i.e., stitching area to compensate the cross term of the boundary caused by separate and independent optimization with OPC in the cell and the peripheral regime. The final patterns were acquired by defining the cell at first and the peripheral region secondly with different defocus and registration in respect to the cell. The actual data on wafer are presented according to defocus and one region's overlay offset relatively to the other region. And the outstanding matching between simulation results and in-line data are shown. Lithography process window for stable patterning is thoroughly investigated in view of depth of focus, energy latitude

  16. Optimization of the EMI shielding effectiveness of fine and ultrafine POFA powder mix with OPC powder using Flower Pollination Algorithm

    Science.gov (United States)

    Narong, L. C.; Sia, C. K.; Yee, S. K.; Ong, P.; Zainudin, A.; Nor, N. H. M.; Kasim, N. A.

    2017-01-01

    In order to solve the electromagnetic interference (EMI) issue and provide a new application for palm oil fuel ash (POFA), POFA was used as the cement filler for enhancing the EMI absorption of cement-based composites. POFA was refined by using water precipitation for 24 hours to remove the filthiness and distinguish the layer 1 (floated) and layer 2 (sink) of POFA. Both layers POFA were dried for 24 hours at 100 ± 5 °C and grind separately for sieve at 140 μm (Fine) and 45 цш sizes (Ultrafine). The micro structure and element content of the both layers POFA were characterized by scanning electron microscope (SEM) and energy-dispersive X-ray spectroscopy (EDS) respectively. The results showed layer 1 POFA has potentialities for EMI shielding effectiveness (SE) due to its higher carbon content and porous structure. The study reveals that EMI SE also influenced by the particle size of POFA, where smaller particle size can increase 5 % to 13 % of EMI SE. When the specimen consists of 50% POFA with passing through 45 μm sieve, the EMI was shield -13.08 dB in between 50 MHz to 2 GHz range. Flower Pollination Algorithm (FPA) proves that POFA passing 45 μm sieve with 50% mixed to OPC is optimal parameter. The error between experimental and FPA simulation data is below 1.2 for both layers POFA.

  17. Design of Service Robot Monitoring System Based on OPC%基于OPC的服务机器人监控系统设计

    Institute of Scientific and Technical Information of China (English)

    智少磊; 夏继强; 张炯

    2012-01-01

    提出一种适用于敬老院环境的助老助残服务机器人监控系统设计方案.基于专为服务机器人制定的助老助残服务机器人以太网协议、OPC技术,实现机器人数据与监控平台的实时传输,为7种服务机器人分别定制其OPC Server,利用ASP技术集成数据库操作与OPCClient,将机器人的实时数据存入数据库,创建Web Server,为浏览器界面提供数据,以此实现远程监控.实际应用证明了该方案的可行性.%This paper proposes a comprehensive monitoring system for the senior and disable people aid service robot which is applied in a nursing home. This system is based on the Ethemet/the Senior and Disable People Aid Robot Protocol(Ethernet/SDARP) and Object Linking and Embedding for Process Control(OPC) technology, can communicate the real-time data between robots and the monitoring platform. Seven service robots' OPC servers are made respectively. This paper uses the ASP technology to integrate database and OPC Client for storing the real-time data of robots into the database. It creates a Web Server to provide data for the browser and realizes the remote monitoring. Actual application proves the feasibility of this method.

  18. Based on ethernet development of OPC client application program%基于以太网的OPC客户端应用程序实现

    Institute of Scientific and Technical Information of China (English)

    段宝利

    2012-01-01

    西门子通过以太网建立起Simatic Net OPC Server与S7系列PLC的S7连接,基于以太网的OPC客户应用程序实现,达到对现场PLC数据的交互访问、远程控制的目的.开发的客户端程序可以成功应用于不同环境中对Siemens、GE PLC数据交互访问,充分达到软件复用性.%Brief description of how Siemens via Ethernet to establish S7 connection between Simatic Net OPC Server and S7 series PLC is also referredlmplementation of OPC client applications based on Ethernet can achieved the objective of field PLC data interactive access and remote control.This client applications has been successfully used in PLC of Siemens and GE data interactive access under different environments,and software reuse is fully realized.

  19. Automatic test of PLC program based on OPC%基于OPC的PLC程序自动化测试

    Institute of Scientific and Technical Information of China (English)

    王达; 赵千川; 马喜春

    2011-01-01

    可编程逻辑控制器(PLC)是一种应用非常广泛的工业控制装置.随着PLC程序的规模和复杂性不断增加,研究PLC程序的自动化测试方法具有重要的意义.将高级语言程序自动化测试的思想引入PLC程序测试中,提出了一种基于OPC的PLC程序自动化测试框架.针对病房监护程序,搭建了一个自动化测试系统,验证了所提测试框架的可行性.最后,结合案例分析了PLC程序自动化测试的优势与可能遇到的困难.%The programmable logic controller (PLC) is a kind of electrical device widely used in the industrial field. With the increasing size and complexity of PLC program, the study of its testing becomes very significant. A framework for the automatic test of PLC program based on OPC is proposed by introducing the idea of automatic test for programs written in advanced programming languages. In order to validate the feasibility of the proposed framework, an automatic test system is set up for a program used for ward care. Finally, based on the experimental study, the advantage of the automatic test for PLC program is analyzed, and the difficulties are discussed.

  20. Your worst nightmare: inspection of aggressive OPC on 14nm masks with emphasis on defect sensitivity and wafer defect print predictability

    Science.gov (United States)

    Badger, Karen D.; Hibbs, Michael; Rankin, Jed; Seki, Kazunori; Stobert, Ian; Dechene, Daniel J.; Bleiman, Ben; Ghosal, Mini; Broadbent, William; Redding, Vincent

    2013-09-01

    To prevent catastrophic failures during wafer manufacturing, mask manufacturers employ sophisticated reticle inspection systems to examine every image on every reticle to identify defects. These advanced systems inspect at resolutions typically 3x higher at the reticle-plane than advanced wafer scanners; thus enabling them to detect the small defects necessary to ensure reticle quality. The most thorough inspection is done using a reticle-to-database comparison that ensures the reticle pattern matches the design pattern. For high defect sensitivity, the database must be carefully modeled to exactly match the reticle pattern. Further, sub-resolution OPC shapes are often at the limit of the mask manufacturing process, which adds subtle variations on such shapes across the reticle. These modeling errors and process variations can cause high numbers of unwanted detections, thereby limiting inspection system defect detection sensitivity.[1] OPC designs are expected to become more aggressive for future generations and may stress the performance of current reticle inspection systems. To systematically assess the capability of various inspection approaches and identify needed areas for improvement, a new "Nightmare" test reticle has been designed by IBM. The test reticle contains various sizes and shapes of sub-resolution features that might appear on reticle generations from today's 22nm to future 7nm. It also contains programmed defects to assess defect detection capability of current and future generation inspection systems. This paper will discuss the design of the "Nightmare" test reticle, and the inspection results of the current generation reticle inspection methods with emphasis on both inspectability and defect sensitivity. The subresolution features will be ranked according to importance for advanced OPC design. The reticle will also be evaluated using wafer print simulation so lithographic impact of features and defects can be measured and compared against

  1. 基于 OPC 通讯和局域网的电动汽车远程控制教学系统设计%Design of the Remote Control Teaching System of Electric Vehicles based on OPC Communications and LAN

    Institute of Scientific and Technical Information of China (English)

    夏加明

    2013-01-01

    Using OPC communications and LAN technology to build electric cars remote control teaching sys -tem can accomplish high speed data transmission and accurate real -time control.This paper mainly elaborates on the function of each part of the system design , and briefly introcluces its use effect .%  运用 OPC 通讯和局域网技术来构建电动汽车远程控制教学系统,以实现高速数据传输及精确实时控制。文章主要对该系统的各部分功能设计进行了详细的阐述,并简要介绍了其使用效果。

  2. Novel Networked Remote Laboratory Architecture for Open Connectivity Based on PLC-OPC-LabVIEW-EJS Integration. Application in Remote Fuzzy Control and Sensors Data Acquisition

    Directory of Open Access Journals (Sweden)

    Isaías González

    2016-10-01

    Full Text Available In this paper the design and implementation of a network for integrating Programmable Logic Controllers (PLC, the Object-Linking and Embedding for Process Control protocol (OPC and the open-source Easy Java Simulations (EJS package is presented. A LabVIEW interface and the Java-Internet-LabVIEW (JIL server complete the scheme for data exchange. This configuration allows the user to remotely interact with the PLC. Such integration can be considered a novelty in scientific literature for remote control and sensor data acquisition of industrial plants. An experimental application devoted to remote laboratories is developed to demonstrate the feasibility and benefits of the proposed approach. The experiment to be conducted is the parameterization and supervision of a fuzzy controller of a DC servomotor. The graphical user interface has been developed with EJS and the fuzzy control is carried out by our own PLC. In fact, the distinctive features of the proposed novel network application are the integration of the OPC protocol to share information with the PLC and the application under control. The user can perform the tuning of the controller parameters online and observe in real time the effect on the servomotor behavior. The target group is engineering remote users, specifically in control- and automation-related tasks. The proposed architecture system is described and experimental results are presented.

  3. Novel Networked Remote Laboratory Architecture for Open Connectivity Based on PLC-OPC-LabVIEW-EJS Integration. Application in Remote Fuzzy Control and Sensors Data Acquisition.

    Science.gov (United States)

    González, Isaías; Calderón, Antonio José; Mejías, Andrés; Andújar, José Manuel

    2016-10-31

    In this paper the design and implementation of a network for integrating Programmable Logic Controllers (PLC), the Object-Linking and Embedding for Process Control protocol (OPC) and the open-source Easy Java Simulations (EJS) package is presented. A LabVIEW interface and the Java-Internet-LabVIEW (JIL) server complete the scheme for data exchange. This configuration allows the user to remotely interact with the PLC. Such integration can be considered a novelty in scientific literature for remote control and sensor data acquisition of industrial plants. An experimental application devoted to remote laboratories is developed to demonstrate the feasibility and benefits of the proposed approach. The experiment to be conducted is the parameterization and supervision of a fuzzy controller of a DC servomotor. The graphical user interface has been developed with EJS and the fuzzy control is carried out by our own PLC. In fact, the distinctive features of the proposed novel network application are the integration of the OPC protocol to share information with the PLC and the application under control. The user can perform the tuning of the controller parameters online and observe in real time the effect on the servomotor behavior. The target group is engineering remote users, specifically in control- and automation-related tasks. The proposed architecture system is described and experimental results are presented.

  4. Computation of X-ray powder diffractograms of cement components and its application to phase analysis and hydration performance of OPC cement

    Indian Academy of Sciences (India)

    Rohan Jadhav; N C Debnath

    2011-08-01

    The importance of computed X-ray diffraction patterns of various polymorphs of alite (3, 1, ), belite (, ), aluminate (cubic, orthorhombic), aluminoferrite, gypsum and hemihydrate in the quantitative phase analysis of cement and its early stage hydration performance is highlighted in this work with three OPC samples. The analysis shows that the predominant silicate phases present in all the samples are 3-alite phase and -belite phase, respectively. Both cubic and orthorhombic phases of C3A, brownmillerite, gypsum and hemihydrates are present at different levels. Quantitative phase analysis of cement by Rietveld refinement method provides more accurate and comprehensive data of the phase composition compared to Bogue method. The comparative hydration performance of these samples was studied with / ratio, 0.5 and the results are interpreted in the light of difference in phase compositions viz. -C2S/C3S ratio, fraction of finer cement particles present in the samples and theoretical modeling of C3S hydration.

  5. Camino hacia la creación de clientes y servidores bajo el estándar UA de la fundación OPC

    Directory of Open Access Journals (Sweden)

    Rubén Darío Sánchez Dams

    2010-01-01

    Full Text Available El presente artículo recorrió la creación de las aplicaciones cliente y servidor OPC, las cuales permiten el acceso a datos de procesos industriales en el campo de forma estandarizada. Se describieron conceptos fundamentales, y las justificaciones de la tecnología analizando las posibilidades e implicaciones con las que se cuenta en la implementación de una nueva aplicación. A su vez se mostró la implementación de una solución de este tipo, para lo cual se expusieron las principales alternativas para la creación de estos clientes y servidores, y finalmente se describió la implementación de ellos.

  6. Steel energy management system based on Web and OPC technology%基于Web和OPC技术的钢厂能源管理系统

    Institute of Scientific and Technical Information of China (English)

    朱永强; 程耕国

    2011-01-01

    采用Web和OPC技术,开发了基于Oracle数据库的钢厂能源数据管理系统,实现了生产数据采集和Web数据发布的功能.系统具有基于B/S架构、远程操作、平台无关性、扩展灵活等特点.该系统结构可广泛应用于工业自动化领域,满足企业日常管理需求.%This paper uses Web and OPC technology, and develops the steel energy management system based on Oracle database. It implements the production data acquisition and Web data publishing features. The system is based on B/S architecture, remote operation, platform independence, scalability and flexible features. The system structure can be widely used in industrial automation to meet the business needs of daily management.

  7. Application of the OPC Technology in Liquid Level Control System%OPC技术在液位控制中的应用

    Institute of Scientific and Technical Information of China (English)

    匡芬芳

    2011-01-01

    Aiming at the the difficulties in implementing communication among internal hardware and software of the computerized control systems, and the system is poor at the expandability, the multi-layer network control system based on OPC technology is proposed. The system is composed of a three-layer network that includes field operator stations, engineer station and expert station, and the internal information of the system can be transmitted among the three-layer network in real time with OPC technology. The structure and implementing method of program are discussed in detail. The design has been applied successfully in liquid level control object. The practice shows that the system is open, expandable and low cost in development; it is ease to implement information interaction and sharing for multiple software and hardware.%针对计算机控制系统内部各软硬件之间通信困难以及系统可扩展性差等问题,提出了一种基于OPC技术的多级网络控制系统.该系统由现场操作级、工程师站和专家站三级网络组成,借助OPC技术,系统内部信息可在三级网络间实时传递.详细探讨了系统结构及程序实现的方法,并将系统成功应用于液位对象的控制.实践表明,系统具有开放、可扩展和开发费用低廉等特点,便于实现多种软硬件之间的信息交互与共享.

  8. 基于OPC技术的网络控制系统仿真平台设计%Design of a simulation platform of networked control system based on OPC technology

    Institute of Scientific and Technical Information of China (English)

    李二超; 李炜; 李战明; 孙增昌

    2012-01-01

    The networked control system (NCS) is a new kind of computer control systems. Though industrial networks different control parts communicate with each other, which leads new problems to control systems such as time delay and scheduling. Based on Matlab and OPC technology, and mediated by campus LAN, Siemens s7-300 PLC is used as experimental platform of the server, the OPC technology, provided by OPC Toolbox of Matlab, is used to achieve OPC server and client network communication. This method realizes the separation of the plant mndel and controller on two computers, thus obtaining a network control system experiment research platform for the study and validation of the advanced controlling algorithms.%网络控制系统(NCS)是一种新型计算机控制系统,通过工业网络实现控制单元之间的数据交换,但这也给控制系统带来了时延等问题.开发了一种基于Matlab和OPC技术,以校园局域网为媒介的虚拟NCS实验平台,利用西门子S7-300 PLC作为实验平台的服务器,用Matlab OPC Toolbox工具箱提供的OPC技术实现OPC服务器与客户端的网络通信,实现了对象模型和控制器在两台计算机的分离,从而获得网络化控制系统仿真平台,为高级控制算法的研究和验证提供了良好的实验平台.

  9. Effective Computing Server Application Based on OPC%基于OPC框架的高效计算服务应用

    Institute of Scientific and Technical Information of China (English)

    张琦; 张春平; 杨志; 刘铭

    2016-01-01

    大数据计算是当前云计算研究的热点之一。在电力信息化、精益化的建设过程中,业务复杂度不断提高,数据量与日俱增,这使得传统的数据加工性能日益劣化。在复杂的业务场景下,由于海量的电力数据,使得数据指标加工计算的效率非常低下,传统方式的加工任务经常耗时数个小时,难以满足用户的体验要求。为了解决这个问题,全面提升数据指标加工任务效率,基于对象化并行计算(Objectification Parallel Computing, OPC)框架实现了一种高效计算服务, OPC是分布式并行内存计算框架。在OPC框架中,大数据集被拆分成小数据集,并分布式地存储在集群内存中。 OPC计算任务借鉴了分而治之和归并树的思想,将计算任务分成两个阶段:本地计算任务和计算结果收集汇总。计算任务基于本地计算数据进行计算,得到本地计算结果,然后将计算结果通过收集结点进行汇总合并,最后得到最终结果。 OPC框架技术应用在国家电网公司工程生产管理系统(PMS)中,应用效果表明该技术稳定、可靠,性能提升几十至数百倍,可满足高效计算需求。%The big data computing is one of the researches focus in the Cloud Computing nowadays. With the development of electric power information, the business complexity continues to increase and the amount of data is increasing quickly which makes the traditional way of computing be worse and worse. This paper provides an effective computing of big data base on the Objectification Parallel Computing (OPC) to solve the above challenges. The small data set is split from Big Data, is distributedly stored in memory of OPC Cluster. In the effective compute server, making use of the thought of divide and rule and tree merging, there are two stages. The first stage is local data calculate. The intermediate calculation result can be obtained. The second stage is multistage summarizing. The final result

  10. Binding Procurement

    Science.gov (United States)

    Rao, Gopalakrishna M.; Vaidyanathan, Hari

    2007-01-01

    This viewgraph presentation reviews the use of the binding procurement process in purchasing Aerospace Flight Battery Systems. NASA Engineering and Safety Center (NESC) requested NASA Aerospace Flight Battery Systems Working Group to develop a set of guideline requirements document for Binding Procurement Contracts.

  11. A phase 1 study of a group B meningococcal native outer membrane vesicle vaccine made from a strain with deleted lpxL2 and synX and stable expression of opcA.

    Science.gov (United States)

    Keiser, Paul B; Gibbs, Barnett T; Coster, Trinka S; Moran, E Ellen; Stoddard, Mark B; Labrie, Joseph E; Schmiel, Deborah H; Pinto, Valerian; Chen, Ping; Zollinger, Wendell D

    2010-10-08

    This phase 1 clinical trial assessed the safety and immunogenicity of a native outer membrane vesicle (NOMV) vaccine prepared from a lpxL2(-) synX(-) mutant of strain 44/76 with opcA expression stabilized. Thirty-four volunteers were assigned to one of the three dose groups (25 mcg, 25 mcg with aluminum hydroxide adjuvant, and 50 mcg) to receive three intramuscular injections at 0, 6 and 24 weeks. Specific local and systemic adverse events (AEs) were solicited by diary and at visits on days 1, 2, 7 and 14 after each vaccination and at the end of the study at 30 weeks. Blood chemistries, complete blood count, and coagulation studies were measured on each vaccination day and again two days later. Blood for antibody measurements and bactericidal assays were drawn 0, 14, and 42 days after each vaccination. The proportion of volunteers who developed a fourfold or greater increase in serum bactericidal activity (SBA) to the wild-type parent of the vaccine strain with high opcA expression at 6 weeks after the third dose was 12/26 (0.46, 95% confidence interval 0.27-0.65). Antibody levels to OpcA were significantly higher in vaccine responders than in non-responders (p=0.008), and there was a trend for higher antibody levels to the lipooligosaccharide (LOS) (p=0.059). Bactericidal depletion assays on sera from volunteers with high-titer responses also indicate a major contribution of anti-OpcA and anti-LOS antibodies to the bactericidal response.These results suggest that genetically modified NOMV vaccines can induce protection against group B meningococcus. Copyright © 2010 Elsevier Ltd. All rights reserved.

  12. Bumetanide-induced NKCC1 inhibition attenuates oxygen-glucose deprivation-induced decrease in proliferative activity and cell cycle progression arrest in cultured OPCs via p-38 MAPKs.

    Science.gov (United States)

    Fu, Peicai; Tang, Ronghua; Yu, Zhiyuan; Huang, Shanshan; Xie, Minjie; Luo, Xiang; Wang, Wei

    2015-07-10

    The Na-K-Cl co-transporter 1 (NKCC1; a member of the cation-chloride co-transporter family) mediates the coupled movement of Na(+) and/or K(+) with Cl(-) across the plasma membrane of cells (Haas and Forbush, 2000, Annu. Rev. Physiol., 62, 515-534; Russell, 2000, Physiol. Rev., 80, 211-276). Although it acts as an important regulator of cell volume, secretion, and modulator of cell apoptosis and proliferation (Chen et al., 2005, J. Cereb. Blood Flow Metab., 25, 54-66; Kahle et al., 2008, Nat. Clin. Pract. Neurol., 4, 490-503; Kidokoro et al., 2014, Am. J. Physiol. Ren. Physiol., 306, F1155-F1160; Wang et al., 2011, Cell. Physiol. Biochem., 28, 703-714), NKCC1׳s effects on oligodendrocyte precursor cells (OPCs) have not been characterized. The aim of this study was to investigate whether and to what extent inhibition of NKCC1 alters oxygen glucose deprivation (OGD)-induced cell cycle progression. In the present study, we demonstrated that inhibition of NKCC1 with bumetanide attenuates the decrease in OGD-induced DNA synthesis in cultured OPCs. Western blots showed that NKCC1 inhibition led to an increased expression of cyclin D1, CDK 4, and cyclin E in OGD-treated cells. Furthermore, our results showed bumetanide attenuated the decrease in OGD-induced proliferation and arrest of cell cycle progression via the P-38 MAPK signaling cascade. Thus, NKCC1 plays important roles in the proliferation of OPCs under OGD-induced stress. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. EFSA Panel on Dietetic Products, Nutrition and Allergies (NDA); Scientific Opinion on the substantiation of health claims related to oligomeric procyanidins (OPCs) from grape (Vitis vinifera L.) seeds and improvement of visual adaptation to the dark (ID 680) pursuant to Article 13(1) of Regulation

    DEFF Research Database (Denmark)

    Tetens, Inge

    Following a request from the European Commission, the Panel on Dietetic Products, Nutrition and Allergies was asked to provide a scientific opinion on a list of health claims pursuant to Article 13 of Regulation (EC) No 1924/2006. This opinion addresses the scientific substantiation of health...... claims in relation to oligomeric procyanidins (OPCs) from grape (Vitis vinifera L.) seeds and improvement of visual adaptation to the dark. The scientific substantiation is based on the information provided by the Member States in the consolidated list of Article 13 health claims and references that EFSA...... has received from Member States or directly from stakeholders. The food constituent that is the subject of the health claim is oligomeric procyanidins (OPCs) from grape (Vitis vinifera L.) seeds. The Panel considers that OPCs from grape (Vitis vinifera L.) seeds are sufficiently characterised...

  14. Study of the Microstructure Evolution of Low-pH Cements Based on Ordinary Portland Cement (OPC) by Mid- and Near-Infrared Spectroscopy, and Their Influence on Corrosion of Steel Reinforcement.

    Science.gov (United States)

    García Calvo, José Luis; Sánchez Moreno, Mercedes; Alonso Alonso, María Cruz; Hidalgo López, Ana; García Olmo, Juan

    2013-06-18

    Low-pH cements are designed to be used in underground repositories for high level waste. When they are based on Ordinary Portland Cements (OPC), high mineral admixture contents must be used which significantly modify their microstructure properties and performance. This paper evaluates the microstructure evolution of low-pH cement pastes based on OPC plus silica fume and/or fly ashes, using Mid-Infrared and Near-Infrared spectroscopy to detect cement pastes mainly composed of high polymerized C-A-S-H gels with low C/S ratios. In addition, the lower pore solution pH of these special cementitious materials have been monitored with embedded metallic sensors. Besides, as the use of reinforced concrete can be required in underground repositories, the influence of low-pH cementitious materials on steel reinforcement corrosion was analysed. Due to their lower pore solution pH and their different pore solution chemical composition a clear influence on steel reinforcement corrosion was detected.

  15. Design and Realization of Keys Manage Panel with POKA-YOKE Base on OPC%基于OPC技术的防误防错用钥匙管理盘设计与实现

    Institute of Scientific and Technical Information of China (English)

    王鹏; 周广宏

    2015-01-01

    With the productive process of many types of manufacturing,the material need to be stored by portable storage.This issue which must be having a solution is Poka-Yoke.This article describes a keys manage panel base on OPC,which manage many mobile vehicles,in order to conifrm correctness and uniqueness of operation process.%多种生产类型的企业在生产过程中,材料需要进行移动式仓储管理,如何防错防误,成为必须要解决的问题.本文提出基于OPC通讯技术的钥匙管理盘,管理移动式仓储车,确保整个操作流程的正确性和唯一性.

  16. 基于OPC与组态技术的自动控制实验教学仿真平台开发%Development of teaching simulation platform of automatic control experiment based on OPC and configuration technology

    Institute of Scientific and Technical Information of China (English)

    胡开明; 傅志坚; 葛远香

    2013-01-01

    以水箱液位和直流电机调速系统作为对象,采用OPC(ole for process control)技术实现Matlab与组态王数据交换,在Matlab中进行对象的算法分析和计算,在组态环境中进行实时监控、操作与动画和数据显示.该改造技术较好地体现了控制理论分析与计算,又能较好地监控对象的实时运行状态,同时减少了自动化实验对硬件的依赖程度,对实验改造起到了较好地示范作用.%In present,the industrial configuration technology is applied more and more widely and dependent on the hardware resource in the field of automatic control.This article takes the tank level and the DC motor speed control system as plant.In the system,the algorithm analysis and calculation are carried in Matlab,and the real time monitoring,operation,animation and data display are operated in configuration environment with Matlab and Kingview data exchanged by OPC technology.This transformation technology can effectively combine advantages of configuration real time monitoring conveniently and reflect the system control algorithm analysis and calculation.At the same time,this technology can also effectively solve the configuration software to hardware support.The experimental transformation played a better demonstration effect.

  17. Analyzing binding data.

    Science.gov (United States)

    Motulsky, Harvey J; Neubig, Richard R

    2010-07-01

    Measuring the rate and extent of radioligand binding provides information on the number of binding sites, and their affinity and accessibility of these binding sites for various drugs. This unit explains how to design and analyze such experiments.

  18. Activation of Sterol Regulatory Element Binding Factors by Fenofibrate and Gemfibrozil Stimulate Myelination in Zebrafish

    Directory of Open Access Journals (Sweden)

    Yuhei Nishimura

    2016-07-01

    Full Text Available Oligodendrocytes are major myelin-producing cells and play essential roles in the function of a healthy nervous system. However, they are also one of the most vulnerable neural cell types in the central nervous system (CNS, and myelin abnormalities in the CNS are found in a wide variety of neurological disorders, including multiple sclerosis, adrenoleukodystrophy, and schizophrenia. There is an urgent need to identify small molecular weight compounds that can stimulate myelination. In this study, we performed comparative transcriptome analysis to identify pharmacodynamic effects common to miconazole and clobetasol, which have been shown to stimulate myelination by mouse oligodendrocyte progenitor cells (OPCs. Of the genes differentially expressed in both miconazole- and clobetasol-treated mouse OPCs compared with untreated cells, we identified differentially expressed genes (DEGs common to both drug treatments. Gene ontology analysis revealed that these DEGs are significantly associated with the sterol biosynthetic pathway, and further bioinformatics analysis suggested that sterol regulatory element binding factors (SREBFs might be key upstream regulators of the DEGs. In silico screening of a public database for chemicals associated with SREBF activation identified fenofibrate, a peroxisome proliferator-activated receptor α (PPARα agonist, as a drug that increases the expression of known SREBF targets, raising the possibility that fenofibrate may also stimulate myelination. To test this, we performed in vivo imaging of zebrafish expressing a fluorescent reporter protein under the control of the myelin basic protein (mbp promoter. Treatment of zebrafish with fenofibrate significantly increased expression of the fluorescent reporter compared with untreated zebrafish. This increase was attenuated by co-treatment with fatostatin, a specific inhibitor of SREBFs, confirming that the fenofibrate effect was mediated via SREBFs. Furthermore, incubation

  19. The Design of Resistance Furnace Temperature Control System based on OPC and MATLAB%基于OPC和MATLAB的电阻炉温度控制系统设计

    Institute of Scientific and Technical Information of China (English)

    叶强

    2014-01-01

    针对电阻炉温度系统具有非线性、大惯性、大滞后等特点,结合常规PID控制器和模糊控制器各自的长处,以MATLAB为计算平台,通过OPC技术实现MATLAB和ECS-700之间的数据交换.提出了基于OPC技术的自适应模糊PID控制方案.自适应模糊PID控制器由MATLAB中的模糊工具箱设计,ECS-700主要负责数据采集和设备驱动.实验结果表明,电阻炉温度控制系统的性能令人满意,该方法调节时间短、超调量小、波动小,OPC通信的性能非常有效可靠,可以有效应用于电阻炉温度控制系统中.

  20. Membrane binding domains

    OpenAIRE

    Hurley, James H.

    2006-01-01

    Eukaryotic signaling and trafficking proteins are rich in modular domains that bind cell membranes. These binding events are tightly regulated in space and time. The structural, biochemical, and biophysical mechanisms for targeting have been worked out for many families of membrane binding domains. This review takes a comparative view of seven major classes of membrane binding domains, the C1, C2, PH, FYVE, PX, ENTH, and BAR domains. These domains use a combination of specific headgroup inter...

  1. Analyzing radioligand binding data.

    Science.gov (United States)

    Motulsky, Harvey; Neubig, Richard

    2002-08-01

    Radioligand binding experiments are easy to perform, and provide useful data in many fields. They can be used to study receptor regulation, discover new drugs by screening for compounds that compete with high affinity for radioligand binding to a particular receptor, investigate receptor localization in different organs or regions using autoradiography, categorize receptor subtypes, and probe mechanisms of receptor signaling, via measurements of agonist binding and its regulation by ions, nucleotides, and other allosteric modulators. This unit reviews the theory of receptor binding and explains how to analyze experimental data. Since binding data are usually best analyzed using nonlinear regression, this unit also explains the principles of curve fitting with nonlinear regression.

  2. Mediaeval manuscript bindings

    Directory of Open Access Journals (Sweden)

    Jedert Vodopivec

    1999-01-01

    Full Text Available The present article represents an excerpt from the final chapters of the research study titled "The development of structures in mediaeval manuscript bindings - interdependence with conservatory methods". In it, aims, methods of work, archive and library materials used and directions for conservatory methods are presented. Besides, the research study includes also a historcial overview of book bindings, detailed analysis of separate structural elements in Slovenian mediaeval bindings, comprehensive presentation of separate structures, the techniques of binding and materials of the preserved mediaeval bindings in Slovenian public archives and libraries, terminological dictionary of specific professional terms related to binding as a segment of a book, and a catalogue of all analysed bindings, containing a survey of ajI detectable data, sketches,graphite prints and photographs.

  3. Ureaplasma urealyticum binds mannose-binding lectin.

    Science.gov (United States)

    Benstein, Barbara D; Ourth, Donald D; Crouse, Dennis T; Shanklin, D Radford

    2004-10-01

    Mannose-binding C-type lectin (MBL) is an important component of innate immunity in mammals. Mannose-binding lectin (MBL), an acute phase protein, acts as an opsonin for phagocytosis and also activates the mannan-binding lectin complement pathway. It may play a particularly significant role during infancy before adequate specific protection can be provided by the adaptive immune system. Ureaplasma urealyticum has been linked to several diseases including pneumonia and chronic lung disease (CLD) in premature infants. We therefore investigated the ability of U. urealyticum to bind MBL. A guinea pig IgG anti-rabbit-MBL antiserum was produced. An immunoblot (dot-blot) assay done on nitrocellulose membrane determined that the anti-MBL antibody had specificity against both rabbit and human MBL. Pure cultures of U. urealyticum, serotype 3, were used to make slide preparations. The slides containing the organisms were then incubated with nonimmune rabbit serum containing MBL. Ureaplasma was shown to bind rabbit MBL with an immunocytochemical assay using the guinea pig IgG anti-rabbit MBL antiserum. Horseradish peroxidase (HRP)-labeled anti-guinea pig IgG was used to localize the reaction. The anti-MBL antiserum was also used in an immunocytochemical assay to localize U. urealyticum in histological sections of lungs from mice specifically infected with this organism. The same method also indicated binding of MBL by ureaplasma in human lung tissue obtained at autopsy from culture positive infants. Our results demonstrate that ureaplasma has the capacity to bind MBL. The absence of MBL may play a role in the predisposition of diseases related to this organism.

  4. Ligand binding mechanics of maltose binding protein.

    Science.gov (United States)

    Bertz, Morten; Rief, Matthias

    2009-11-13

    In the past decade, single-molecule force spectroscopy has provided new insights into the key interactions stabilizing folded proteins. A few recent studies probing the effects of ligand binding on mechanical protein stability have come to quite different conclusions. While some proteins seem to be stabilized considerably by a bound ligand, others appear to be unaffected. Since force acts as a vector in space, it is conceivable that mechanical stabilization by ligand binding is dependent on the direction of force application. In this study, we vary the direction of the force to investigate the effect of ligand binding on the stability of maltose binding protein (MBP). MBP consists of two lobes connected by a hinge region that move from an open to a closed conformation when the ligand maltose binds. Previous mechanical experiments, where load was applied to the N and C termini, have demonstrated that MBP is built up of four building blocks (unfoldons) that sequentially detach from the folded structure. In this study, we design the pulling direction so that force application moves the two MBP lobes apart along the hinge axis. Mechanical unfolding in this geometry proceeds via an intermediate state whose boundaries coincide with previously reported MBP unfoldons. We find that in contrast to N-C-terminal pulling experiments, the mechanical stability of MBP is increased by ligand binding when load is applied to the two lobes and force breaks the protein-ligand interactions directly. Contour length measurements indicate that MBP is forced into an open conformation before unfolding even if ligand is bound. Using mutagenesis experiments, we demonstrate that the mechanical stabilization effect is due to only a few key interactions of the protein with its ligand. This work illustrates how varying the direction of the applied force allows revealing important details about the ligand binding mechanics of a large protein.

  5. Protein Binding Pocket Dynamics.

    Science.gov (United States)

    Stank, Antonia; Kokh, Daria B; Fuller, Jonathan C; Wade, Rebecca C

    2016-05-17

    The dynamics of protein binding pockets are crucial for their interaction specificity. Structural flexibility allows proteins to adapt to their individual molecular binding partners and facilitates the binding process. This implies the necessity to consider protein internal motion in determining and predicting binding properties and in designing new binders. Although accounting for protein dynamics presents a challenge for computational approaches, it expands the structural and physicochemical space for compound design and thus offers the prospect of improved binding specificity and selectivity. A cavity on the surface or in the interior of a protein that possesses suitable properties for binding a ligand is usually referred to as a binding pocket. The set of amino acid residues around a binding pocket determines its physicochemical characteristics and, together with its shape and location in a protein, defines its functionality. Residues outside the binding site can also have a long-range effect on the properties of the binding pocket. Cavities with similar functionalities are often conserved across protein families. For example, enzyme active sites are usually concave surfaces that present amino acid residues in a suitable configuration for binding low molecular weight compounds. Macromolecular binding pockets, on the other hand, are located on the protein surface and are often shallower. The mobility of proteins allows the opening, closing, and adaptation of binding pockets to regulate binding processes and specific protein functionalities. For example, channels and tunnels can exist permanently or transiently to transport compounds to and from a binding site. The influence of protein flexibility on binding pockets can vary from small changes to an already existent pocket to the formation of a completely new pocket. Here, we review recent developments in computational methods to detect and define binding pockets and to study pocket dynamics. We introduce five

  6. High risk of adrenal toxicity of N1-desoxy quinoxaline 1,4-dioxide derivatives and the protection of oligomeric proanthocyanidins (OPC) in the inhibition of the expression of aldosterone synthetase in H295R cells.

    Science.gov (United States)

    Wang, Xu; Yang, Chunhui; Ihsan, Awais; Luo, Xun; Guo, Pu; Cheng, Guyue; Dai, Menghong; Chen, Dongmei; Liu, Zhenli; Yuan, Zonghui

    2016-02-01

    Quinoxaline 1,4-dioxide derivatives (QdNOs) with a wide range of biological activities are used in animal husbandry worldwide. It was found that QdNOs significantly inhibited the gene expression of CYP11B1 and CYP11B2, the key aldosterone synthases, and thus reduced aldosterone levels. However, whether the metabolites of QdNOs have potential adrenal toxicity and the role of oxidative stress in the adrenal toxicity of QdNOs remains unclear. The relatively new QdNOs, cyadox (CYA), mequindox (MEQ), quinocetone (QCT) and their metabolites, were selected for elucidation of their toxic mechanisms in H295R cells. Interestingly, the results showed that the main toxic metabolites of QCT, MEQ, and CYA were their N1-desoxy metabolites, which were more harmful than other metabolites and evoked dose and time-dependent cell damage on adrenal cells and inhibited aldosterone production. Gene and protein expression of CYP11B1 and CYP11B2 and mRNA expression of transcription factors, such as NURR1, NGFIB, CREB, SF-1, and ATF-1, were down regulated by N1-desoxy QdNOs. The natural inhibitors of oxidant stress, oligomeric proanthocyanidins (OPC), could upregulate the expression of diverse transcription factors, including CYP11B1 and CYP11B2, and elevated aldosterone levels to reduce adrenal toxicity. This study demonstrated for the first time that N1-desoxy QdNOs have the potential to be the major toxic metabolites in adrenal toxicity, which may shed new light on the adrenal toxicity of these fascinating compounds and help to provide a basic foundation for the formulation of safety controls for animal products and the design of new QdNOs with less harmful effects.

  7. Python bindings for libcloudph++

    OpenAIRE

    Jarecka, Dorota; Arabas, Sylwester; Del Vento, Davide

    2015-01-01

    This technical note introduces the Python bindings for libcloudph++. The libcloudph++ is a C++ library of algorithms for representing atmospheric cloud microphysics in numerical models. The bindings expose the complete functionality of the library to the Python users. The bindings are implemented using the Boost.Python C++ library and use NumPy arrays. This note includes listings with Python scripts exemplifying the use of selected library components. An example solution for using the Python ...

  8. DNS & Bind Cookbook

    CERN Document Server

    Liu, Cricket

    2011-01-01

    The DNS & BIND Cookbook presents solutions to the many problems faced by network administrators responsible for a name server. Following O'Reilly's popular problem-and-solution cookbook format, this title is an indispensable companion to DNS & BIND, 4th Edition, the definitive guide to the critical task of name server administration. The cookbook contains dozens of code recipes showing solutions to everyday problems, ranging from simple questions, like, "How do I get BIND?" to more advanced topics like providing name service for IPv6 addresses. It's full of BIND configuration files that yo

  9. Python bindings for libcloudph++

    CERN Document Server

    Jarecka, Dorota; Del Vento, Davide

    2015-01-01

    This technical note introduces the Python bindings for libcloudph++. The libcloudph++ is a C++ library of algorithms for representing atmospheric cloud microphysics in numerical models. The bindings expose the complete functionality of the library to the Python users. The bindings are implemented using the Boost.Python C++ library and use NumPy arrays. This note includes listings with Python scripts exemplifying the use of selected library components. An example solution for using the Python bindings to access libcloudph++ from Fortran is presented.

  10. On Binding Domains

    NARCIS (Netherlands)

    Everaert, M.B.H.

    2005-01-01

    In this paper I want to explore reasons for replacing Binding Theory based on the anaphor-pronoun dichotomy by a Binding Theory allowing more domains restricting/defining anaphoric dependencies. This will, thus, have consequences for the partitioning of anaphoric elements, presupposing more types of

  11. Melanin-binding radiopharmaceuticals

    Energy Technology Data Exchange (ETDEWEB)

    Packer, S; Fairchild, R G; Watts, K P; Greenberg, D; Hannon, S J

    1980-01-01

    The scope of this paper is limited to an analysis of the factors that are important to the relationship of radiopharmaceuticals to melanin. While the authors do not attempt to deal with differences between melanin-binding vs. melanoma-binding, a notable variance is assumed. (PSB)

  12. DNS BIND Server Configuration

    Directory of Open Access Journals (Sweden)

    Radu MARSANU

    2011-01-01

    Full Text Available After a brief presentation of the DNS and BIND standard for Unix platforms, the paper presents an application which has a principal objective, the configuring of the DNS BIND 9 server. The general objectives of the application are presented, follow by the description of the details of designing the program.

  13. Thermodynamics of fragment binding.

    Science.gov (United States)

    Ferenczy, György G; Keserű, György M

    2012-04-23

    The ligand binding pockets of proteins have preponderance of hydrophobic amino acids and are typically within the apolar interior of the protein; nevertheless, they are able to bind low complexity, polar, water-soluble fragments. In order to understand this phenomenon, we analyzed high resolution X-ray data of protein-ligand complexes from the Protein Data Bank and found that fragments bind to proteins with two near optimal geometry H-bonds on average. The linear extent of the fragment binding site was found not to be larger than 10 Å, and the H-bonding region was found to be restricted to about 5 Å on average. The number of conserved H-bonds in proteins cocrystallized with multiple different fragments is also near to 2. These fragment binding sites that are able to form limited number of strong H-bonds in a hydrophobic environment are identified as hot spots. An estimate of the free-energy gain of H-bond formation versus apolar desolvation supports that fragment sized compounds need H-bonds to achieve detectable binding. This suggests that fragment binding is mostly enthalpic that is in line with their observed binding thermodynamics documented in Isothermal Titration Calorimetry (ITC) data sets and gives a thermodynamic rationale for fragment based approaches. The binding of larger compounds tends to more rely on apolar desolvation with a corresponding increase of the entropy content of their binding free-energy. These findings explain the reported size-dependence of maximal available affinity and ligand efficiency both behaving differently in the small molecule region featured by strong H-bond formation and in the larger molecule region featured by apolar desolvation.

  14. Diseño e Implementación de un Control de Planta de Nivel Gunt RT450 utilizando un Plc Simatic S7 1200 con (TIA PORTAL) e Implementación de una Interfaz para Usuario diseñada en Labview con Comunicación mediante OPC

    OpenAIRE

    Molina Pearanda, Jorge Manuel; Barreiro Chevez, Lenin Jair

    2015-01-01

    En la industria es frecuente que se utilicen equipos de automatización de procesos como PLCs HMIs, de diferentes fabricantes y en ocasiones que utilizan diferentes protocolos dependiendo de cada fabricante, esto constituye el problema de protocolos propietarios para el cual en este proyecto diseñaremos una soluciòn, uno de lo s objetivos es usar el recurso NI OPC Servers para comunicar: un PLC Simatic S7 1200 que actúa como Fuente de Datos, con una Interfaz para Usuario ...

  15. SHBG (Sex Hormone Binding Globulin)

    Science.gov (United States)

    ... as: Testosterone-estrogen Binding Globulin; TeBG Formal name: Sex Hormone Binding Globulin Related tests: Testosterone , Free Testosterone, ... I should know? How is it used? The sex hormone binding globulin (SHBG) test may be used ...

  16. The SAMPL5 host-guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method

    Science.gov (United States)

    Yin, Jian; Henriksen, Niel M.; Slochower, David R.; Gilson, Michael K.

    2017-01-01

    The absolute binding free energies and binding enthalpies of twelve host-guest systems in the SAMPL5 blind challenge were computed using our attach-pull-release (APR) approach. This method has previously shown good correlations between experimental and calculated binding data in retrospective studies of cucurbit[7]uril (CB7) and β-cyclodextrin (βCD) systems. In the present work, the computed binding free energies for host octa acid (OA or OAH) and tetra-endo-methyl octa-acid (TEMOA or OAMe) with guests are in good agreement with prospective experimental data, with a coefficient of determination (R2) of 0.8 and root-mean-squared error of 1.7 kcal/mol using the TIP3P water model. The binding enthalpy calculations achieve moderate correlations, with R2 of 0.5 and RMSE of 2.5 kcal/mol, for TIP3P water. Calculations using the newly developed OPC water model also show good performance. Furthermore, the present calculations semi-quantitatively capture the experimental trend of enthalpy-entropy compensation observed, and successfully predict guests with the strongest and weakest binding affinity. The most populated binding poses of all twelve systems, based on clustering analysis of 750 ns molecular dynamics (MD) trajectories, were extracted and analyzed. Computational methods using MD simulations and explicit solvent models in a rigorous statistical thermodynamic framework, like APR, can generate reasonable predictions of binding thermodynamics. Especially with continuing improvement in simulation force fields, such methods hold the promise of making substantial contributions to hit identification and lead optimization in the drug discovery process.

  17. Binding enthalpy calculations for a neutral host-guest pair yield widely divergent salt effects across water models.

    Science.gov (United States)

    Gao, Kaifu; Yin, Jian; Henriksen, Niel M; Fenley, Andrew T; Gilson, Michael K

    2015-10-13

    Dissolved salts are a part of the physiological milieu and can significantly influence the kinetics and thermodynamics of various biomolecular processes, such as binding and catalysis; thus, it is important for molecular simulations to reliably describe their effects. The present study uses a simple, nonionized host-guest model system to study the sensitivity of computed binding enthalpies to the choice of water and salt models. Molecular dynamics simulations of a cucurbit[7]uril host with a neutral guest molecule show striking differences in the salt dependency of the binding enthalpy across four water models, TIP3P, SPC/E, TIP4P-Ew, and OPC, with additional sensitivity to the choice of parameters for sodium and chloride. In particular, although all of the models predict that binding will be less exothermic with increasing NaCl concentration, the strength of this effect varies by 7 kcal/mol across models. The differences appear to result primarily from differences in the number of sodium ions displaced from the host upon binding the guest rather than from differences in the enthalpy associated with this displacement, and it is the electrostatic energy that contributes most to the changes in enthalpy with increasing salt concentration. That a high sensitivity of salt affecting the choice of water model, as observed for the present host-guest system despite it being nonionized, raises issues regarding the selection and adjustment of water models for use with biological macromolecules, especially as these typically possess multiple ionized groups that can interact relatively strongly with ions in solution.

  18. CARBOHYDRATE-CONTAINING COMPOUNDS WHICH BIND TO CARBOHYDRATE BINDING RECEPTORS

    DEFF Research Database (Denmark)

    1995-01-01

    Carbohydrate-containing compounds which contain saccharides or derivatives thereof and which bind to carbohydrate binding receptors are useful in pharmaceutical products for treatment of inflammatory diseases and other diseases.......Carbohydrate-containing compounds which contain saccharides or derivatives thereof and which bind to carbohydrate binding receptors are useful in pharmaceutical products for treatment of inflammatory diseases and other diseases....

  19. Terms of Binding

    NARCIS (Netherlands)

    Sevcenco, A.

    2006-01-01

    The present dissertation aimed at achieving two goals. First, it constitutes an attempt to widen the search for phenomena that bear relevance to the idea that binding has a syntactic residue and is not, therefore, an exclusively semantic matter. Second, it tried to provide the technical means to acc

  20. Cellulose binding domain proteins

    Science.gov (United States)

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc; Doi, Roy

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  1. MD-2 binds cholesterol.

    Science.gov (United States)

    Choi, Soo-Ho; Kim, Jungsu; Gonen, Ayelet; Viriyakosol, Suganya; Miller, Yury I

    2016-02-19

    Cholesterol is a structural component of cellular membranes, which is transported from liver to peripheral cells in the form of cholesterol esters (CE), residing in the hydrophobic core of low-density lipoprotein. Oxidized CE (OxCE) is often found in plasma and in atherosclerotic lesions of subjects with cardiovascular disease. Our earlier studies have demonstrated that OxCE activates inflammatory responses in macrophages via toll-like receptor-4 (TLR4). Here we demonstrate that cholesterol binds to myeloid differentiation-2 (MD-2), a TLR4 ancillary molecule, which is a binding receptor for bacterial lipopolysaccharide (LPS) and is indispensable for LPS-induced TLR4 dimerization and signaling. Cholesterol binding to MD-2 was competed by LPS and by OxCE-modified BSA. Furthermore, soluble MD-2 in human plasma and MD-2 in mouse atherosclerotic lesions carried cholesterol, the finding supporting the biological significance of MD-2 cholesterol binding. These results help understand the molecular basis of TLR4 activation by OxCE and mechanisms of chronic inflammation in atherosclerosis.

  2. Binding and Bulgarian

    NARCIS (Netherlands)

    Schürcks-Grozeva, Lilia Lubomirova

    2003-01-01

    In haar proefschrift analyseert Lilia Schürcks de anaforische verschijnselen in de Bulgaarse taal. Het gaat dan om wederkerende aspecten, uitgedrukt bij woorden als ‘zich’ en ‘elkaar’. De situatie in het Bulgaars blijkt moeilijk in te passen in de klassieke Binding Theory van Noam Chomsky. Bron: RUG

  3. Sequential memory: Binding dynamics

    Science.gov (United States)

    Afraimovich, Valentin; Gong, Xue; Rabinovich, Mikhail

    2015-10-01

    Temporal order memories are critical for everyday animal and human functioning. Experiments and our own experience show that the binding or association of various features of an event together and the maintaining of multimodality events in sequential order are the key components of any sequential memories—episodic, semantic, working, etc. We study a robustness of binding sequential dynamics based on our previously introduced model in the form of generalized Lotka-Volterra equations. In the phase space of the model, there exists a multi-dimensional binding heteroclinic network consisting of saddle equilibrium points and heteroclinic trajectories joining them. We prove here the robustness of the binding sequential dynamics, i.e., the feasibility phenomenon for coupled heteroclinic networks: for each collection of successive heteroclinic trajectories inside the unified networks, there is an open set of initial points such that the trajectory going through each of them follows the prescribed collection staying in a small neighborhood of it. We show also that the symbolic complexity function of the system restricted to this neighborhood is a polynomial of degree L - 1, where L is the number of modalities.

  4. Megalin binds and mediates cellular internalization of folate binding protein

    DEFF Research Database (Denmark)

    Birn, Henrik; Zhai, Xiaoyue; Holm, Jan

    2005-01-01

    Folate is an essential vitamin involved in a number of biological processes. High affinity folate binding proteins (FBPs) exist both as glycosylphosphatidylinositol-linked, membrane associated folate binding proteins and as soluble FBPs in plasma and some secretory fluids such as milk, saliva...... to bind and mediate cellular uptake of FBP. Surface plasmon resonance analysis shows binding of bovine and human milk FBP to immobilized megalin, but not to low density lipoprotein receptor related protein. Binding of (125)I-labeled folate binding protein (FBP) to sections of kidney proximal tubule, known...

  5. Binding Principles A and B

    Institute of Scientific and Technical Information of China (English)

    陈源

    2014-01-01

    This paper focuses on the discussion of how Binding Principle A and Binding Principe B help with the interpretation of reference in English and Chinese. They are supposedly universal across languages.

  6. Neisseria meningitidis Adhesin NadA Targets β1 Integrins: FUNCTIONAL SIMILARITY TO YERSINIA INVASIN*

    OpenAIRE

    Nägele, Virginie; Heesemann, Jürgen; Schielke, Stephanie; Luisa F Jiménez-Soto; Kurzai, Oliver; Ackermann, Nikolaus

    2011-01-01

    Meningococci are facultative-pathogenic bacteria endowed with a set of adhesins allowing colonization of the human upper respiratory tract, leading to fulminant meningitis and septicemia. The Neisseria adhesin NadA was identified in about 50% of N. meningitidis isolates and is closely related to the Yersinia adhesin YadA, the prototype of the oligomeric coiled-coil adhesin (Oca) family. NadA is known to be involved in cell adhesion, invasion, and induction of proinflammatory cytokines. Becaus...

  7. Neisseria meningitidis adhesin NadA targets beta1 integrins: functional similarity to Yersinia invasin.

    Science.gov (United States)

    Nägele, Virginie; Heesemann, Jürgen; Schielke, Stephanie; Jiménez-Soto, Luisa F; Kurzai, Oliver; Ackermann, Nikolaus

    2011-06-10

    Meningococci are facultative-pathogenic bacteria endowed with a set of adhesins allowing colonization of the human upper respiratory tract, leading to fulminant meningitis and septicemia. The Neisseria adhesin NadA was identified in about 50% of N. meningitidis isolates and is closely related to the Yersinia adhesin YadA, the prototype of the oligomeric coiled-coil adhesin (Oca) family. NadA is known to be involved in cell adhesion, invasion, and induction of proinflammatory cytokines. Because of the enormous diversity of neisserial cell adhesins the analysis of the specific contribution of NadA in meningococcal host interactions is limited. Therefore, we used a non-invasive Y. enterocolitica mutant as carrier to study the role of NadA in host cell interaction. NadA was shown to be efficiently produced and localized in its oligomeric form on the bacterial surface of Y. enterocolitica. Additionally, NadA mediated a β1 integrin-dependent adherence with subsequent internalization of yersiniae by a β1 integrin-positive cell line. Using recombinant NadA(24-210) protein and human and murine β1 integrin-expressing cell lines we could demonstrate the role of the β1 integrin subunit as putative receptor for NadA. Subsequent inhibition assays revealed specific interaction of NadA(24-210) with the human β1 integrin subunit. Cumulatively, these results indicate that Y. enterocolitica is a suitable toolbox system for analysis of the adhesive properties of NadA, revealing strong evidence that β1 integrins are important receptors for NadA. Thus, this study demonstrated for the first time a direct interaction between the Oca-family member NadA and human β1 integrins.

  8. Neisseria meningitidis Adhesin NadA Targets β1 Integrins: FUNCTIONAL SIMILARITY TO YERSINIA INVASIN*

    OpenAIRE

    Nägele, Virginie; Heesemann, Jürgen; Schielke, Stephanie; Jiménez-Soto, Luisa F.; Kurzai, Oliver; Ackermann, Nikolaus

    2011-01-01

    Meningococci are facultative-pathogenic bacteria endowed with a set of adhesins allowing colonization of the human upper respiratory tract, leading to fulminant meningitis and septicemia. The Neisseria adhesin NadA was identified in about 50% of N. meningitidis isolates and is closely related to the Yersinia adhesin YadA, the prototype of the oligomeric coiled-coil adhesin (Oca) family. NadA is known to be involved in cell adhesion, invasion, and induction of proinflammatory cytokines. Becaus...

  9. Carboplatin binding to histidine

    Energy Technology Data Exchange (ETDEWEB)

    Tanley, Simon W. M. [University of Manchester, Brunswick Street, Manchester M13 9PL (United Kingdom); Diederichs, Kay [University of Konstanz, D-78457 Konstanz (Germany); Kroon-Batenburg, Loes M. J. [Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands); Levy, Colin [University of Manchester, 131 Princess Street, Manchester M1 7DN (United Kingdom); Schreurs, Antoine M. M. [Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands); Helliwell, John R., E-mail: john.helliwell@manchester.ac.uk [University of Manchester, Brunswick Street, Manchester M13 9PL (United Kingdom)

    2014-08-29

    An X-ray crystal structure showing the binding of purely carboplatin to histidine in a model protein has finally been obtained. This required extensive crystallization trials and various novel crystal structure analyses. Carboplatin is a second-generation platinum anticancer agent used for the treatment of a variety of cancers. Previous X-ray crystallographic studies of carboplatin binding to histidine (in hen egg-white lysozyme; HEWL) showed the partial conversion of carboplatin to cisplatin owing to the high NaCl concentration used in the crystallization conditions. HEWL co-crystallizations with carboplatin in NaBr conditions have now been carried out to confirm whether carboplatin converts to the bromine form and whether this takes place in a similar way to the partial conversion of carboplatin to cisplatin observed previously in NaCl conditions. Here, it is reported that a partial chemical transformation takes place but to a transplatin form. Thus, to attempt to resolve purely carboplatin binding at histidine, this study utilized co-crystallization of HEWL with carboplatin without NaCl to eliminate the partial chemical conversion of carboplatin. Tetragonal HEWL crystals co-crystallized with carboplatin were successfully obtained in four different conditions, each at a different pH value. The structural results obtained show carboplatin bound to either one or both of the N atoms of His15 of HEWL, and this particular variation was dependent on the concentration of anions in the crystallization mixture and the elapsed time, as well as the pH used. The structural details of the bound carboplatin molecule also differed between them. Overall, the most detailed crystal structure showed the majority of the carboplatin atoms bound to the platinum centre; however, the four-carbon ring structure of the cyclobutanedicarboxylate moiety (CBDC) remained elusive. The potential impact of the results for the administration of carboplatin as an anticancer agent are described.

  10. Evaluation of binding strength depending on the adhesive binding methods

    Directory of Open Access Journals (Sweden)

    Suzana Pasanec Preprotić

    2015-05-01

    Full Text Available A book with a personal value is worth remembering since it represents specific interests of an individual - author of the book. Therefore the original is the first issue of a book which is always bound manually. Due to cost-effectiveness, adhesive binding is most commonly used in author’s edition in paperback and hardback. Adhesive binding methods differ only if a paper leaf is a binding unit in adhesive binding form. The subject of the research is the quality of book block binding for two binding methods with/without mull fabric. The assumption is that double-fan adhesive binding method shows an extraordinary binding quality as compared to the rough spine method. For the needs of this research book block parameters remained unaltered: paper type, size and book volume. The results related to strength were obtained by using an experimental method of tensile strength for individual paper leaves. The rating of book block quality was conducted in accordance with FOGRA Nr.71006 guidelines for page pull-test. Furthermore, strength results for both methods were compared in order to evaluate the importance of changing the quality of adhesive binding. Statistical method ANOVA analysis of variance and Fisher’s F-test were used to evaluate the quality of book block binding.

  11. Analytic QCD Binding Potentials

    CERN Document Server

    Fried, H M; Grandou, T; Sheu, Y -M

    2011-01-01

    This paper applies the analytic forms of a recent non-perturbative, manifestly gauge- and Lorentz-invariant description (of the exchange of all possible virtual gluons between quarks ($Q$) and/or anti-quarks ($\\bar{Q}$) in a quenched, eikonal approximation) to extract analytic forms for the binding potentials generating a model $Q$-$\\bar{Q}$ "pion", and a model $QQQ$ "nucleon". Other, more complicated $Q$, $\\bar{Q}$ contributions to such color-singlet states may also be identified analytically. An elementary minimization technique, relevant to the ground states of such bound systems, is adopted to approximate the solutions to a more proper, but far more complicated Schroedinger/Dirac equation; the existence of possible contributions to the pion and nucleon masses due to spin, angular momentum, and "deformation" degrees of freedom is noted but not pursued. Neglecting electromagnetic and weak interactions, this analysis illustrates how the one new parameter making its appearance in this exact, realistic formali...

  12. Identification of consensus binding sites clarifies FMRP binding determinants.

    Science.gov (United States)

    Anderson, Bart R; Chopra, Pankaj; Suhl, Joshua A; Warren, Stephen T; Bassell, Gary J

    2016-08-19

    Fragile X mental retardation protein (FMRP) is a multifunctional RNA-binding protein with crucial roles in neuronal development and function. Efforts aimed at elucidating how FMRP target mRNAs are selected have produced divergent sets of target mRNA and putative FMRP-bound motifs, and a clear understanding of FMRP's binding determinants has been lacking. To clarify FMRP's binding to its target mRNAs, we produced a shared dataset of FMRP consensus binding sequences (FCBS), which were reproducibly identified in two published FMRP CLIP sequencing datasets. This comparative dataset revealed that of the various sequence and structural motifs that have been proposed to specify FMRP binding, the short sequence motifs TGGA and GAC were corroborated, and a novel TAY motif was identified. In addition, the distribution of the FCBS set demonstrates that FMRP preferentially binds to the coding region of its targets but also revealed binding along 3' UTRs in a subset of target mRNAs. Beyond probing these putative motifs, the FCBS dataset of reproducibly identified FMRP binding sites is a valuable tool for investigating FMRP targets and function. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. Binding Energy and Enzymatic Catalysis.

    Science.gov (United States)

    Hansen, David E.; Raines, Ronald T.

    1990-01-01

    Discussed is the fundamental role that the favorable free energy of binding of the rate-determining transition state plays in catalysis. The principle that all of the catalytic factors discussed are realized by the use of this binding energy is reviewed. (CW)

  14. Cooperative binding: a multiple personality.

    Science.gov (United States)

    Martini, Johannes W R; Diambra, Luis; Habeck, Michael

    2016-06-01

    Cooperative binding has been described in many publications and has been related to or defined by several different properties of the binding behavior of the ligand to the target molecule. In addition to the commonly used Hill coefficient, other characteristics such as a sigmoidal shape of the overall titration curve in a linear plot, a change of ligand affinity of the other binding sites when a site of the target molecule becomes occupied, or complex roots of the binding polynomial have been used to define or to quantify cooperative binding. In this work, we analyze how the different properties are related in the most general model for binding curves based on the grand canonical partition function and present several examples which highlight differences between the cooperativity characterizing properties which are discussed. Our results mainly show that among the presented definitions there are not two which fully coincide. Moreover, this work poses the question whether it can make sense to distinguish between positive and negative cooperativity based on the macroscopic binding isotherm only. This article shall emphasize that scientists who investigate cooperative effects in biological systems could help avoiding misunderstandings by stating clearly which kind of cooperativity they discuss.

  15. Asymmetric cation-binding catalysis

    DEFF Research Database (Denmark)

    Oliveira, Maria Teresa; Lee, Jiwoong

    2017-01-01

    and KCN, are selectively bound to the catalyst, providing exceptionally high enantioselectivities for kinetic resolutions, elimination reactions (fluoride base), and Strecker synthesis (cyanide nucleophile). Asymmetric cation-binding catalysis was recently expanded to silicon-based reagents, enabling...... solvents, thus increasing their applicability in synthesis. The expansion of this concept to chiral polyethers led to the emergence of asymmetric cation-binding catalysis, where chiral counter anions are generated from metal salts, particularly using BINOL-based polyethers. Alkali metal salts, namely KF...

  16. Ion binding to biological macromolecules.

    Science.gov (United States)

    Petukh, Marharyta; Alexov, Emil

    2014-11-01

    Biological macromolecules carry out their functions in water and in the presence of ions. The ions can bind to the macromolecules either specifically or non-specifically, or can simply to be a part of the water phase providing physiological gradient across various membranes. This review outlines the differences between specific and non-specific ion binding in terms of the function and stability of the corresponding macromolecules. Furthermore, the experimental techniques to identify ion positions and computational methods to predict ion binding are reviewed and their advantages compared. It is indicated that specifically bound ions are relatively easier to be revealed while non-specifically associated ions are difficult to predict. In addition, the binding and the residential time of non-specifically bound ions are very much sensitive to the environmental factors in the cells, specifically to the local pH and ion concentration. Since these characteristics differ among the cellular compartments, the non-specific ion binding must be investigated with respect to the sub-cellular localization of the corresponding macromolecule.

  17. The prion protein binds thiamine.

    Science.gov (United States)

    Perez-Pineiro, Rolando; Bjorndahl, Trent C; Berjanskii, Mark V; Hau, David; Li, Li; Huang, Alan; Lee, Rose; Gibbs, Ebrima; Ladner, Carol; Dong, Ying Wei; Abera, Ashenafi; Cashman, Neil R; Wishart, David S

    2011-11-01

    Although highly conserved throughout evolution, the exact biological function of the prion protein is still unclear. In an effort to identify the potential biological functions of the prion protein we conducted a small-molecule screening assay using the Syrian hamster prion protein [shPrP(90-232)]. The screen was performed using a library of 149 water-soluble metabolites that are known to pass through the blood-brain barrier. Using a combination of 1D NMR, fluorescence quenching and surface plasmon resonance we identified thiamine (vitamin B1) as a specific prion ligand with a binding constant of ~60 μM. Subsequent studies showed that this interaction is evolutionarily conserved, with similar binding constants being seen for mouse, hamster and human prions. Various protein construct lengths, both with and without the unstructured N-terminal region in the presence and absence of copper, were examined. This indicates that the N-terminus has no influence on the protein's ability to interact with thiamine. In addition to thiamine, the more biologically abundant forms of vitamin B1 (thiamine monophosphate and thiamine diphosphate) were also found to bind the prion protein with similar affinity. Heteronuclear NMR experiments were used to determine thiamine's interaction site, which is located between helix 1 and the preceding loop. These data, in conjunction with computer-aided docking and molecular dynamics, were used to model the thiamine-binding pharmacophore and a comparison with other thiamine binding proteins was performed to reveal the common features of interaction.

  18. Cholesterol binding to ion channels

    Directory of Open Access Journals (Sweden)

    Irena eLevitan

    2014-02-01

    Full Text Available Numerous studies demonstrated that membrane cholesterol is a major regulator of ion channel function. The goal of this review is to discuss significant advances that have been recently achieved in elucidating the mechanisms responsible for cholesterol regulation of ion channels. The first major insight that comes from growing number of studies that based on the sterol specificity of cholesterol effects, show that several types of ion channels (nAChR, Kir, BK, TRPV are regulated by specific sterol-protein interactions. This conclusion is supported by demonstrating direct saturable binding of cholesterol to a bacterial Kir channel. The second major advance in the field is the identification of putative cholesterol binding sites in several types of ion channels. These include sites at locations associated with the well-known cholesterol binding motif CRAC and its reversed form CARC in nAChR, BK, and TRPV, as well as novel cholesterol binding regions in Kir channels. Notably, in the majority of these channels, cholesterol is suggested to interact mainly with hydrophobic residues in non-annular regions of the channels being embedded in between transmembrane protein helices. We also discuss how identification of putative cholesterol binding sites is an essential step to understand the mechanistic basis of cholesterol-induced channel regulation. Clearly, however, these are only the first few steps in obtaining a general understanding of cholesterol-ion channels interactions and their roles in cellular and organ functions.

  19. Candida glabrata Binding to Candida albicans Hyphae Enables Its Development in Oropharyngeal Candidiasis.

    Science.gov (United States)

    Tati, Swetha; Davidow, Peter; McCall, Andrew; Hwang-Wong, Elizabeth; Rojas, Isolde G; Cormack, Brendan; Edgerton, Mira

    2016-03-01

    Pathogenic mechanisms of Candida glabrata in oral candidiasis, especially because of its inability to form hyphae, are understudied. Since both Candida albicans and C. glabrata are frequently co-isolated in oropharyngeal candidiasis (OPC), we examined their co-adhesion in vitro and observed adhesion of C. glabrata only to C. albicans hyphae microscopically. Mice were infected sublingually with C. albicans or C. glabrata individually, or with both species concurrently, to study their ability to cause OPC. Infection with C. glabrata alone resulted in negligible infection of tongues; however, colonization by C. glabrata was increased by co-infection or a pre-established infection with C. albicans. Furthermore, C. glabrata required C. albicans for colonization of tongues, since decreasing C. albicans burden with fluconazole also reduced C. glabrata. C. albicans hyphal wall adhesins Als1 and Als3 were important for in vitro adhesion of C. glabrata and to establish OPC. C. glabrata cell wall protein coding genes EPA8, EPA19, AWP2, AWP7, and CAGL0F00181 were implicated in mediating adhesion to C. albicans hyphae and remarkably, their expression was induced by incubation with germinated C. albicans. Thus, we found a near essential requirement for the presence of C. albicans for both initial colonization and establishment of OPC infection by C. glabrata.

  20. Galectin-3-Binding and Metastasis

    Science.gov (United States)

    Nangia-Makker, Pratima; Balan, Vitaly; Raz, Avraham

    2013-01-01

    i. Summary Galectin-3 is a member of a family of carbohydrate-binding proteins. It is present in the nucleus, the cytoplasm and also extracellular matrix of many normal and neoplastic cell types. Arrays of reports show an upregulation of this protein in transformed and metastatic cell lines (1, 2). Moreover, in many human carcinomas, an increased expression of galectin-3 correlates with progressive tumor stages (3–6). Several lines of analysis have demonstrated that the galectins participate in cell-cell and cell-matrix interactions by recognizing and binding complimentary glycoconjugates and thereby play a crucial role in normal and pathological processes. Elevated expression of the protein is associated with an increased capacity for anchorage-independent growth, homotypic aggregation, and tumor cell lung colonization (7–9). In this chapter we describe the methods of purification of galectin-3 from transformed E. coli and some of the commonly used functional assays for analyzing galectin-3 binding. PMID:22674139

  1. Computational Prediction of RNA-Binding Proteins and Binding Sites

    Directory of Open Access Journals (Sweden)

    Jingna Si

    2015-11-01

    Full Text Available Proteins and RNA interaction have vital roles in many cellular processes such as protein synthesis, sequence encoding, RNA transfer, and gene regulation at the transcriptional and post-transcriptional levels. Approximately 6%–8% of all proteins are RNA-binding proteins (RBPs. Distinguishing these RBPs or their binding residues is a major aim of structural biology. Previously, a number of experimental methods were developed for the determination of protein–RNA interactions. However, these experimental methods are expensive, time-consuming, and labor-intensive. Alternatively, researchers have developed many computational approaches to predict RBPs and protein–RNA binding sites, by combining various machine learning methods and abundant sequence and/or structural features. There are three kinds of computational approaches, which are prediction from protein sequence, prediction from protein structure, and protein-RNA docking. In this paper, we review all existing studies of predictions of RNA-binding sites and RBPs and complexes, including data sets used in different approaches, sequence and structural features used in several predictors, prediction method classifications, performance comparisons, evaluation methods, and future directions.

  2. Computational Prediction of RNA-Binding Proteins and Binding Sites.

    Science.gov (United States)

    Si, Jingna; Cui, Jing; Cheng, Jin; Wu, Rongling

    2015-01-01

    Proteins and RNA interaction have vital roles in many cellular processes such as protein synthesis, sequence encoding, RNA transfer, and gene regulation at the transcriptional and post-transcriptional levels. Approximately 6%-8% of all proteins are RNA-binding proteins (RBPs). Distinguishing these RBPs or their binding residues is a major aim of structural biology. Previously, a number of experimental methods were developed for the determination of protein-RNA interactions. However, these experimental methods are expensive, time-consuming, and labor-intensive. Alternatively, researchers have developed many computational approaches to predict RBPs and protein-RNA binding sites, by combining various machine learning methods and abundant sequence and/or structural features. There are three kinds of computational approaches, which are prediction from protein sequence, prediction from protein structure, and protein-RNA docking. In this paper, we review all existing studies of predictions of RNA-binding sites and RBPs and complexes, including data sets used in different approaches, sequence and structural features used in several predictors, prediction method classifications, performance comparisons, evaluation methods, and future directions.

  3. Synthetic heparin-binding growth factor analogs

    Science.gov (United States)

    Pena, Louis A.; Zamora, Paul; Lin, Xinhua; Glass, John D.

    2007-01-23

    The invention provides synthetic heparin-binding growth factor analogs having at least one peptide chain that binds a heparin-binding growth factor receptor, covalently bound to a hydrophobic linker, which is in turn covalently bound to a non-signaling peptide that includes a heparin-binding domain. The synthetic heparin-binding growth factor analogs are useful as soluble biologics or as surface coatings for medical devices.

  4. Scientific Opinion on the substantiation of a health claim related to the combination of artichoke leaf dry extract standardised in caffeoylquinic acids, monacolin K in red yeast rice, sugar-cane derived policosanols, OPC from French maritime pine bark, garlic dry extract standardised in allicin, d-α-tocopheryl hydrogen succinate, riboflavin and inositol hexanicotinate in Limicol® and reduction of blood LDL-cholesterol concentrations pursuant to Article 14 of Regulation (EC No 1924/2006

    Directory of Open Access Journals (Sweden)

    EFSA Panel on Dietetic Products, Nutrition and Allergies (NDA

    2013-07-01

    Full Text Available Following an application from Laboratoire Lescuyer, submitted pursuant to Article 14 of Regulation (EC No 1924/2006 via the Competent Authority of France, the Panel on Dietetic Products, Nutrition and Allergies (NDA was asked to deliver an opinion on the scientific substantiation of a health claim related to the combination of artichoke leaf dry extract standardised in caffeoylquinic acids, monacolin K in red yeast rice, sugar-cane derived policosanols, OPC from French maritime pine bark, garlic dry extract standardised in allicin, d-α-tocopheryl hydrogen succinate, riboflavin and inositol hexanicotinate in Limicol® and reduction of blood LDL-cholesterol concentrations. The Panel considers that the food which is the subject of the claim is sufficiently characterised. The Panel considers that reduction of blood LDL-cholesterol concentrations is a beneficial physiological effect. High LDL-cholesterol is a risk factor in the development of coronary heart disease. In weighing the evidence, the Panel took into account that, although no evidence was provided for an LDL-cholesterol lowering effect of any of the single food constituents in Limicol® at the proposed conditions of use or as to how the ingredients individually or in any combination could contribute to the claimed effect and despite the lack of a dose-response relationship observed in one human intervention study, three human intervention studies conducted by two independent research groups showed an effect of the combination of food ingredients in Limicol® on blood LDL-cholesterol concentrations. The Panel concludes that a cause and effect relationship has been established between the consumption of the combination of artichoke leaf dry extract standardised in caffeoylquinic acids, monacolin K in red yeast rice, sugar-cane derived policosanols, OPC from French maritime pine bark, garlic dry extract standardised in allicin, d-α-tocopheryl hydrogen succinate, riboflavin and inositol

  5. Cellulose binding domain fusion proteins

    Science.gov (United States)

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc A.; Doi, Roy H.

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  6. Bacterial oligopeptide-binding proteins.

    Science.gov (United States)

    Monnet, V

    2003-10-01

    This review focuses on bacterial oligopeptide-binding proteins, which form part of the oligopeptide transport system belonging to the ATP-binding cassette family of transporters. Depending on the bacterial species, these binding proteins (OppA) capture peptides ranging in size from 2 to 18 amino acids from the environment and pass them on to the other components of the oligopeptide transport system for internalisation. Bacteria have developed several strategies to produce these binding proteins, which are periplasmic in Gram- bacteria and membrane-anchored in Gram+, with a higher stoichiometry (probably necessary for efficient transport) than the other components in the transport system. The expression of OppA-encoding genes is clearly modulated by external factors, especially nitrogen compounds, but the mechanisms of regulation are not always clear. The best-understood roles played by OppAs are internalisation of peptides for nutrition and recycling of muropeptides. It has, however, recently become clear that OppAs are also involved in sensing the external medium via specific or non-specific peptides.

  7. Protein binding assay for hyaluronate

    Energy Technology Data Exchange (ETDEWEB)

    Lacy, B.E.; Underhill, C.B.

    1986-11-01

    A relatively quick and simple assay for hyaluronate was developed using the specific binding protein, hyaluronectin. The hyaluronectin was obtained by homogenizing the brains of Sprague-Dawley rats, and then centrifuging the homogenate. The resulting supernatant was used as a source of crude hyaluronectin. In the binding assay, the hyaluronectin was mixed with (/sup 3/H)hyaluronate, followed by an equal volume of saturated (NH/sub 4/)/sub 2/SO/sub 4/, which precipitated the hyaluronectin and any (/sup 3/H)hyaluronate associated with it, but left free (/sup 3/H)hyaluronate in solution. The mixture was then centrifuged, and the amount of bound (/sup 3/H)hyaluronate in the precipitate was determined. Using this assay, the authors found that hyaluronectin specifically bound hyaluronate, since other glycosaminoglycans failed to compete for the binding protein. In addition, the interaction between hyaluronectin and hyaluronate was of relatively high affinity, and the size of the hyaluronate did not appear to substantially alter the amount of binding. To determine the amount of hyaluronate in an unknown sample, they used a competition assay in which the binding of a set amount of (/sup 3/H)hyaluronate was blocked by the addition of unlabeled hyaluronate. By comparing the degree of competition of the unknown samples with that of known amounts of hyaluronate, it was possible to determine the amount of hyaluronate in the unknowns. They have found that this method is sensitive to 1 ..mu..g or less of hyaluronate, and is unaffected by the presence of proteins.

  8. Human plasminogen binding protein tetranectin

    DEFF Research Database (Denmark)

    Kastrup, J S; Rasmussen, H; Nielsen, B B;

    1997-01-01

    The recombinant human plasminogen binding protein tetranectin (TN) and the C-type lectin CRD of this protein (TN3) have been crystallized. TN3 crystallizes in the tetragonal space group P4(2)2(1)2 with cell dimensions a = b = 64.0, c = 75.7 A and with one molecule per asymmetric unit. The crystals...... to at least 2.5 A. A full data set has been collected to 3.0 A. The asymmetric unit contains one monomer of TN. Molecular replacement solutions for TN3 and TN have been obtained using the structure of the C-type lectin CRD of rat mannose-binding protein as search model. The rhombohedral space group indicates...

  9. Probing protein phosphatase substrate binding

    DEFF Research Database (Denmark)

    Højlys-Larsen, Kim B.; Sørensen, Kasper Kildegaard; Jensen, Knud Jørgen;

    2012-01-01

    Proteomics and high throughput analysis for systems biology can benefit significantly from solid-phase chemical tools for affinity pull-down of proteins from complex mixtures. Here we report the application of solid-phase synthesis of phosphopeptides for pull-down and analysis of the affinity...... around the phosphorylated residue are important for the binding affinity of ILKAP. We conclude that solid-phase affinity pull-down of proteins from complex mixtures can be applied in phosphoproteomics and systems biology....

  10. BINDING ISOTHERMS SURFACTANT-PROTEINS

    Directory of Open Access Journals (Sweden)

    Elena Irina Moater

    2011-12-01

    Full Text Available The interactions between surfactants and proteins shows some similarities with interactions between surfactants and polymers, but the hydrophobic amphoteric nature of proteins and their secondary and tertiary structure components make them different from conventional polymer systems. Many studies from the past about surfactant - proteins bonding used the dialysis techniques. Other techniques used to determine the binding isotherm, included ultrafiltration, ultracentrifugation, potentiometry, ion-selective electrode method and surface tension. High affinity isotherms which are typical of an anionic surfactant - protein bonding, exhibit an initial increase steep followed by a slow growth region and then a vertical growth above a certain concentration. This isotherm is typical of ionic surfactant to protein binding. Often the high affinity initial bond appears at very low concentrations of surfactant and therefore in some protein-surfactant systems, the exact shape of the isotherm in this region may be missing. The surfactant - protein binding is influenced by a number of variables such as the nature and chain length of surfactant, pH, ionic strength, temperature, nature of this protein and additives.

  11. Anion binding in biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Feiters, Martin C [Department of Organic Chemistry, Institute for Molecules and Materials, Faculty of Science, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands); Meyer-Klaucke, Wolfram [EMBL Hamburg Outstation at DESY, Notkestrasse 85, D-22607 Hamburg (Germany); Kostenko, Alexander V; Soldatov, Alexander V [Faculty of Physics, Southern Federal University, Sorge 5, Rostov-na-Donu, 344090 (Russian Federation); Leblanc, Catherine; Michel, Gurvan; Potin, Philippe [Centre National de la Recherche Scientifique and Universite Pierre et Marie Curie Paris-VI, Station Biologique de Roscoff, Place Georges Teissier, BP 74, F-29682 Roscoff cedex, Bretagne (France); Kuepper, Frithjof C [Scottish Association for Marine Science, Dunstaffnage Marine Laboratory, Oban, Argyll PA37 1QA, Scotland (United Kingdom); Hollenstein, Kaspar; Locher, Kaspar P [Institute of Molecular Biology and Biophysics, ETH Zuerich, Schafmattstrasse 20, Zuerich, 8093 (Switzerland); Bevers, Loes E; Hagedoorn, Peter-Leon; Hagen, Wilfred R, E-mail: m.feiters@science.ru.n [Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft (Netherlands)

    2009-11-15

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L{sub 3} (2p{sub 3/2}) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  12. Anion binding in biological systems

    Science.gov (United States)

    Feiters, Martin C.; Meyer-Klaucke, Wolfram; Kostenko, Alexander V.; Soldatov, Alexander V.; Leblanc, Catherine; Michel, Gurvan; Potin, Philippe; Küpper, Frithjof C.; Hollenstein, Kaspar; Locher, Kaspar P.; Bevers, Loes E.; Hagedoorn, Peter-Leon; Hagen, Wilfred R.

    2009-11-01

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L3 (2p3/2) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  13. Engineering RNA-binding proteins for biology

    OpenAIRE

    Chen,Yu; Varani, Gabriele

    2013-01-01

    RNA-binding proteins play essential roles in the regulation of gene expression. Many have modular structures and combine relatively few common domains in various arrangements to recognize RNA sequences and/or structures. Recent progress in engineering the specificity of the PUF class RNA-binding proteins has shown that RNA-binding domains may be combined with various effector or functional domains to regulate the metabolism of targeted RNAs. Designer RNA-binding proteins with tailored sequenc...

  14. Rat Mannose-Binding Protein A Binds CD14

    OpenAIRE

    Chiba, Hirofumi; Sano, Hitomi; Iwaki, Daisuke; Murakami, Seiji; Mitsuzawa, Hiroaki; Takahashi, Toru; Konishi, Masanori; Takahashi, Hiroki; Kuroki, Yoshio

    2001-01-01

    Lipopolysaccharide (LPS) has been known to induce inflammation by interacting with CD14, which serves as a receptor for LPS. Mannose-binding protein (MBP) belongs to the collectin subgroup of the C-type lectin superfamily, along with surfactant proteins SP-A and SP-D. We have recently demonstrated that SP-A modulates LPS-induced cellular responses by interaction with CD14 (H. Sano, H. Sohma, T. Muta, S. Nomura, D. R. Voelker, and Y. Kuroki, J. Immunol. 163:387–395, 2000) and that SP-D also in...

  15. Feature-Based Binding and Phase Theory

    Science.gov (United States)

    Antonenko, Andrei

    2012-01-01

    Current theories of binding cannot provide a uniform account for many facts associated with the distribution of anaphors, such as long-distance binding effects and the subject-orientation of monomorphemic anaphors. Further, traditional binding theory is incompatible with minimalist assumptions. In this dissertation I propose an analysis of…

  16. OPC Paste Samples Exposed To Aggressive Solutions. Cementitious Barriers Partnership

    Energy Technology Data Exchange (ETDEWEB)

    Langton, C. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2014-11-01

    The study presented in this report focused on a low-activity wasteform containing a high pH pore solution with a significant level of sulfate. The purpose of the study was to improve understanding of the complex concrete/wasteform reactive transport problem, in particular the role of pH in sulfate attack. Paste samples prepared at three different water-to-cement ratios were tested. The mixtures were prepared with ASTM Type I cement, without additional admixtures. The samples were exposed to two different sodium sulfate contact solutions. The first solution was prepared at 0.15M Na2SO4. The second solution also incorporated 0.5M NaOH, to mimic the high pH conditions found in Saltstone. The data collected indicated that in Na2SO4 solution, damage occurs to the pastes. In the case of the high pH sulfate solution (Na2SO4 + NaOH), no signs of damage was observed on any of the paste mixtures. These results indicate that the high sulfate content found in the wasteform pore solution will not necessarily lead to severe damage to concrete. Good-quality mixtures could thus prove durable over the long term, and act as an effective barrier to prevent radionuclides from reaching the environment.

  17. OPC Paste Samples Exposed To Aggressive Solutions. Cementitious Barriers Partnership

    Energy Technology Data Exchange (ETDEWEB)

    Langton, C. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2014-11-01

    The study presented in this report focused on a low-activity wasteform containing a high-pH pore solution with a significant level of sulfate. The purpose of the study was to improve understanding of the complex concrete/wasteform reactive transport problem, in particular, the role of pH in sulfate attack. Paste samples prepared at three different water-to-cement ratios were tested. The mixtures were prepared with ASTM Type I cement, without additional admixtures. The samples were exposed to two different sodium sulfate contact solutions. The first solution was prepared at 0.15M Na2SO4. The second solution also incorporated 0.5M NaOH, to mimic the high pH conditions found in Saltstone. The data collected indicated that, in Na2SO4 solution, damage occurs to the pastes. In the case of the high-pH sulfate solution (Na2SO4 + NaOH), no signs of damage were observed on any of the paste mixtures. These results indicate that the high sulfate content found in the wasteform pore solution will not necessarily lead to severe damage to concrete. Good-quality mixtures could thus prove durable over the long term, and act as an effective barrier to prevent radionuclides from reaching the environment.

  18. Manufacturability evaluation of model-based OPC masks

    Science.gov (United States)

    Jang, Sung-Hoon; Zinn, Sonny Y.; Ki, Won-Tai; Choi, Ji-Hyun; Jeon, Chan-Uk; Choi, Seong-Woon; Yoon, Hee-Sun; Sohn, Jung-Min; Oh, Yong-Ho; Lee, Jai-Cheol; Lim, Sungwoo

    2002-12-01

    A systematic method for the model-based optical proximity correction in presented. This is called optical proximity effect reducing algorithm (OPERA) and has been implemented to TOPO, an in-house program for optical lithography simulations. Comparing simulational results as well as experimental results, we found that OPERA is not only suitable for shape restoration but also for resolution enhancement. However, the resulting optimized patterns have a high degree of complexity and this brought up a number of issues for mask manufacturing. First, data volume and exposure time were dramatically increased for conventional e-beam file formats. This was solved by using the MODE6 format that preserves data hierarchy. Second, due to excessive shot divisions, a variable-shaped beam machine could not finish the exposure process. A raster-scan beam machine successfully finished the exposure. Finally, a die-to-die inspection was performed but many false defects that do not affect wafer printing were defected. This will be solved by a new type of tool that inspects a mask by evaluating its aerial image.

  19. Biodiscovery of Aluminum Binding Peptides

    Science.gov (United States)

    2013-08-01

    for an additional 35-45 min. After induction, 5 µL cells were added to 25µL 250 nM YPet-Mona for 45 min. on ice. Cells were then pelleted and...binding mechanism of phage particles displaying a constrained heptapeptide with specific affinity to SiO2 and TiO2 ," Anal. Chem. 78(14), 4872-4879 (2006...hydroxyapatite crystals," Langmuir 27(12), 7620-7628 (2011). [15] Dickerson, M. B. A., et al., Peptide-induced room temperature formation of nanostructured TiO2

  20. Statistics for Transcription Factor Binding Sites

    OpenAIRE

    2008-01-01

    Transcription factors (TFs) play a key role in gene regulation. They interact with specific binding sites or motifs on the DNA sequence and regulate expression of genes downstream of these binding sites. In silico prediction of potential binding of a TF to a binding site is an important task in computational biology. From a statistical point of view, the DNA sequence is a long text consisting of four different letters ('A','C','G', and 'T'). The binding of a TF to the sequence corresponds to ...

  1. Defining Starch Binding by Glucan Phosphatases

    DEFF Research Database (Denmark)

    Auger, Kyle; Raththagala, Madushi; Wilkens, Casper

    2015-01-01

    phosphatases. The main objective of this study was to quantify the binding affinity of different enzymes that are involved in this cyclic process. We established a protocol to quickly, reproducibly, and quantitatively measure the binding of the enzymes to glucans utilizing Affinity Gel Electrophoresis (AGE...... glucan phosphatases showed similar affinities for the short oligosaccharide β-cyclodextrin. We performed structure-guided mutagenesis to define the mechanism of these differences. We found that the carbohydrate binding module (CBM) domain provided a stronger binding affinity compared to surface binding...

  2. Synthetic heparin-binding factor analogs

    Science.gov (United States)

    Pena, Louis A.; Zamora, Paul O.; Lin, Xinhua; Glass, John D.

    2010-04-20

    The invention provides synthetic heparin-binding growth factor analogs having at least one peptide chain, and preferably two peptide chains branched from a dipeptide branch moiety composed of two trifunctional amino acid residues, which peptide chain or chains bind a heparin-binding growth factor receptor and are covalently bound to a non-signaling peptide that includes a heparin-binding domain, preferably by a linker, which may be a hydrophobic linker. The synthetic heparin-binding growth factor analogs are useful as pharmaceutical agents, soluble biologics or as surface coatings for medical devices.

  3. Domain Modeling: NP_000486.1 [SAHG[Archive

    Lifescience Database Archive (English)

    Full Text Available NP_000486.1 chrX CRYSTAL STRUCTURE OF INVASIN: A BACTERIAL INTEGRIN-BINDING PROTEIN c1cwva_ chrX/NP_000486....1/NP_000486.1_holo_16-473.pdb swppa 16A,17L,18S,19L,98P,99G,100F CIT 0 ...

  4. Domain Modeling: NP_671766.1 [SAHG[Archive

    Lifescience Database Archive (English)

    Full Text Available NP_671766.1 chr2 CRYSTAL STRUCTURE OF INVASIN: A BACTERIAL INTEGRIN-BINDING PROTEIN c1cwva_ chr2/NP_671766....1/NP_671766.1_holo_978-1439.pdb swppa 978A,979T,980P,981P,1039Q,1040P,1041R CIT 0 ...

  5. Domain Modeling: NP_059984.2 [SAHG[Archive

    Lifescience Database Archive (English)

    Full Text Available NP_059984.2 chrX CRYSTAL STRUCTURE OF INVASIN: A BACTERIAL INTEGRIN-BINDING PROTEIN c1cwva_ chrX/NP_059984....2/NP_059984.2_holo_551-1231.pdb swppa 551V,552T,553S,554P,634V,635F,636Y,637N,667P,668H CIT 0 ...

  6. Domain Modeling: NP_612482.2 [SAHG[Archive

    Lifescience Database Archive (English)

    Full Text Available NP_612482.2 chr12 CRYSTAL STRUCTURE OF INVASIN: A BACTERIAL INTEGRIN-BINDING PROTEI...N c1cwva_ chr12/NP_612482.2/NP_612482.2_holo_9-579.pdb swppa 9D,10E,11M,12T,35F,91G,92E,93L CIT 0 ...

  7. Domain Modeling: NP_001098662.1 [SAHG[Archive

    Lifescience Database Archive (English)

    Full Text Available NP_001098662.1 chr15 CRYSTAL STRUCTURE OF INVASIN: A BACTERIAL INTEGRIN-BINDING PRO...TEIN c1cwva_ chr15/NP_001098662.1/NP_001098662.1_holo_2-439.pdb swppa 50L,51A,52N 433S,434S,435L,436A,437S,438I,439P CIT 0 ...

  8. Domain Modeling: NP_060252.3 [SAHG[Archive

    Lifescience Database Archive (English)

    Full Text Available NP_060252.3 chr10 CRYSTAL STRUCTURE OF INVASIN: A BACTERIAL INTEGRIN-BINDING PROTEI...N c1cwva_ chr10/NP_060252.3/NP_060252.3_holo_16-498.pdb swppa 16V,17L,18M,19S,20P,98S,99N,100R CIT 0 ...

  9. Domain Modeling: NP_001091977.1 [SAHG[Archive

    Lifescience Database Archive (English)

    Full Text Available NP_001091977.1 chr17 CRYSTAL STRUCTURE OF INVASIN: A BACTERIAL INTEGRIN-BINDING PRO...TEIN c1cwva_ chr17/NP_001091977.1/NP_001091977.1_holo_22-493.pdb swppa 22D,23E,24K,25I,104S,105Q,106K CIT 0 ...

  10. Domain Modeling: NP_065961.1 [SAHG[Archive

    Lifescience Database Archive (English)

    Full Text Available NP_065961.1 chr7 CRYSTAL STRUCTURE OF INVASIN: A BACTERIAL INTEGRIN-BINDING PROTEIN c1cwva_ chr7/NP_065961.1.../NP_065961.1_holo_340-822.pdb swppa 340T,341S,342E,343L,366R,422S,423E,424F CIT 0 ...

  11. DBD2BS: connecting a DNA-binding protein with its binding sites

    OpenAIRE

    2012-01-01

    By binding to short and highly conserved DNA sequences in genomes, DNA-binding proteins initiate, enhance or repress biological processes. Accurately identifying such binding sites, often represented by position weight matrices (PWMs), is an important step in understanding the control mechanisms of cells. When given coordinates of a DNA-binding domain (DBD) bound with DNA, a potential function can be used to estimate the change of binding affinity after base substitutions, where the changes c...

  12. Infinite sets and double binds.

    Science.gov (United States)

    Arden, M

    1984-01-01

    There have been many attempts to bring psychoanalytical theory up to date. This paper approaches the problem by discussing the work of Gregory Bateson and Ignacio Matte-Blanco, with particular reference to the use made by these authors of Russell's theory of logical types. Bateson's theory of the double bind and Matte-Blanco's bilogic are both based on concepts of logical typing. It is argued that the two theories can be linked by the idea that neurotic symptoms are based on category errors in thinking. Clinical material is presented from the analysis of a middle-aged woman. The intention is to demonstrate that the process of making interpretations can be thought of as revealing errors in thinking. Changes in the patient's inner world are then seen to be the result of clarifying childhood experiences based on category errors. Matte-Blanco's theory of bilogic and infinite experiences is a re-evaluation of the place of the primary process in mental life. It is suggested that a combination of bilogic and double bind theory provides a possibility of reformulating psychoanalytical theory.

  13. Adaptive evolution of transcription factor binding sites

    Directory of Open Access Journals (Sweden)

    Berg Johannes

    2004-10-01

    Full Text Available Abstract Background The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks in the evolution of complex regulatory networks. We study a theoretical model for the sequence evolution of binding sites by point mutations. The approach is based on biophysical models for the binding of transcription factors to DNA. Hence we derive empirically grounded fitness landscapes, which enter a population genetics model including mutations, genetic drift, and selection. Results We show that the selection for factor binding generically leads to specific correlations between nucleotide frequencies at different positions of a binding site. We demonstrate the possibility of rapid adaptive evolution generating a new binding site for a given transcription factor by point mutations. The evolutionary time required is estimated in terms of the neutral (background mutation rate, the selection coefficient, and the effective population size. Conclusions The efficiency of binding site formation is seen to depend on two joint conditions: the binding site motif must be short enough and the promoter region must be long enough. These constraints on promoter architecture are indeed seen in eukaryotic systems. Furthermore, we analyse the adaptive evolution of genetic switches and of signal integration through binding cooperativity between different sites. Experimental tests of this picture involving the statistics of polymorphisms and phylogenies of sites are discussed.

  14. Actin binding proteins and spermiogenesis

    Science.gov (United States)

    Mruk, Dolores D

    2011-01-01

    Drebrin E, an actin-binding protein lacking intrinsic activity in the regulation of actin dynamics (e.g., polymerization, capping, nucleation, branching, cross-linking, bundling and severing), is known to recruit actin regulatory proteins to a specific cellular site. Herein, we critically evaluate recent findings in the field which illustrate that drebrin E works together with two other actin-binding proteins, namely Arp3 (actin-related protein 3, a component of the Arp2/3 complex that simultaneously controls actin nucleation for polymerization and branching of actin filaments) and Eps8 (epidermal growth factor receptor pathway substrate 8 that controls capping of the barbed ends of actin filaments, as well as actin filament bundling) to regulate the homeostasis of F-actin filament bundles at the ectoplasmic specialization (ES), a testis-specific atypical adherens junction (AJ) in the seminiferous epithelium. This is mediated by the strict temporal and spatial expression of these three actin-binding proteins at the apical and basal ES at the Sertoli cell-spermatid (step 8–19) and Sertoli-Sertoli cell interface, respectively, during the seminiferous epithelial cycle of spermatogenesis. In this Commentary, we put forth a possible model by which drebrin E may be acting as a platform upon which proteins (e.g., Arp3) that are needed to alter the conformation of actin filament bundles at the ES can be recruited to the site, thus facilitating changes in cell shape and cell position in the epithelium during spermiogenesis and spermiation. In short, drebrin E may be acting as a “logistic” distribution center to manage different regulatory proteins at the apical ES, thereby regulating the dynamics of actin filament bundles and modulating the plasticity of the apical ES. This would allow adhesion to be altered continuously throughout the epithelial cycle to accommodate spermatid movement in the seminiferous epithelium during spermiogenesis and spermiation. We also

  15. Sex hormone binding globulin phenotypes

    DEFF Research Database (Denmark)

    Cornelisse, M M; Bennett, Patrick; Christiansen, M

    1994-01-01

    Human sex hormone binding globulin (SHBG) is encoded by a normal and a variant allele. The resulting SHBG phenotypes (the homozygous normal SHBG, the heterozygous SHBG and the homozygous variant SHBG phenotype) can be distinguished by their electrophoretic patterns. We developed a novel detection....... This method of detection was used to determine the distribution of SHBG phenotypes in healthy controls of both sexes and in five different pathological conditions characterized by changes in the SHBG level or endocrine disturbances (malignant and benign ovarian neoplasms, hirsutism, liver cirrhosis...... on the experimental values. Differences in SHBG phenotypes do not appear to have any clinical significance and no sex difference was found in the SHBG phenotype distribution....

  16. Gamma Oscillations and Visual Binding

    Science.gov (United States)

    Robinson, Peter A.; Kim, Jong Won

    2006-03-01

    At the root of visual perception is the mechanism the brain uses to analyze features in a scene and bind related ones together. Experiments show this process is linked to oscillations of brain activity in the 30-100 Hz gamma band. Oscillations at different sites have correlation functions (CFs) that often peak at zero lag, implying simultaneous firing, even when conduction delays are large. CFs are strongest between cells stimulated by related features. Gamma oscillations are studied here by modeling mm-scale patchy interconnections in the visual cortex. Resulting predictions for gamma responses to stimuli account for numerous experimental findings, including why oscillations and zero-lag synchrony are associated, observed connections with feature preferences, the shape of the zero-lag peak, and variations of CFs with attention. Gamma waves are found to obey the Schroedinger equation, opening the possibility of cortical analogs of quantum phenomena. Gamma instabilities are tied to observations of gamma activity linked to seizures and hallucinations.

  17. DNA binding hydroxyl radical probes

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Vicky J.; Konigsfeld, Katie M.; Aguilera, Joe A. [Department of Radiology, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0610 (United States); Milligan, Jamie R., E-mail: jmilligan@ucsd.edu [Department of Radiology, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0610 (United States)

    2012-01-15

    The hydroxyl radical is the primary mediator of DNA damage by the indirect effect of ionizing radiation. It is a powerful oxidizing agent produced by the radiolysis of water and is responsible for a significant fraction of the DNA damage associated with ionizing radiation. There is therefore an interest in the development of sensitive assays for its detection. The hydroxylation of aromatic groups to produce fluorescent products has been used for this purpose. We have examined four different chromophores, which produce fluorescent products when hydroxylated. Of these, the coumarin system suffers from the fewest disadvantages. We have therefore examined its behavior when linked to a cationic peptide ligand designed to bind strongly to DNA. - Highlights: > Examined four aromatic groups as a means to detect hydroxyl radicals by fluorescence. > Coumarin system suffers from the fewest disadvantages. > Characterized its reactivity when linked to a hexa-arginine peptide.

  18. Why tight-binding theory?

    Science.gov (United States)

    Harrison, Walter A.

    2002-12-01

    In the context of computational physics other methods are more accurate, but tight-binding theory allows very direct physical interpretation and is simple enough to allow much more realistic treatments beyond the local density approximation. We address several important questions of this last category: How does the gap enhancement from Coulomb correlations vary from material to material? Should the enhanced gap be used for calculating the dielectric constant? For calculating the effective mass in k-dot-p theory? How valid is the scissors approximation? How does one line up bands at an interface? How should we match the envelope function at interfaces in effective-mass theory? Why can the resulting quantum-well states seem to violate the uncertainty principle? How should f-shell electrons be treated when they are intermediate between band-like and core-like? The answers to all of these questions are given and discussed.

  19. Synthetic LPS-Binding Polymer Nanoparticles

    Science.gov (United States)

    Jiang, Tian

    Lipopolysaccharide (LPS), one of the principal components of most gram-negative bacteria's outer membrane, is a type of contaminant that can be frequently found in recombinant DNA products. Because of its strong and even lethal biological effects, selective LPS removal from bioproducts solution is of particular importance in the pharmaceutical and health care industries. In this thesis, for the first time, a proof-of-concept study on preparing LPS-binding hydrogel-like NPs through facile one-step free-radical polymerization was presented. With the incorporation of various hydrophobic (TBAm), cationic (APM, GUA) monomers and cross-linkers (BIS, PEG), a small library of NPs was constructed. Their FITC-LPS binding behaviors were investigated and compared with those of commercially available LPS-binding products. Moreover, the LPS binding selectivity of the NPs was also explored by studying the NPs-BSA interactions. The results showed that all NPs obtained generally presented higher FITC-LPS binding capacity in lower ionic strength buffer than higher ionic strength. However, unlike commercial poly-lysine cellulose and polymyxin B agarose beads' nearly linear increase of FITC-LPS binding with particle concentration, NPs exhibited serious aggregation and the binding quickly saturated or even decreased at high particle concentration. Among various types of NPs, higher FITC-LPS binding capacity was observed for those containing more hydrophobic monomers (TBAm). However, surprisingly, more cationic NPs with higher content of APM exhibited decreased FITC-LPS binding in high ionic strength conditions. Additionally, when new cationic monomer and cross-linker, GUA and PEG, were applied to replace APM and BIS, the obtained NPs showed improved FITC-LPS binding capacity at low NP concentration. But compared with APM- and BIS-containing NPs, the FITC-LPS binding capacity of GUA- and PEG-containing NPs saturated earlier. To investigate the NPs' binding to proteins, we tested the NPs

  20. Peptide binding specificity of the chaperone calreticulin

    DEFF Research Database (Denmark)

    Sandhu, N.; Duus, K.; Jorgensen, C.S.;

    2007-01-01

    Calreticulin is a molecular chaperone with specificity for polypeptides and N-linked monoglucosylated glycans. In order to determine the specificity of polypeptide binding, the interaction of calreticulin with polypeptides was investigated using synthetic peptides of different length and composit......Calreticulin is a molecular chaperone with specificity for polypeptides and N-linked monoglucosylated glycans. In order to determine the specificity of polypeptide binding, the interaction of calreticulin with polypeptides was investigated using synthetic peptides of different length...... and composition. A large set of available synthetic peptides (n=127) was tested for binding to calreticulin and the results analysed by multivariate data analysis. The parameter that correlated best with binding was hydrophobicity while beta-turn potential disfavoured binding. Only hydrophobic peptides longer...... a peptide-binding specificity for hydrophobic sequences and delineate the fine specificity of calreticulin for hydrophobic amino acid residues....

  1. An RNA motif that binds ATP

    Science.gov (United States)

    Sassanfar, M.; Szostak, J. W.

    1993-01-01

    RNAs that contain specific high-affinity binding sites for small molecule ligands immobilized on a solid support are present at a frequency of roughly one in 10(10)-10(11) in pools of random sequence RNA molecules. Here we describe a new in vitro selection procedure designed to ensure the isolation of RNAs that bind the ligand of interest in solution as well as on a solid support. We have used this method to isolate a remarkably small RNA motif that binds ATP, a substrate in numerous biological reactions and the universal biological high-energy intermediate. The selected ATP-binding RNAs contain a consensus sequence, embedded in a common secondary structure. The binding properties of ATP analogues and modified RNAs show that the binding interaction is characterized by a large number of close contacts between the ATP and RNA, and by a change in the conformation of the RNA.

  2. The helical structure of DNA facilitates binding

    Science.gov (United States)

    Berg, Otto G.; Mahmutovic, Anel; Marklund, Emil; Elf, Johan

    2016-09-01

    The helical structure of DNA imposes constraints on the rate of diffusion-limited protein binding. Here we solve the reaction-diffusion equations for DNA-like geometries and extend with simulations when necessary. We find that the helical structure can make binding to the DNA more than twice as fast compared to a case where DNA would be reactive only along one side. We also find that this rate advantage remains when the contributions from steric constraints and rotational diffusion of the DNA-binding protein are included. Furthermore, we find that the association rate is insensitive to changes in the steric constraints on the DNA in the helix geometry, while it is much more dependent on the steric constraints on the DNA-binding protein. We conclude that the helical structure of DNA facilitates the nonspecific binding of transcription factors and structural DNA-binding proteins in general.

  3. Binding of TH-iloprost to rat gastric mucosa: a pitfall in performing radioligand binding assays

    Energy Technology Data Exchange (ETDEWEB)

    Beinborn, M.; Kromer, W.; Staar, U.; Sewing, K.F.

    1985-09-01

    Binding of TH-iloprost was studied in a 20,000 x g sediment of the rat gastric mucosa. When pH in both test tubes for total and non-specific binding was kept identical, no displaceable binding of iloprost could be detected. When no care was taken to keep the pH identical in corresponding test tubes of the binding assay, changes in pH simulated specific and displaceable binding of iloprost. Therefore it is concluded that - in contrast to earlier reports - it is not possible to demonstrate specific iloprost binding using the given method.

  4. Predicted metal binding sites for phytoremediation

    OpenAIRE

    Sharma, Ashok; Roy, Sudeep; Tripathi, Kumar Parijat; Roy, Pratibha; Mishra, Manoj; Khan, Feroz; Meena, Abha

    2009-01-01

    Metal ion binding domains are found in proteins that mediate transport, buffering or detoxification of metal ions. The objective of the study is to design and analyze metal binding motifs against the genes involved in phytoremediation. This is being done on the basis of certain pre-requisite amino-acid residues known to bind metal ions/metal complexes in medicinal and aromatic plants (MAP's). Earlier work on MAP's have shown that heavy metals accumulated by aromatic and medicinal plants do no...

  5. A computational model for feature binding

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The "Binding Problem" is an important problem across many disciplines, including psychology, neuroscience, computational modeling, and even philosophy. In this work, we proposed a novel computational model, Bayesian Linking Field Model, for feature binding in visual perception, by combining the idea of noisy neuron model, Bayesian method, Linking Field Network and competitive mechanism. Simulation Experiments demonstrated that our model perfectly fulfilled the task of feature binding in visual perception and provided us some enlightening idea for future research.

  6. A computational model for feature binding

    Institute of Scientific and Technical Information of China (English)

    SHI ZhiWei; SHI ZhongZhi; LIU Xi; SHI ZhiPing

    2008-01-01

    The "Binding Problem" is an important problem across many disciplines, including psychology, neuroscience, computational modeling, and even philosophy. In this work, we proposed a novel computational model, Bayesian Linking Field Model, for feature binding in visual perception, by combining the idea of noisy neuron model, Bayesian method, Linking Field Network and competitive mechanism.Simulation Experiments demonstrated that our model perfectly fulfilled the task of feature binding in visual perception and provided us some enlightening idea for future research.

  7. Characterization of feline serum-cobalt binding.

    Science.gov (United States)

    Schnelle, Amy N; Barger, Anne M; MacNeill, Amy L; Mitchell, Mark M; Solter, Philip

    2015-06-01

    Oxidative stress inhibits albumin's ability to complex with cobalt. Feline serum-cobalt binding has not been described. The objective was to develop a cobalt binding test for use with feline serum, and correlate the results with other biochemical and cellular constituents in blood, and with clinical diseases of cats. A colorimetric test of cobalt binding, based on the oxidation-reduction reaction of Co(+2) and dithiothreitol, was developed using feline serum. The test was used to measure cobalt binding in stored serum from 176 cats presented to the University of Illinois Veterinary Teaching Hospital for a variety of disease conditions. Time-matched hematology and biochemical data, and clinical information, were obtained from the medical record of each cat and correlated with the serum-cobalt binding results. Serial dilution of feline serum with phosphate-buffered saline resulted in a highly linear decrease in serum-cobalt binding (r(2)  = .9984). Serum-cobalt binding of the clinical samples also correlated with albumin concentrations in a stepwise linear regression model (r(2)  = .425), and both cobalt binding and albumin were significantly decreased in cases of inflammation. Albumin and cobalt binding also shared significant correlations with several erythron variables, and serum concentration of total calcium and bilirubin. The correlation of cobalt binding measured by a colorimetric test with albumin concentration in the clinical samples and with serum dilution is consistent with feline albumin-cobalt complex formation. Hypoalbuminemia is the likely cause of reduced serum-cobalt binding in inflammation and the correlations observed between cobalt binding and other variables. © 2015 American Society for Veterinary Clinical Pathology.

  8. Norfloxacin binds to human fecal material.

    Science.gov (United States)

    Edlund, C; Lindqvist, L; Nord, C E

    1988-01-01

    Earlier studies have reported very high (120 to 2,700 mg/kg) concentrations of norfloxacin in feces after therapeutic doses. MICs for fecal microorganisms are with few exceptions far below these levels. Nevertheless, clinical investigations show that the main part of the aerobic gram-positive and the anaerobic microflora remains unaffected after norfloxacin administration. In this study, the binding of [14C]norfloxacin to fecal material was analyzed. The binding of a group of nonlabeled quinolones to feces and the interactions between Enterococcus faecium, Bacteroides fragilis, and norfloxacin were also investigated. The results showed that norfloxacin has the ability to bind to feces. The specific binding was reversible, saturated after 90 min of incubation at 37 degrees C, and increased linearly with fecal concentration. Scatchard plots and nonlinear regression computer analyses revealed two different binding classes. The primary specific binding had a dissociation constant (KD) of 1.0 microM and a maximal binding capacity (Bmax) of 0.12 mumol/g of feces. The KD and Bmax of the secondary, more unspecific binding were 450 microM and 11.8 mumol/g of feces, respectively. The binding of unlabeled ciprofloxacin, enoxacin, ofloxacin, pefloxacin, and norfloxacin to feces was comparable to that of [14C]norfloxacin. The results of norfloxacin binding to suspensions of B. fragilis suggested that the main part of the binding is to the bacterial fraction of feces. In the presence of 8.0 g (dry weight) of B. fragilis per liter, the MBC of norfloxacin for E. faecium increased from 8 to 256 micrograms/ml. The finding of the present study indicated that binding of norfloxacin to feces may explain the paradox of high fecal concentrations of norfloxacin versus the actual effect on the normal gastrointestinal microflora. PMID:2854456

  9. Drug binding properties of neonatal albumin

    DEFF Research Database (Denmark)

    Brodersen, R; Honoré, B

    1989-01-01

    Neonatal and adult albumin was isolated by gel chromatography on Sephacryl S-300, from adult and umbilical cord serum, respectively. Binding of monoacetyl-diamino-diphenyl sulfone, warfarin, sulfamethizole, and diazepam was studied by means of equilibrium dialysis and the binding data were analyzed...... by the method of several acceptable fitted curves. It was found that the binding affinity to neonatal albumin is less than to adult albumin for monoacetyl-diamino-diphenyl sulfone and warfarin. Sulfamethizole binding to the neonatal protein is similarly reduced when more than one molecule of the drug is bound...

  10. Advances on Plant Pathogenic Mycotoxin Binding Proteins

    Institute of Scientific and Technical Information of China (English)

    WANG Chao-hua; DONG Jin-gao

    2002-01-01

    Toxin-binding protein is one of the key subjects in plant pathogenic mycotoxin research. In this paper, new advances in toxin-binding proteins of 10 kinds of plant pathogenic mycotoxins belonging to Helminthosporium ,Alternaria ,Fusicoccum ,Verticillium were reviewed, especially the techniques and methods of toxin-binding proteins of HS-toxin, HV-toxin, HMT-toxin, HC-toxin. It was proposed that the isotope-labeling technique and immunological chemistry technique should be combined together in research of toxin-binding protein, which will be significant to study the molecular recognition mechanism between host and pathogenic fungus.

  11. Lead-Binding Proteins: A Review

    Directory of Open Access Journals (Sweden)

    Harvey C. Gonick

    2011-01-01

    Full Text Available Lead-binding proteins are a series of low molecular weight proteins, analogous to metallothionein, which segregate lead in a nontoxic form in several organs (kidney, brain, lung, liver, erythrocyte. Whether the lead-binding proteins in every organ are identical or different remains to be determined. In the erythrocyte, delta-aminolevulinic acid dehydratase (ALAD isoforms have commanded the greatest attention as proteins and enzymes that are both inhibitable and inducible by lead. ALAD-2, although it binds lead to a greater degree than ALAD-1, appears to bind lead in a less toxic form. What may be of greater significance is that a low molecular weight lead-binding protein, approximately 10 kDa, appears in the erythrocyte once blood lead exceeds 39 μg/dL and eventually surpasses the lead-binding capacity of ALAD. In brain and kidney of environmentally exposed humans and animals, a cytoplasmic lead-binding protein has been identified as thymosin β4, a 5 kDa protein. In kidney, but not brain, another lead-binding protein has been identified as acyl-CoA binding protein, a 9 kDa protein. Each of these proteins, when coincubated with liver ALAD and titrated with lead, diminishes the inhibition of ALAD by lead, verifying their ability to segregate lead in a nontoxic form.

  12. Retinoid-binding proteins: similar protein architectures bind similar ligands via completely different ways.

    Directory of Open Access Journals (Sweden)

    Yu-Ru Zhang

    Full Text Available BACKGROUND: Retinoids are a class of compounds that are chemically related to vitamin A, which is an essential nutrient that plays a key role in vision, cell growth and differentiation. In vivo, retinoids must bind with specific proteins to perform their necessary functions. Plasma retinol-binding protein (RBP and epididymal retinoic acid binding protein (ERABP carry retinoids in bodily fluids, while cellular retinol-binding proteins (CRBPs and cellular retinoic acid-binding proteins (CRABPs carry retinoids within cells. Interestingly, although all of these transport proteins possess similar structures, the modes of binding for the different retinoid ligands with their carrier proteins are different. METHODOLOGY/PRINCIPAL FINDINGS: In this work, we analyzed the various retinoid transport mechanisms using structure and sequence comparisons, binding site analyses and molecular dynamics simulations. Our results show that in the same family of proteins and subcellular location, the orientation of a retinoid molecule within a binding protein is same, whereas when different families of proteins are considered, the orientation of the bound retinoid is completely different. In addition, none of the amino acid residues involved in ligand binding is conserved between the transport proteins. However, for each specific binding protein, the amino acids involved in the ligand binding are conserved. The results of this study allow us to propose a possible transport model for retinoids. CONCLUSIONS/SIGNIFICANCE: Our results reveal the differences in the binding modes between the different retinoid-binding proteins.

  13. Tissue specificity of endothelin binding sites

    Energy Technology Data Exchange (ETDEWEB)

    Bolger, G.T.; Liard, F.; Krogsrud, R.; Thibeault, D.; Jaramillo, J. (BioMega, Inc., Laval, Quebec (Canada))

    1990-09-01

    A measurement was made of the binding of 125I-labeled endothelin (125I-ET) to crude membrane fractions prepared from rat aorta, atrium, ventricle, portal vein, trachea, lung parenchyma, vas deferens, ileum, bladder, and guinea-pig taenia coli and lung parenchyma. Scatchard analysis of 125I-ET binding in all tissues indicated binding to a single class of saturable sites. The affinity and density of 125I-ET binding sites varied between tissues. The Kd of 125I-ET binding was approximately 0.5 nM for rat aorta, trachea, lung parenchyma, ventricle, bladder, and vas deferens, and guinea-pig taenia coli and lung parenchyma, 1.8 nM for rat portal vein and atrium, and 3.3 nM for ileum. The Bmax of 125I-ET binding had the following rank order of density in rat tissues: trachea greater than lung parenchyma = vas deferens much greater than aorta = portal vein = atrium greater than bladder greater than ventricle = ileum. The properties of 125I-ET endothelin binding were characterized in rat ventricular membranes. 125I-ET binding was time dependent, reaching a maximum within 45-60 min at 25 degrees C. The calculated microassociation constant was 9.67 x 10(5) s-1 M-1. Only 15-20% of 125I-ET dissociated from its binding site even when dissociation was studied as long as 3 h. Preincubation of ventricular membranes with ET prevented binding of 125I-ET. 125I-ET binding was destroyed by boiling of ventricular membranes and was temperature, pH, and cation (Ca2+, Mg2+, and Na+) dependent.

  14. Biodiscovery of aluminum binding peptides

    Science.gov (United States)

    Adams, Bryn L.; Sarkes, Deborah A.; Finch, Amethist S.; Hurley, Margaret M.; Stratis-Cullum, Dimitra

    2013-05-01

    Cell surface peptide display systems are large and diverse libraries of peptides (7-15 amino acids) which are presented by a display scaffold hosted by a phage (virus), bacteria, or yeast cell. This allows the selfsustaining peptide libraries to be rapidly screened for high affinity binders to a given target of interest, and those binders quickly identified. Peptide display systems have traditionally been utilized in conjunction with organic-based targets, such as protein toxins or carbon nanotubes. However, this technology has been expanded for use with inorganic targets, such as metals, for biofabrication, hybrid material assembly and corrosion prevention. While most current peptide display systems employ viruses to host the display scaffold, we have recently shown that a bacterial host, Escherichia coli, displaying peptides in the ubiquitous, membrane protein scaffold eCPX can also provide specific peptide binders to an organic target. We have, for the first time, extended the use of this bacterial peptide display system for the biodiscovery of aluminum binding 15mer peptides. We will present the process of biopanning with macroscopic inorganic targets, binder enrichment, and binder isolation and discovery.

  15. The Aryl Hydrocarbon Receptor Governs Epithelial Cell Invasion during Oropharyngeal Candidiasis

    Science.gov (United States)

    Solis, Norma V.; Swidergall, Marc; Bruno, Vincent M.; Gaffen, Sarah L.

    2017-01-01

    ABSTRACT Oropharyngeal candidiasis (OPC), caused predominantly by Candida albicans, is a prevalent infection in patients with advanced AIDS, defects in Th17 immunity, and head and neck cancer. A characteristic feature of OPC is fungal invasion of the oral epithelial cells. One mechanism by which C. albicans hyphae can invade oral epithelial cells is by expressing the Als3 and Ssa1 invasins that interact with the epidermal growth factor receptor (EGFR) on epithelial cells and stimulate endocytosis of the organism. However, the signaling pathways that function downstream of EGFR and mediate C. albicans endocytosis are poorly defined. Here, we report that C. albicans infection activates the aryl hydrocarbon receptor (AhR), leading to activation of Src family kinases (SFKs), which in turn phosphorylate EGFR and induce endocytosis of the fungus. Furthermore, treatment of oral epithelial cells with interferon gamma inhibits fungal endocytosis by inducing the synthesis of kynurenines, which cause prolonged activation of AhR and SFKs, thereby interfering with C. albicans-induced EGFR signaling. Treatment of both immunosuppressed and immunocompetent mice with an AhR inhibitor decreases phosphorylation of SFKs and EGFR in the oral mucosa, reduces fungal invasion, and lessens the severity of OPC. Thus, our data indicate that AhR plays a central role in governing the pathogenic interactions of C. albicans with oral epithelial cells during OPC and suggest that this receptor is a potential therapeutic target. PMID:28325761

  16. 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.

    1984-08-01

    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.

  17. Binding Principle for Long-Distance Anaphors.

    Science.gov (United States)

    Choi, Dong-Ik

    1997-01-01

    An analysis of long-distance anaphora, a binding phenomenon in which reflexives find their antecedents outside their local domain, is presented, using data from English, Chinese, Japanese, Korean, Russian, Icelandic, and Italian. It is found that no approach deals with long-distance anaphors exclusively and elegantly. The binding domain…

  18. Triazatriangulene as binding group for molecular electronics

    DEFF Research Database (Denmark)

    Wei, Zhongming; Wang, Xintai; Borges, Anders

    2014-01-01

    The triazatriangulene (TATA) ring system was investigated as a binding group for tunnel junctions of molecular wires on gold surfaces. Self-assembled monolayers (SAMs) of TATA platforms with three different lengths of phenylene wires were fabricated, and their electrical conductance was recorded ...... with its high stability and directionality make this binding group very attractive for molecular electronic measurements and devices. (Figure Presented)....

  19. Localization-enhanced biexciton binding in semiconductors

    DEFF Research Database (Denmark)

    Langbein, Wolfgang Werner; Hvam, Jørn Märcher

    1999-01-01

    The influence of excitonic localization on the binding energy of biexcitons is investigated for quasi-three-dimensional and quasi-two-dimensional AlxGa1-xAs structures. An increase of the biexciton binding energy is observed for localization energies comparable to or larger than the free biexcito...

  20. CTCF Binding Polarity Determines Chromatin Looping

    NARCIS (Netherlands)

    de Wit, Elzo; Vos, Erica S M; Holwerda, Sjoerd J B|info:eu-repo/dai/nl/344682218; Valdes-Quezada, Christian; Verstegen, Marjon J A M; Teunissen, Hans; Splinter, Erik; Wijchers, Patrick J; Krijger, Peter H L; de Laat, Wouter|info:eu-repo/dai/nl/169934497

    2015-01-01

    CCCTC-binding factor (CTCF) is an architectural protein involved in the three-dimensional (3D) organization of chromatin. In this study, we assayed the 3D genomic contact profiles of a large number of CTCF binding sites with high-resolution 4C-seq. As recently reported, our data also suggest that ch

  1. Binding of anandamide to bovine serum albumin

    DEFF Research Database (Denmark)

    Bojesen, I.N.; Hansen, Harald S.

    2003-01-01

    The endocannabinoid anandamide is of lipid nature and may thus bind to albumin in the vascular system, as do fatty acids. The knowledge of the free water-phase concentration of anandamide is essential for the investigations of its transfer from the binding protein to cellular membranes, because...

  2. Multiple binding modes of ibuprofen in human serum albumin identified by absolute binding free energy calculations

    KAUST Repository

    Evoli, Stefania

    2016-11-10

    Human serum albumin possesses multiple binding sites and transports a wide range of ligands that include the anti-inflammatory drug ibuprofen. A complete map of the binding sites of ibuprofen in albumin is difficult to obtain in traditional experiments, because of the structural adaptability of this protein in accommodating small ligands. In this work, we provide a set of predictions covering the geometry, affinity of binding and protonation state for the pharmaceutically most active form (S-isomer) of ibuprofen to albumin, by using absolute binding free energy calculations in combination with classical molecular dynamics (MD) simulations and molecular docking. The most favorable binding modes correctly reproduce several experimentally identified binding locations, which include the two Sudlow\\'s drug sites (DS2 and DS1) and the fatty acid binding sites 6 and 2 (FA6 and FA2). Previously unknown details of the binding conformations were revealed for some of them, and formerly undetected binding modes were found in other protein sites. The calculated binding affinities exhibit trends which seem to agree with the available experimental data, and drastically degrade when the ligand is modeled in a protonated (neutral) state, indicating that ibuprofen associates with albumin preferentially in its charged form. These findings provide a detailed description of the binding of ibuprofen, help to explain a wide range of results reported in the literature in the last decades, and demonstrate the possibility of using simulation methods to predict ligand binding to albumin.

  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

    1996-01-01

    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-...

  4. Acyl-CoA-binding protein/diazepam-binding inhibitor gene and pseudogenes

    DEFF Research Database (Denmark)

    Mandrup, S; Hummel, R; Ravn, S

    1992-01-01

    Acyl-CoA-binding protein (ACBP) is a 10 kDa protein isolated from bovine liver by virtue of its ability to bind and induce the synthesis of medium-chain acyl-CoA esters. Surprisingly, it turned out to be identical to a protein named diazepam-binding Inhibitor (DBI) claimed to be an endogenous mod...

  5. Bacterial periplasmic sialic acid-binding proteins exhibit a conserved binding site

    Energy Technology Data Exchange (ETDEWEB)

    Gangi Setty, Thanuja [Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065 (India); Cho, Christine [Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109 (United States); Govindappa, Sowmya [Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065 (India); Apicella, Michael A. [Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109 (United States); Ramaswamy, S., E-mail: ramas@instem.res.in [Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065 (India)

    2014-07-01

    Structure–function studies of sialic acid-binding proteins from F. nucleatum, P. multocida, V. cholerae and H. influenzae reveal a conserved network of hydrogen bonds involved in conformational change on ligand binding. Sialic acids are a family of related nine-carbon sugar acids that play important roles in both eukaryotes and prokaryotes. These sialic acids are incorporated/decorated onto lipooligosaccharides as terminal sugars in multiple bacteria to evade the host immune system. Many pathogenic bacteria scavenge sialic acids from their host and use them for molecular mimicry. The first step of this process is the transport of sialic acid to the cytoplasm, which often takes place using a tripartite ATP-independent transport system consisting of a periplasmic binding protein and a membrane transporter. In this paper, the structural characterization of periplasmic binding proteins from the pathogenic bacteria Fusobacterium nucleatum, Pasteurella multocida and Vibrio cholerae and their thermodynamic characterization are reported. The binding affinities of several mutations in the Neu5Ac binding site of the Haemophilus influenzae protein are also reported. The structure and the thermodynamics of the binding of sugars suggest that all of these proteins have a very well conserved binding pocket and similar binding affinities. A significant conformational change occurs when these proteins bind the sugar. While the C1 carboxylate has been identified as the primary binding site, a second conserved hydrogen-bonding network is involved in the initiation and stabilization of the conformational states.

  6. Specific insulin binding in bovine chromaffin cells; demonstration of preferential binding to adrenalin-storing cells

    Energy Technology Data Exchange (ETDEWEB)

    Serck-Hanssen, G.; Soevik, O.

    1987-12-28

    Insulin binding was studied in subpopulations of bovine chromaffin cells enriched in adrenalin-producing cells (A-cells) or noradrenalin-producing cells (NA-cells). Binding of /sup 125/I-insulin was carried out at 15/sup 0/C for 3 hrs in the absence or presence of excess unlabeled hormone. Four fractions of cells were obtained by centrifugation on a stepwise bovine serum albumin gradient. The four fractions were all shown to bind insulin in a specific manner and the highest binding was measured in the cell layers of higher densities, containing mainly A-cells. The difference in binding of insulin to the four subpopulations of chromaffin cells seemed to be related to differences in numbers of receptors as opposed to receptor affinities. The authors conclude that bovine chromaffin cells possess high affinity binding sites for insulin and that these binding sites are mainly confined to A-cells. 24 references, 2 figures, 1 table.

  7. Predicted metal binding sites for phytoremediation.

    Science.gov (United States)

    Sharma, Ashok; Roy, Sudeep; Tripathi, Kumar Parijat; Roy, Pratibha; Mishra, Manoj; Khan, Feroz; Meena, Abha

    2009-09-05

    Metal ion binding domains are found in proteins that mediate transport, buffering or detoxification of metal ions. The objective of the study is to design and analyze metal binding motifs against the genes involved in phytoremediation. This is being done on the basis of certain pre-requisite amino-acid residues known to bind metal ions/metal complexes in medicinal and aromatic plants (MAP's). Earlier work on MAP's have shown that heavy metals accumulated by aromatic and medicinal plants do not appear in the essential oil and that some of these species are able to grow in metal contaminated sites. A pattern search against the UniProtKB/Swiss-Prot and UniProtKB/TrEMBL databases yielded true positives in each case showing the high specificity of the motifs designed for the ions of nickel, lead, molybdenum, manganese, cadmium, zinc, iron, cobalt and xenobiotic compounds. Motifs were also studied against PDB structures. Results of the study suggested the presence of binding sites on the surface of protein molecules involved. PDB structures of proteins were finally predicted for the binding sites functionality in their respective phytoremediation usage. This was further validated through CASTp server to study its physico-chemical properties. Bioinformatics implications would help in designing strategy for developing transgenic plants with increased metal binding capacity. These metal binding factors can be used to restrict metal update by plants. This helps in reducing the possibility of metal movement into the food chain.

  8. [Binding to chicken liver lactatedehydrogenase (author's transl)].

    Science.gov (United States)

    Lluís, C; Bozal, J

    1976-06-01

    Some information about the lactate dehydrogenase NAD binding site has been obtained by working with coenzymes analogs of incomplete molecules. 5'AMP, 5'-ADP, ATP, 5'-c-AMP and 3'(2)-AMP inhibit chicken liver LDH activity competitively with NADH. 5"-AMP and 5'-ADP show a stronger inhibition power than ATP, suggesting that the presence of one or two phosphate groups at the 5' position of adenosine, is essential for the binding of the coenzyme analogs at the enzyme binding site. Ribose and ribose-5'-P do not appear to inhibit the LDH activity, proving that purine base lacking mononucleotides do not bind to the enzyme. 5"-ADPG inhibits LDH activity in the exactly as 5'-ADP, showing that ribose moiety may be replaced by glucose, without considerable effects on the coenzyme analog binding. 2'-desoxidenosin-5'-phosphate proves to be a poorer inhibitor of the LDH activity than 5'-AMP, indicating that an interaction between the--OH groups and the amino-acids of the LDH active center takes place. Nicotinamide does not produce any inhibition effect, while NMN and CMP induce a much weaker inhibition than the adenine analogues, thus indicating a lesser binding capacity to the enzyme. Therefore, the LDH binding site seems to show some definite specificity towards the adenina groups of the coenzyme.

  9. Measuring Binding Affinity of Protein-Ligand Interaction Using Spectrophotometry: Binding of Neutral Red to Riboflavin-Binding Protein

    Science.gov (United States)

    Chenprakhon, Pirom; Sucharitakul, Jeerus; Panijpan, Bhinyo; Chaiyen, Pimchai

    2010-01-01

    The dissociation constant, K[subscript d], of the binding of riboflavin-binding protein (RP) with neutral red (NR) can be determined by titrating RP to a fixed concentration of NR. Upon adding RP to the NR solution, the maximum absorption peak of NR shifts to 545 nm from 450 nm for the free NR. The change of the absorption can be used to determine…

  10. Estradiol Binds to Insulin and Insulin Receptor Decreasing Insulin Binding in vitro

    Directory of Open Access Journals (Sweden)

    Robert eRoot-Bernstein

    2014-07-01

    Full Text Available Rationale: Insulin resistance associated with hyperestrogenemias occurs in gestational diabetes mellitus, polycystic ovary syndrome, ovarian hyperstimulation syndrome, estrogen therapies, metabolic syndrome and obesity. The mechanism by which insulin and estrogen interact is unknown. We hypothesize that estrogen binds directly to insulin and the insulin receptor producing insulin resistance.Objectives: To determine the binding constants of steroid hormones to insulin, the insulin receptor, and insulin-like peptides derived from the insulin receptor; and to investigate the effect of estrogens on the binding of insulin to its receptor.Methods: Ultraviolet spectroscopy, capillary electrophoresis and NMR demonstrated estrogen binding to insulin and its receptor. Horse-radish peroxidase-linked insulin was used in an ELISA-like procedure to measure the effect of estradiol on binding of insulin to its receptor. Measurements: Binding constants for estrogens to insulin and the insulin receptor were determined by concentration-dependent spectral shifts. The effect of estradiol on insulin-HRP binding to its receptor was determined by shifts in the insulin binding curve. Main Results: Estradiol bound to insulin with a Kd of 12 x 10-9 M and to the insulin receptor with a Kd of 24 x 10-9 M, while other hormones had significantly less affinity. 200 nM estradiol shifted the binding curve of insulin to its receptor 0.8 log units to the right. Conclusions: Estradiol concentrations in many hyperestrogenemic syndromes are sufficient to interfere with insulin binding to its receptor producing significant insulin resistance.

  11. On Reflexive Binding in North Sami

    Directory of Open Access Journals (Sweden)

    Hanna Outakoski

    2004-01-01

    Full Text Available Principle A of the Binding Theory states that an anaphor must be A-bound in the local domain containing it, its governor and an accessible subject. However, if the anaphor is contained in an infinitival complement clause, it may, in North Sami, be bound either by the clause-mate subject or by the subject of the tensed clause. Thus, it appears that there is a larger binding domain for anaphors in addition to that determined by the condition A of standard binding theory. This domain can in some languages, as in North Sami, be defined by the notion of Tense whereas in other languages this need not be case, as in English. This supports the approach that the characterization of binding domains is parameterized and that languages pick different values of the parameter.

  12. Tau Induces Cooperative Taxol Binding to Microtubules

    Science.gov (United States)

    Ross, Jennifer; Santangelo, Christian; Victoria, Makrides; Fygenson, Deborah

    2004-03-01

    Taxol and tau are two ligands which stabilize the microtubule (MT) lattice. Taxol is an anti-mitotic drug that binds β tubulin in the MT interior. Tau is a MT-associated protein that binds both α and β tubulin on the MT exterior. Both taxol and tau reduce MT dynamics and promote tubulin polymerization. Tau alone also acts as a buttress to bundle, stiffen, and space MTs. A structural study recently suggested that taxol and tau may interact by binding to the same site. Using fluorescence recovery after photobleaching, we find that tau induces taxol to bind MTs cooperatively depending on the tau concentration. We develop a model that correctly fits the data in the absence of tau and yields a measure of taxol cooperativity when tau is present.

  13. Motion transparency promotes synchronous perceptual binding.

    Science.gov (United States)

    Clifford, Colin W G; Spehar, Branka; Pearson, Joel

    2004-12-01

    While identified regions of human extrastriate visual cortex are functionally specialized for processing different attributes of an object, the cognitive and neural mechanisms by which these attributes are dynamically bound into integrated percepts are still largely mysterious. Here, we report that perceptual organization influences the dynamics of binding. Specifically, the perception of motion transparency promotes the synchronous perceptual binding of colour and motion, which otherwise exhibits considerable asynchronies. In addition, we demonstrate that perceptual asynchrony can be reinstated by manipulating stereoscopic disparity or speed within the stimulus. Our findings suggest that the phenomenology of colour-motion binding parallels the known physiology of motion processing in area MT of primate visual cortex, supporting the view that the dynamics of perceptual binding is a direct reflection of the time course of the underlying neural processing.

  14. System Support for Managing Invalid Bindings

    CERN Document Server

    Das, Lachhman; Shah, Azhar; Khoumbati, Khalil; 10.5121/iju.2011.2303

    2011-01-01

    Context-aware adaptation is a central aspect of pervasive computing applications, enabling them to adapt and perform tasks based on contextual information. One of the aspects of context-aware adaptation is reconfiguration in which bindings are created between application component and remote services in order to realize new behaviour in response to contextual information. Various research efforts provide reconfiguration support and allow the development of adaptive context-aware applications from high-level specifications, but don't consider failure conditions that might arise during execution of such applications, making bindings between application and remote services invalid. To this end, we propose and implement our design approach to reconfiguration to manage invalid bindings. The development and modification of adaptive context-aware applications is a complex task, and an issue of an invalidity of bindings further complicates development efforts. To reduce the development efforts, our approach provides ...

  15. Receptor binding profile of Otilonium bromide.

    Science.gov (United States)

    Evangelista, S; Giachetti, A; Chapelain, B; Neliat, G; Maggi, C A

    1998-08-01

    The interaction of Otilonium bromide (OB) with binding sites for 63 different receptors and ion channels in appropriate preparations has been investigated. Experiments were also performed in rat colon, the preferred tissue for OB 'in vivo' uptake after oral administration. Among the receptors investigated OB binds with sub microM affinity to muscarinic M1, M2, M4, M5 and PAF receptors and with microM affinity to the diltiazem binding site on L type Ca2+ channels. In the rat colon OB shows competitive interaction with the verapamil binding site on L type Ca2+ channels and with muscarinic M2 receptors with IC50 of 1020 and 1220 nM, respectively. These findings provide a molecular rationale to explain the spasmolytic action exerted by OB on intestinal smooth muscle. In particular, a combination of antimuscarinic and Ca2+ channel blocker properties seems to best account for the action of this compound.

  16. HEAVY QUARK POTENTIALS AND QUARKONIA BINDING.

    Energy Technology Data Exchange (ETDEWEB)

    PETRECZKY,P.

    2004-11-04

    The author reviews recent progress in studying in-medium modification of inter-quark forces at finite temperature in lattice QCD. Some applications to the problem of quarkonium binding in potential models is also discussed.

  17. Hardware device binding and mutual authentication

    Energy Technology Data Exchange (ETDEWEB)

    Hamlet, Jason R; Pierson, Lyndon G

    2014-03-04

    Detection and deterrence of device tampering and subversion by substitution may be achieved by including a cryptographic unit within a computing device for binding multiple hardware devices and mutually authenticating the devices. The cryptographic unit includes a physically unclonable function ("PUF") circuit disposed in or on the hardware device, which generates a binding PUF value. The cryptographic unit uses the binding PUF value during an enrollment phase and subsequent authentication phases. During a subsequent authentication phase, the cryptographic unit uses the binding PUF values of the multiple hardware devices to generate a challenge to send to the other device, and to verify a challenge received from the other device to mutually authenticate the hardware devices.

  18. Adjustment of legally binding local plans

    DEFF Research Database (Denmark)

    Hvingel, Line Træholt; Aunsborg, Christian; Christensen, Finn Kjær

    2012-01-01

    Traditionally, and by law, new urban areas in Denmark are regulated and planned through legally binding local plans. Recently a tendency has occurred: The municipalities make the legally binding local plans quite open for future adjustment, and they are using a substantial amount of ‘empowerment......, which seem to be beyond the scope of the Danish Planning Act. This paper deals with this problem through case studies and a legal analysis of present law. If the combination of the legally binding local plan and subsequent added requirements is misused, it will weaken the legal rights of the citizens...... the considerations of legal rights, the extend of the legal use of empowerment provisions and the combination of the use of legal binding local plans and other legal instruments such as easements and sales agreements....

  19. Imidazole binding to human serum albumin.

    Science.gov (United States)

    Rodrigo, M C; Ceballos, A; Mariño, E; Cachaza, J M; Domínguez-Gil, A; Kuemmerle, H P

    1988-06-01

    Imidazole is a substance released by the organism when a new salicylate derivative, imidazole salicylate is administered. A study was made of the binding of imidazole to human serum albumin by an in vitro assay employing an ultrafiltration technique. For the concentration range that imidazole was found in plasma following administration of the drug to healthy volunteers, the mean binding percentages were: 12.1 +/- 1.8 and 19.7 +/- 3.1 at 37 degrees C and 25 degrees C, respectively. The results obtained in the study follow a model entailing three equal and independent binding sites of imidazole to serum albumin and the values of the corresponding constants were determined. Apparently, the presence in the plasma samples of sodium salicylate at a concentration of 100 micrograms/ml does not affect the binding of imidazole to human serum albumin.

  20. Acyl-coenzyme A binding protein, ACBP

    DEFF Research Database (Denmark)

    Kragelund, Birthe Brandt; Knudsen, J.; Poulsen, Flemming

    1999-01-01

    Acyl-coenzyme A binding proteins are known from a large group of eukaryote species and to bind a long chain length acyl-CoA ester with very high affinity. Detailed biochemical mapping of ligand binding properties has been obtained as well as in-depth structural studies on the bovine apo-protein...... and of the complex with palmitoyl-CoA using NMR spectroscopy. In the four a-helix bundle structure, a set of 21 highly conserved residues present in more that 90% of all known sequences of acyl-coenzyme A binding proteins constitutes three separate mini-cores. These residues are predominantly located at the helix......-helix interfaces. From studies of a large set of mutant proteins the role of the conserved residues has been related to structure, function, folding and stability....

  1. Acyl-coenzyme A binding protein (ACBP)

    DEFF Research Database (Denmark)

    Kragelund, B B; Knudsen, J; Poulsen, F M

    1999-01-01

    and of the complex with palmitoyl-CoA using NMR spectroscopy. In the four alpha-helix bundle structure, a set of 21 highly conserved residues present in more that 90% of all known sequences of acyl-coenzyme A binding proteins constitutes three separate mini-cores. These residues are predominantly located......Acyl-coenzyme A binding proteins are known from a large group of eukaryote species and to bind a long chain length acyl-CoA ester with very high affinity. Detailed biochemical mapping of ligand binding properties has been obtained as well as in-depth structural studies on the bovine apo-protein...... at the helix-helix interfaces. From studies of a large set of mutant proteins the role of the conserved residues has been related to structure, function, folding and stability....

  2. Binding capacity: cooperativity and buffering in biopolymers.

    Science.gov (United States)

    Di Cera, E; Gill, S J; Wyman, J

    1988-01-01

    The group of linkage potentials resulting from the energy of a physicochemical system expressed per mol of a reference component, say a polyfunctional macromolecule, leads to the concept of binding capacity. This concept applies equally to both chemical and physical ligands and opens the way to consideration of higher-order linkage relationships. It provides a means of exploring the consequences of thermodynamic stability on generalized binding phenomena in biopolymers. PMID:3422436

  3. Supramolecular electron transfer by anion binding.

    Science.gov (United States)

    Fukuzumi, Shunichi; Ohkubo, Kei; D'Souza, Francis; Sessler, Jonathan L

    2012-10-11

    Anion binding has emerged as an attractive strategy to construct supramolecular electron donor-acceptor complexes. In recent years, the level of sophistication in the design of these systems has advanced to the point where it is possible to create ensembles that mimic key aspects of the photoinduced electron-transfer events operative in the photosynthetic reaction centre. Although anion binding is a reversible process, kinetic studies on anion binding and dissociation processes, as well as photoinduced electron-transfer and back electron-transfer reactions in supramolecular electron donor-acceptor complexes formed by anion binding, have revealed that photoinduced electron transfer and back electron transfer occur at time scales much faster than those associated with anion binding and dissociation. This difference in rates ensures that the linkage between electron donor and acceptor moieties is maintained over the course of most forward and back electron-transfer processes. A particular example of this principle is illustrated by electron-transfer ensembles based on tetrathiafulvalene calix[4]pyrroles (TTF-C4Ps). In these ensembles, the TTF-C4Ps act as donors, transferring electrons to various electron acceptors after anion binding. Competition with non-redox active substrates is also observed. Anion binding to the pyrrole amine groups of an oxoporphyrinogen unit within various supramolecular complexes formed with fullerenes also results in acceleration of the photoinduced electron-transfer process but deceleration of the back electron transfer; again, this is ascribed to favourable structural and electronic changes. Anion binding also plays a role in stabilizing supramolecular complexes between sulphonated tetraphenylporphyrin anions ([MTPPS](4-): M = H(2) and Zn) and a lithium ion encapsulated C(60) (Li(+)@C(60)); the resulting ensemble produces long-lived charge-separated states upon photoexcitation of the porphyrins.

  4. Predicting zinc binding at the proteome level

    Directory of Open Access Journals (Sweden)

    Rosato Antonio

    2007-02-01

    Full Text Available Abstract Background Metalloproteins are proteins capable of binding one or more metal ions, which may be required for their biological function, for regulation of their activities or for structural purposes. Metal-binding properties remain difficult to predict as well as to investigate experimentally at the whole-proteome level. Consequently, the current knowledge about metalloproteins is only partial. Results The present work reports on the development of a machine learning method for the prediction of the zinc-binding state of pairs of nearby amino-acids, using predictors based on support vector machines. The predictor was trained using chains containing zinc-binding sites and non-metalloproteins in order to provide positive and negative examples. Results based on strong non-redundancy tests prove that (1 zinc-binding residues can be predicted and (2 modelling the correlation between the binding state of nearby residues significantly improves performance. The trained predictor was then applied to the human proteome. The present results were in good agreement with the outcomes of previous, highly manually curated, efforts for the identification of human zinc-binding proteins. Some unprecedented zinc-binding sites could be identified, and were further validated through structural modelling. The software implementing the predictor is freely available at: http://zincfinder.dsi.unifi.it Conclusion The proposed approach constitutes a highly automated tool for the identification of metalloproteins, which provides results of comparable quality with respect to highly manually refined predictions. The ability to model correlations between pairwise residues allows it to obtain a significant improvement over standard 1D based approaches. In addition, the method permits the identification of unprecedented metal sites, providing important hints for the work of experimentalists.

  5. Fractal aspects of calcium binding protein structures

    Energy Technology Data Exchange (ETDEWEB)

    Isvoran, Adriana [West University of Timisoara, Department of Chemistry, Pestalozzi 16, 300115 Timisoara (Romania)], E-mail: aisvoran@cbg.uvt.ro; Pitulice, Laura [West University of Timisoara, Department of Chemistry, Pestalozzi 16, 300115 Timisoara (Romania); Craescu, Constantin T. [INSERM U759/Institute Curie-Recherche, Centre Universitaire Paris-Sud, Batiment 112, 91405 Orsay (France); Chiriac, Adrian [West University of Timisoara, Department of Chemistry, Pestalozzi 16, 300115 Timisoara (Romania)

    2008-03-15

    The structures of EF-hand calcium binding proteins may be classified into two distinct groups: extended and compact structures. In this paper we studied 20 different structures of calcium binding proteins using the fractal analysis. Nine structures show extended shapes, one is semi-compact and the other 10 have compact shapes. Our study reveals different fractal characteristics for protein backbones belonging to different structural classes and these observations may be correlated to the physicochemical forces governing the protein folding.

  6. Ligand Binding to Macromolecules: Allosteric and Sequential Models of Cooperativity.

    Science.gov (United States)

    Hess, V. L.; Szabo, Attila

    1979-01-01

    A simple model is described for the binding of ligands to macromolecules. The model is applied to the cooperative binding by hemoglobin and aspartate transcarbamylase. The sequential and allosteric models of cooperative binding are considered. (BB)

  7. EFSA NDA Panel (EFSA Panel on Dietetic Products, Nutrition and Allergies ), 2013. Scientific Opinion on the substantiation of a health claim related to the combination of artichoke leaf dry extract standardised in caffeoylquinic acids, monacolin K in red yeast ric e, sugar - cane derived, policosanols, OPC from French maritime pine bark, garlic dry extract standardised in allicin, d - α - tocopheryl hydrogen succinate , riboflavin and inositol hexanicotinate in Limicol ® and reduction of blood LDL - cholesterol concentrations pursuant to Article 14 of Regulation (EC) No 1924/2006

    DEFF Research Database (Denmark)

    Tetens, Inge

    claim related to the combination of artichoke leaf dry extract standardised in caffeoylquinic acids, monacolin K in red yeast rice, sugar-cane derived policosanols, OPC from French maritime pine bark, garlic dry extract standardised in allicin, d-α-tocopheryl hydrogen succinate, riboflavin and inositol...... hexanicotinate in Limicol® and reduction of blood LDL-cholesterol concentrations. The Panel considers that the food which is the subject of the claim is sufficiently characterised. The Panel considers that reduction of blood LDL-cholesterol concentrations is a beneficial physiological effect. High LDL...... ingredients in Limicol® on blood LDL-cholesterol concentrations. The Panel concludes that a cause and effect relationship has been established between the consumption of the combination of artichoke leaf dry extract standardised in caffeoylquinic acids, monacolin K in red yeast rice, sugar-cane derived...

  8. The readiness potential reflects intentional binding

    Directory of Open Access Journals (Sweden)

    Han-Gue eJo

    2014-06-01

    Full Text Available When a voluntary action is causally linked with a sensory outcome, the action and its consequent effect are perceived as being closer together in time. This effect is called intentional binding. Although many experiments were conducted on this phenomenon, the underlying neural mechanisms are not well understood. While intentional binding is specific to voluntary action, we presumed that preconscious brain activity (the readiness potential, RP, which occurs before an action is made, might play an important role in this binding effect. In this study, the brain dynamics were recorded with electroencephalography (EEG and analyzed in single-trials in order to estimate whether intentional binding is correlated with the early neural processes. Moreover, we were interested in different behavioral performance between meditators and non-meditators since meditators are expected to be able to keep attention more consistently on a task. Thus, we performed the intentional binding paradigm with twenty mindfulness meditators and compared them to matched controls. Although, we did not observe a group effect on either behavioral data or EEG recordings, we found that self-initiated movements following ongoing negative deflections of slow cortical potentials (SCPs result in a stronger binding effect compared to positive potentials, especially regarding the perceived time of the consequent effect. Our results provide the first direct evidence that the early neural activity within the range of SCPs affects perceived time of a sensory outcome that is caused by intentional action.

  9. Comparative serum protein binding of anthracycline derivatives.

    Science.gov (United States)

    Chassany, O; Urien, S; Claudepierre, P; Bastian, G; Tillement, J P

    1996-01-01

    The binding of doxorubicin, iododoxorubicin, daunorubicin, epirubicin, pirarubicin, zorubicin, aclarubicin, and mitoxantrone to 600 microM human serum albumin and 50 microM alpha 1-acid glycoprotein was studied by ultrafiltration at 37 degrees C and pH 7.4. Anthracycline concentrations (total and free) were determined by high-performance liquid chromatography (HPLC) with fluorometric detection. Binding to albumin (600 microM) varied from 61% (daunorubicin) to 94% (iododoxorubicin). The binding to alpha 1-acid glycoprotein (50 microM) was more variable, ranging from 31% (epirubicin) to 64% (zorubicin), and was essentially related to the hydrophobicity of the derivatives. Simulations showed that the total serum binding varied over a broad range from 71% (doxorubicin) to 96% (iododoxorubicin). We recently reported that the binding to lipoproteins of a series of eight anthracycline analogues could be ascribed to chemicophysical determinants of lipophilicity [2]. The present study was conducted to evaluate in vitro the contribution of albumin and alpha 1-acid glycoprotein to the total serum binding of these drugs.

  10. Zinc Binding by Lactic Acid Bacteria

    Directory of Open Access Journals (Sweden)

    Jasna Mrvčić

    2009-01-01

    Full Text Available Zinc is an essential trace element in all organisms. A common method for the prevention of zinc deficiency is pharmacological supplementation, especially in a highly available form of a metalloprotein complex. The potential of different microbes to bind essential and toxic heavy metals has recently been recognized. In this work, biosorption of zinc by lactic acid bacteria (LAB has been investigated. Specific LAB were assessed for their ability to bind zinc from a water solution. Significant amount of zinc ions was bound, and this binding was found to be LAB species-specific. Differences among the species in binding performance at a concentration range between 10–90 mg/L were evaluated with Langmuir model for biosorption. Binding of zinc was a fast process, strongly influenced by ionic strength, pH, biomass concentration, and temperature. The most effective metal-binding LAB species was Leuconostoc mesenteroides (27.10 mg of Zn2+ per gram of dry mass bound at pH=5 and 32 °C, during 24 h. FT-IR spectroscopy analysis and electron microscopy demonstrated that passive adsorption and active uptake of the zinc ions were involved.

  11. DNA-Aptamers Binding Aminoglycoside Antibiotics

    Directory of Open Access Journals (Sweden)

    Nadia Nikolaus

    2014-02-01

    Full Text Available Aptamers are short, single stranded DNA or RNA oligonucleotides that are able to bind specifically and with high affinity to their non-nucleic acid target molecules. This binding reaction enables their application as biorecognition elements in biosensors and assays. As antibiotic residues pose a problem contributing to the emergence of antibiotic-resistant pathogens and thereby reducing the effectiveness of the drug to fight human infections, we selected aptamers targeted against the aminoglycoside antibiotic kanamycin A with the aim of constructing a robust and functional assay that can be used for water analysis. With this work we show that aptamers that were derived from a Capture-SELEX procedure targeting against kanamycin A also display binding to related aminoglycoside antibiotics. The binding patterns differ among all tested aptamers so that there are highly substance specific aptamers and more group specific aptamers binding to a different variety of aminoglycoside antibiotics. Also the region of the aminoglycoside antibiotics responsible for aptamer binding can be estimated. Affinities of the different aptamers for their target substance, kanamycin A, are measured with different approaches and are in the micromolar range. Finally, the proof of principle of an assay for detection of kanamycin A in a real water sample is given.

  12. Electrostatically biased binding of kinesin to microtubules.

    Directory of Open Access Journals (Sweden)

    Barry J Grant

    2011-11-01

    Full Text Available The minimum motor domain of kinesin-1 is a single head. Recent evidence suggests that such minimal motor domains generate force by a biased binding mechanism, in which they preferentially select binding sites on the microtubule that lie ahead in the progress direction of the motor. A specific molecular mechanism for biased binding has, however, so far been lacking. Here we use atomistic Brownian dynamics simulations combined with experimental mutagenesis to show that incoming kinesin heads undergo electrostatically guided diffusion-to-capture by microtubules, and that this produces directionally biased binding. Kinesin-1 heads are initially rotated by the electrostatic field so that their tubulin-binding sites face inwards, and then steered towards a plus-endwards binding site. In tethered kinesin dimers, this bias is amplified. A 3-residue sequence (RAK in kinesin helix alpha-6 is predicted to be important for electrostatic guidance. Real-world mutagenesis of this sequence powerfully influences kinesin-driven microtubule sliding, with one mutant producing a 5-fold acceleration over wild type. We conclude that electrostatic interactions play an important role in the kinesin stepping mechanism, by biasing the diffusional association of kinesin with microtubules.

  13. The readiness potential reflects intentional binding.

    Science.gov (United States)

    Jo, Han-Gue; Wittmann, Marc; Hinterberger, Thilo; Schmidt, Stefan

    2014-01-01

    When a voluntary action is causally linked with a sensory outcome, the action and its consequent effect are perceived as being closer together in time. This effect is called intentional binding. Although many experiments were conducted on this phenomenon, the underlying neural mechanisms are not well understood. While intentional binding is specific to voluntary action, we presumed that preconscious brain activity (the readiness potential, RP), which occurs before an action is made, might play an important role in this binding effect. In this study, the brain dynamics were recorded with electroencephalography (EEG) and analyzed in single-trials in order to estimate whether intentional binding is correlated with the early neural processes. Moreover, we were interested in different behavioral performance between meditators and non-meditators since meditators are expected to be able to keep attention more consistently on a task. Thus, we performed the intentional binding paradigm with 20 mindfulness meditators and compared them to matched controls. Although, we did not observe a group effect on either behavioral data or EEG recordings, we found that self-initiated movements following ongoing negative deflections of slow cortical potentials (SCPs) result in a stronger binding effect compared to positive potentials, especially regarding the perceived time of the consequent effect. Our results provide the first direct evidence that the early neural activity within the range of SCPs affects perceived time of a sensory outcome that is caused by intentional action.

  14. To Bind or not to Bind: It’s in the Contract

    DEFF Research Database (Denmark)

    Tvarnø, Christina D.

    2015-01-01

    discusses, in a theoretical perspective, the legal reasoning behind the different partnering approaches, both from a historical and contract law perspective, and furthermore applies a game theoretical approach in evaluating binding versus non-binding partnering contracts. The analysis focuses on private......This article discusses the formalization of collaboration through partnering contracts in the construction industry in the USA, Great Britain and Denmark. The article compares the different types of collaborative partnering contracts in the three countries, and provides a conclusion on whether...... the collaborative partnering contract should be binding or non-binding, based on the three empirical contracts analyzed in this article. The partnering contracts in Great Britain and Denmark are legally binding, while in the USA the partnering agreements are non-binding charters or letters of intent. This article...

  15. Theoretical studies of binding of mannose-binding protein to monosaccharides

    Science.gov (United States)

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

    2004-11-01

    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. Mannose-Binding Lectin Binds to Amyloid Protein and Modulates Inflammation

    Directory of Open Access Journals (Sweden)

    Mykol Larvie

    2012-01-01

    Full Text Available Mannose-binding lectin (MBL, a soluble factor of the innate immune system, is a pattern recognition molecule with a number of known ligands, including viruses, bacteria, and molecules from abnormal self tissues. In addition to its role in immunity, MBL also functions in the maintenance of tissue homeostasis. We present evidence here that MBL binds to amyloid β peptides. MBL binding to other known carbohydrate ligands is calcium-dependent and has been attributed to the carbohydrate-recognition domain, a common feature of other C-type lectins. In contrast, we find that the features of MBL binding to Aβ are more similar to the reported binding characteristics of the cysteine-rich domain of the unrelated mannose receptor and therefore may involve the MBL cysteine-rich domain. Differences in MBL ligand binding may contribute to modulation of inflammatory response and may correlate with the function of MBL in processes such as coagulation and tissue homeostasis.

  17. Solution Structure and Backbone Dynamics of Human Liver Fatty Acid Binding Protein: Fatty Acid Binding Revisited

    OpenAIRE

    Cai, Jun; Lücke, Christian; Chen, Zhongjing; Qiao, Ye; Klimtchuk, Elena; Hamilton, James A.

    2012-01-01

    Liver fatty acid binding protein (L-FABP), a cytosolic protein most abundant in liver, is associated with intracellular transport of fatty acids, nuclear signaling, and regulation of intracellular lipolysis. Among the members of the intracellular lipid binding protein family, L-FABP is of particular interest as it can i), bind two fatty acid molecules simultaneously and ii), accommodate a variety of bulkier physiological ligands such as bilirubin and fatty acyl CoA. To better understand the p...

  18. Automatic Binding Time Analysis for a Typed Lambda-Calculus

    DEFF Research Database (Denmark)

    Nielson, Hanne Riis; Nielson, Flemming

    1988-01-01

    analysis of the binding times of a typed lambda-calculus with products, sums, lists and general recursive types. Given partial information about the binding times of some of the subexpressions it will complete that information such that (i) early bindings may be turned into late bindings but not vice versa......, (ii) the resulting two-level lambda-expression reflects our intuition about binding times, e.g. that early bindings are performed before late bindings, and (iii) as few changes as possible have been made compared with the initial binding information. The results can be applied in the implementation...

  19. Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species.

    Directory of Open Access Journals (Sweden)

    Robert K Bradley

    2010-03-01

    Full Text Available Changes in gene expression play an important role in evolution, yet the molecular mechanisms underlying regulatory evolution are poorly understood. Here we compare genome-wide binding of the six transcription factors that initiate segmentation along the anterior-posterior axis in embryos of two closely related species: Drosophila melanogaster and Drosophila yakuba. Where we observe binding by a factor in one species, we almost always observe binding by that factor to the orthologous sequence in the other species. Levels of binding, however, vary considerably. The magnitude and direction of the interspecies differences in binding levels of all six factors are strongly correlated, suggesting a role for chromatin or other factor-independent forces in mediating the divergence of transcription factor binding. Nonetheless, factor-specific quantitative variation in binding is common, and we show that it is driven to a large extent by the gain and loss of cognate recognition sequences for the given factor. We find only a weak correlation between binding variation and regulatory function. These data provide the first genome-wide picture of how modest levels of sequence divergence between highly morphologically similar species affect a system of coordinately acting transcription factors during animal development, and highlight the dominant role of quantitative variation in transcription factor binding over short evolutionary distances.

  20. Crystal Structure of the Botulinum Neurotoxin Type G Binding Domain: Insight into Cell Surface Binding

    Energy Technology Data Exchange (ETDEWEB)

    Stenmark, Pål; Dong, Min; Dupuy, Jérôme; Chapman, Edwin R.; Stevens, Raymond C. (Scripps); (UW)

    2011-11-02

    Botulinum neurotoxins (BoNTs) typically bind the neuronal cell surface via dual interactions with both protein receptors and gangliosides. We present here the 1.9-{angstrom} X-ray structure of the BoNT serotype G (BoNT/G) receptor binding domain (residues 868-1297) and a detailed view of protein receptor and ganglioside binding regions. The ganglioside binding motif (SxWY) has a conserved structure compared to the corresponding regions in BoNT serotype A and BoNT serotype B (BoNT/B), but several features of interactions with the hydrophilic face of the ganglioside are absent at the opposite side of the motif in the BoNT/G ganglioside binding cleft. This may significantly reduce the affinity between BoNT/G and gangliosides. BoNT/G and BoNT/B share the protein receptor synaptotagmin (Syt) I/II. The Syt binding site has a conserved hydrophobic plateau located centrally in the proposed protein receptor binding interface (Tyr1189, Phe1202, Ala1204, Pro1205, and Phe1212). Interestingly, only 5 of 14 residues that are important for binding between Syt-II and BoNT/B are conserved in BoNT/G, suggesting that the means by which BoNT/G and BoNT/B bind Syt diverges more than previously appreciated. Indeed, substitution of Syt-II Phe47 and Phe55 with alanine residues had little effect on the binding of BoNT/G, but strongly reduced the binding of BoNT/B. Furthermore, an extended solvent-exposed hydrophobic loop, located between the Syt binding site and the ganglioside binding cleft, may serve as a third membrane association and binding element to contribute to high-affinity binding to the neuronal membrane. While BoNT/G and BoNT/B are homologous to each other and both utilize Syt-I/Syt-II as their protein receptor, the precise means by which these two toxin serotypes bind to Syt appears surprisingly divergent.

  1. CaMELS: In silico prediction of calmodulin binding proteins and their binding sites.

    Science.gov (United States)

    Abbasi, Wajid Arshad; Asif, Amina; Andleeb, Saiqa; Minhas, Fayyaz Ul Amir Afsar

    2017-09-01

    Due to Ca(2+) -dependent binding and the sequence diversity of Calmodulin (CaM) binding proteins, identifying CaM interactions and binding sites in the wet-lab is tedious and costly. Therefore, computational methods for this purpose are crucial to the design of such wet-lab experiments. We present an algorithm suite called CaMELS (CalModulin intEraction Learning System) for predicting proteins that interact with CaM as well as their binding sites using sequence information alone. CaMELS offers state of the art accuracy for both CaM interaction and binding site prediction and can aid biologists in studying CaM binding proteins. For CaM interaction prediction, CaMELS uses protein sequence features coupled with a large-margin classifier. CaMELS models the binding site prediction problem using multiple instance machine learning with a custom optimization algorithm which allows more effective learning over imprecisely annotated CaM-binding sites during training. CaMELS has been extensively benchmarked using a variety of data sets, mutagenic studies, proteome-wide Gene Ontology enrichment analyses and protein structures. Our experiments indicate that CaMELS outperforms simple motif-based search and other existing methods for interaction and binding site prediction. We have also found that the whole sequence of a protein, rather than just its binding site, is important for predicting its interaction with CaM. Using the machine learning model in CaMELS, we have identified important features of protein sequences for CaM interaction prediction as well as characteristic amino acid sub-sequences and their relative position for identifying CaM binding sites. Python code for training and evaluating CaMELS together with a webserver implementation is available at the URL: http://faculty.pieas.edu.pk/fayyaz/software.html#camels. © 2017 Wiley Periodicals, Inc.

  2. Computational search for aflatoxin binding proteins

    Science.gov (United States)

    Wang, Ying; Liu, Jinfeng; Zhang, Lujia; He, Xiao; Zhang, John Z. H.

    2017-10-01

    Aflatoxin is one of the mycotoxins that contaminate various food products. Among various aflatoxin types (B1, B2, G1, G2 and M1), aflatoxin B1 is the most important and the most toxic one. In this study, through computational screening, we found that several proteins may bind specifically with different type of aflatoxins. Combination of theoretical methods including target fishing, molecular docking, molecular dynamics (MD) simulation, MM/PBSA calculation were utilized to search for new aflatoxin B1 binding proteins. A recently developed method for calculating entropic contribution to binding free energy called interaction entropy (IE) was employed to compute the binding free energy between the protein and aflatoxin B1. Through comprehensive comparison, three proteins, namely, trihydroxynaphthalene reductase, GSK-3b, and Pim-1 were eventually selected as potent aflatoxin B1 binding proteins. GSK-3b and Pim-1 are drug targets of cancers or neurological diseases. GSK-3b is the strongest binder for aflatoxin B1.

  3. Haptenation: Chemical Reactivity and Protein Binding

    Directory of Open Access Journals (Sweden)

    Itai Chipinda

    2011-01-01

    Full Text Available Low molecular weight chemical (LMW allergens are commonly referred to as haptens. Haptens must complex with proteins to be recognized by the immune system. The majority of occupationally related haptens are reactive, electrophilic chemicals, or are metabolized to reactive metabolites that form covalent bonds with nucleophilic centers on proteins. Nonelectrophilic protein binding may occur through disulfide exchange, coordinate covalent binding onto metal ions on metalloproteins or of metal allergens, themselves, to the major histocompatibility complex. Recent chemical reactivity kinetic studies suggest that the rate of protein binding is a major determinant of allergenic potency; however, electrophilic strength does not seem to predict the ability of a hapten to skew the response between Th1 and Th2. Modern proteomic mass spectrometry methods that allow detailed delineation of potential differences in protein binding sites may be valuable in predicting if a chemical will stimulate an immediate or delayed hypersensitivity. Chemical aspects related to both reactivity and protein-specific binding are discussed.

  4. Conformational heterogeneity of the calmodulin binding interface

    Science.gov (United States)

    Shukla, Diwakar; Peck, Ariana; Pande, Vijay S.

    2016-04-01

    Calmodulin (CaM) is a ubiquitous Ca2+ sensor and a crucial signalling hub in many pathways aberrantly activated in disease. However, the mechanistic basis of its ability to bind diverse signalling molecules including G-protein-coupled receptors, ion channels and kinases remains poorly understood. Here we harness the high resolution of molecular dynamics simulations and the analytical power of Markov state models to dissect the molecular underpinnings of CaM binding diversity. Our computational model indicates that in the absence of Ca2+, sub-states in the folded ensemble of CaM's C-terminal domain present chemically and sterically distinct topologies that may facilitate conformational selection. Furthermore, we find that local unfolding is off-pathway for the exchange process relevant for peptide binding, in contrast to prior hypotheses that unfolding might account for binding diversity. Finally, our model predicts a novel binding interface that is well-populated in the Ca2+-bound regime and, thus, a candidate for pharmacological intervention.

  5. Endocytosis of Integrin-Binding Human Picornaviruses

    Directory of Open Access Journals (Sweden)

    Pirjo Merilahti

    2012-01-01

    Full Text Available Picornaviruses that infect humans form one of the largest virus groups with almost three hundred virus types. They include significant enteroviral pathogens such as rhino-, polio-, echo-, and coxsackieviruses and human parechoviruses that cause wide range of disease symptoms. Despite the economic importance of picornaviruses, there are no antivirals. More than ten cellular receptors are known to participate in picornavirus infection, but experimental evidence of their role in cellular infection has been shown for only about twenty picornavirus types. Three enterovirus types and one parechovirus have experimentally been shown to bind and use integrin receptors in cellular infection. These include coxsackievirus A9 (CV-A9, echovirus 9, and human parechovirus 1 that are among the most common and epidemic human picornaviruses and bind to αV-integrins via RGD motif that resides on virus capsid. In contrast, echovirus 1 (E-1 has no RGD and uses integrin α2β1 as cellular receptor. Endocytosis of CV-A9 has recently been shown to occur via a novel Arf6- and dynamin-dependent pathways, while, contrary to collagen binding, E-1 binds inactive β1 integrin and enters via macropinocytosis. In this paper, we review what is known about receptors and endocytosis of integrin-binding human picornaviruses.

  6. Optical binding between dielectric nanowires (Conference Presentation)

    Science.gov (United States)

    Hanna, Simon; Simpson, Stephen H.

    2016-09-01

    Optical binding occurs when micron-sized particles interact through the exchange of scattered photons. It has been observed both in systems of colloidal dielectric particles and between metallic nanoparticles, and can result in the formation of clusters and coupled dynamical behaviour. Optical binding between spherical particles has been studied in some detail, but little work has appeared in the literature to describe binding effects in lower symmetry systems. In the present paper we discuss recent theoretical work and computer simulations of optical binding effects operating between dielectric nanowires in counter propagating beams. The reduction in symmetry from simple spheres introduces new opportunities for binding, including different types of orientational ordering and anisotropies in the spatial arrangements that are possible for the bound particles. Various ordered configurations are possible, including ladder-like structures and oriented lattices. The stability of these structures to thermal perturbations will be discussed. Asymmetric arrangements of the nanowires are also possible, as a consequence of interactions between the nanowires and the underlying counter-propagating laser field. These configurations lead to a diversity of non-conservative effects, including uniform translation in linearly polarised beams and synchronous rotations in circularly polarised beams, suggesting potential applications of such bound structures in micro-machines.

  7. An extended database of keratin binding.

    Science.gov (United States)

    Hansen, Steffi; Selzer, Dominik; Schaefer, Ulrich F; Kasting, Gerald B

    2011-05-01

    Diffusion modeling of dermal absorption relies in large part on high quality input data. Currently, estimates of corneocyte-phase partitioning are based on an analysis of a dataset of limited size and diversity. Therefore, we have updated and broadened the analysis. For this purpose, binding coefficients to different keratins, namely, bovine hoof and horn, human delipidized callus, human delipidized stratum corneum (SC), human nail, human hair, and sheep wool were collected from the literature. In addition, binding coefficients to hoof/horn and delipidized SC were measured for eight hydrophilic compounds including three ionizable compounds that were measured at different pH values. Important results are: (i) only hoof/horn, callus, and delipidized SC are suitable keratins for estimating corneocyte protein binding; (ii) binding coefficients to hoof/horn, callus, and delipidized SC can be predicted from the octanol-water partition coefficients log K(o/w) confirming the analysis of the limited dataset; (iii) binding of ionizable compounds can be predicted by correcting log K(o/w) for pH; (iv) the correlation derived for the extended database is steeper than the relationship derived for the limited dataset. This has consequences for the estimates of SC partition and diffusion coefficients for diffusion modeling of dermal absorption. .

  8. Endocytosis of integrin-binding human picornaviruses.

    Science.gov (United States)

    Merilahti, Pirjo; Koskinen, Satu; Heikkilä, Outi; Karelehto, Eveliina; Susi, Petri

    2012-01-01

    Picornaviruses that infect humans form one of the largest virus groups with almost three hundred virus types. They include significant enteroviral pathogens such as rhino-, polio-, echo-, and coxsackieviruses and human parechoviruses that cause wide range of disease symptoms. Despite the economic importance of picornaviruses, there are no antivirals. More than ten cellular receptors are known to participate in picornavirus infection, but experimental evidence of their role in cellular infection has been shown for only about twenty picornavirus types. Three enterovirus types and one parechovirus have experimentally been shown to bind and use integrin receptors in cellular infection. These include coxsackievirus A9 (CV-A9), echovirus 9, and human parechovirus 1 that are among the most common and epidemic human picornaviruses and bind to αV-integrins via RGD motif that resides on virus capsid. In contrast, echovirus 1 (E-1) has no RGD and uses integrin α2β1 as cellular receptor. Endocytosis of CV-A9 has recently been shown to occur via a novel Arf6- and dynamin-dependent pathways, while, contrary to collagen binding, E-1 binds inactive β1 integrin and enters via macropinocytosis. In this paper, we review what is known about receptors and endocytosis of integrin-binding human picornaviruses.

  9. DNA binding studies of tartrazine food additive.

    Science.gov (United States)

    Kashanian, Soheila; Zeidali, Sahar Heidary

    2011-07-01

    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).

  10. On the Orientation Problem in Korean 'CAKI' Binding and the Typology of X Reflexive Binding.

    Science.gov (United States)

    Cho, Mi-Hui

    1994-01-01

    The purpose of this paper is to demonstrate the existence of nonsubject binding of the so-called long distance anaphor in languages like Korean and Japanese and to give a principled account of why and when it happens. The Korean reflexive pronoun "caki" ('self') is bound by local and long-distance antecedents. Nonsubject binding occurs…

  11. CTCF: the protein, the binding partners, the binding sites and their chromatin loops

    NARCIS (Netherlands)

    Holwerda, S.J.; de Laat, W.

    2013-01-01

    CTCF has it all. The transcription factor binds to tens of thousands of genomic sites, some tissue-specific, others ultra-conserved. It can act as a transcriptional activator, repressor and insulator, and it can pause transcription. CTCF binds at chromatin domain boundaries, at enhancers and gene pr

  12. The interrelationship between ligand binding and self-association of the folate binding protein

    DEFF Research Database (Denmark)

    Holm, Jan; Schou, Christian; Babol, Linnea N.

    2011-01-01

    The folate binding protein (FBP) regulates homeostasis and intracellular trafficking of folic acid, a vitamin of decisive importance in cell division and growth. We analyzed whether interrelationship between ligand binding and self-association of FBP plays a significant role in the physiology...

  13. Ancestral Protein Reconstruction Yields Insights into Adaptive Evolution of Binding Specificity in Solute-Binding Proteins.

    Science.gov (United States)

    Clifton, Ben E; Jackson, Colin J

    2016-02-18

    The promiscuous functions of proteins are an important reservoir of functional novelty in protein evolution, but the molecular basis for binding promiscuity remains elusive. We used ancestral protein reconstruction to experimentally characterize evolutionary intermediates in the functional expansion of the polar amino acid-binding protein family, which has evolved to bind a variety of amino acids with high affinity and specificity. High-resolution crystal structures of an ancestral arginine-binding protein in complex with l-arginine and l-glutamine show that the promiscuous binding of l-glutamine is enabled by multi-scale conformational plasticity, water-mediated interactions, and selection of an alternative conformational substate productive for l-glutamine binding. Evolution of specialized glutamine-binding proteins from this ancestral protein was achieved by displacement of water molecules from the protein-ligand interface, reducing the entropic penalty associated with the promiscuous interaction. These results provide a structural and thermodynamic basis for the co-option of a promiscuous interaction in the evolution of binding specificity.

  14. Asporin competes with decorin for collagen binding, binds calcium and promotes osteoblast collagen mineralization

    DEFF Research Database (Denmark)

    Kalamajski, Sebastian; Aspberg, Anders; Lindblom, Karin

    2009-01-01

    The interactions of the ECM (extracellular matrix) protein asporin with ECM components have previously not been investigated. Here, we show that asporin binds collagen type I. This binding is inhibited by recombinant asporin fragment LRR (leucine-rich repeat) 10-12 and by full-length decorin, but...

  15. Opioid binding sites in the guinea pig and rat kidney: Radioligand homogenate binding and autoradiography

    Energy Technology Data Exchange (ETDEWEB)

    Dissanayake, V.U.; Hughes, J.; Hunter, J.C. (Parke-Davis Research Unit, Addenbrookes Hospital Site, Cambridge (England))

    1991-07-01

    The specific binding of the selective {mu}-, {delta}-, and {kappa}-opioid ligands (3H)(D-Ala2,MePhe4,Gly-ol5)enkephalin ((3H) DAGOL), (3H)(D-Pen2,D-Pen5)enkephalin ((3H)DPDPE), and (3H)U69593, respectively, to crude membranes of the guinea pig and rat whole kidney, kidney cortex, and kidney medulla was investigated. In addition, the distribution of specific 3H-opioid binding sites in the guinea pig and rat kidney was visualized by autoradiography. Homogenate binding and autoradiography demonstrated the absence of {mu}- and {kappa}-opioid binding sites in the guinea pig kidney. No opioid binding sites were demonstrable in the rat kidney. In the guinea pig whole kidney, cortex, and medulla, saturation studies demonstrated that (3H)DPDPE bound with high affinity (KD = 2.6-3.5 nM) to an apparently homogeneous population of binding sites (Bmax = 8.4-30 fmol/mg of protein). Competition studies using several opioid compounds confirmed the nature of the {delta}-opioid binding site. Autoradiography experiments demonstrated that specific (3H)DPDPE binding sites were distributed radially in regions of the inner and outer medulla and at the corticomedullary junction of the guinea pig kidney. Computer-assisted image analysis of saturation data yielded KD values (4.5-5.0 nM) that were in good agreement with those obtained from the homogenate binding studies. Further investigation of the {delta}-opioid binding site in medulla homogenates, using agonist ((3H)DPDPE) and antagonist ((3H)diprenorphine) binding in the presence of Na+, Mg2+, and nucleotides, suggested that the {delta}-opioid site is linked to a second messenger system via a GTP-binding protein. Further studies are required to establish the precise localization of the {delta} binding site in the guinea pig kidney and to determine the nature of the second messenger linked to the GTP-binding protein in the medulla.

  16. ABP: a novel AMPA receptor binding protein.

    Science.gov (United States)

    Srivastava, S; Ziff, E B

    1999-04-30

    We review the cloning of a novel AMPA receptor binding protein (ABP) that interacts with GluR2/3 and is homologous to GRIP. ABP is enriched in the PSD with GluR2 and is localized to the PSD by EM. ABP binds GluR2 via the C-terminal VXI motif through a Class I PDZ interaction. ABP and GRIP can also homo- and heteromultimerize. Thus, ABP and GRIP may be involved in AMPA receptor regulation and localization, by linking it to other cytoskeletal or signaling molecules. We suggest that the ABP/GRIP and PSD-95 families form distinct scaffolds that anchor, respectively, AMPA and NMDA receptors. We are currently investigating proteins that bind ABP and that may regulate the AMPA receptor.

  17. Arsenic binding to Fucus vesiculosus metallothionein.

    Science.gov (United States)

    Merrifield, Maureen E; Ngu, Thanh; Stillman, Martin J

    2004-11-05

    The seaweed Fucus vesiculosus is a member of the brown algae family. Kille and co-workers [Biochem. J. 338 (1999) 553] reported that this species contains the gene for metallothionein. Metallothionein is a metalloprotein having low molecular weight, and high cysteine content, which binds a range of metals. F. vesiculosus bioaccumulates arsenic from the aquatic environment [Mar. Chem. 18 (1986) 321]. In this paper we describe arsenic binding to F. vesiculosus metallothionein, characterized by electrospray ionization mass spectrometry. Five arsenic-MT species were detected with increasing As to protein ratios. These results provide important information about the metal-chelation behaviour of this novel algal metallothionein which is a putative model for arsenic binding to F. vesiculosus in vivo.

  18. Asymmetry of calmodulin revealed by peptide binding.

    Science.gov (United States)

    Leclerc, E; Leclerc, L; Marden, M C

    1993-03-01

    The binding of amphiphilic peptides to calmodulin has been studied using fluorescence energy transfer techniques. Calmodulin has no tryptophan residues but possesses two tyrosines (at positions 99 and 138) in the C-terminal half of the protein. The peptides have a single tryptophan which serves as energy acceptor for the protein tyrosine fluorescence. For the binding of mastoparan or peptide Baa17, with a tryptophan at position 3, the observed quenching of the tyrosine fluorescence of over a factor of 2 corresponds to an average tyrosine-trytophan distance of less than 14 Å. These results indicate that the peptides binds preferentially with the tryptophan in the C-terminal half of the protein.

  19. A review of albumin binding in CKD.

    Science.gov (United States)

    Meijers, Björn K I; Bammens, Bert; Verbeke, Kristin; Evenepoel, Pieter

    2008-05-01

    Hypoalbuminemia is associated with excess mortality in patients with kidney disease. Albumin is an important oxidant scavenger and an abundant carrier protein for numerous endogenous and exogenous compounds. Several specific binding sites for anionic, neutral, and cationic ligands were described. Overall, the extent of binding depends on the ligand and albumin concentration, albumin-binding affinity, and presence of competing ligands. Chronic kidney disease affects all these determinants. This may result in altered pharmacokinetics and increased risk of toxicity. Renal clearance of albumin-bound solutes mainly depends on tubular clearance. Dialytic clearance by means of conventional hemodialysis/hemofiltration and peritoneal dialysis is limited. Other epuration techniques combining hemodialysis with adsorption have been developed. However, the benefit of these techniques remains to be proved.

  20. Conformation-controlled binding kinetics of antibodies

    Science.gov (United States)

    Galanti, Marta; Fanelli, Duccio; Piazza, Francesco

    2016-01-01

    Antibodies are large, extremely flexible molecules, whose internal dynamics is certainly key to their astounding ability to bind antigens of all sizes, from small hormones to giant viruses. In this paper, we build a shape-based coarse-grained model of IgG molecules and show that it can be used to generate 3D conformations in agreement with single-molecule Cryo-Electron Tomography data. Furthermore, we elaborate a theoretical model that can be solved exactly to compute the binding rate constant of a small antigen to an IgG in a prescribed 3D conformation. Our model shows that the antigen binding process is tightly related to the internal dynamics of the IgG. Our findings pave the way for further investigation of the subtle connection between the dynamics and the function of large, flexible multi-valent molecular machines.

  1. Heavy quark interactions and quarkonium binding

    Science.gov (United States)

    Satz, Helmut

    2009-06-01

    We consider heavy quark interactions in quenched and unquenched lattice QCD. In a region just above the deconfinement point, non-Abelian gluon polarization leads to a strong increase in the binding. Comparing quark-antiquark and quark-quark interaction, the dependence of the binding on the separation distance r is found to be the same for the colorless singlet Q{\\skew3\\bar{Q}} and the colored anti-triplet QQ state. In a potential model description of in-medium J/ψ behavior, this enhancement of the binding leads to a survival up to temperatures of 1.5 Tc or higher; it could also result in J/ψ flow. Based on joint work with O Kaczmarek and F Karsch.

  2. Defining Starch Binding by Glucan Phosphatases

    DEFF Research Database (Denmark)

    Auger, Kyle; Raththagala, Madushi; Wilkens, Casper;

    2015-01-01

    Starch is a vital energy molecule in plants that has a wide variety of uses in industry, such as feedstock for biomaterial processing and biofuel production. Plants employ a three enzyme cyclic process utilizing kinases, amylases, and phosphatases to degrade starch in a diurnal manner. Starch...... is comprised of the branched glucan amylopectin and the more linear glucan amylose. Our lab has determined the first structures of these glucan phosphatases and we have defined their enzymatic action. Despite this progress, we lacked a means to quickly and efficiently quantify starch binding to glucan...... phosphatases. The main objective of this study was to quantify the binding affinity of different enzymes that are involved in this cyclic process. We established a protocol to quickly, reproducibly, and quantitatively measure the binding of the enzymes to glucans utilizing Affinity Gel Electrophoresis (AGE...

  3. Adjustment of legally binding local plans

    DEFF Research Database (Denmark)

    Hvingel, Line Træholt; Aunsborg, Christian; Christensen, Finn Kjær

    2012-01-01

    Traditionally, and by law, new urban areas in Denmark are regulated and planned through legally binding local plans. Recently a tendency has occurred: The municipalities make the legally binding local plans quite open for future adjustment, and they are using a substantial amount of ‘empowerment...... provisions’ which empower the municipalities to later ruling. This way of making plans postpones the actual regulation of an area (i.e. the planning permission) making it an individual ruling for instance at the application of building permits. Case studies show examples of this way of regulating an area......, which seem to be beyond the scope of the Danish Planning Act. This paper deals with this problem through case studies and a legal analysis of present law. If the combination of the legally binding local plan and subsequent added requirements is misused, it will weaken the legal rights of the citizens...

  4. Predicting binding free energies in solution

    CERN Document Server

    Jensen, Jan H

    2015-01-01

    Recent predictions of absolute binding free energies of host-guest complexes in aqueous solution using electronic structure theory have been encouraging for some systems, while other systems remain problematic for others. In paper I summarize some of the many factors that could easily contribute 1-3 kcal/mol errors at 298 K: three-body dispersion effects, molecular symmetry, anharmonicity, spurious imaginary frequencies, insufficient conformational sampling, wrong or changing ionization states, errors in the solvation free energy of ions, and explicit solvent (and ion) effects that are not well-represented by continuum models. While the paper is primarily a synthesis of previously published work there are two new results: the adaptation of Legendre transformed free energies to electronic structure theory and a use of water clusters that maximizes error cancellation in binding free energies computed using explicit solvent molecules. While I focus on binding free energies in aqueous solution the approach also a...

  5. Mercury-binding proteins of Mytilus edulis

    Energy Technology Data Exchange (ETDEWEB)

    Roesijadi, G.; Morris, J. E.; Calabrese, A.

    1981-11-01

    Mytilus edulis possesses low molecular weight, mercury-binding proteins. The predominant protein isolated from gill tissue is enriched in cysteinyl residues (8%) and possesses an amino acid composition similar to cadmium-binding proteins of mussels and oysters. Continuous exposure of mussels to 5 ..mu..g/l mercury results in spillover of mercury from these proteins to high molecular weight proteins. Antibodies to these proteins have been isolated, and development of immunoassays is presently underway. Preliminary studies to determine whether exposure of adult mussels to mercury will result in induction of mercury-binding proteins in offspring suggest that such proteins occur in larvae although additional studies are indicated for a conclusive demonstration.

  6. 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))

    1990-12-01

    {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.

  7. Potential of goat probiotic to bind mutagens.

    Science.gov (United States)

    Apás, Ana Lidia; González, Silvia Nelina; Arena, Mario Eduardo

    2014-08-01

    The mutagen binding ability of the goat probiotics (Lactobacillus reuteri DDL 19, Lactobacillus alimentarius DDL 48, Enterococcus faecium DDE 39, and Bifidobacterium bifidum DDBA) was evaluated. The oral administration of these probiotics reduced fecal mutagens and intestinal cancer markers in goats. Secondly, the effects of probiotics against the mutagenesis induced by sodium azide (SA), and Benzopyrene (B[α]P) by performing the modified Ames test using Salmonella typhimurium TA 100 was investigated. The capacity to bind benzopyrene and the stability of the bacterial-mutagen complex was analyzed by HPLC. The dismutagenic potential against both mutagens was proportional to probiotic concentration. Results showed that probiotic antimutagenic capacity against SA was ranging from 13 to 78%. The mixture of four goat probiotics (MGP) displayed higher antimutagenic activity against SA than any individual strains at the same cell concentration. This study shows that the highest diminution of mutagenicity in presence of B[α]P (74%) was observed in presence of MGP. The antimutagenic activity of nearly all the individual probiotic and the MGP were in concordance with the B[α]P binding determined by HPLC. According to our results, the B[α]P binding to probiotic was irreversible still after being washed with DMSO solution. The stability of the toxic compounds-bacterial cell binding is a key consideration when probiotic antimutagenic property is evaluated. MGP exhibits the ability to bind and detoxify potent mutagens, and this property can be useful in supplemented foods for goats since it can lead to the removal of potent mutagens and protect and enhance ruminal health and hence food safety of consumers.

  8. Binding of alkylpyridinium chloride surfactants to sodium polystyrene sulfonate

    NARCIS (Netherlands)

    Ishiguro, M.; Koopal, L.K.

    2009-01-01

    Binding of cationic surfactants to anionic polymers is well studied. However, the surfactant binding characteristics at very low concentration near the start of binding and at high concentration, where charge compensation may Occur. are less well known. Therefore, the binding characteristics of

  9. High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints.

    Directory of Open Access Journals (Sweden)

    Yuchun Guo

    Full Text Available An essential component of genome function is the syntax of genomic regulatory elements that determine how diverse transcription factors interact to orchestrate a program of regulatory control. A precise characterization of in vivo spacing constraints between key transcription factors would reveal key aspects of this genomic regulatory language. To discover novel transcription factor spatial binding constraints in vivo, we developed a new integrative computational method, genome wide event finding and motif discovery (GEM. GEM resolves ChIP data into explanatory motifs and binding events at high spatial resolution by linking binding event discovery and motif discovery with positional priors in the context of a generative probabilistic model of ChIP data and genome sequence. GEM analysis of 63 transcription factors in 214 ENCODE human ChIP-Seq experiments recovers more known factor motifs than other contemporary methods, and discovers six new motifs for factors with unknown binding specificity. GEM's adaptive learning of binding-event read distributions allows it to further improve upon previous methods for processing ChIP-Seq and ChIP-exo data to yield unsurpassed spatial resolution and discovery of closely spaced binding events of the same factor. In a systematic analysis of in vivo sequence-specific transcription factor binding using GEM, we have found hundreds of spatial binding constraints between factors. GEM found 37 examples of factor binding constraints in mouse ES cells, including strong distance-specific constraints between Klf4 and other key regulatory factors. In human ENCODE data, GEM found 390 examples of spatially constrained pair-wise binding, including such novel pairs as c-Fos:c-Jun/USF1, CTCF/Egr1, and HNF4A/FOXA1. The discovery of new factor-factor spatial constraints in ChIP data is significant because it proposes testable models for regulatory factor interactions that will help elucidate genome function and the

  10. High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints.

    Science.gov (United States)

    Guo, Yuchun; Mahony, Shaun; Gifford, David K

    2012-01-01

    An essential component of genome function is the syntax of genomic regulatory elements that determine how diverse transcription factors interact to orchestrate a program of regulatory control. A precise characterization of in vivo spacing constraints between key transcription factors would reveal key aspects of this genomic regulatory language. To discover novel transcription factor spatial binding constraints in vivo, we developed a new integrative computational method, genome wide event finding and motif discovery (GEM). GEM resolves ChIP data into explanatory motifs and binding events at high spatial resolution by linking binding event discovery and motif discovery with positional priors in the context of a generative probabilistic model of ChIP data and genome sequence. GEM analysis of 63 transcription factors in 214 ENCODE human ChIP-Seq experiments recovers more known factor motifs than other contemporary methods, and discovers six new motifs for factors with unknown binding specificity. GEM's adaptive learning of binding-event read distributions allows it to further improve upon previous methods for processing ChIP-Seq and ChIP-exo data to yield unsurpassed spatial resolution and discovery of closely spaced binding events of the same factor. In a systematic analysis of in vivo sequence-specific transcription factor binding using GEM, we have found hundreds of spatial binding constraints between factors. GEM found 37 examples of factor binding constraints in mouse ES cells, including strong distance-specific constraints between Klf4 and other key regulatory factors. In human ENCODE data, GEM found 390 examples of spatially constrained pair-wise binding, including such novel pairs as c-Fos:c-Jun/USF1, CTCF/Egr1, and HNF4A/FOXA1. The discovery of new factor-factor spatial constraints in ChIP data is significant because it proposes testable models for regulatory factor interactions that will help elucidate genome function and the implementation of combinatorial

  11. Binding energies of hypernuclei and hypernuclear interactions

    Energy Technology Data Exchange (ETDEWEB)

    Bodmer, A.R. [Argonne National Lab., IL (United States)]|[Univ. of Illinois, Chicago, IL (United States). Dept. of Physics; Murali, S.; Usmani, Q.N. [Jamia Millia Islamia, New Delhi (India). Dept. of Physics

    1996-05-01

    In part 1 the effect of nuclear core dynamics on the binding energies of {Lambda} hypernuclei is discussed in the framework of variational correlated wave functions. In particular, the authors discuss a new rearrangement energy contribution and its effect on the core polarization. In part 2 they consider the interpretation of the {Lambda} single-particle energy in terms of basic {Lambda}-nuclear interactions using a local density approximation based on a Fermi hypernetted chain calculation of the A binding to nuclear matter. To account for the data strongly repulsive 3-body {Lambda}NN forces are required. Also in this framework they discuss core polarization for medium and heavier hypernuclei.

  12. The binding energy and bonding in dialane.

    Science.gov (United States)

    Goebbert, Daniel J; Hernandez, Heriberto; Francisco, Joseph S; Wenthold, Paul G

    2005-08-24

    The binding energy of dialane, Al2H6, has been measured using mass spectrometric techniques to be 33 +/- 5 kcal/mol. This represents the first measurement of the thermochemical properties of dialane, which has only recently been observed in low-temperature matricies. High-level quantum mechanical calculations give a binding energy in agreement with the measured value. Experimental and quantum mechanical calculations show that dialane is chemically similar to diborane, B2H6, even though the bonding for these two systems shows significant differences.

  13. Perceptual-binding and persistent surface segregation.

    Science.gov (United States)

    Moradi, Farshad; Shimojo, Shinsuke

    2004-11-01

    Visual input is segregated in the brain into subsystems that process different attributes such as motion and color. At the same time, visual information is perceptually segregated into objects and surfaces. Here we demonstrate that perceptual segregation of visual entities based on a transparency cue precedes and affects perceptual binding of attributes. Adding an irrelevant transparency cue paradoxically improved the pairing of color and motion for rapidly alternating surfaces. Subsequent experiments show: (1) Attributes are registered over the temporal window defined by the perceptual persistence of segregation, resulting in asynchrony in binding, and (2) attention is necessary for correct registration of attributes in the presence of ambiguity.

  14. Binding energy of two-dimensional biexcitons

    DEFF Research Database (Denmark)

    Singh, Jai; Birkedal, Dan; Vadim, Lyssenko;

    1996-01-01

    Using a model structure for a two-dimensional (2D) biexciton confined in a quantum well, it is shown that the form of the Hamiltonian of the 2D biexciton reduces into that of an exciton. The binding energies and Bohr radii of a 2D biexciton in its various internal energy states are derived...... analytically using the fractional dimension approach. The ratio of the binding energy of a 2D biexciton to that of a 2D exciton is found to be 0.228, which agrees very well with the recent experimental value. The results of our approach are compared with those of earlier theories....

  15. Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy Estimation.

    Science.gov (United States)

    Mentes, Ahmet; Deng, Nan-Jie; Vijayan, R S K; Xia, Junchao; Gallicchio, Emilio; Levy, Ronald M

    2016-05-10

    Molecular dynamics modeling of complex biological systems is limited by finite simulation time. The simulations are often trapped close to local energy minima separated by high energy barriers. Here, we introduce Hamiltonian replica exchange (H-REMD) with torsional flattening in the Binding Energy Distribution Analysis Method (BEDAM), to reduce energy barriers along torsional degrees of freedom and accelerate sampling of intramolecular degrees of freedom relevant to protein-ligand binding. The method is tested on a standard benchmark (T4 Lysozyme/L99A/p-xylene complex) and on a library of HIV-1 integrase complexes derived from the SAMPL4 blind challenge. We applied the torsional flattening strategy to 26 of the 53 known binders to the HIV Integrase LEDGF site found to have a binding energy landscape funneled toward the crystal structure. We show that our approach samples the conformational space more efficiently than the original method without flattening when starting from a poorly docked pose with incorrect ligand dihedral angle conformations. In these unfavorable cases convergence to a binding pose within 2-3 Å from the crystallographic pose is obtained within a few nanoseconds of the Hamiltonian replica exchange simulation. We found that torsional flattening is insufficient in cases where trapping is due to factors other than torsional energy, such as the formation of incorrect intramolecular hydrogen bonds and stacking. Work is in progress to generalize the approach to handle these cases and thereby make it more widely applicable.

  16. Solution structure and binding specificity of the p63 DNA binding domain.

    Science.gov (United States)

    Enthart, Andreas; Klein, Christian; Dehner, Alexander; Coles, Murray; Gemmecker, Gerd; Kessler, Horst; Hagn, Franz

    2016-05-26

    p63 is a close homologue of p53 and, together with p73, is grouped into the p53 family of transcription factors. p63 is known to be involved in the induction of controlled apoptosis important for differentiation processes, germ line integrity and development. Despite its high homology to p53, especially within the DNA binding domain (DBD), p63-DBD does not show cooperative DNA binding properties and is significantly more stable against thermal and chemical denaturation. Here, we determined the solution structure of p63-DBD and show that it is markedly less dynamic than p53-DBD. In addition, we also investigate the effect of a double salt bridge present in p53-DBD, but not in p63-DBD on the cooperative binding behavior and specificity to various DNA sites. Restoration of the salt bridges in p63-DBD by mutagenesis leads to enhanced binding affinity to p53-specific, but not p63-specific response elements. Furthermore, we show that p63-DBD is capable of binding to anti-apoptotic BclxL via its DNA binding interface, a feature that has only been shown for p53 so far. These data suggest that all p53 family members - despite alterations in the specificity and binding affinity - are capable of activating pro-apoptotic pathways in a tissue specific manner.

  17. Generation of metal-binding staphylococci through surface display of combinatorially engineered cellulose-binding domains.

    Science.gov (United States)

    Wernérus, H; Lehtiö, J; Teeri, T; Nygren, P A; Ståhl, S

    2001-10-01

    Ni(2+)-binding staphylococci were generated through surface display of combinatorially engineered variants of a fungal cellulose-binding domain (CBD) from Trichoderma reesei cellulase Cel7A. Novel CBD variants were generated by combinatorial protein engineering through the randomization of 11 amino acid positions, and eight potentially Ni(2+)-binding CBDs were selected by phage display technology. These new variants were subsequently genetically introduced into chimeric surface proteins for surface display on Staphylococcus carnosus cells. The expressed chimeric proteins were shown to be properly targeted to the cell wall of S. carnosus cells, since full-length proteins could be extracted and affinity purified. Surface accessibility for the chimeric proteins was demonstrated, and furthermore, the engineered CBDs, now devoid of cellulose-binding capacity, were shown to be functional with regard to metal binding, since the recombinant staphylococci had gained Ni(2+)-binding capacity. Potential environmental applications for such tailor-made metal-binding bacteria as bioadsorbents in biofilters or biosensors are discussed.

  18. ALG-2, a multifunctional calcium binding protein?

    DEFF Research Database (Denmark)

    Tarabykina, Svetlana; Mollerup, Jens; Winding Gojkovic, P.;

    2004-01-01

    ALG-2 was originally discovered as a pro-apoptotic protein in a genetic screen. Due to its ability to bind calcium with high affinity it was postulated to provide a link between the known effect of calcium in programmed cell death and the molecular death execution machinery. This review article...

  19. Alkali binding in hydrated Portland cement paste

    NARCIS (Netherlands)

    Chen, W.; Brouwers, H.J.H.

    2010-01-01

    The alkali-binding capacity of C–S–H in hydrated Portland cement pastes is addressed in this study. The amount of bound alkalis in C–S–H is computed based on the alkali partition theories firstly proposed by Taylor (1987) and later further developed by Brouwers and Van Eijk (2003). Experimental data

  20. Information flow through calcium binding proteins

    Science.gov (United States)

    Bak, Ji Hyun; Bialek, William

    2013-03-01

    Calcium signaling is a ubiquitous mode of biological communication, which regulates a great variety of vital processes in living systems. Such a signal typically begins with an elementary event, in which calcium ions bind to a protein, inducing a change in the protein's structure. Information can only be lost, from what was conveyed through this initial event, as the signal is further transduced through the downstream networks. In the present work we analyze and optimize the information flow in the calcium binding process. We explicitly calculate the mutual information between the calcium concentration and the states of the protein, using a simple model for allosteric regulation in a dimeric protein. The optimal solution depends on the dynamic range of the input as well as on the timescale of signal integration. According to our result, the optimizing strategy involves allowing the calcium-binding protein to be ``activated'' by a partial occupation of its sites, and tuning independently the strengths of cooperative interactions in the binding and unbinding processes.

  1. Binding of flavonoids to staphylococcal enterotoxin B.

    Science.gov (United States)

    Benedik, Evgen; Skrt, Mihaela; Podlipnik, Crtomir; Ulrih, Nataša Poklar

    2014-12-01

    Staphylococcal enterotoxins are metabolic products of Staphylococcus aureus that are responsible for the second-most-commonly reported type of food poisoning. Polyphenols are known to interact with proteins to form complexes, the properties of which depend on the structures of both the polyphenols and the protein. In the present study, we investigated the binding of four flavonoid polyphenols to Staphylococcal enterotoxin B (SEB) at pH 7.5 and 25 °C: (-)-epigallocatechin-3-gallate (EGCG), (-)-epigallocatechin (EGC), kaempferol-3-glucoside (KAM-G) and kaempferol (KAM). Fluorescence emission spectrometry and molecular docking were applied to compare experimentally determined binding parameters with molecular modeling. EGCG showed an order of magnitude higher binding constant (1.4 × 10(5) M(-1)) than the other studied polyphenols. Our blind-docking results showed that EGCG and similar polyphenolic ligands is likely to bind to the channel at the surface of SEB that is responsible for the recognition of the T-cell beta chain fragment and influence the adhesion of SEB to T cells.

  2. Binding of cationic surfactants to humic substances

    NARCIS (Netherlands)

    Ishiguro, M.; Tan, W.; Koopal, L.K.

    2007-01-01

    Commercial surfactants are introduced into the environment either through waste products or site-specific contamination. The amphiphilic nature of both surfactants and humic substances (HS) leads to their mutual attraction especially when surfactant and HS are oppositely charged. Binding of the cati

  3. Oxytocin binding sites in bovine mammary tissue

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Xin.

    1989-01-01

    Oxytocin binding sites were identified and characterized in bovine mammary tissue. ({sup 3}H)-oxytocin binding reached equilibrium by 50 min at 20{degree}C and by 8 hr at 4{degree}C. The half-time of displacement at 20{degree}C was approximately 1 hr. Thyrotropin releasing hormone, adrenocorticotropin, angiotensin I, angiotensin II, pentagastrin, bradykinin, xenopsin and L-valyl-histidyl-L-leucyl-L-threonyl-L-prolyl-L-valyl-L-glutamyl-L-lysine were not competitive. In the presence of 10 nM LiCl, addition of oxytocin to dispersed bovine mammary cells, in which phosphatidylinositol was pre-labelled, caused a time and dose-dependent increase in radioactive inositiol monophosphate incorporation. The possibility that there are distinct vasopressin receptors in bovine mammary tissue was investigated. ({sup 3}H)-vasopressin binding reached equilibrium by 40 min at 20{degree}. The half-time of displacement at 20{degree}C was approximately 1 hr. The ability of the peptides to inhibit ({sup 3}H)-vasopressin binding was: (Thr{sup 4},Gly{sup 7})-oxytocin > Arg{sup 8}-vasopressin > (lys{sup 8})-vasopressin > (Deamino{sup 1},D-arg{sup 8})-vasopressin > oxytocin > d (CH{sub 2}){sub 5}Tyr(Me)AVP.

  4. Binding Hydrated Anions with Hydrophobic Pockets.

    Science.gov (United States)

    Sokkalingam, Punidha; Shraberg, Joshua; Rick, Steven W; Gibb, Bruce C

    2016-01-13

    Using a combination of isothermal titration calorimetry and quantum and molecular dynamics calculations, we demonstrate that relatively soft anions have an affinity for hydrophobic concavity. The results are consistent with the anions remaining partially hydrated upon binding, and suggest a novel strategy for anion recognition.

  5. Lipid binding proteins from parasitic platyhelminthes.

    Science.gov (United States)

    Alvite, Gabriela; Esteves, Adriana

    2012-01-01

    TWO MAIN FAMILIES OF LIPID BINDING PROTEINS HAVE BEEN IDENTIFIED IN PARASITIC PLATYHELMINTHES: hydrophobic ligand binding proteins (HLBPs) and fatty acid binding proteins (FABPs). Members of the former family of proteins are specific to the Cestoda class, while FABPs are conserved across a wide range of animal species. Because Platyhelminthes are unable to synthesize their own lipids, these lipid-binding proteins are important molecules in these organisms. HLBPs are a high molecular mass complex of proteins and lipids. They are composed of subunits of low molecular mass proteins and a wide array of lipid molecules ranging from CoA esters to cholesterol. These proteins are excretory-secretory molecules and are key serological tools for diagnosis of diseases caused by cestodes. FABPs are mainly intracellular proteins of low molecular weight. They are also vaccine candidates. Despite that the knowledge of their function is scarce, the differences in their molecular organization, ligand preferences, intra/extracellular localization, evolution, and phylogenetic distribution, suggest that platyhelminths HLBPs and FABPs should play different functions. FABPs might be involved in the removal of fatty acids from the inner surface of the cell membrane and in their subsequent targeting to specific cellular destinations. In contrast, HLBPs might be involved in fatty acid uptake from the host environment.

  6. Nucleic acids encoding a cellulose binding domain

    Energy Technology Data Exchange (ETDEWEB)

    Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc A. (Davis, CA); Doi, Roy H. (Davis, CA)

    1996-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  7. Development of a glucose binding protein biosensor

    Science.gov (United States)

    Dweik, M.; Milanick, M.; Grant, S.

    2007-09-01

    Glucose binding protein (GBP) is a monomeric periplasmic protein. It is synthesized in the cytoplasm of Escherichia coli which functions as a receptor for transport D-glucose. GBP binds glucose with high affinity. The binding mechanism is based on a hinge motion due to the protein conformational change. This change was utilized as an optical sensing mechanism by applying Fluorescence Resonance Energy Transfer (FRET). The wild-type GBP lacks cysteine in its structure, but by introducing a single cysteine at a specific site by site-directed mutagenesis, this ensured single-label attachment at specific sites with a fluorescent probe. The other sites were amino sites, which were labeled with second fluorophore. The near IR FRET pair, Alexa Fluor 680 (AF680) and Alexa Fluor 750(AF750), was utilized. The AF680 targeted the amine sites, which was the donor fluorophore, while the AF750 labeled the single cysteine site, which was the acceptor fluorophore. The sensing system strategy was based on the fluorescence changes of the probe as the protein undergoes a structural change upon binding. This biosensor had the ability to detect down to 10 uM concentrations of glucose. Next the probes were uploaded into red blood cells via hypo osmotic dialysis. The sensor responded to glucose while encapsulated with the red cells. These results showed the feasibility of an intracellular glucose biosensor.

  8. Tension-induced binding of semiflexible biopolymers

    CERN Document Server

    Benetatos, Panayotis; Zippelius, Annette

    2014-01-01

    We investigate theoretically the effect of polymer tension on the collective behavior of reversibly binding cross-links. For this purpose, we employ a model of two weakly bending wormlike chains aligned in parallel by a tensile force, with a sequence of inter-chain binding sites regularly spaced along the contours. Reversible cross-links attach and detach at the sites with an affinity controlled by a chemical potential. In a mean-field approach, we calculate the free energy of the system and find the emergence of a free-energy barrier which controls the reversible (un)binding. The tension affects the conformational entropy of the chains which competes with the binding energy of the cross-links. This competition gives rise to a sudden increase in the fraction of bound sites as the tension increases. We show that this transition is related to the cross-over between weak and strong localization of a directed polymer in a pinning potential. The cross-over to the strongly bound state can be interpreted as a mechan...

  9. Singular Value Decomposition and Ligand Binding Analysis

    Directory of Open Access Journals (Sweden)

    André Luiz Galo

    2013-01-01

    Full Text Available Singular values decomposition (SVD is one of the most important computations in linear algebra because of its vast application for data analysis. It is particularly useful for resolving problems involving least-squares minimization, the determination of matrix rank, and the solution of certain problems involving Euclidean norms. Such problems arise in the spectral analysis of ligand binding to macromolecule. Here, we present a spectral data analysis method using SVD (SVD analysis and nonlinear fitting to determine the binding characteristics of intercalating drugs to DNA. This methodology reduces noise and identifies distinct spectral species similar to traditional principal component analysis as well as fitting nonlinear binding parameters. We applied SVD analysis to investigate the interaction of actinomycin D and daunomycin with native DNA. This methodology does not require prior knowledge of ligand molar extinction coefficients (free and bound, which potentially limits binding analysis. Data are acquired simply by reconstructing the experimental data and by adjusting the product of deconvoluted matrices and the matrix of model coefficients determined by the Scatchard and McGee and von Hippel equation.

  10. Binding of cholera toxin to Giardia lamblia.

    OpenAIRE

    McCardell, B. A.; Madden, J M; Stanfield, J T; Tall, B D; Stephens, M. J.

    1987-01-01

    Binding of cholera toxin to Giardia lamblia was demonstrated by two slightly different methods: an immunofluorescence technique using antibody to cholera toxin and anti-rabbit immunoglobulin G conjugated to fluorescein isothiocyanate, and a one-step fluorescence method in which G. lamblia was incubated with the B subunit of cholera toxin conjugated to fluorescein isothiocyanate.

  11. The Double Bind: The next Generation

    Science.gov (United States)

    Malcom, Lindsey E.; Malcom, Shirley M.

    2011-01-01

    In this foreword, Shirley Malcom and Lindsey Malcom speak to the history and current status of women of color in science, technology, engineering, and mathematics (STEM) fields. As the author of the seminal report "The Double Bind: The Price of Being a Minority Woman in Science", Shirley Malcom is uniquely poised to give us an insightful…

  12. Factor VIIa binding and internalization in hepatocytes

    DEFF Research Database (Denmark)

    Hjortoe, G; Sorensen, B B; Petersen, L C

    2005-01-01

    The liver is believed to be the primary clearance organ for coagulation proteases, including factor VIIa (FVIIa). However, at present, clearance mechanisms for FVIIa in liver are unknown. To obtain information on the FVIIa clearance mechanism, we investigated the binding and internalization...

  13. Lipid Binding Proteins from Parasitic Platyhelmithes

    Directory of Open Access Journals (Sweden)

    Gabriela eAlvite

    2012-09-01

    Full Text Available Two main families of lipid binding proteins have been identified in parasitic Platyhelminthes: hydrophobic ligand binding proteins (HLBPs and fatty acid binding proteins (FABPs. Members of the former family of proteins are specific to the Cestoda class, while FABPs are conserved across a wide range of animal species. Because Platyhelminthes are unable to synthesise their own lipids, these lipid-binding proteins are important molecules in these organisms.HLBPs are a high molecular mass complex of proteins and lipids. They are composed of subunits of low molecular mass proteins and a wide array of lipid molecules ranging from CoA esters to cholesterol. These proteins are excretory-secretory molecules and are key serological tools for diagnosis of diseases caused by cestodes. FABPs are mainly intracellular proteins of low molecular weight. They are also vaccine candidates.Despite that the knowledge of their function is scarce, the differences in their molecular organisation, ligand preferences, intra/extracellular localisation, evolution, and phylogenetic distribution, suggest that platyhelminths HLBPs and FABPs should play different functions. FABPs might be involved in the removal of fatty acids from the inner surface of the cell membrane and in their subsequent targeting to specific cellular destinations. In contrast, HLBPs might be involved in fatty acid uptake from the host environment.

  14. CD36 binds oxidized low density lipoprotein (LDL) in a mechanism dependent upon fatty acid binding.

    Science.gov (United States)

    Jay, Anthony G; Chen, Alexander N; Paz, Miguel A; Hung, Justin P; Hamilton, James A

    2015-02-20

    The association of unesterified fatty acid (FA) with the scavenger receptor CD36 has been actively researched, with focuses on FA and oxidized low density lipoprotein (oxLDL) uptake. CD36 has been shown to bind FA, but this interaction has been poorly characterized to date. To gain new insights into the physiological relevance of binding of FA to CD36, we characterized FA binding to the ectodomain of CD36 by the biophysical method surface plasmon resonance. Five structurally distinct FAs (saturated, monounsaturated (cis and trans), polyunsaturated, and oxidized) were pulsed across surface plasmon resonance channels, generating association and dissociation binding curves. Except for the oxidized FA HODE, all FAs bound to CD36, with rapid association and dissociation kinetics similar to HSA. Next, to elucidate the role that each FA might play in CD36-mediated oxLDL uptake, we used a fluorescent oxLDL (Dii-oxLDL) live cell assay with confocal microscopy imaging. CD36-mediated uptake in serum-free medium was very low but greatly increased when serum was present. The addition of exogenous FA in serum-free medium increased oxLDL binding and uptake to levels found with serum and affected CD36 plasma membrane distribution. Binding/uptake of oxLDL was dependent upon the FA dose, except for docosahexaenoic acid, which exhibited binding to CD36 but did not activate the uptake of oxLDL. HODE also did not affect oxLDL uptake. High affinity FA binding to CD36 and the effects of each FA on oxLDL uptake have important implications for protein conformation, binding of other ligands, functional properties of CD36, and high plasma FA levels in obesity and type 2 diabetes.

  15. Retinoblastoma-binding protein 1 has an interdigitated double Tudor domain with DNA binding activity.

    Science.gov (United States)

    Gong, Weibin; Wang, Jinfeng; Perrett, Sarah; Feng, Yingang

    2014-02-21

    Retinoblastoma-binding protein 1 (RBBP1) is a tumor and leukemia suppressor that binds both methylated histone tails and DNA. Our previous studies indicated that RBBP1 possesses a Tudor domain, which cannot bind histone marks. In order to clarify the function of the Tudor domain, the solution structure of the RBBP1 Tudor domain was determined by NMR and is presented here. Although the proteins are unrelated, the RBBP1 Tudor domain forms an interdigitated double Tudor structure similar to the Tudor domain of JMJD2A, which is an epigenetic mark reader. This indicates the functional diversity of Tudor domains. The RBBP1 Tudor domain structure has a significant area of positively charged surface, which reveals a capability of the RBBP1 Tudor domain to bind nucleic acids. NMR titration and isothermal titration calorimetry experiments indicate that the RBBP1 Tudor domain binds both double- and single-stranded DNA with an affinity of 10-100 μM; no apparent DNA sequence specificity was detected. The DNA binding mode and key interaction residues were analyzed in detail based on a model structure of the Tudor domain-dsDNA complex, built by HADDOCK docking using the NMR data. Electrostatic interactions mediate the binding of the Tudor domain with DNA, which is consistent with NMR experiments performed at high salt concentration. The DNA-binding residues are conserved in Tudor domains of the RBBP1 protein family, resulting in conservation of the DNA-binding function in the RBBP1 Tudor domains. Our results provide further insights into the structure and function of RBBP1.

  16. Chromate Binding and Removal by the Molybdate-Binding Protein ModA.

    Science.gov (United States)

    Karpus, Jason; Bosscher, Michael; Ajiboye, Ifedayo; Zhang, Liang; He, Chuan

    2017-04-04

    Effective and cheap methods and techniques for the safe removal of hexavalent chromate from the environment are in increasingly high demand. High concentrations of hexavalent chromate have been shown to have numerous harmful effects on human biology. We show that the E. coli molybdate-binding protein ModA is a genetically encoded tool capable of removing chromate from aqueous solutions. Although previously reported to not bind chromate, we show that ModA binds chromate tightly and is capable of removing chromate to levels well below current US federal standards. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. STARD4 Membrane Interactions and Sterol Binding.

    Science.gov (United States)

    Iaea, David B; Dikiy, Igor; Kiburu, Irene; Eliezer, David; Maxfield, Frederick R

    2015-08-01

    The steroidogenic acute regulatory protein-related lipid transfer (START) domain family is defined by a conserved 210-amino acid sequence that folds into an α/β helix-grip structure. Members of this protein family bind a variety of ligands, including cholesterol, phospholipids, sphingolipids, and bile acids, with putative roles in nonvesicular lipid transport, metabolism, and cell signaling. Among the soluble START proteins, STARD4 is expressed in most tissues and has previously been shown to transfer sterol, but the molecular mechanisms of membrane interaction and sterol binding remain unclear. In this work, we use biochemical techniques to characterize regions of STARD4 and determine their role in membrane interaction and sterol binding. Our results show that STARD4 interacts with anionic membranes through a surface-exposed basic patch and that introducing a mutation (L124D) into the Omega-1 (Ω1) loop, which covers the sterol binding pocket, attenuates sterol transfer activity. To gain insight into the attenuating mechanism of the L124D mutation, we conducted structural and biophysical studies of wild-type and L124D STARD4. These studies show that the L124D mutation reduces the conformational flexibility of the protein, resulting in a diminished level of membrane interaction and sterol transfer. These studies also reveal that the C-terminal α-helix, and not the Ω1 loop, partitions into the membrane bilayer. On the basis of these observations, we propose a model of STARD4 membrane interaction and sterol binding and release that requires dynamic movement of both the Ω1 loop and membrane insertion of the C-terminal α-helix.

  18. Automatic Binding Time Analysis for a Typed Lambda-Calculus

    DEFF Research Database (Denmark)

    Nielson, Hanne Riis; Nielson, Flemming

    1988-01-01

    A binding time analysis imposes a distinction between the computations to be performed early (e.g. at compile-time) and those to be performed late (e.g. at run-time). For the lambda-calculus this distinction is formalized by a two-level lambda-calculus. The authors present an algorithm for static...... analysis of the binding times of a typed lambda-calculus with products, sums, lists and general recursive types. Given partial information about the binding times of some of the subexpressions it will complete that information such that (i) early bindings may be turned into late bindings but not vice versa......, (ii) the resulting two-level lambda-expression reflects our intuition about binding times, e.g. that early bindings are performed before late bindings, and (iii) as few changes as possible have been made compared with the initial binding information. The results can be applied in the implementation...

  19. Isothermal titration calorimetry: general formalism using binding polynomials.

    Science.gov (United States)

    Freire, Ernesto; Schön, Arne; Velazquez-Campoy, Adrian

    2009-01-01

    The theory of the binding polynomial constitutes a very powerful formalism by which many experimental biological systems involving ligand binding can be analyzed under a unified framework. The analysis of isothermal titration calorimetry (ITC) data for systems possessing more than one binding site has been cumbersome because it required the user to develop a binding model to fit the data. Furthermore, in many instances, different binding models give rise to identical binding isotherms, making it impossible to discriminate binding mechanisms using binding data alone. One of the main advantages of the binding polynomials is that experimental data can be analyzed by employing a general model-free methodology that provides essential information about the system behavior (e.g., whether there exists binding cooperativity, whether the cooperativity is positive or negative, and the magnitude of the cooperative energy). Data analysis utilizing binding polynomials yields a set of binding association constants and enthalpy values that conserve their validity after the correct model has been determined. In fact, once the correct model is validated, the binding polynomial parameters can be immediately translated into the model specific constants. In this chapter, we describe the general binding polynomial formalism and provide specific theoretical and experimental examples of its application to isothermal titration calorimetry.

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

    DEFF Research Database (Denmark)

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

    2015-01-01

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

  1. The inhibition of anti-DNA binding to DNA by nucleic acid binding polymers.

    Directory of Open Access Journals (Sweden)

    Nancy A Stearns

    Full Text Available Antibodies to DNA (anti-DNA are the serological hallmark of systemic lupus erythematosus (SLE and can mediate disease pathogenesis by the formation of immune complexes. Since blocking immune complex formation can attenuate disease manifestations, the effects of nucleic acid binding polymers (NABPs on anti-DNA binding in vitro were investigated. The compounds tested included polyamidoamine dendrimer, 1,4-diaminobutane core, generation 3.0 (PAMAM-G3, hexadimethrine bromide, and a β-cylodextrin-containing polycation. As shown with plasma from patients with SLE, NABPs can inhibit anti-DNA antibody binding in ELISA assays. The inhibition was specific since the NABPs did not affect binding to tetanus toxoid or the Sm protein, another lupus autoantigen. Furthermore, the polymers could displace antibody from preformed complexes. Together, these results indicate that NABPs can inhibit the formation of immune complexes and may represent a new approach to treatment.

  2. A new zinc binding fold underlines the versatility of zinc binding modules in protein evolution.

    Science.gov (United States)

    Sharpe, Belinda K; Matthews, Jacqueline M; Kwan, Ann H Y; Newton, Anthea; Gell, David A; Crossley, Merlin; Mackay, Joel P

    2002-05-01

    Many different zinc binding modules have been identified. Their abundance and variety suggests that the formation of zinc binding folds might be relatively common. We have determined the structure of CH1(1), a 27-residue peptide derived from the first cysteine/histidine-rich region (CH1) of CREB binding protein (CBP). This peptide forms a highly ordered zinc-dependent fold that is distinct from known folds. The structure differs from a subsequently determined structure of a larger region from the CH3 region of CBP, and the CH1(1) fold probably represents a nonphysiologically active form. Despite this, the fold is thermostable and tolerant to both multiple alanine mutations and changes in the zinc-ligand spacing. Our data support the idea that zinc binding domains may arise frequently. Additionally, such structures may prove useful as scaffolds for protein design, given their stability and robustness.

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

    Directory of Open Access Journals (Sweden)

    Bitter István

    2010-10-01

    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

  4. Studies on the biotin-binding site of avidin. Minimized fragments that bind biotin.

    OpenAIRE

    Hiller, Y; Bayer, E A; Wilchek, M

    1991-01-01

    The object of this study was to define minimized biotin-binding fragments, or 'prorecognition sites', of either the egg-white glycoprotein avidin or its bacterial analogue streptavidin. Because of the extreme stability to enzymic hydrolysis, fragments of avidin were prepared by chemical means and examined for their individual biotin-binding capacity. Treatment of avidin with hydroxylamine was shown to result in new cleavage sites in addition to the known Asn-Gly cleavage site (position 88-89 ...

  5. Cobalamin and its binding protein in rat milk

    DEFF Research Database (Denmark)

    Raaberg, Lasse; Nexø, Ebba; Poulsen, Steen Seier

    1989-01-01

    Cobalamin and its binding protein, haptocorrin, are present in rat milk throughout the lactation period. The concentration of cobalamin is approximately 0.3-times the concentration of the unsaturated binding protein. The concentration of the unsaturated cobalamin-binding protein varies between 18...... nmol l-1 and 16 nmol l-1. The binding protein has a Stokes radius of 2.49 nm when saturated with cobalamin and 2.61 nm when unsaturated. It binds cobalamin over a broad range of pH and is able to bind cobinamide also. With immunohistochemistry, we find haptocorrin immunoreactivity in the mammary glands...

  6. Is there a link between selectivity and binding thermodynamics profiles?

    Science.gov (United States)

    Tarcsay, Ákos; Keserű, György M

    2015-01-01

    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.

  7. The biotin repressor: thermodynamic coupling of corepressor binding, protein assembly, and sequence-specific DNA binding.

    Science.gov (United States)

    Streaker, Emily D; Gupta, Aditi; Beckett, Dorothy

    2002-12-03

    The Escherichia coli biotin repressor, an allosteric transcriptional regulator, is activated for binding to the biotin operator by the small molecule biotinyl-5'-AMP. Results of combined thermodynamic, kinetic, and structural studies of the protein have revealed that corepressor binding results in disorder to order transitions in the protein monomer that facilitate tighter dimerization. The enhanced stability of the dimer leads to stabilization of the resulting biotin repressor-biotin operator complex. It is not clear, however, that the allosteric response in the system is transmitted solely through the protein-protein interface. In this work, the allosteric mechanism has been quantitatively probed by measuring the biotin operator binding and dimerization properties of three biotin repressor species: the apo or unliganded form, the biotin-bound form, and the holo or bio-5'-AMP-bound form. Comparisons of the pairwise differences in the bioO binding and dimerization energetics for the apo and holo species reveal that the enhanced DNA binding energetics resulting from adenylate binding track closely with the enhanced assembly energetics. However, when the results for repressor pairs that include the biotin-bound species are compared, no such equivalence is observed.

  8. CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins.

    Science.gov (United States)

    Khorshid, Mohsen; Rodak, Christoph; Zavolan, Mihaela

    2011-01-01

    The stability, localization and translation rate of mRNAs are regulated by a multitude of RNA-binding proteins (RBPs) that find their targets directly or with the help of guide RNAs. Among the experimental methods for mapping RBP binding sites, cross-linking and immunoprecipitation (CLIP) coupled with deep sequencing provides transcriptome-wide coverage as well as high resolution. However, partly due to their vast volume, the data that were so far generated in CLIP experiments have not been put in a form that enables fast and interactive exploration of binding sites. To address this need, we have developed the CLIPZ database and analysis environment. Binding site data for RBPs such as Argonaute 1-4, Insulin-like growth factor II mRNA-binding protein 1-3, TNRC6 proteins A-C, Pumilio 2, Quaking and Polypyrimidine tract binding protein can be visualized at the level of the genome and of individual transcripts. Individual users can upload their own sequence data sets while being able to limit the access to these data to specific users, and analyses of the public and private data sets can be performed interactively. CLIPZ, available at http://www.clipz.unibas.ch, aims to provide an open access repository of information for post-transcriptional regulatory elements.

  9. Sugar-Binding Profiles of Chitin-Binding Lectins from the Hevein Family: A Comprehensive Study

    Directory of Open Access Journals (Sweden)

    Yoko Itakura

    2017-05-01

    Full Text Available Chitin-binding lectins form the hevein family in plants, which are defined by the presence of single or multiple structurally conserved GlcNAc (N-acetylglucosamine-binding domains. Although they have been used as probes for chito-oligosaccharides, their detailed specificities remain to be investigated. In this study, we analyzed six chitin-binding lectins, DSA, LEL, PWM, STL, UDA, and WGA, by quantitative frontal affinity chromatography. Some novel features were evident: WGA showed almost comparable affinity for pyridylaminated chitotriose and chitotetraose, while LEL and UDA showed much weaker affinity, and DSA, PWM, and STL had no substantial affinity for the former. WGA showed selective affinity for hybrid-type N-glycans harboring a bisecting GlcNAc residue. UDA showed extensive binding to high-mannose type N-glycans, with affinity increasing with the number of Man residues. DSA showed the highest affinity for highly branched N-glycans consisting of type II LacNAc (N-acetyllactosamine. Further, multivalent features of these lectins were investigated by using glycoconjugate and lectin microarrays. The lectins showed substantial binding to immobilized LacNAc as well as chito-oligosaccharides, although the extents to which they bound varied among them. WGA showed strong binding to heavily sialylated glycoproteins. The above observations will help interpret lectin-glycoprotein interactions in histochemical studies and glyco-biomarker investigations.

  10. Ligand Binding and Conformational Changes in the Purine-Binding Riboswitch Aptamer Domains

    Science.gov (United States)

    Noeske, Jonas; Buck, Janina; Wöhnert, Jens; Schwalbe, Harald

    Riboswitches are highly structured mRNA elements that regulate gene expression upon specific binding of small metabolite molecules. The purine-binding riboswitches bind different purine ligands by forming both canonical Watson—Crick and non-canonical intermolecular base pairs, involving a variety of hydrogen bonds between the riboswitch aptamer domain and the purine ligand. Here, we summarize work on the ligand binding modes of both purine-binding aptamer domains, their con-formational characteristics in the free and ligand-bound forms, and their ligand-induced folding. The adenine- and guanine-binding riboswitch aptamer domains display different conformations in their free forms, despite nearly identical nucleotide loop sequences that form a loop—loop interaction in the ligand-bound forms. Interestingly, the stability of helix II is crucial for the formation of the loop—loop interaction in the free form. A more stable helix II in the guanine riboswitch leads to a preformed loop—loop interaction in its free form. In contrast, a less stable helix II in the adenine riboswitch results in a lack of this loop—loop interaction in the absence of ligand and divalent cations.

  11. Fucosyl neoglycoprotein binds to mouse epididymal spermatozoa and inhibits sperm binding to the egg zona pellucida.

    Science.gov (United States)

    Oh, Y S; Ahn, H S; Gye, M C

    2013-12-01

    Glycan epitopes of cellular glycoconjugates act as versatile biochemical signals, and this sugar coding plays an important role in cell-to-cell recognition processes. In this study, our aims were to determine the distribution of sperm receptors with activity for fucosyl- and galactosyl glycans and to address whether monosugar neoglycoproteins functionally mimic the binding between zona pellucida (ZP) glycoproteins and spermatozoa. In mouse epididymal spermatozoa with intact acrosomes, fucopyranosyl bovine serum albumin (BSA-Fuc) bound to the segment of the acrosome, the equatorial segment, and the postacrosome region of the sperm head. Galactosyl BSA (BSA-Gal) binding activity was similar to that of BSA-Fuc, but was weaker. In acrosome-reacted spermatozoa treated with the Ca(2+) ionophore A23187, BSA-zuc binding was lost in the apical segment of the acrosome but remained in the equatorial segment and postacrosome regions. BSA-Gal binding to the equatorial region was increased. In the presence of 2.5 μg ml(-1) BSA-Fuc, in vitro sperm-ZP binding was significantly decreased, indicating that fucosyl BSA functionally mimics ZP glycoproteins during sperm-egg ZP interactions. At the same concentration, BSA-Gal was not effective. Fucosyl BSA that efficiently inhibited the sperm-ZP binding can mimic the ZP glycoconjugate and has potential for use as a sperm fertility control agent in mouse.

  12. Being a binding site: characterizing residue composition of binding sites on proteins.

    Science.gov (United States)

    Iván, Gábor; Szabadka, Zoltán; Grolmusz, Vince

    2007-12-30

    The Protein Data Bank contains the description of more than 45,000 three-dimensional protein and nucleic-acid structures today. Started to exist as the computer-readable depository of crystallographic data complementing printed articles, the proper interpretation of the content of the individual files in the PDB still frequently needs the detailed information found in the citing publication. This fact implies that the fully automatic processing of the whole PDB is a very hard task. We first cleaned and re-structured the PDB data, then analyzed the residue composition of the binding sites in the whole PDB for frequency and for hidden association rules. Main results of the paper: (i) the cleaning and repairing algorithm (ii) redundancy elimination from the data (iii) application of association rule mining to the cleaned non-redundant data set. We have found numerous significant relations of the residue-composition of the ligand binding sites on protein surfaces, summarized in two figures. One of the classical data-mining methods for exploring implication-rules, the association-rule mining, is capable to find previously unknown residue-set preferences of bind ligands on protein surfaces. Since protein-ligand binding is a key step in enzymatic mechanisms and in drug discovery, these uncovered preferences in the study of more than 19,500 binding sites may help in identifying new binding protein-ligand pairs.

  13. Essential mechanisms in the triton binding

    Energy Technology Data Exchange (ETDEWEB)

    Brandenburg, R.A.; Chulick, G.S.; Machleidt, R.; Picklesimer, A.; Thaler, R.M.

    1988-03-01

    The recent successful prediction of the triton binding energy, E/sub t/, with the static Bonn potential is examined. Modified versions of the potential are introduced to isolate separately the effects of the deuteron D-state admixture and the /sup 1/S/sub 0/ scattering length on E/sub t/. Within this model study we find a monotonic relation between E/sub t/ and the /sup 1/S/sub 0/ scattering length and a strict linear dependence of E/sub t/ on the D-state admixture, in accordance with general well-known trends and earlier separable-potential model studies. The mechanism through which the weaker tensor force (lower D-state admixture) leads to a stronger binding of the triton is investigated by the introduction and study of effective energy-dependent central potentials

  14. Autologous antibodies that bind neuroblastoma cells.

    Science.gov (United States)

    Sun, Yujing; Sholler, Giselle S; Shukla, Girja S; Pero, Stephanie C; Carman, Chelsea L; Zhao, Ping; Krag, David N

    2015-11-01

    Antibody therapy of neuroblastoma is promising and our goal is to derive antibodies from patients with neuroblastoma for developing new therapeutic antibodies. The feasibility of using residual bone marrow obtained for clinical indications as a source of tumor cells and a source of antibodies was assessed. From marrow samples, neuroblastoma cells were recovered, grown in cell culture and also implanted into mice to create xenografts. Mononuclear cells from the marrow were used as a source to generate phage display antibody libraries and also hybridomas. Growth of neuroblastoma patient cells was possible both in vitro and as xenografts. Antibodies from the phage libraries and from the monoclonal hybridomas bound autologous neuroblastoma cells with some selectivity. It appears feasible to recover neuroblastoma cells from residual marrow specimens and to generate human antibodies that bind autologous neuroblastoma cells. Expansion of this approach is underway to collect more specimens, optimize methods to generate antibodies, and to evaluate the bioactivity of neuroblastoma-binding antibodies.

  15. Lectin binding in normal donkey eyeball

    Directory of Open Access Journals (Sweden)

    Khaled Aly

    2013-10-01

    Full Text Available In the present study, the distribution of various sugar residues in the eyeball tissues of sexually mature donkey was examined by employing fluorescein isothiocyanate-conjugated lectins. Our results revealed the presence of mannose (labeled by lectins ConA, galactose (labeled by PNA, GSAI, ECA, GalNAc (labeled by SBA, VVA, and GlcNAc (labeled by WGA residues in the donkey ocular tissues. The epithelium and stroma of the ocular tissues were labeled with mannose (ConA and GlcNAc (WGA binding lectins. Binding sites for WGA and PNA to the rod and cone cells of the retina were evident. The lectins Con A, WGA and GSAI are bound strongly to the endothelium of blood vessels and to smooth muscle cells of the iris. In conclusion, the findings of the present study clearly indicate that the donkey eyeball contains a wide range of glycoconjugates (bearing mannosyl, galactosyl and glucosly residues, and it lacks fucosyl residues.

  16. K- nuclear states: Binding energies and widths

    Science.gov (United States)

    Hrtánková, J.; Mareš, J.

    2017-07-01

    K- optical potentials relevant to calculations of K- nuclear quasibound states were developed within several chiral meson-baryon coupled-channels interaction models. The applied models yield quite different K- binding energies and widths. Then the K- multinucleon interactions were incorporated by a phenomenological optical potential fitted recently to kaonic atom data. Though the applied K- interaction models differ significantly in the K-N subthreshold region, our self-consistent calculations of kaonic nuclei across the periodic table lead to conclusions valid quite generally. Due to K- multinucleon absorption in the nuclear medium, the calculated widths of K- nuclear states are sizable, ΓK-≥90 MeV, and exceed substantially their binding energies in all considered nuclei.

  17. Comparison of Transcription Factor Binding Site Models

    KAUST Repository

    Bhuyan, Sharifulislam

    2012-05-01

    Modeling of transcription factor binding sites (TFBSs) and TFBS prediction on genomic sequences are important steps to elucidate transcription regulatory mechanism. Dependency of transcription regulation on a great number of factors such as chemical specificity, molecular structure, genomic and epigenetic characteristics, long distance interaction, makes this a challenging problem. Different experimental procedures generate evidence that DNA-binding domains of transcription factors show considerable DNA sequence specificity. Probabilistic modeling of TFBSs has been moderately successful in identifying patterns from a family of sequences. In this study, we compare performances of different probabilistic models and try to estimate their efficacy over experimental TFBSs data. We build a pipeline to calculate sensitivity and specificity from aligned TFBS sequences for several probabilistic models, such as Markov chains, hidden Markov models, Bayesian networks. Our work, containing relevant statistics and evaluation for the models, can help researchers to choose the most appropriate model for the problem at hand.

  18. Quantifying drug-protein binding in vivo.

    Energy Technology Data Exchange (ETDEWEB)

    Buchholz, B; Bench, G; Keating III, G; Palmblad, M; Vogel, J; Grant, P G; Hillegonds, D

    2004-02-17

    Accelerator mass spectrometry (AMS) provides precise quantitation of isotope labeled compounds that are bound to biological macromolecules such as DNA or proteins. The sensitivity is high enough to allow for sub-pharmacological (''micro-'') dosing to determine macromolecular targets without inducing toxicities or altering the system under study, whether it is healthy or diseased. We demonstrated an application of AMS in quantifying the physiologic effects of one dosed chemical compound upon the binding level of another compound in vivo at sub-toxic doses [4].We are using tissues left from this study to develop protocols for quantifying specific binding to isolated and identified proteins. We also developed a new technique to quantify nanogram to milligram amounts of isolated protein at precisions that are comparable to those for quantifying the bound compound by AMS.

  19. Causal binding of actions to their effects.

    Science.gov (United States)

    Buehner, Marc J; Humphreys, Gruffydd R

    2009-10-01

    According to widely held views in cognitive science harking back to David Hume, causality cannot be perceived directly, but instead is inferred from patterns of sensory experience, and the quality of these inferences is determined by perceivable quantities such as contingency and contiguity. We report results that suggest a reversal of Hume's conjecture: People's sense of time is warped by the experience of causality. In a stimulus-anticipation task, participants' response behavior reflected a shortened experience of time in the case of target stimuli participants themselves had generated, relative to equidistant, equally predictable stimuli they had not caused. These findings suggest that causality in the mind leads to temporal binding of cause and effect, and extend and generalize beyond earlier claims of intentional binding between action and outcome.

  20. Binding of ampholine to transfer RNA.

    Science.gov (United States)

    Galante, E; Caravaggio, T; Righetti, P G

    1976-09-06

    The melting temperature of isoaccepting tRNAfMet is affected by Ampholine. The plot of Tm versus the logarithm of Ampholine concentration shows clearly an increasing effect of Ampholine when the pH changes from 7.4 to 4.2. This result is interpreted as binding of Ampholine to the nucleic acid. The effects of Ampholine have been compared with those of soidum, magnesium and tetraethylene pentamine. Ampholine carrier ampholytes at pH 4.2 bind to tRNA with the same affinity as magnesium; at higher pH values they are less active. An hypothesis for the mechanism of action of Ampholine on nucleic acids during isoelectric focusing is proposed.

  1. Insulin-induced lipid binding to hemoglobin

    Directory of Open Access Journals (Sweden)

    VESNA NIKETIC

    2003-01-01

    Full Text Available Under hypoglycemic conditions, concomitant hyperinsulinism causes an apparent modification of hemoglobin (Hb which is manifested by its aggregation (Niketi} et al., Clin. Chim. Acta 197 (1991 47. In the present work the causes and mechanisms underlying this Hb modification were studied. Hemoglobin isolated from normal erythrocytes incubated with insulin was analyzed by applying 31P-spectrometry and lipid extraction and analysis. To study the dynamics of the plasma membrane during hyperinsulinism, a fluorescent lipid-analog was applied. In the presence of insulin, phosphatidylserine (PS, phosphatidylethanolamine (PE and cholesterol were found to bind to Hb. Lipid binding resulted in Hb aggregation, a condition that can be reproduced when phospholipids are incubated with Hb in vitro. Using a fluorescent lipid-analog, it was also shown that exposing erythrocytes to supraphysiological concentrations of insulin in vitro resulted in the internalization of lipids. The results presented in this work may have relevance to cases of diabetes mellitus and hypoglycemia.

  2. Engineering knottins as novel binding agents.

    Science.gov (United States)

    Moore, Sarah J; Cochran, Jennifer R

    2012-01-01

    Cystine-knot miniproteins, also known as knottins, contain a conserved core of three tightly woven disulfide bonds which impart extraordinary thermal and proteolytic stability. Interspersed between their conserved cysteine residues are constrained loops that possess high levels of sequence diversity among knottin family members. Together these attributes make knottins promising molecular scaffolds for protein engineering and translational applications. While naturally occurring knottins have shown potential as both diagnostic agents and therapeutics, protein engineering is playing an important and increasing role in creating designer molecules that bind to a myriad of biomedical targets. Toward this goal, rational and combinatorial approaches have been used to engineer knottins with novel molecular recognition properties. Here, methods are described for creating and screening knottin libraries using yeast surface display and fluorescence-activated cell sorting. Protocols are also provided for producing knottins by synthetic and recombinant methods, and for measuring the binding affinity of knottins to target proteins expressed on the cell surface.

  3. Tight-binding treatment of conjugated polymers

    DEFF Research Database (Denmark)

    Lynge, Thomas Bastholm

    This PhD thesis concerns conjugated polymers which constitute a constantly growing research area. Today, among other things, conjugated polymers play a role in plastic based solar cells, photodetectors and light emitting diodes, and even today such plastic-based components constitute an alternative...... of tomorrow. This thesis specifically treats the three conjugated polymers trans-polyacetylene (tPA), poly(para-phenylene) (PPP) and poly(para-phe\\-nylene vinylene) (PPV). The present results, which are derived within the tight-binding model, are divided into two parts. In one part, analytic results...... are derived for the optical properties of the polymers expressed in terms of the optical susceptibility both in the presence and in the absence of a static electric field. In the other part, the cumputationally efficient Density Functional-based Tight-Binding (DFTB) model is applied to the description...

  4. Polypeptide binding properties of the chaperone calreticulin

    DEFF Research Database (Denmark)

    Jørgensen, C S; Heegaard, N H; Holm, A

    2000-01-01

    to be elucidated. We have investigated the interactions of human calreticulin with denatured ovalbumin, proteolytic digests of ovalbumin, and different available peptides by solid phase assays, size-exclusion chromatography, capillary electrophoresis, and MS. The results show that calreticulin interacts better...... with unfolded ovalbumin than with native ovalbumin, that calreticulin strongly binds components in proteolytic digests of denatured ovalbumin, and that calreticulin interacts strongly with certain synthetic peptides....

  5. Perceptual-binding and persistent surface segregation

    OpenAIRE

    2004-01-01

    Visual input is segregated in the brain into subsystems that process different attributes such as motion and color. At the same time, visual information is perceptually segregated into objects and surfaces. Here we demonstrate that perceptual segregation of visual entities based on a transparency cue precedes and affects perceptual binding of attributes. Adding an irrelevant transparency cue paradoxically improved the pairing of color and motion for rapidly alternating surfaces. Subsequent ex...

  6. Brain hyaluronan binding protein inhibits tumor growth

    Institute of Scientific and Technical Information of China (English)

    高锋; 曹曼林; 王蕾

    2004-01-01

    Background Great efforts have been made to search for the angiogenic inhibitors in avascular tissues. Several proteins isolated from cartilage have been proved to have anti-angiogenic or anti-tumour effects. Because cartilage contains a great amount of hyaluronic acid (HA) oligosaccharides and abundant HA binding proteins (HABP), therefore, we speculated that HABP might be one of the factors regulating vascularization in cartilage or anti-angiogenesis in tumours. The purpose of this research was to evaluale the effects of hyaluronan binding protein on inhibiting tumour growth both in vivo and vitro. Methods A unique protein termed human brain hyaluronan (HA) binding protein (b-HABP) was cloned from human brain cDNA library. MDA-435 human breast cancer cell line was chosen as a transfectant. The in vitro underlying mechanisms were investigated by determining the possibilities of MDA-435/b-HABP colony formation on soft agar, the effects of the transfectant on the proliferation of endothelial cells and the expression levels of caspase 3 and FasL from MDA-435/b-HABP. The in vivo study included tumour growth on the chorioallantoic membrane (CAM) of chicken embryos and nude mice. Results Colony formation assay revealed that the colonies formed by MDA-435/b-HABP were greatly reduced compared to mock transfectants. The conditioned media from MDA-435/b-HABP inhibited the growth of endothelial cells in culture. Caspase 3 and FasL expressions were induced by MDA-435/b-HABP. The size of tumours of MDA-435/b-HABP in both CAM and nude mice was much smaller than that of MDA-435 alone. Conclusions Human brain hyaluronan binding protein (b-HABP) may represent a new kind of naturally existing anti-tumour substance. This brain-derived glycoprotein may block tumour growth by inducing apoptosis of cancer cells or by decreasing angiogenesis in tumour tissue via inhibiting proliferation of endothelial cells.

  7. Oxygen binding to partially nitrosylated hemoglobin.

    Science.gov (United States)

    Fago, Angela; Crumbliss, Alvin L; Hendrich, Michael P; Pearce, Linda L; Peterson, Jim; Henkens, Robert; Bonaventura, Celia

    2013-09-01

    Reactions of nitric oxide (NO) with hemoglobin (Hb) are important elements in protection against nitrosative damage. NO in the vasculature is depleted by the oxidative reaction with oxy Hb or by binding to deoxy Hb to generate partially nitrosylated Hb (Hb-NO). Many aspects of the formation and persistence of Hb-NO are yet to be clarified. In this study, we used a combination of EPR and visible absorption spectroscopy to investigate the interactions of partially nitrosylated Hb with O2. Partially nitrosylated Hb samples had predominantly hexacoordinate NO-heme geometry and resisted oxidation when exposed to O2 in the absence of anionic allosteric effectors. Faster oxidation occurred in the presence of 2,3-diphosphoglycerate (DPG) or inositol hexaphosphate (IHP), where the NO-heme derivatives had higher levels of pentacoordinate heme geometry. The anion-dependence of the NO-heme geometry also affected O2 binding equilibria. O2-binding curves of partially nitrosylated Hb in the absence of anions were left-shifted at low saturations, indicating destabilization of the low O2 affinity T-state of the Hb by increasing percentages of NO-heme, much as occurs with increasing levels of CO-heme. Samples containing IHP showed small decreases in O2 affinity, indicating shifts toward the low-affinity T-state and formation of inert α-NO/β-met tetramers. Most remarkably, O2-equilibria in the presence of the physiological effector DPG were essentially unchanged by up to 30% NO-heme in the samples. As will be discussed, under physiological conditions the interactions of Hb with NO provide protection against nitrosative damage without impairing O2 transport by Hb's unoccupied heme sites. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins. Copyright © 2013 Elsevier B.V. All rights reserved.

  8. Simultaneous optimal experimental design for in vitro binding parameter estimation.

    Science.gov (United States)

    Ernest, C Steven; Karlsson, Mats O; Hooker, Andrew C

    2013-10-01

    Simultaneous optimization of in vitro ligand binding studies using an optimal design software package that can incorporate multiple design variables through non-linear mixed effect models and provide a general optimized design regardless of the binding site capacity and relative binding rates for a two binding system. Experimental design optimization was employed with D- and ED-optimality using PopED 2.8 including commonly encountered factors during experimentation (residual error, between experiment variability and non-specific binding) for in vitro ligand binding experiments: association, dissociation, equilibrium and non-specific binding experiments. Moreover, a method for optimizing several design parameters (ligand concentrations, measurement times and total number of samples) was examined. With changes in relative binding site density and relative binding rates, different measurement times and ligand concentrations were needed to provide precise estimation of binding parameters. However, using optimized design variables, significant reductions in number of samples provided as good or better precision of the parameter estimates compared to the original extensive sampling design. Employing ED-optimality led to a general experimental design regardless of the relative binding site density and relative binding rates. Precision of the parameter estimates were as good as the extensive sampling design for most parameters and better for the poorly estimated parameters. Optimized designs for in vitro ligand binding studies provided robust parameter estimation while allowing more efficient and cost effective experimentation by reducing the measurement times and separate ligand concentrations required and in some cases, the total number of samples.

  9. SUMO-1 possesses DNA binding activity

    Directory of Open Access Journals (Sweden)

    Wieruszeski Jean-Michel

    2010-05-01

    Full Text Available Abstract Background Conjugation of small ubiquitin-related modifiers (SUMOs is a frequent post-translational modification of proteins. SUMOs can also temporally associate with protein-targets via SUMO binding motifs (SBMs. Protein sumoylation has been identified as an important regulatory mechanism especially in the regulation of transcription and the maintenance of genome stability. The precise molecular mechanisms by which SUMO conjugation and association act are, however, not understood. Findings Using NMR spectroscopy and protein-DNA cross-linking experiments, we demonstrate here that SUMO-1 can specifically interact with dsDNA in a sequence-independent fashion. We also show that SUMO-1 binding to DNA can compete with other protein-DNA interactions at the example of the regulatory domain of Thymine-DNA Glycosylase and, based on these competition studies, estimate the DNA binding constant of SUMO1 in the range 1 mM. Conclusion This finding provides an important insight into how SUMO-1 might exert its activity. SUMO-1 might play a general role in destabilizing DNA bound protein complexes thereby operating in a bottle-opener way of fashion, explaining its pivotal role in regulating the activity of many central transcription and DNA repair complexes.

  10. Mesic retardation and the triton binding energy

    Energy Technology Data Exchange (ETDEWEB)

    Brandenburg, R.A.; Chulick, G.S.; Machleidt, R.; Picklesimer, A.; Thaler, R.M.

    1988-09-01

    The relationship between the apparently successful result for the triton binding energy obtained from the static Bonn potentials and the underlying meson theory is investigated. The triton binding is shown to be strongly dependent upon mesic retardation and associated explicit energy dependences in the meson theory of the nucleon-nucleon interaction. Because it is a much closer representation of the full interaction than are its energy-independent counterparts, the energy-dependent one-boson-exchange potential representation of the Bonn interaction is used to gauge the implications of the full interaction. This one-boson-exchange potential, with or without corrections to adapt it for use in conjunction with nonrelativistic (Schroedinger) three-body equations, predicts a triton binding of only approx.6.7 MeV, as compared to a result of about 8.4 MeV obtained with the energy-independent potentials. This difference is traced to the combination of the explicit energy-dependence and the implicit energy dependence introduced through the tensor force, especially in the /sup 3/S/sub 1/ partial wave. This provides a new perspective on the success of the static Bonn potentials relative to other realistic potentials and relative to the meson-theoretic framework. Implications, especially with regard to the need for investigations of consistent three-body forces, are discussed.

  11. Mesic retardation and the triton binding energy

    Science.gov (United States)

    Brandenburg, R. A.; Chulick, G. S.; Machleidt, R.; Picklesimer, A.; Thaler, R. M.

    1988-09-01

    The relationship between the apparently successful result for the triton binding energy obtained from the static Bonn potentials and the underlying meson theory is investigated. The triton binding is shown to be strongly dependent upon mesic retardation and associated explicit energy dependences in the meson theory of the nucleon-nucleon interaction. Because it is a much closer representation of the full interaction than are its energy-independent counterparts, the energy-dependent one-boson-exchange potential representation of the Bonn interaction is used to gauge the implications of the full interaction. This one-boson-exchange potential, with or without corrections to adapt it for use in conjunction with nonrelativistic (Schrödinger) three-body equations, predicts a triton binding of only ~6.7 MeV, as compared to a result of about 8.4 MeV obtained with the energy-independent potentials. This difference is traced to the combination of the explicit energy-dependence and the implicit energy dependence introduced through the tensor force, especially in the 3S1 partial wave. This provides a new perspective on the success of the static Bonn potentials relative to other realistic potentials and relative to the meson-theoretic framework. Implications, especially with regard to the need for investigations of consistent three-body forces, are discussed.

  12. Binding Energy and Equilibrium of Compact Objects

    Directory of Open Access Journals (Sweden)

    Germano M.

    2014-04-01

    Full Text Available The theoretical analysis of the existence of a limit mass for compact astronomic ob- jects requires the solution of the Einstein’s equations of g eneral relativity together with an appropriate equation of state. Analytical solutions exi st in some special cases like the spherically symmetric static object without energy sou rces that is here considered. Solutions, i.e. the spacetime metrics, can have a singular m athematical form (the so called Schwarzschild metric due to Hilbert or a nonsingula r form (original work of Schwarzschild. The former predicts a limit mass and, conse quently, the existence of black holes above this limit. Here it is shown that, the origi nal Schwarzschild met- ric permits compact objects, without mass limit, having rea sonable values for central density and pressure. The lack of a limit mass is also demonst rated analytically just imposing reasonable conditions on the energy-matter densi ty, of positivity and decreas- ing with radius. Finally the ratio between proper mass and to tal mass tends to 2 for high values of mass so that the binding energy reaches the lim it m (total mass seen by a distant observer. As it is known the negative binding energ y reduces the gravitational mass of the object; the limit of m for the binding energy provides a mechanism for stable equilibrium of any amount of mass to contrast the gravitatio nal collapse.

  13. Studies on the biotin-binding site of avidin. Minimized fragments that bind biotin.

    Science.gov (United States)

    Hiller, Y; Bayer, E A; Wilchek, M

    1991-09-01

    The object of this study was to define minimized biotin-binding fragments, or 'prorecognition sites', of either the egg-white glycoprotein avidin or its bacterial analogue streptavidin. Because of the extreme stability to enzymic hydrolysis, fragments of avidin were prepared by chemical means and examined for their individual biotin-binding capacity. Treatment of avidin with hydroxylamine was shown to result in new cleavage sites in addition to the known Asn-Gly cleavage site (position 88-89 in avidin). Notably, the Asn-Glu and Asp-Lys peptide bonds (positions 42-43 and 57-58 respectively) were readily cleaved; in addition, lesser levels of hydrolysis of the Gln-Pro (61-62) and Asn-Asp (12-13 and 104-105) bonds could be detected. The smallest biotin-binding peptide fragment, derived from hydroxylamine cleavage of either native or non-glycosylated avidin, was identified to comprise residues 1-42. CNBr cleavage resulted in a 78-amino acid-residue fragment (residues 19-96) that still retained activity. The data ascribe an important biotin-binding function to the overlapping region (residues 19-42) of avidin, which bears the single tyrosine moiety. This contention was corroborated by synthesizing a tridecapeptide corresponding to residues 26-38 of avidin; this peptide was shown to recognize biotin. Streptavidin was not susceptible to either enzymic or chemical cleavage methods used in this work. The approach taken in this study enabled the experimental distinction between the chemical and structural elements of the binding site. The capacity to assign biotin-binding activity to the tyrosine-containing domain of avidin underscores its primary chemical contribution to the binding of biotin by avidin.

  14. STUDY OF ESTROGEN BINDING SITE ON HUMAN EJACULATED SPERMATOZOA

    Institute of Scientific and Technical Information of China (English)

    CHUJin-Shong; WANGYi-Fei

    1989-01-01

    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

  15. Molecular modelling and competition binding study of Br-noscapine and colchicine provide insight into noscapinoid-tubulin binding site.

    Science.gov (United States)

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

    2011-06-01

    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.

  16. Quantitative analysis of pheromone-binding protein specificity

    OpenAIRE

    Katti, S.; Lokhande, N.; D González; Cassill, A.; Renthal, R

    2012-01-01

    Many pheromones have very low water solubility, posing experimental difficulties for quantitative binding measurements. A new method is presented for determining thermodynamically valid dissociation constants for ligands binding to pheromone-binding proteins (OBPs), using β-cyclodextrin as a solubilizer and transfer agent. The method is applied to LUSH, a Drosophila OBP that binds the pheromone 11-cis vaccenyl acetate (cVA). Refolding of LUSH expressed in E. coli was assessed by measuring N-p...

  17. Enhanced human receptor binding by H5 haemagglutinins

    OpenAIRE

    Xiong, Xiaoli; Xiao, Haixia; Martin, Stephen R.; Coombs, Peter J.; Liu, Junfeng; Collins, Patrick J.; Vachieri, Sebastien G.; Walker, Philip A.; Lin, Yi Pu; McCauley, John W.; Gamblin, Steven J.; John J Skehel

    2014-01-01

    Mutant H5N1 influenza viruses have been isolated from humans that have increased human receptor avidity. We have compared the receptor binding properties of these mutants with those of wild-type viruses, and determined the structures of their haemagglutinins in complex with receptor analogues. Mutants from Vietnam bind tighter to human receptor by acquiring basic residues near the receptor binding site. They bind more weakly to avian receptor because they lack specific interactions between As...

  18. A structural classification of substrate-binding proteins

    NARCIS (Netherlands)

    Berntsson, Ronnie P. -A.; Smits, Sander H. J.; Schmitt, Lutz; Slotboom, Dirk-Jan; Poolman, Bert

    2010-01-01

    Substrate-binding proteins (SBP) are associated with a wide variety of protein complexes. The proteins are part of ATP-binding cassette transporters for substrate uptake, ion gradient driven transporters, DNA-binding proteins, as well as channels and receptors from both pro-and eukaryotes. A wealth

  19. The binding interactions of imidacloprid with earthworm fibrinolytic enzyme

    Science.gov (United States)

    Wang, Yan-Qing; Zhang, Hong-Mei; Chen, Tao

    2014-08-01

    In this paper, several studies were conducted to elucidate the binding mechanism of earthworm fibrinolytic enzyme (EFE) with imidocloprid (IMI) by using theoretical calculation, fluorescence, UV-vis, circular dichroism spectroscopy and an enzymatic inhibition assay. The spectral data showed that the binding interactions existed between IMI and EFE. The binding constants, binding site, thermodynamic parameters and binding forces were analyzed in detail. The results indicate a single class of binding sites for IMI in EFE and that this binding interaction is a spontaneous process with the estimated enthalpy and entropy changes being 2.195 kJ mol-1 and 94.480 J mol-1 K-1, respectively. A single class of binding site existed for IMI in EFE. The tertiary or secondary structure of EFE was partly destroyed by IMI. The visualized binding details were also exhibited by the theoretical calculation and the results indicated that the interaction between IMI and Phe (Tyr, or Trp) or EFE occurred. Combining the experimental data with the theoretical calculation data, we showed that the binding forces between IMI and EFE were mainly hydrophobic force accompanied by hydrogen binding, and π-π stacking. In addition, IMI did not obviously influence the activity of EFE. In a word, the above analysis offered insights into the binding mechanism of IMI with EFE and could provide some important information for the molecular toxicity of IMI for earthworms.

  20. Biomimetic supramolecular metallohosts for binding and activation of dioxygen

    NARCIS (Netherlands)

    Sprakel, Vera Stefanie Irene

    2004-01-01

    Host-guest chemistry involves the binding of a specific substrate in a receptor via molecular recognition based on supramolecular interactions. Metal-containing derivatives of receptors for the selective supramolecular binding of dihydroxybenzene substrates, which receptors model oxygen binding enz

  1. Binding of disodium cromoglycate to human serum albumin

    Science.gov (United States)

    Ochoa de Aspuru, Eduardo; Zatón, Ana M. L.

    1998-07-01

    The binding of several benzopiranone derivatives to human serum albumin was determined. The antiallergic drug disodium cromoglycate binds weakly to serum albumin. However, its precursors, chromones of smaller size, were able to bind in a hydrophobic pocket in the protein, and are carried by serum albumin in blood.

  2. Landscape of protein-small ligand binding modes.

    Science.gov (United States)

    Kasahara, Kota; Kinoshita, Kengo

    2016-09-01

    Elucidating the mechanisms of specific small-molecule (ligand) recognition by proteins is a long-standing conundrum. While the structures of these molecules, proteins and ligands, have been extensively studied, protein-ligand interactions, or binding modes, have not been comprehensively analyzed. Although methods for assessing similarities of binding site structures have been extensively developed, the methods for the computational treatment of binding modes have not been well established. Here, we developed a computational method for encoding the information about binding modes as graphs, and assessing their similarities. An all-against-all comparison of 20,040 protein-ligand complexes provided the landscape of the protein-ligand binding modes and its relationships with protein- and chemical spaces. While similar proteins in the same SCOP Family tend to bind relatively similar ligands with similar binding modes, the correlation between ligand and binding similarities was not very high (R(2)  = 0.443). We found many pairs with novel relationships, in which two evolutionally distant proteins recognize dissimilar ligands by similar binding modes (757,474 pairs out of 200,790,780 pairs were categorized into this relationship, in our dataset). In addition, there were an abundance of pairs of homologous proteins binding to similar ligands with different binding modes (68,217 pairs). Our results showed that many interesting relationships between protein-ligand complexes are still hidden in the structure database, and our new method for assessing binding mode similarities is effective to find them.

  3. Peptide Nucleic Acids Having Enhanced Binding Affinity and Sequence Specificity

    DEFF Research Database (Denmark)

    1998-01-01

    A novel class of compounds, known as peptide nucleic acids, bind complementary DNA and RNA strands more strongly than a corresponding DNA strand, and exhibit increased sequence specificity and binding affinity. Methods of increasing binding affinity and sequence specificity of peptide nucleic aci...

  4. The Receptor Binding Domain of Botulinum Neurotoxin Stereotype C Binds Phosphoinositides

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yanfeng; Varnum, Susan M.

    2012-03-01

    Botulinum neurotoxins (BoNTs) are the most toxic proteins known for humans and animals with an extremely low LD50 of {approx} 1 ng/kg. BoNTs generally require a protein and a ganglioside on the cell membrane surface for binding, which is known as a 'dual receptor' mechanism for host intoxication. Recent studies have suggested that in addition to gangliosides, other membrane lipids such as phosphoinositides may be involved in the interactions with the receptor binding domain (HCR) of BoNTs for better membrane penetration. Here, using two independent lipid-binding assays, we tested the interactions of BoNT/C-HCR with lipids in vitro. BoNT/C-HCR was found to bind negatively charged phospholipids, preferentially phosphoinositides. Additional interactions to phosphoinositides may help BoNT/C bind membrane more tightly and transduct signals for subsequent steps of intoxication. Our results provide new insights into the mechanisms of host cell membrane recognition by BoNTs.

  5. Steered molecular dynamics study of inhibitor binding in the internal binding site in dehaloperoxidase-hemoglobin.

    Science.gov (United States)

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

    2016-04-01

    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.

  6. The Staphylococcus aureus extracellular adherence protein promotes bacterial internalization by keratinocytes independent of fibronectin-binding proteins.

    Science.gov (United States)

    Bur, Stephanie; Preissner, Klaus T; Herrmann, Mathias; Bischoff, Markus

    2013-08-01

    Staphylococcus aureus, the leading causal pathogen of skin infections, is strongly associated with skin atopy, and a number of bacterial adhesins allow the microbe to adhere to and invade eukaryotic cells. One of these adhesive molecules is the multifunctional extracellular adherence protein (Eap), which is overexpressed in situ in authentic human wounds and was shown to delay wound healing in experimental models. Yet, its role during invasion of keratinocytes is not clearly defined. By using a gentamicin/lysostaphin protection assay we demonstrate here that preincubation of HaCaT cells or primary keratinocytes with Eap results in a concentration-dependent significant increase in staphylococcal adhesion, followed by an even more pronounced internalization of bacteria by eukaryotic cells. Flow cytometric analysis revealed that Eap increased both the number of infected eukaryotic cells and the bacterial load per infected cell. Moreover, treatment of keratinocytes with Eap strongly enhanced the internalization of coagulase-negative staphylococci, as well as of E. coli, and markedly promoted staphylococcal invasion into extended-culture keratinocytes, displaying expression of keratin 10 and involucrin as differentiation markers. Thus, wound-related staphylococcal Eap may provide a major cellular invasin function, thereby enhancing the pathogen's ability to hide from the host immune system during acute and chronic skin infection.

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

    OpenAIRE

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

    2011-01-01

    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)...

  8. Palmitate and stearate binding to human serum albumin. Determination of relative binding constants

    DEFF Research Database (Denmark)

    Vorum, H; Fisker, K; Honoré, B

    1997-01-01

    . The experimental data were analysed by a computerised curve fitting procedure using equilibrium equations for multiple binding of ligands, containing relative binding constants, valid whether the ligands are truly insoluble or are slightly soluble and irrespective of aggregation in aqueous solution. A best-fit set...... of relative binding constants was found, and subsequently 30 sets of acceptable constants for each set of data in order to evaluate the variation. The data were first fitted by the relative Scatchard's equation, then by the relative, stoichiometric equation. Scatchard's equation is deduced on the presumption...... that cooperativity is absent while the stoichiometric equation is valid even when cooperativity is present. It was found with palmitate as well as with stearate that the two equations fitted the data equally well, and it was concluded that the observations were compatible with absence of cooperativity. The relative...

  9. Dengue virus binding and replication by platelets.

    Science.gov (United States)

    Simon, Ayo Y; Sutherland, Michael R; Pryzdial, Edward L G

    2015-07-16

    Dengue virus (DENV) infection causes ∼200 million cases of severe flulike illness annually, escalating to life-threatening hemorrhagic fever or shock syndrome in ∼500,000. Although thrombocytopenia is typical of both mild and severe diseases, the mechanism triggering platelet reduction is incompletely understood. As a probable initiating event, direct purified DENV-platelet binding was followed in the current study by quantitative reverse transcription-polymerase chain reaction and confirmed antigenically. Approximately 800 viruses specifically bound per platelet at 37°C. Fewer sites were observed at 25°C, the blood bank storage temperature (∼350 sites), or 4°C, known to attenuate virus cell entry (∼200 sites). Dendritic cell-specific intercellular adhesion molecule-3-grabbing nonintegrin (DC-SIGN) and heparan sulfate proteoglycan were implicated as coreceptors because only the combination of anti-DC-SIGN and low-molecular-weight heparin prevented binding. Interestingly, at 37°C and 25°C, platelets replicated the positive sense single-stranded RNA genome of DENV by up to ∼4-fold over 7 days. Further time course experiments demonstrated production of viral NS1 protein, which is known to be highly antigenic in patient serum. The infectivity of DENV intrinsically decayed in vitro, which was moderated by platelet-mediated generation of viable progeny. This was shown using a transcription inhibitor and confirmed by freeze-denatured platelets being incapable of replicating the DENV genome. For the first time, these data demonstrate that platelets directly bind DENV saturably and produce infectious virus. Thus, expression of antigen encoded by DENV is a novel consideration in the pathogen-induced thrombocytopenia mechanism. These results furthermore draw attention to the possibility that platelets may produce permissive RNA viruses in addition to DENV.

  10. Antioxidant flavonoids bind human serum albumin

    Science.gov (United States)

    Kanakis, C. D.; Tarantilis, P. A.; Polissiou, M. G.; Diamantoglou, S.; Tajmir-Riahi, H. A.

    2006-10-01

    Human serum albumin (HSA) is a principal extracellular protein with a high concentration in blood plasma and carrier for many drugs to different molecular targets. Flavonoids are powerful antioxidants and prevent DNA damage. The antioxidative protections are related to their binding modes to DNA duplex and complexation with free radicals in vivo. However, flavonoids are known to inhibit the activities of several enzymes such as calcium phospholipid-dependent protein kinase, tyrosine protein kinase from rat lung, phosphorylase kinase, phosphatidylinositol 3-kinase and DNA topoisomerases that exhibit the importance of flavonoid-protein interaction. This study was designed to examine the interaction of human serum albumin (HSA) with quercetin (que), kaempferol (kae) and delphinidin (del) in aqueous solution at physiological conditions, using constant protein concentration of 0.25 mM (final) and various drug contents of 1 μM-1 mM. FTIR and UV-vis spectroscopic methods were used to determine the polyphenolic binding mode, the binding constant and the effects of flavonoid complexation on protein secondary structure. The spectroscopic results showed that flavonoids are located along the polypeptide chains through H-bonding interactions with overall affinity constant of Kque = 1.4 × 10 4 M -1, Kkae = 2.6 × 10 5 M -1 and Kdel = 4.71 × 10 5 M -1. The protein secondary structure showed no alterations at low pigment concentration (1 μM), whereas at high flavonoid content (1 mM), major reduction of α-helix from 55% (free HSA) to 42-46% and increase of β-sheet from 15% (free HSA) to 17-19% and β-anti from 7% (free HSA) to 10-20% occurred in the flavonoid-HSA adducts. The major reduction of HSA α-helix is indicative of a partial protein unfolding upon flavonoid interaction.

  11. DNA and RNA Quadruplex-Binding Proteins

    Directory of Open Access Journals (Sweden)

    Václav Brázda

    2014-09-01

    Full Text Available Four-stranded DNA structures were structurally characterized in vitro by NMR, X-ray and Circular Dichroism spectroscopy in detail. Among the different types of quadruplexes (i-Motifs, minor groove quadruplexes, G-quadruplexes, etc., the best described are G-quadruplexes which are featured by Hoogsteen base-paring. Sequences with the potential to form quadruplexes are widely present in genome of all organisms. They are found often in repetitive sequences such as telomeric ones, and also in promoter regions and 5' non-coding sequences. Recently, many proteins with binding affinity to G-quadruplexes have been identified. One of the initially portrayed G-rich regions, the human telomeric sequence (TTAGGGn, is recognized by many proteins which can modulate telomerase activity. Sequences with the potential to form G-quadruplexes are often located in promoter regions of various oncogenes. The NHE III1 region of the c-MYC promoter has been shown to interact with nucleolin protein as well as other G-quadruplex-binding proteins. A number of G-rich sequences are also present in promoter region of estrogen receptor alpha. In addition to DNA quadruplexes, RNA quadruplexes, which are critical in translational regulation, have also been predicted and observed. For example, the RNA quadruplex formation in telomere-repeat-containing RNA is involved in interaction with TRF2 (telomere repeat binding factor 2 and plays key role in telomere regulation. All these fundamental examples suggest the importance of quadruplex structures in cell processes and their understanding may provide better insight into aging and disease development.

  12. Structural basis for PECAM-1 homophilic binding

    Energy Technology Data Exchange (ETDEWEB)

    Paddock, C.; Zhou, D.; Lertkiatmongkol, P.; Newman, P. J.; Zhu, J.

    2015-12-23

    Platelet endothelial cell adhesion molecule-1 (PECAM-1) is a 130-kDa member of the immunoglobulin gene superfamily (IgSF) that is present on the surface of circulating platelets and leukocytes, and highly expressed at the junctions of confluent endothelial cell monolayers. PECAM-1–mediated homophilic interactions, known to be mediated by its 2 amino-terminal immunoglobulin homology domains, are essential for concentrating PECAM-1 at endothelial cell intercellular junctions, where it functions to facilitate diapedesis, maintain vascular integrity, and transmit survival signals into the cell. Given the importance of PECAM-1–mediated homophilic interactions in mediating each of these cell physiological events, and to reveal the nature and orientation of the PECAM-1–PECAM-1 homophilic-binding interface, we undertook studies aimed at determining the crystal structure of the PECAM-1 homophilic-binding domain, which is composed of amino-terminal immunoglobulin homology domains 1 and 2 (IgD1 and IgD2). The crystal structure revealed that both IgD1 and IgD2 exhibit a classical IgSF fold, having a β-sandwich topology formed by 2 sheets of antiparallel β strands stabilized by the hallmark disulfide bond between the B and F strands. Interestingly, despite previous assignment to the C2 class of immunoglobulin-like domains, the structure of IgD1 reveals that it actually belongs to the I2 set of IgSF folds. Both IgD1 and IgD2 participate importantly in the formation of the trans homophilic-binding interface, with a total buried interface area of >2300 Å2. These and other unique structural features of PECAM-1 allow for the development of an atomic-level model of the interactions that PECAM-1 forms during assembly of endothelial cell intercellular junctions.

  13. Zooming into the binding groove of HLA molecules : which positions and which substitutions change peptide binding most?

    NARCIS (Netherlands)

    van Deutekom, Hanneke W M; Kesmir, C.

    2015-01-01

    Human leukocyte antigen (HLA) genes are the most polymorphic genes in the human genome. Almost all polymorphic residues are located in the peptide-binding groove, resulting in different peptide-binding preferences. Whether a single amino acid change can alter the peptide-binding repertoire of an HLA

  14. Loss of cargo binding in the human myosin VI deafness mutant (R1166X) leads to increased actin filament binding.

    Science.gov (United States)

    Arden, Susan D; Tumbarello, David A; Butt, Tariq; Kendrick-Jones, John; Buss, Folma

    2016-10-01

    Mutations in myosin VI have been associated with autosomal-recessive (DFNB37) and autosomal-dominant (DFNA22) deafness in humans. Here, we characterise an myosin VI nonsense mutation (R1166X) that was identified in a family with hereditary hearing loss in Pakistan. This mutation leads to the deletion of the C-terminal 120 amino acids of the myosin VI cargo-binding domain, which includes the WWY-binding motif for the adaptor proteins LMTK2, Tom1 as well as Dab2. Interestingly, compromising myosin VI vesicle-binding ability by expressing myosin VI with the R1166X mutation or with single point mutations in the adaptor-binding sites leads to increased F-actin binding of this myosin in vitro and in vivo As our results highlight the importance of cargo attachment for regulating actin binding to the motor domain, we perform a detailed characterisation of adaptor protein binding and identify single amino acids within myosin VI required for binding to cargo adaptors. We not only show that the adaptor proteins can directly interact with the cargo-binding tail of myosin VI, but our in vitro studies also suggest that multiple adaptor proteins can bind simultaneously to non-overlapping sites in the myosin VI tail. In conclusion, our characterisation of the human myosin VI deafness mutant (R1166X) suggests that defects in cargo binding may leave myosin VI in a primed/activated state with an increased actin-binding ability.

  15. PRBP: Prediction of RNA-Binding Proteins Using a Random Forest Algorithm Combined with an RNA-Binding Residue Predictor.

    Science.gov (United States)

    Ma, Xin; Guo, Jing; Xiao, Ke; Sun, Xiao

    2015-01-01

    The prediction of RNA-binding proteins is an incredibly challenging problem in computational biology. Although great progress has been made using various machine learning approaches with numerous features, the problem is still far from being solved. In this study, we attempt to predict RNA-binding proteins directly from amino acid sequences. A novel approach, PRBP predicts RNA-binding proteins using the information of predicted RNA-binding residues in conjunction with a random forest based method. For a given protein, we first predict its RNA-binding residues and then judge whether the protein binds RNA or not based on information from that prediction. If the protein cannot be identified by the information associated with its predicted RNA-binding residues, then a novel random forest predictor is used to determine if the query protein is a RNA-binding protein. We incorporated features of evolutionary information combined with physicochemical features (EIPP) and amino acid composition feature to establish the random forest predictor. Feature analysis showed that EIPP contributed the most to the prediction of RNA-binding proteins. The results also showed that the information from the RNA-binding residue prediction improved the overall performance of our RNA-binding protein prediction. It is anticipated that the PRBP method will become a useful tool for identifying RNA-binding proteins. A PRBP Web server implementation is freely available at http://www.cbi.seu.edu.cn/PRBP/.

  16. The Plasminogen-Binding Group A Streptococcal M Protein-Related Protein Prp Binds Plasminogen via Arginine and Histidine Residues▿

    Science.gov (United States)

    Sanderson-Smith, Martina L.; Dowton, Mark; Ranson, Marie; Walker, Mark J.

    2007-01-01

    The migration of the human pathogen Streptococcus pyogenes (group A streptococcus) from localized to deep tissue sites may result in severe invasive disease, and sequestration of the host zymogen plasminogen appears crucial for virulence. Here, we describe a novel plasminogen-binding M protein, the plasminogen-binding group A streptococcal M protein (PAM)-related protein (Prp). Prp is phylogenetically distinct from previously described plasminogen-binding M proteins of group A, C, and G streptococci. While competition experiments indicate that Prp binds plasminogen with a lower affinity than PAM (50% effective concentration = 0.34 μM), Prp nonetheless binds plasminogen with high affinity and at physiologically relevant concentrations of plasminogen (Kd = 7.8 nM). Site-directed mutagenesis of the putative plasminogen binding site indicates that unlike the majority of plasminogen receptors, Prp does not interact with plasminogen exclusively via lysine residues. Mutagenesis to alanine of lysine residues Lys96 and Lys101 reduced but did not abrogate plasminogen binding by Prp. Plasminogen binding was abolished only with the additional mutagenesis of Arg107 and His108 to alanine. Furthermore, mutagenesis of Arg107 and His108 abolished plasminogen binding by Prp despite the presence of Lys96 and Lys101 in the binding site. Thus, binding to plasminogen via arginine and histidine residues appears to be a conserved mechanism among plasminogen-binding M proteins. PMID:17012384

  17. The plasminogen-binding group A streptococcal M protein-related protein Prp binds plasminogen via arginine and histidine residues.

    Science.gov (United States)

    Sanderson-Smith, Martina L; Dowton, Mark; Ranson, Marie; Walker, Mark J

    2007-02-01

    The migration of the human pathogen Streptococcus pyogenes (group A streptococcus) from localized to deep tissue sites may result in severe invasive disease, and sequestration of the host zymogen plasminogen appears crucial for virulence. Here, we describe a novel plasminogen-binding M protein, the plasminogen-binding group A streptococcal M protein (PAM)-related protein (Prp). Prp is phylogenetically distinct from previously described plasminogen-binding M proteins of group A, C, and G streptococci. While competition experiments indicate that Prp binds plasminogen with a lower affinity than PAM (50% effective concentration = 0.34 microM), Prp nonetheless binds plasminogen with high affinity and at physiologically relevant concentrations of plasminogen (K(d) = 7.8 nM). Site-directed mutagenesis of the putative plasminogen binding site indicates that unlike the majority of plasminogen receptors, Prp does not interact with plasminogen exclusively via lysine residues. Mutagenesis to alanine of lysine residues Lys(96) and Lys(101) reduced but did not abrogate plasminogen binding by Prp. Plasminogen binding was abolished only with the additional mutagenesis of Arg(107) and His(108) to alanine. Furthermore, mutagenesis of Arg(107) and His(108) abolished plasminogen binding by Prp despite the presence of Lys(96) and Lys(101) in the binding site. Thus, binding to plasminogen via arginine and histidine residues appears to be a conserved mechanism among plasminogen-binding M proteins.

  18. Glycan masking of Plasmodium vivax Duffy Binding Protein for probing protein binding function and vaccine development.

    Directory of Open Access Journals (Sweden)

    Sowmya Sampath

    Full Text Available Glycan masking is an emerging vaccine design strategy to focus antibody responses to specific epitopes, but it has mostly been evaluated on the already heavily glycosylated HIV gp120 envelope glycoprotein. Here this approach was used to investigate the binding interaction of Plasmodium vivax Duffy Binding Protein (PvDBP and the Duffy Antigen Receptor for Chemokines (DARC and to evaluate if glycan-masked PvDBPII immunogens would focus the antibody response on key interaction surfaces. Four variants of PVDBPII were generated and probed for function and immunogenicity. Whereas two PvDBPII glycosylation variants with increased glycan surface coverage distant from predicted interaction sites had equivalent binding activity to wild-type protein, one of them elicited slightly better DARC-binding-inhibitory activity than wild-type immunogen. Conversely, the addition of an N-glycosylation site adjacent to a predicted PvDBP interaction site both abolished its interaction with DARC and resulted in weaker inhibitory antibody responses. PvDBP is composed of three subdomains and is thought to function as a dimer; a meta-analysis of published PvDBP mutants and the new DBPII glycosylation variants indicates that critical DARC binding residues are concentrated at the dimer interface and along a relatively flat surface spanning portions of two subdomains. Our findings suggest that DARC-binding-inhibitory antibody epitope(s lie close to the predicted DARC interaction site, and that addition of N-glycan sites distant from this site may augment inhibitory antibodies. Thus, glycan resurfacing is an attractive and feasible tool to investigate protein structure-function, and glycan-masked PvDBPII immunogens might contribute to P. vivax vaccine development.

  19. Thermodynamic analysis of DNA binding by a Bacillus single stranded DNA binding protein

    Directory of Open Access Journals (Sweden)

    Biswas-Fiss Esther E

    2012-06-01

    Full Text Available Abstract Background Single-stranded DNA binding proteins (SSB are essential for DNA replication, repair, and recombination in all organisms. SSB works in concert with a variety of DNA metabolizing enzymes such as DNA polymerase. Results We have cloned and purified SSB from Bacillus anthracis (SSBBA. In the absence of DNA, at concentrations ≤100 μg/ml, SSBBA did not form a stable tetramer and appeared to resemble bacteriophage T4 gene 32 protein. Fluorescence anisotropy studies demonstrated that SSBBA bound ssDNA with high affinity comparable to other prokaryotic SSBs. Thermodynamic analysis indicated both hydrophobic and ionic contributions to ssDNA binding. FRET analysis of oligo(dT70 binding suggested that SSBBA forms a tetrameric assembly upon ssDNA binding. This report provides evidence of a bacterial SSB that utilizes a novel mechanism for DNA binding through the formation of a transient tetrameric structure. Conclusions Unlike other prokaryotic SSB proteins, SSBBA from Bacillus anthracis appeared to be monomeric at concentrations ≤100 μg/ml as determined by SE-HPLC. SSBBA retained its ability to bind ssDNA with very high affinity, comparable to SSB proteins which are tetrameric. In the presence of a long ssDNA template, SSBBA appears to form a transient tetrameric structure. Its unique structure appears to be due to the cumulative effect of multiple key amino acid changes in its sequence during evolution, leading to perturbation of stable dimer and tetramer formation. The structural features of SSBBA could promote facile assembly and disassembly of the protein-DNA complex required in processes such as DNA replication.

  20. Oligomerization of Mannan-binding Lectin Dictates Binding Properties and Complement Activation.

    Science.gov (United States)

    Kjaer, T R; Jensen, L; Hansen, A; Dani, R; Jensenius, J C; Dobó, J; Gál, P; Thiel, S

    2016-07-01

    The complement system is a part of the innate immune system and is involved in recognition and clearance of pathogens and altered-self structures. The lectin pathway of the complement system is initiated when soluble pattern recognition molecules (PRMs) with collagen-like regions bind to foreign or altered self-surfaces. Associated with the collagen-like stems of these PRMs are three mannan-binding lectin (MBL)-associated serine proteases (MASPs) and two MBL-associated proteins (MAps). The most studied of the PRMs, MBL, is present in serum mainly as trimeric and tetrameric oligomers of the structural subunit. We hypothesized that oligomerization of MBL may influence both the potential to bind to micro organisms and the interaction with the MASPs and MAps, thus influencing the ability to initiate complement activation. When testing binding at 37 °C, we found higher binding of tetrameric MBL to Staphylococcus aureus (S. aureus) than trimeric and dimeric MBL. In serum, we found that tetrameric MBL was the main oligomeric form present in complexes with the MASPs and MAp44. Such preference was confirmed using purified forms of recombinant MBL (rMBL) oligomers, where tetrameric rMBL interacted stronger with all of the MASPs and MAp44, compared to trimeric MBL. As a direct consequence of the weaker interaction with the MASPs, we found that trimeric rMBL was inferior to tetrameric rMBL in activating the complement system. Our data suggest that the oligomeric state of MBL is crucial both for the binding properties and the effector function of MBL.

  1. Human pentraxin 3 binds to the complement regulator c4b-binding protein.

    Directory of Open Access Journals (Sweden)

    Anne Braunschweig

    Full Text Available The long pentraxin 3 (PTX3 is a soluble recognition molecule with multiple functions including innate immune defense against certain microbes and the clearance of apoptotic cells. PTX3 interacts with recognition molecules of the classical and lectin complement pathways and thus initiates complement activation. In addition, binding of PTX3 to the alternative complement pathway regulator factor H was shown. Here, we show that PTX3 binds to the classical and lectin pathway regulator C4b-binding protein (C4BP. A PTX3-binding site was identified within short consensus repeats 1-3 of the C4BP α-chain. PTX3 did not interfere with the cofactor activity of C4BP in the fluid phase and C4BP maintained its complement regulatory activity when bound to PTX3 on surfaces. While C4BP and factor H did not compete for PTX3 binding, the interaction of C4BP with PTX3 was inhibited by C1q and by L-ficolin. PTX3 bound to human fibroblast- and endothelial cell-derived extracellular matrices and recruited functionally active C4BP to these surfaces. Whereas PTX3 enhanced the activation of the classical/lectin pathway and caused enhanced C3 deposition on extracellular matrix, deposition of terminal pathway components and the generation of the inflammatory mediator C5a were not increased. Furthermore, PTX3 enhanced the binding of C4BP to late apoptotic cells, which resulted in an increased rate of inactivation of cell surface bound C4b and a reduction in the deposition of C5b-9. Thus, in addition to complement activators, PTX3 interacts with complement inhibitors including C4BP. This balanced interaction on extracellular matrix and on apoptotic cells may prevent excessive local complement activation that would otherwise lead to inflammation and host tissue damage.

  2. Computational identification of uncharacterized cruzain binding sites.

    Directory of Open Access Journals (Sweden)

    Jacob D Durrant

    Full Text Available Chagas disease, caused by the unicellular parasite Trypanosoma cruzi, claims 50,000 lives annually and is the leading cause of infectious myocarditis in the world. As current antichagastic therapies like nifurtimox and benznidazole are highly toxic, ineffective at parasite eradication, and subject to increasing resistance, novel therapeutics are urgently needed. Cruzain, the major cysteine protease of Trypanosoma cruzi, is one attractive drug target. In the current work, molecular dynamics simulations and a sequence alignment of a non-redundant, unbiased set of peptidase C1 family members are used to identify uncharacterized cruzain binding sites. The two sites identified may serve as targets for future pharmacological intervention.

  3. Biolabeling and Binding Evaluation of Amphiphilic Nanocrystallopolymers

    Directory of Open Access Journals (Sweden)

    Kwang-Suk Jang

    2016-01-01

    Full Text Available Surfactant-like inorganic-organic hybrid molecules named as nanocrystallopolymers were designed by conjugation of the hydrophilic synthetic poly(amino acid, poly-α,β-(N-(2-hydroxyethyll-aspartamide, with hydrophobic inorganic nanoparticles. In aqueous media, amphiphilic nanocrystallopolymers form self-aggregates with unique morphologies. Here, a simple biolabeling method of nanocrystallopolymers was developed. Biotin was selected as a model biomolecule. The specific binding of biotin-labeled nanocrystallopolymers to the targeted surface was evaluated with a surface plasmon resonance sensor.

  4. Mannose Binding Lectin Deficiency and Clinical Features

    Directory of Open Access Journals (Sweden)

    Ertugrul Erken

    2013-08-01

    Full Text Available Innate immunity consists of macrophages, neutrophils, natural killer cells, mucosal immunuglobulins and the comlement system. Mannose binding lectin (MBL takes part in innate immunity through opsonisation and complement activation. MBL deficiency is associated with some infections and autoimmune disorders. However some studies indicate that MBL deficiency alone is not essential for immunity but it may intensify the clinic picture of an immune deficiency that already exists. This article refers to clincal studies related to MBL and brings up the clinical importance of MBL deficiency. [Archives Medical Review Journal 2013; 22(4.000: 565-574

  5. DNS and BIND on IPv6

    CERN Document Server

    Liu, Cricket

    2011-01-01

    If you're preparing to roll out IPv6 on your network, this concise book provides the essentials you need to support this protocol with DNS. You'll learn how DNS was extended to accommodate IPv6 addresses, and how you can configure a BIND name server to run on the network. This book also features methods for troubleshooting problems with IPv6 forward- and reverse-mapping, and techniques for helping islands of IPv6 clients communicate with IPv4 resources. Topics include: DNS and IPv6-Learn the structure and representation of IPv6 addresses, and the syntaxes of AAAA and PTR records in the ip6.a

  6. Polynucleotides encoding TRF1 binding proteins

    Science.gov (United States)

    Campisi, Judith; Kim, Sahn-Ho

    2002-01-01

    The present invention provides a novel telomere associated protein (Trf1-interacting nuclear protein 2 "Tin2") that hinders the binding of Trf1 to its specific telomere repeat sequence and mediates the formation of a Tin2-Trf1-telomeric DNA complex that limits telomerase access to the telomere. Also included are the corresponding nucleic acids that encode the Tin2 of the present invention, as well as mutants of Tin2. Methods of making, purifying and using Tin2 of the present invention are described. In addition, drug screening assays to identify drugs that mimic and/or complement the effect of Tin2 are presented.

  7. TIGHT-BINDING DESCRIPTION OF TICx

    Directory of Open Access Journals (Sweden)

    V.I.Ivashchenko

    2004-01-01

    Full Text Available A parametrized non-orthogonal tight-binding (TB method combined with the coherent-potential-approximation is applied to the study of the electronic structure of disordered off-stoichiometric TiCx, the lattice relaxation and the electronic spectra of the TiC (001 surface, the local relaxation and energetic states of TiC structures with one or two vacancies in both the non-metal and metal sublattices. The calculated results are in good agreement with available experimental and theoretical data. The importance of the overlap matrix elements of the TB Hamiltonian in describing the electronic structure of this class of compounds is emphasized.

  8. Transferable Tight-Binding Potential for Hydrocarbons

    CERN Document Server

    Wang, Y; Wang, Yang

    1994-01-01

    A transferable tight-binding potential has been constructed for heteroatomic systems containing carbon and hydrogen. The electronic degree of freedom is treated explicitly in this potential using a small set of transferable parameters which has been fitted to small hydrocarbons and radicals. Transferability to other higher hydrocarbons were tested by comparison with ab initio calculations and experimental data. The potential can correctly reproduce changes in the electronic configuration as a function of the local bonding geometry around each carbon atom. This type of potential is well suited for computer simulations of covalently bonded systems in both gas-phase and condensed-phase systems.

  9. The binding of bovine factor XII to kaolin.

    Science.gov (United States)

    Kirby, E P; McDevitt, P J

    1983-04-01

    Purified bovine factor XII was radiolabeled with iodine-125 and its binding to kaolin studied. Binding was rapid and was not readily reversible upon adding unlabeled factor XII. The optimum pH for binding was in the region of pH 5-7. The isoelectric point of factor XII was pH 5.7. High concentrations of urea or increasing the ionic strength of the medium did not inhibit binding. Polyvalent macromolecules, such as Polybrene and polylysine, were effective inhibitors of factor XII binding to kaolin. Polylysine caused the release of factor XII that had bound to the kaolin surface.

  10. Factor XII binding to endothelial cells depends on caveolae

    DEFF Research Database (Denmark)

    Schousboe, Inger; Thomsen, Peter; van Deurs, Bo

    2004-01-01

    to human umbilical vein endothelial cells (HUVEC) has never been shown to be localized to these specialized membrane structures. Using microscopical techniques, we here report that FXII binds to specific patches of the HUVEC plasma membrane with a high density of caveolae. Further investigations of FXII...... lipid rafts. Accordingly, cholesterol-depleted cells were found to bind significantly reduced amounts of FXII. These observations, combined with the presence of a minority of u-PAR in caveolae concomitant with FXII binding, indicate that FXII binding to u-PAR may be secondary and depends upon...... the structural elements within caveolae. Thus, FXII binding to HUVEC depends on intact caveolae on the cellular surface....

  11. Dual chain synthetic heparin-binding growth factor analogs

    Science.gov (United States)

    Zamora, Paul O.; Pena, Louis A.; Lin, Xinhua

    2009-10-06

    The invention provides synthetic heparin-binding growth factor analogs having two peptide chains each branched from a branch moiety, such as trifunctional amino acid residues, the branch moieties separated by a first linker of from 3 to about 20 backbone atoms, which peptide chains bind a heparin-binding growth factor receptor and are covalently bound to a non-signaling peptide that includes a heparin-binding domain, preferably by a second linker, which may be a hydrophobic second linker. The synthetic heparin-binding growth factor analogs are useful as pharmaceutical agents, soluble biologics or as surface coatings for medical devices.

  12. Dual chain synthetic heparin-binding growth factor analogs

    Energy Technology Data Exchange (ETDEWEB)

    Zamora, Paul O. (Gaithersburg, MD); Pena, Louis A. (Poquott, NY); Lin, Xinhua (Plainview, NY)

    2012-04-24

    The invention provides synthetic heparin-binding growth factor analogs having two peptide chains each branched from a branch moiety, such as trifunctional amino acid residues, the branch moieties separated by a first linker of from 3 to about 20 backbone atoms, which peptide chains bind a heparin-binding growth factor receptor and are covalently bound to a non-signaling peptide that includes a heparin-binding domain, preferably by a second linker, which may be a hydrophobic second linker. The synthetic heparin-binding growth factor analogs are useful as pharmaceutical agents, soluble biologics or as surface coatings for medical devices.

  13. A unique bivalent binding and inhibition mechanism by the yatapoxvirus interleukin 18 binding protein.

    Directory of Open Access Journals (Sweden)

    Brian Krumm

    Full Text Available Interleukin 18 (IL18 is a cytokine that plays an important role in inflammation as well as host defense against microbes. Mammals encode a soluble inhibitor of IL18 termed IL18 binding protein (IL18BP that modulates IL18 activity through a negative feedback mechanism. Many poxviruses encode homologous IL18BPs, which contribute to virulence. Previous structural and functional studies on IL18 and IL18BPs revealed an essential binding hot spot involving a lysine on IL18 and two aromatic residues on IL18BPs. The aromatic residues are conserved among the very diverse mammalian and poxviruses IL18BPs with the notable exception of yatapoxvirus IL18BPs, which lack a critical phenylalanine residue. To understand the mechanism by which yatapoxvirus IL18BPs neutralize IL18, we solved the crystal structure of the Yaba-Like Disease Virus (YLDV IL18BP and IL18 complex at 1.75 Å resolution. YLDV-IL18BP forms a disulfide bonded homo-dimer engaging IL18 in a 2∶2 stoichiometry, in contrast to the 1∶1 complex of ectromelia virus (ECTV IL18BP and IL18. Disruption of the dimer interface resulted in a functional monomer, however with a 3-fold decrease in binding affinity. The overall architecture of the YLDV-IL18BP:IL18 complex is similar to that observed in the ECTV-IL18BP:IL18 complex, despite lacking the critical lysine-phenylalanine interaction. Through structural and mutagenesis studies, contact residues that are unique to the YLDV-IL18BP:IL18 binding interface were identified, including Q67, P116 of YLDV-IL18BP and Y1, S105 and D110 of IL18. Overall, our studies show that YLDV-IL18BP is unique among the diverse family of mammalian and poxvirus IL-18BPs in that it uses a bivalent binding mode and a unique set of interacting residues for binding IL18. However, despite this extensive divergence, YLDV-IL18BP binds to the same surface of IL18 used by other IL18BPs, suggesting that all IL18BPs use a conserved inhibitory mechanism by blocking a putative receptor-binding

  14. Antineoplastic DNA-binding compounds: intercalating and minor groove binding drugs.

    Science.gov (United States)

    Mišković, Katarina; Bujak, Maro; Baus Lončar, Mirela; Glavaš-Obrovac, Ljubica

    2013-12-01

    DNA intercalating and minor groove binding compounds are new weapons in the battle against malignant diseases. These antineoplastic agents target the DNA molecule and interfere with the cell cycle leading to rapidly proliferating cell death. They are mainly derivates of a naturally occurring organic compound derived from a microorganism or plant. Intercalators usually act as topoisomerase I and/or II poisons, while the mechanisms of DNA minor groove binders are a combination of several steps including topoisomerase poisoning. This paper gives an overview of some of the developed DNA intercalating and minor groove binding compounds, as well as an explanation of their chemical structures, origins, and application in chemotherapy.

  15. Detection of secondary binding sites in proteins using fragment screening.

    Science.gov (United States)

    Ludlow, R Frederick; Verdonk, Marcel L; Saini, Harpreet K; Tickle, Ian J; Jhoti, Harren

    2015-12-29

    Proteins need to be tightly regulated as they control biological processes in most normal cellular functions. The precise mechanisms of regulation are rarely completely understood but can involve binding of endogenous ligands and/or partner proteins at specific locations on a protein that can modulate function. Often, these additional secondary binding sites appear separate to the primary binding site, which, for example for an enzyme, may bind a substrate. In previous work, we have uncovered several examples in which secondary binding sites were discovered on proteins using fragment screening approaches. In each case, we were able to establish that the newly identified secondary binding site was biologically relevant as it was able to modulate function by the binding of a small molecule. In this study, we investigate how often secondary binding sites are located on proteins by analyzing 24 protein targets for which we have performed a fragment screen using X-ray crystallography. Our analysis shows that, surprisingly, the majority of proteins contain secondary binding sites based on their ability to bind fragments. Furthermore, sequence analysis of these previously unknown sites indicate high conservation, which suggests that they may have a biological function, perhaps via an allosteric mechanism. Comparing the physicochemical properties of the secondary sites with known primary ligand binding sites also shows broad similarities indicating that many of the secondary sites may be druggable in nature with small molecules that could provide new opportunities to modulate potential therapeutic targets.

  16. RNA recognition by the DNA end-binding Ku heterodimer.

    Science.gov (United States)

    Dalby, Andrew B; Goodrich, Karen J; Pfingsten, Jennifer S; Cech, Thomas R

    2013-06-01

    Most nucleic acid-binding proteins selectively bind either DNA or RNA, but not both nucleic acids. The Saccharomyces cerevisiae Ku heterodimer is unusual in that it has two very different biologically relevant binding modes: (1) Ku is a sequence-nonspecific double-stranded DNA end-binding protein with prominent roles in nonhomologous end-joining and telomeric capping, and (2) Ku associates with a specific stem-loop of TLC1, the RNA subunit of budding yeast telomerase, and is necessary for proper nuclear localization of this ribonucleoprotein enzyme. TLC1 RNA-binding and dsDNA-binding are mutually exclusive, so they may be mediated by the same site on Ku. Although dsDNA binding by Ku is well studied, much less is known about what features of an RNA hairpin enable specific recognition by Ku. To address this question, we localized the Ku-binding site of the TLC1 hairpin with single-nucleotide resolution using phosphorothioate footprinting, used chemical modification to identify an unpredicted motif within the hairpin secondary structure, and carried out mutagenesis of the stem-loop to ascertain the critical elements within the RNA that permit Ku binding. Finally, we provide evidence that the Ku-binding site is present in additional budding yeast telomerase RNAs and discuss the possibility that RNA binding is a conserved function of the Ku heterodimer.

  17. Characterization of the DNA binding properties of polyomavirus capsid protein

    Science.gov (United States)

    Chang, D.; Cai, X.; Consigli, R. A.; Spooner, B. S. (Principal Investigator)

    1993-01-01

    The DNA binding properties of the polyomavirus structural proteins VP1, VP2, and VP3 were studied by Southwestern analysis. The major viral structural protein VP1 and host-contributed histone proteins of polyomavirus virions were shown to exhibit DNA binding activity, but the minor capsid proteins VP2 and VP3 failed to bind DNA. The N-terminal first five amino acids (Ala-1 to Lys-5) were identified as the VP1 DNA binding domain by genetic and biochemical approaches. Wild-type VP1 expressed in Escherichia coli (RK1448) exhibited DNA binding activity, but the N-terminal truncated VP1 mutants (lacking Ala-1 to Lys-5 and Ala-1 to Cys-11) failed to bind DNA. The synthetic peptide (Ala-1 to Cys-11) was also shown to have an affinity for DNA binding. Site-directed mutagenesis of the VP1 gene showed that the point mutations at Pro-2, Lys-3, and Arg-4 on the VP1 molecule did not affect DNA binding properties but that the point mutation at Lys-5 drastically reduced DNA binding affinity. The N-terminal (Ala-1 to Lys-5) region of VP1 was found to be essential and specific for DNA binding, while the DNA appears to be non-sequence specific. The DNA binding domain and the nuclear localization signal are located in the same N-terminal region.

  18. Methyl-CpG binding proteins in the nervous system

    Institute of Scientific and Technical Information of China (English)

    Guoping FAN; Leah HUTNICK

    2005-01-01

    Classical methyl-CpG binding proteins contain the conserved DNA binding motif methyl-cytosine binding domain (MBD), which preferentially binds to methylated CpG dinucleotides. These proteins serve as transcriptional repressors,mediating gene silencing via DNA cytosine methylation. Mutations in methyl-CpG binding protein 2 (MeCP2) have been linked to the human mental retardation disorder Rett syndrome, suggesting an important role for methyl-CpG binding proteins in brain development and function. This mini-review summarizes the recent advances in studying the diverse functions of MeCP2 as a prototype for other methyl-CpG binding proteins in the development and function of the vertebrate nervous system.

  19. Structural Analysis of Botulinum Neurotoxin Type G Receptor Binding

    Energy Technology Data Exchange (ETDEWEB)

    Schmitt, John; Karalewitz, Andrew; Benefield, Desire A.; Mushrush, Darren J.; Pruitt, Rory N.; Spiller, Benjamin W.; Barbieri, Joseph T.; Lacy, D. Borden (Vanderbilt); (MCW)

    2010-10-19

    Botulinum neurotoxin (BoNT) binds peripheral neurons at the neuromuscular junction through a dual-receptor mechanism that includes interactions with ganglioside and protein receptors. The receptor identities vary depending on BoNT serotype (A-G). BoNT/B and BoNT/G bind the luminal domains of synaptotagmin I and II, homologous synaptic vesicle proteins. We observe conditions under which BoNT/B binds both Syt isoforms, but BoNT/G binds only SytI. Both serotypes bind ganglioside G{sub T1b}. The BoNT/G receptor-binding domain crystal structure provides a context for examining these binding interactions and a platform for understanding the physiological relevance of different Syt receptor isoforms in vivo.

  20. Substrate and drug binding sites in LeuT.

    Science.gov (United States)

    Nyola, Ajeeta; Karpowich, Nathan K; Zhen, Juan; Marden, Jennifer; Reith, Maarten E; Wang, Da-Neng

    2010-08-01

    LeuT is a member of the neurotransmitter/sodium symporter family, which includes the neuronal transporters for serotonin, norepinephrine, and dopamine. The original crystal structure of LeuT shows a primary leucine-binding site at the center of the protein. LeuT is inhibited by different classes of antidepressants that act as potent inhibitors of the serotonin transporter. The newly determined crystal structures of LeuT-antidepressant complexes provide opportunities to probe drug binding in the serotonin transporter, of which the exact position remains controversial. Structure of a LeuT-tryptophan complex shows an overlapping binding site with the primary substrate site. A secondary substrate binding site was recently identified, where the binding of a leucine triggers the cytoplasmic release of the primary substrate. This two binding site model presents opportunities for a better understanding of drug binding and the mechanism of inhibition for mammalian transporters.

  1. Cue integration and the perception of action in intentional binding

    DEFF Research Database (Denmark)

    Wolpe, Noham; Haggard, Patrick; Siebner, Hartwig R

    2013-01-01

    'Intentional binding' describes the perceived temporal attraction between a voluntary action and its sensory consequence. Binding has been used in health and disease as an indirect measure of awareness of action or agency, that is, the sense that one controls one's own actions. It has been proposed...... that binding results from cue integration, in which a voluntary action provides information about the timing of its consequences or vice versa. The perception of the timing of either event is then a weighted average, determined according to the reliability of each of these two cues. Here we tested...... the contribution of cue integration to the perception of action and its sensory effect in binding, that is, action and tone binding, by manipulating the sensory reliability of the outcome tone. As predicted, when tone reliability was reduced, action binding was diminished and tone binding was increased. However...

  2. Oligosaccharide binding to barley alpha-amylase 1

    DEFF Research Database (Denmark)

    Robert, X.; Haser, R.; Mori, H.;

    2005-01-01

    Enzymatic subsite mapping earlier predicted 10 binding subsites in the active site substrate binding cleft of barley alpha-amylase isozymes. The three-dimensional structures of the oligosaccharide complexes with barley alpha-amylase isozyme 1 (AMY1) described here give for the first time a thorough...... insight into the substrate binding by describing residues defining 9 subsites, namely -7 through +2. These structures support that the pseudotetrasaccharide inhibitor acarbose is hydrolyzed by the active enzymes. Moreover, sugar binding was observed to the starch granule-binding site previously determined...... in barley alpha-amylase isozyme 2 (AMY2), and the sugar binding modes are compared between the two isozymes. The "sugar tongs" surface binding site discovered in the AMY1-thio-DP4 complex is confirmed in the present work. A site that putatively serves as an entrance for the substrate to the active site...

  3. Electrochemical binding and wiring in battery materials

    Energy Technology Data Exchange (ETDEWEB)

    Pejovnik, S. [National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana (Slovenia); Faculty of Chemistry and Chemical Technology, Askerceva 5, SI-1000 Ljubljana (Slovenia); Dominko, R.; Bele, M.; Gaberscek, M.; Jamnik, J. [National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana (Slovenia)

    2008-10-01

    Binders in battery electrodes not only provide mechanical cohesiveness during battery operation but can also affect the electrode properties via the surface modification. Using atomic force microscopy (AFM), we study the surface structuring of three binders: polyvinylidene fluoride (PVdF), carboxymethyl cellulose (CMC) and gelatin. We try to find correlation between the observed structures and the measured electrochemical charge-discharge characteristics. We further measure the binding ability of gelatin adsorbed from solutions of different pHs. While the best binding ability of gelatin is obtained at pH about 9, the least polarization is observed at pH 12. Both properties are explained based on the observed gelatin structuring as a function of pH. In the second part of this study, gelatin is used as a surface agent that dictates the organization of nanometre-sized carbon black particles around micrometre-sized cathodic active particles. Using microcontact impedance measurements on polished pellets we show that using gelatin-forced carbon black deposition the average electronic resistance around LiMn{sub 2}O{sub 4} particles is decreased by more than two orders of magnitude. We believe that it is this decrease in resistance that improves significantly the rate performance of various cathode materials, such as LiMn{sub 2}O{sub 4} and LiCoO{sub 2}. (author)

  4. Characterizing the morphology of protein binding patches.

    Science.gov (United States)

    Malod-Dognin, Noël; Bansal, Achin; Cazals, Frédéric

    2012-12-01

    Let the patch of a partner in a protein complex be the collection of atoms accounting for the interaction. To improve our understanding of the structure-function relationship, we present a patch model decoupling the topological and geometric properties. While the geometry is classically encoded by the atomic positions, the topology is recorded in a graph encoding the relative position of concentric shells partitioning the interface atoms. The topological-geometric duality provides the basis of a generic dynamic programming-based algorithm comparing patches at the shell level, which may favor topological or geometric features. On the biological side, we address four questions, using 249 cocrystallized heterodimers organized in biological families. First, we dissect the morphology of binding patches and show that Nature enjoyed the topological and geometric degrees of freedom independently while retaining a finite set of qualitatively distinct topological signatures. Second, we argue that our shell-based comparison is effective to perform atomic-level comparisons and show that topological similarity is a less stringent than geometric similarity. We also use the topological versus geometric duality to exhibit topo-rigid patches, whose topology (but not geometry) remains stable upon docking. Third, we use our comparison algorithms to infer specificity-related information amidst a database of complexes. Finally, we exhibit a descriptor outperforming its contenders to predict the binding affinities of the affinity benchmark. The softwares developed with this article are availablefrom http://team.inria.fr/abs/vorpatch_compatch/.

  5. Grafting of protein-protein binding sites

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A strategy for grafting protein-protein binding sites is described. Firstly, key interaction residues at the interface of ligand protein to be grafted are identified and suitable positions in scaffold protein for grafting these key residues are sought. Secondly, the scaffold proteins are superposed onto the ligand protein based on the corresponding Ca and Cb atoms. The complementarity between the scaffold protein and the receptor protein is evaluated and only matches with high score are accepted. The relative position between scaffold and receptor proteins is adjusted so that the interface has a reasonable packing density. Then the scaffold protein is mutated to corresponding residues in ligand protein at each candidate position. And the residues having bad steric contacts with the receptor proteins, or buried charged residues not involved in the formation of any salt bridge are mutated. Finally, the mutated scaffold protein in complex with receptor protein is co-minimized by Charmm. In addition, we deduce a scoring function to evaluate the affinity between mutated scaffold protein and receptor protein by statistical analysis of rigid binding data sets.

  6. Chloride binding site of neurotransmitter sodium symporters.

    Science.gov (United States)

    Kantcheva, Adriana K; Quick, Matthias; Shi, Lei; Winther, Anne-Marie Lund; Stolzenberg, Sebastian; Weinstein, Harel; Javitch, Jonathan A; Nissen, Poul

    2013-05-21

    Neurotransmitter:sodium symporters (NSSs) play a critical role in signaling by reuptake of neurotransmitters. Eukaryotic NSSs are chloride-dependent, whereas prokaryotic NSS homologs like LeuT are chloride-independent but contain an acidic residue (Glu290 in LeuT) at a site where eukaryotic NSSs have a serine. The LeuT-E290S mutant displays chloride-dependent activity. We show that, in LeuT-E290S cocrystallized with bromide or chloride, the anion is coordinated by side chain hydroxyls from Tyr47, Ser290, and Thr254 and the side chain amide of Gln250. The bound anion and the nearby sodium ion in the Na1 site organize a connection between their coordinating residues and the extracellular gate of LeuT through a continuous H-bond network. The specific insights from the structures, combined with results from substrate binding studies and molecular dynamics simulations, reveal an anion-dependent occlusion mechanism for NSS and shed light on the functional role of chloride binding.

  7. DC-SIGN:Binding receptor for HCV?

    Institute of Scientific and Technical Information of China (English)

    Zhi-Hua Feng; Quan-Chu Wang; Qing-He Nie; Zhan-Sheng Jia; Yong-Xin Zhou

    2004-01-01

    DC-SIGN, a dendritic Cell-specific adhesion receptor and a type Ⅱ transmembrane mannose-binding C-type lectin, is very important in the function of DC, both in mediating naive T cell interactions through ICAM-3 and as a rolling receptor that mediates the DC-specific ICAM-2-dependent migration processes. It can be used by viral and bacterial pathogens including Human Immunodeficiency Virus (HIV), HCV, Ebola Virus, CMV and Mycobacterium tuberculosis to facilitate infection. Both DC-SIGN and DC-SIGNR can act either in cis,by concentrating virus on target cells, or in trans, by transmission of bound virus to a target cell expressing appropropriate entry receptors. Recent work showed that DC-SIGN are highaffinity binding receptors for HCV. Besides playing a role in entry into DC, HCV E2 interaction with DC-SIGN might also be detrimental for the interaction of DC with T cells during antigen presentation. The clinical strategies that target DCSIGN may be successful in restricting HCV dissemination and pathogenesis as well as directing the migration of DCs to manipulate appropriate immune responses in autoimmunity and tumorigenic situations.

  8. Quinine binding by the cocaine-binding aptamer. Thermodynamic and hydrodynamic analysis of high-affinity binding of an off-target ligand.

    Science.gov (United States)

    Reinstein, Oren; Yoo, Mina; Han, Chris; Palmo, Tsering; Beckham, Simone A; Wilce, Matthew C J; Johnson, Philip E

    2013-12-03

    The cocaine-binding aptamer is unusual in that it tightly binds molecules other than the ligand it was selected for. Here, we study the interaction of the cocaine-binding aptamer with one of these off-target ligands, quinine. Isothermal titration calorimetry was used to quantify the quinine-binding affinity and thermodynamics of a set of sequence variants of the cocaine-binding aptamer. We find that the affinity of the cocaine-binding aptamer for quinine is 30-40 times stronger than it is for cocaine. Competitive-binding studies demonstrate that both quinine and cocaine bind at the same site on the aptamer. The ligand-induced structural-switching binding mechanism of an aptamer variant that contains three base pairs in stem 1 is retained with quinine as a ligand. The short stem 1 aptamer is unfolded or loosely folded in the free form and becomes folded when bound to quinine. This folding is confirmed by NMR spectroscopy and by the short stem 1 construct having a more negative change in heat capacity of quinine binding than is seen when stem 1 has six base pairs. Small-angle X-ray scattering (SAXS) studies of the free aptamer and both the quinine- and the cocaine-bound forms show that, for the long stem 1 aptamers, the three forms display similar hydrodynamic properties, and the ab initio shape reconstruction structures are very similar. For the short stem 1 aptamer there is a greater variation among the SAXS-derived ab initio shape reconstruction structures, consistent with the changes expected with its structural-switching binding mechanism.

  9. BindUP: a web server for non-homology-based prediction of DNA and RNA binding proteins.

    Science.gov (United States)

    Paz, Inbal; Kligun, Efrat; Bengad, Barak; Mandel-Gutfreund, Yael

    2016-07-08

    Gene expression is a multi-step process involving many layers of regulation. The main regulators of the pathway are DNA and RNA binding proteins. While over the years, a large number of DNA and RNA binding proteins have been identified and extensively studied, it is still expected that many other proteins, some with yet another known function, are awaiting to be discovered. Here we present a new web server, BindUP, freely accessible through the website http://bindup.technion.ac.il/, for predicting DNA and RNA binding proteins using a non-homology-based approach. Our method is based on the electrostatic features of the protein surface and other general properties of the protein. BindUP predicts nucleic acid binding function given the proteins three-dimensional structure or a structural model. Additionally, BindUP provides information on the largest electrostatic surface patches, visualized on the server. The server was tested on several datasets of DNA and RNA binding proteins, including proteins which do not possess DNA or RNA binding domains and have no similarity to known nucleic acid binding proteins, achieving very high accuracy. BindUP is applicable in either single or batch modes and can be applied for testing hundreds of proteins simultaneously in a highly efficient manner.

  10. Identification of actin binding protein, ABP-280, as a binding partner of human Lnk adaptor protein.

    Science.gov (United States)

    He, X; Li, Y; Schembri-King, J; Jakes, S; Hayashi, J

    2000-08-01

    Human Lnk (hLnk) is an adaptor protein with multiple functional domains that regulates T cell activation signaling. In order to identify cellular Lnk binding partners, a yeast two-hybrid screening of human spleen cDNA library was carried out using human hLnk as bait. A polypeptide sequence identical to the C-terminal segment of the actin binding protein (ABP-280) was identified as a hLnk binding protein. The expressed hLnk and the FLAG tagged C-terminal 673 amino acid residues of ABP-280 or the endogenous ABP-280 in COS-7 cells could be co-immunoprecipitated using antibodies either to hLnk, FLAG or ABP-280, respectively. Furthermore, immunofluorescence confocal microscope showed that hLnk and ABP-280 co-localized at the plasma membrane and at juxtanuclear region of COS-7 cells. In Jurkat cells, the endogenous hLnk also associates with the endogenous ABP-280 indicating that the association of these two proteins is physiological. The interacting domains of both proteins were mapped using yeast two-hybrid assays. Our results indicate that hLnk binds to the residues 2006-2454 (repeats 19-23C) of ABP-280. The domain in hLnk that associates with ABP-280 was mapped to an interdomain region of 56 amino acids between pleckstrin homology and Src homology 2 domains. These results suggest that hLnk may exert its regulatory role through its association with ABP-280.

  11. Understanding enzymic binding affinity : thermodynamics of binding of benzamidinium chloride inhibitors to trypsin

    NARCIS (Netherlands)

    Talhout, Reinskje

    2003-01-01

    Understanding enzymic binding affinity is of fundamental scientific importance as well as a prerequisite for structure-based drug design. In this study, the interactions of the serine proteinase trypsin with several artificial, benzamidinium-based inhibitors have been studied in aqueous solutions. I

  12. The complex interplay between ligand binding and conformational structure of the folate binding protein (folate receptor)

    DEFF Research Database (Denmark)

    Holm, Jan; Bruun, Susanne Wrang; Hansen, Steen I.

    2015-01-01

    , and the binding induces a conformational change with formation of hydrophilic and stable holo-FBP. Holo-FBP exhibits a ligand-mediated concentration-dependent self-association into multimers of great thermal and chemical stability due to strong intermolecular forces. Both ligand and FBP are thus protected against...

  13. Cooperative binding of copper(I) to the metal binding domains in Menkes disease protein

    DEFF Research Database (Denmark)

    Jensen, P Y; Bonander, N; Møller, L B

    1999-01-01

    We have optimised the overexpression and purification of the N-terminal end of the Menkes disease protein expressed in Escherichia coli, containing one, two and six metal binding domains (MBD), respectively. The domain(s) have been characterised using circular dichroism (CD) and fluorescence spec...

  14. Mechanical unfolding of ribose binding protein and its comparison with other periplasmic binding proteins.

    Science.gov (United States)

    Kotamarthi, Hema Chandra; Narayan, Satya; Ainavarapu, Sri Rama Koti

    2014-10-01

    Folding and unfolding studies on large, multidomain proteins are still rare despite their high abundance in genomes of prokaryotes and eukaryotes. Here, we investigate the unfolding properties of a 271 residue, two-domain ribose binding protein (RBP) from the bacterial periplasm using single-molecule force spectroscopy. We observe that RBP predominately unfolds via a two-state pathway with an unfolding force of ∼80 pN and an unfolding contour length of ∼95 nm. Only a small population (∼15%) of RBP follows three-state pathways. The ligand binding neither increases the mechanical stability nor influences the unfolding flux of RBP through different pathways. The kinetic partitioning between two-state and three-state pathways, which has been reported earlier for other periplasmic proteins, is also observed in RBP, albeit to a lesser extent. These results provide important insights into the mechanical stability and unfolding processes of large two-domain proteins and highlight the contrasting features upon ligand binding. Protein structural topology diagrams are used to explain the differences in the mechanical unfolding behavior of RBP with other periplasmic binding proteins.

  15. Analysis of the ligand binding properties of recombinant bovine liver-type fatty acid binding protein

    DEFF Research Database (Denmark)

    Rolf, B; Oudenampsen-Krüger, E; Börchers, T

    1995-01-01

    The coding part of the cDNA for bovine liver-type fatty acid binding protein (L-FABP) has been amplified by RT-PCR, cloned and used for the construction of an Escherichia coli (E. coli) expression system. The recombinant protein made up to 25% of the soluble E. coli proteins and could be isolated...

  16. A novel DNA-binding domain in the Shrunken initiator-binding protein (IBP1).

    Science.gov (United States)

    Lugert, T; Werr, W

    1994-06-01

    South-western screening of lambda gt11 expression library with a fragment of the Shrunken promoter containing the initiator element resulted in cloning of a novel maize gene. The encoded initiator-binding protein (IBP1) interacts at the transcription start site of the Shrunken promoter. Analysis of the 680 amino acid (aa) long polypeptide revealed a novel bipartite DNA-binding domain at the carboxyl terminus. In its amino-terminal part, it is weakly related to Myb R-repeats but the following basic region is also essential for DNA binding. A region of similarity to the conserved 2.1 and 2.2 motifs in bacterial sigma-factors is located close to the IBP1 amino terminus. Two putative nuclear localization signals are compatible with the presence of antigenically related polypeptides in nuclear protein extracts. The IBP1 gene was mapped to the long arm of chromosome 9 (9L095); a second highly related gene IBP2 is located on the short arm of chromosome 1 (1S014). Both genes encode proteins sharing 93% similarity and are transcribed with similar activity in different plant organs. A small 82 nucleotide intron in the IBP2 transcript is found unspliced to a variable degree in different tissues. Translation of this incompletely processed transcript would result in a truncated amino-terminal polypeptide lacking the DNA-binding domain.

  17. Structural Basis of Rnd1 Binding to Plexin Rho GTPase Binding Domains (RBDs)

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Hui; Hota, Prasanta K.; Tong, Yufeng; Li, Buren; Shen, Limin; Nedyalkova, Lyudmila; Borthakur, Susmita; Kim, SoonJeung; Tempel, Wolfram; Buck, Matthias; Park, Hee-Won (Toronto); (Case Western U.-Med)

    2011-09-20

    Plexin receptors regulate cell adhesion, migration, and guidance. The Rho GTPase binding domain (RBD) of plexin-A1 and -B1 can bind GTPases, including Rnd1. By contrast, plexin-C1 and -D1 reportedly bind Rnd2 but associate with Rnd1 only weakly. The structural basis of this differential Rnd1 GTPase binding to plexin RBDs remains unclear. Here, we solved the structure of the plexin-A2 RBD in complex with Rnd1 and the structures of the plexin-C1 and plexin-D1 RBDs alone, also compared with the previously determined plexin-B1 RBD.Rnd1 complex structure. The plexin-A2 RBD {center_dot} Rnd1 complex is a heterodimer, whereas plexin-B1 and -A2 RBDs homodimerize at high concentration in solution, consistent with a proposed model for plexin activation. Plexin-C1 and -D1 RBDs are monomeric, consistent with major residue changes in the homodimerization loop. In plexin-A2 and -B1, the RBD {beta}3-{beta}4 loop adjusts its conformation to allow Rnd1 binding, whereas minimal structural changes occur in Rnd1. The plexin-C1 and -D1 RBDs lack several key non-polar residues at the corresponding GTPase binding surface and do not significantly interact with Rnd1. Isothermal titration calorimetry measurements on plexin-C1 and -D1 mutants reveal that the introduction of non-polar residues in this loop generates affinity for Rnd1. Structure and sequence comparisons suggest a similar mode of Rnd1 binding to the RBDs, whereas mutagenesis suggests that the interface with the highly homologous Rnd2 GTPase is different in detail. Our results confirm, from a structural perspective, that Rnd1 does not play a role in the activation of plexin-C1 and -D1. Plexin functions appear to be regulated by subfamily-specific mechanisms, some of which involve different Rho family GTPases.

  18. DBD2BS: connecting a DNA-binding protein with its binding sites.

    Science.gov (United States)

    Chien, Ting-Ying; Lin, Chih-Kang; Lin, Chih-Wei; Weng, Yi-Zhong; Chen, Chien-Yu; Chang, Darby Tien-Hao

    2012-07-01

    By binding to short and highly conserved DNA sequences in genomes, DNA-binding proteins initiate, enhance or repress biological processes. Accurately identifying such binding sites, often represented by position weight matrices (PWMs), is an important step in understanding the control mechanisms of cells. When given coordinates of a DNA-binding domain (DBD) bound with DNA, a potential function can be used to estimate the change of binding affinity after base substitutions, where the changes can be summarized as a PWM. This technique provides an effective alternative when the chromatin immunoprecipitation data are unavailable for PWM inference. To facilitate the procedure of predicting PWMs based on protein-DNA complexes or even structures of the unbound state, the web server, DBD2BS, is presented in this study. The DBD2BS uses an atom-level knowledge-based potential function to predict PWMs characterizing the sequences to which the query DBD structure can bind. For unbound queries, a list of 1066 DBD-DNA complexes (including 1813 protein chains) is compiled for use as templates for synthesizing bound structures. The DBD2BS provides users with an easy-to-use interface for visualizing the PWMs predicted based on different templates and the spatial relationships of the query protein, the DBDs and the DNAs. The DBD2BS is the first attempt to predict PWMs of DBDs from unbound structures rather than from bound ones. This approach increases the number of existing protein structures that can be exploited when analyzing protein-DNA interactions. In a recent study, the authors showed that the kernel adopted by the DBD2BS can generate PWMs consistent with those obtained from the experimental data. The use of DBD2BS to predict PWMs can be incorporated with sequence-based methods to discover binding sites in genome-wide studies. Available at: http://dbd2bs.csie.ntu.edu.tw/, http://dbd2bs.csbb.ntu.edu.tw/, and http://dbd2bs.ee.ncku.edu.tw.

  19. Structural Signatures of Enzyme Binding Pockets from Order-Independent Surface Alignment: A Study of Metalloendopeptidase and NAD Binding Proteins

    Science.gov (United States)

    Dundas, Joe; Adamian, Larisa; Liang, Jie

    2011-01-01

    Detecting similarities between local binding surfaces can facilitate identification of enzyme binding sites, prediction of enzyme functions, as well as aid in our understanding of enzyme mechanisms. A challenging task is to construct a template of local surface characteristics for a specific enzyme function or binding activity, as the size and shape of binding surfaces of a biochemical function often varies. Here we introduce the concept of signature binding pockets, which captures information about preserved and varied atomic positions at multi-resolution levels. For proteins with complex enzyme binding and activity, multiple signatures arise naturally in our model, which form a signature basis set that characterize this class of proteins. Both signatures and signature basis set can be automatically constructed by a method called Solar (Signature Of Local Active Regions). This method is based on a sequence order independent alignment of computed binding surface pockets. Solar also provides a structure based multiple sequence fragment alignment (MSFA) to facilitate interpretation of computed signatures. For studying a family of evolutionary related proteins, we show that for metzincin metalloendopeptidase, which has a broad spectrum of substrate binding, signature and basis set pockets can be used to discriminate metzincins from other enzymes, to predict the subclass of enzyme functions, and to identify the specific binding surfaces. For studying unrelated proteins which have evolved to bind to the same NAD co-factor, signatures of NAD binding pockets can be constructed and can be used to predict NAD binding proteins and to locate NAD binding pockets. By measuring preservation ratio and location variation, our method can identify residues and atoms important for binding affinity and specificity. In both cases, we show that signatures and signature basis set reveal significant biological insight. PMID:21145898

  20. Kinetics characterization of c-Src binding to lipid membranes: Switching from labile to persistent binding.

    Science.gov (United States)

    Le Roux, Anabel-Lise; Busquets, Maria Antònia; Sagués, Francesc; Pons, Miquel

    2016-02-01

    Cell signaling by the c-Src proto-oncogen requires the attachment of the protein to the inner side of the plasma membrane through the myristoylated N-terminal region, known as the SH4 domain. Additional binding regions of lower affinity are located in the neighbor intrinsically disordered Unique domain and the structured SH3 domain. Here we present a surface plasmon resonance study of the binding of a myristoylated protein including the SH4, Unique and SH3 domains of c-Src to immobilized liposomes. Two distinct binding processes were observed: a fast and a slow one. The second process lead to a persistently bound form (PB) with a slower binding and a much slower dissociation rate than the first one. The association and dissociation of the PB form could be detected using an anti-SH4 antibody. The kinetic analysis revealed that binding of the PB form follows a second order rate law suggesting that it involves the formation of c-Src dimers on the membrane surface. A kinetically equivalent PB form is observed in a myristoylated peptide containing only the SH4 domain but not in a construct including the three domains but with a 12-carbon lauroyl substituent instead of the 14-carbon myristoyl group. The PB form is observed with neutral lipids but its population increases when the immobilized liposomes contain negatively charged lipids. We suggest that the PB form may represent the active signaling form of c-Src while the labile form provides the capacity for fast 2D search of the target signaling site on the membrane surface.

  1. The platelet glycoprotein thrombospondin binds specifically to sulfated glycolipids.

    Science.gov (United States)

    Roberts, D D; Haverstick, D M; Dixit, V M; Frazier, W A; Santoro, S A; Ginsburg, V

    1985-08-05

    The human platelet glycoprotein thrombospondin (TSP) binds specifically and with high affinity to sulfatides (galactosylceramide-I3-sulfate). Binding of 125I-TSP to lipids from sheep and human erythrocytes and human platelets resolved on thin layer chromatograms indicates that sulfatides are the only lipids in the membrane which bind TSP. Binding to less than 2 ng of sulfatide could be detected. TSP failed to bind to other purified lipids including cholesterol 3-sulfate, phospholipids, neutral glycolipids, and gangliosides. Binding of 125I-TSP was inhibited by unlabeled TSP, by low pH, and by reduction of intersubunit disulfide bonds with dithiothreitol. A monoclonal antibody against TSP (A2.5), which inhibits hemagglutination and agglutination of fixed activated platelets by TSP, strongly inhibited TSP binding to sulfatides. A second monoclonal antibody (C6.7), which inhibits hemagglutination and aggregation of thrombin-activated live platelets, weakly inhibited sulfatide binding. Binding was inhibited by high ionic strength and by some monosaccharide sulfates including methyl-alpha-D-GlcNAc-3-sulfate. Neutral sugars did not inhibit. Fucoidan, a sulfated fucan, strongly inhibited binding with 50% inhibition at 0.3 micrograms/ml fucoidan. Other sulfated polysaccharides including heparin and dextran sulfates were good inhibitors, whereas hyaluronic acid and keratan sulfate were very weak.

  2. An Electrostatic Funnel in the GABA-Binding Pathway.

    Directory of Open Access Journals (Sweden)

    Timothy S Carpenter

    2016-04-01

    Full Text Available The γ-aminobutyric acid type A receptor (GABAA-R is a major inhibitory neuroreceptor that is activated by the binding of GABA. The structure of the GABAA-R is well characterized, and many of the binding site residues have been identified. However, most of these residues are obscured behind the C-loop that acts as a cover to the binding site. Thus, the mechanism by which the GABA molecule recognizes the binding site, and the pathway it takes to enter the binding site are both unclear. Through the completion and detailed analysis of 100 short, unbiased, independent molecular dynamics simulations, we have investigated this phenomenon of GABA entering the binding site. In each system, GABA was placed quasi-randomly near the binding site of a GABAA-R homology model, and atomistic simulations were carried out to observe the behavior of the GABA molecules. GABA fully entered the binding site in 19 of the 100 simulations. The pathway taken by these molecules was consistent and non-random; the GABA molecules approach the binding site from below, before passing up behind the C-loop and into the binding site. This binding pathway is driven by long-range electrostatic interactions, whereby the electrostatic field acts as a 'funnel' that sweeps the GABA molecules towards the binding site, at which point more specific atomic interactions take over. These findings define a nuanced mechanism whereby the GABAA-R uses the general zwitterionic features of the GABA molecule to identify a potential ligand some 2 nm away from the binding site.

  3. Method And Apparatus For Detecting Chemical Binding

    Energy Technology Data Exchange (ETDEWEB)

    Warner, Benjamin P. (Los Alamos, NM); Havrilla, George J. (Los Alamos, NM); Miller, Thomasin C. (Los Alamos, NM); Wells, Cyndi A. (Los Alamos, NM)

    2005-02-22

    The method for screening binding between a target binder and potential pharmaceutical chemicals involves sending a solution (preferably an aqueous solution) of the target binder through a conduit to a size exclusion filter, the target binder being too large to pass through the size exclusion filter, and then sending a solution of one or more potential pharmaceutical chemicals (preferably an aqueous solution) through the same conduit to the size exclusion filter after target binder has collected on the filter. The potential pharmaceutical chemicals are small enough to pass through the filter. Afterwards, x-rays are sent from an x-ray source to the size exclusion filter, and if the potential pharmaceutical chemicals form a complex with the target binder, the complex produces an x-ray fluorescence signal having an intensity that indicates that a complex has formed.

  4. Method and apparatus for detecting chemical binding

    Energy Technology Data Exchange (ETDEWEB)

    Warner, Benjamin P. (Los Alamos, NM); Havrilla, George J. (Los Alamos, NM); Miller, Thomasin C. (Los Alamos, NM); Wells, Cyndi A. (Los Alamos, NM)

    2007-07-10

    The method for screening binding between a target binder and potential pharmaceutical chemicals involves sending a solution (preferably an aqueous solution) of the target binder through a conduit to a size exclusion filter, the target binder being too large to pass through the size exclusion filter, and then sending a solution of one or more potential pharmaceutical chemicals (preferably an aqueous solution) through the same conduit to the size exclusion filter after target binder has collected on the filter. The potential pharmaceutical chemicals are small enough to pass through the filter. Afterwards, x-rays are sent from an x-ray source to the size exclusion filter, and if the potential pharmaceutical chemicals form a complex with the target binder, the complex produces an x-ray fluorescence signal having an intensity that indicates that a complex has formed.

  5. Asymmetric Aminalization via Cation-Binding Catalysis

    DEFF Research Database (Denmark)

    Park, Sang Yeon; Liu, Yidong; Oh, Joong Suk

    2017-01-01

    Asymmetric cation-binding catalysis, in principle, can generate "chiral" anionic nucleophiles, where the counter cations are coordinated within chiral environments. Nitrogen-nucleophiles are intrinsically basic, therefore, its use as nucleophiles is often challenging and limiting the scope...... of the reaction. Particularly, a formation of configurationally labile aminal centers with alkyl substituents has been a formidable challenge due to the enamine/imine equilibrium of electrophilic substrates. Herein, we report enantioselective nucleophilic addition reactions of potassium phthalimides to Boc......-protected alkyl- and aryl-substituted α-amido sulfones. In-situ generated imines smoothly reacted with the nitrogen nucleophiles to corresponding aminals with good to excellent enantioselectivitiy under mild reaction conditions. In addition, transformation of aminal products gave biologically relevant...

  6. Variations of nuclear binding with quark masses

    Science.gov (United States)

    Carrillo-Serrano, M. E.; Cloët, I. C.; Tsushima, K.; Thomas, A. W.; Afnan, I. R.

    2013-01-01

    We investigate the variation with light quark mass of the mass of the nucleon as well as the masses of the mesons commonly used in a one-boson-exchange model of the nucleon-nucleon force. Care is taken to evaluate the meson mass shifts at the kinematic point relevant to that problem. Using these results, we evaluate the corresponding changes in the energy of the 1S0 antibound state and the binding energies of the deuteron, triton, and selected finite nuclei by using a one-boson exchange model. The results are discussed in the context of possible corrections to the standard scenario for Big Bang nucleosynthesis in the case where, as suggested by recent observations of quasar absorption spectra, the quark masses may have changed over the age of the Universe.

  7. LNA effects on DNA binding and conformation

    DEFF Research Database (Denmark)

    Pabon-Martinez, Y Vladimir; Xu, You; Villa, Alessandra

    2017-01-01

    hybridization analysis and electrophoretic mobility shift assay with molecular dynamics (MD) simulations to better understand the underlying structural features of modified ONs in stabilizing duplex- and triplex structures. Particularly, we investigated the role played by the position and number of locked...... nucleic acid (LNA) substitutions in the ON when targeting a c-MYC or FXN (Frataxin) sequence. We found that LNA-containing single strand TFOs are conformationally pre-organized for major groove binding. Reduced content of LNA at consecutive positions at the 3'-end of a TFO destabilizes the triplex...... structure, whereas the presence of Twisted Intercalating Nucleic Acid (TINA) at the 3'-end of the TFO increases the rate and extent of triplex formation. A triplex-specific intercalating benzoquinoquinoxaline (BQQ) compound highly stabilizes LNA-containing triplex structures. Moreover, LNA...

  8. FHA domains: Phosphopeptide binding and beyond.

    Science.gov (United States)

    Almawi, Ahmad W; Matthews, Lindsay A; Guarné, Alba

    2017-08-01

    Forkhead-associated (FHA) domains are small phosphopeptide recognition modules found in eubacterial and eukaryotic, but not archeal, genomes. Although they were originally found in forkhead-type transcription factors, they have now been identified in many other signaling proteins. FHA domains share a remarkably conserved fold despite very low sequence conservation. They only have five conserved amino acids that are important for binding to phosphorylated epitopes. Recent work from several laboratories has demonstrated that FHA domains can mediate many interactions that do not depend on their ability to recognize a phosphorylated threonine. In this review, we present structural and biochemical work that has unveiled novel interaction interfaces on FHA domains. We discuss how these non-canonical interactions modulate the recognition of phosphorylated and non-phosphorylated substrates, as well as protein oligomerization - events that collectively determine FHA function. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Chaperone binding at the ribosomal exit tunnel

    DEFF Research Database (Denmark)

    Kristensen, Ole; Gajhede, Michael

    2003-01-01

    The exit tunnel region of the ribosome is well established as a focal point for interaction between the components that guide the fate of nascent polypeptides. One of these, the chaperone trigger factor (TF), associates with the 50S ribosomal subunit through its N-terminal domain. Targeting of TF...... to ribosomes is crucial to achieve its remarkable efficiency in protein folding. A similar tight coupling to translation is found in signal recognition particle (SRP)-dependent protein translocation. Here, we report crystal structures of the E. coli TF ribosome binding domain. TF is structurally related...... to the Hsp33 chaperone but has a prominent ribosome anchor located as a tip of the molecule. This tip includes the previously established unique TF signature motif. Comparison reveals that this feature is not found in SRP structures. We identify a conserved helical kink as a hallmark of the TF structure...

  10. Variations of nuclear binding with quark masses

    CERN Document Server

    Carrillo-Serrano, M E; Tsushima, K; Thomas, A W; Afnan, I R

    2012-01-01

    We investigate the variation with light quark mass of the mass of the nucleon as well as the masses of the mesons commonly used in a one-boson-exchange model of the nucleon-nucleon force. Care is taken to evaluate the meson mass shifts at the kinematic point relevant to that problem. Using these results, the corresponding changes in the energy of the 1 S0 anti-bound state, the binding energies of the deuteron, triton and selected finite nuclei are evaluated using a one-boson exchange model. The results are discussed in the context of possible corrections to the standard scenario for big bang nucleosynthesis in the case where, as suggested by recent observations of quasar absorption spectra, the quark masses may have changed over the age of the Universe.

  11. Physical factors affecting chloroquine binding to melanin.

    Science.gov (United States)

    Schroeder, R L; Pendleton, P; Gerber, J P

    2015-10-01

    Chloroquine is an antimalarial drug but is also prescribed for conditions such as rheumatoid arthritis. Long-term users risk toxic side effects, including retinopathy, thought to be caused by chloroquine accumulation on ocular melanin. Although the binding potential of chloroquine to melanin has been investigated previously, our study is the first to demonstrate clear links between chloroquine adsorption by melanin and system factors including temperature, pH, melanin type, and particle size. In the current work, two Sepia melanins were compared with bovine eye as a representative mammalian melanin. Increasing the surface anionic character due to a pH change from 4.7 to 7.4 increased each melanin's affinity for chloroquine. Although the chloroquine isotherms exhibited an apparently strong interaction with each melanin, isosteric heat analysis indicated a competitive interaction. Buffer solution cations competed effectively at low surface coverage; chloroquine adsorption occurs via buffer cation displacement and is promoted by temperature-influenced secondary structure swelling.

  12. Monoclonal Anti—CD4 Antibody MT310 Binds HIV-1 gp120 Binding Site on CD4

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Tests show the monoclonal anti—CD4 antibody (mAb) MT310 recognizes the gp120-binding site on CD4 as part of its mechanism for strongly inhibiting human immunodeficiency virus type 1 (HIV-1) infection of CD4+ T cells. In competition tests, mAb MT310 and mAb Leu3a (an anti-CD4 mAb recognizing the gp120-binding site) all inhibited gp120-binding to CD4+ T lymphocytes, while mAb MT405 did not. This result suggests that MT310, like Leu3a, recognizes the gp120-binding site on CD4. To further confirm whether MT310 recognizes the gp120-binding site on CD4, we prepared rabbit anti-idiotypic antisera (Ab2) against MT310 (Ab1). The anti-idiotypic antisera against MT310 inhibited binding of MT310 and Leu3a to human CD4+ T lymphocytes, but did not block binding of MT151 with the second domain of CD4, while rabbit anti-idiotypic antisera to MT151 could block binding of itself to these cells, but could not inhibit the binding of MT310 and Leu3a, further indicating that MT310 recognized the gp120-binding site on CD4.

  13. A model for positron binding to polar molecules

    CERN Document Server

    Gribakin, G F

    2015-01-01

    A model for positron binding to polar molecules is considered by combining the dipole potential outside the molecule with a strongly repulsive core of a given radius. Using existing experimental data on binding energies leads to unphysically small core radii for all of the molecules studied. This suggests that electron-positron correlations neglected in the simple model play a large role in determining the binding energy. We account for these by including polarization potential via perturbation theory. The improved model enables reliable predictions of binding energies to be made for a range of polar organic molecules and hydrogen cyanide, whose binding energy is known from accurate quantum chemistry calculations. The model explains the linear dependence of the binding energies on the polarizability inferred from the experimental data [Danielson et al 2009 J. Phys. B: At. Mol. Opt. Phys. 42 235203].

  14. Gliadins bind to reticulin in a lectin-like manner.

    Science.gov (United States)

    Unsworth, D J; Leonard, J N; Hobday, C M; Griffiths, C E; Powles, A V; Haffenden, G P; Fry, L

    1987-01-01

    It has previously been reported that gliadins bind to reticulin in tissue sections. Three lines of evidence are reported in this study which indicate that the gliadins bind to reticulins because they are lectins which bind to sugars expressed on glycoproteins in reticulin and other sites. First, immunofluorescence studies on tissue sections showed that although gliadin binding is largely confined to areas rich in reticulin, it is, nonetheless, also seen in one or two other sites devoid of reticulin. Second, by using fluorescein-labelled lectins of known specificity, it has been shown that the areas to which gliadins bind in tissue sections (including those sites devoid of reticulin) are rich in particular sugars. Third, it has been shown that one of these sugars, alpha-D-mannose, partially inhibited gliadin binding to tissue sections.

  15. DNA-binding specificities of human transcription factors.

    Science.gov (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

    2013-01-17

    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.

  16. Hardware device to physical structure binding and authentication

    Energy Technology Data Exchange (ETDEWEB)

    Hamlet, Jason R.; Stein, David J.; Bauer, Todd M.

    2013-08-20

    Detection and deterrence of device tampering and subversion may be achieved by including a cryptographic fingerprint unit within a hardware device for authenticating a binding of the hardware device and a physical structure. The cryptographic fingerprint unit includes an internal physically unclonable function ("PUF") circuit disposed in or on the hardware device, which generate an internal PUF value. Binding logic is coupled to receive the internal PUF value, as well as an external PUF value associated with the physical structure, and generates a binding PUF value, which represents the binding of the hardware device and the physical structure. The cryptographic fingerprint unit also includes a cryptographic unit that uses the binding PUF value to allow a challenger to authenticate the binding.

  17. Structure and localisation of drug binding sites on neurotransmitter transporters.

    Science.gov (United States)

    Ravna, Aina W; Sylte, Ingebrigt; Dahl, Svein G

    2009-10-01

    The dopamine (DAT), serotontin (SERT) and noradrenalin (NET) transporters are molecular targets for different classes of psychotropic drugs. The crystal structure of Aquifex aeolicus LeuT(Aa) was used as a template for molecular modeling of DAT, SERT and NET, and two putative drug binding sites (pocket 1 and 2) in each transporter were identified. Cocaine was docked into binding pocket 1 of DAT, corresponding to the leucine binding site in LeuT(Aa), which involved transmembrane helices (TMHs) 1, 3, 6 and 8. Clomipramine was docked into binding pocket 2 of DAT, involving TMHs 1, 3, 6, 10 and 11, and extracellular loops 4 and 6, corresponding to the clomipramine binding site in a crystal structure of a LeuT(Aa)-clomipramine complex. The structures of the proposed cocaine- and tricyclic antidepressant-binding sites may be of particular interest for the design of novel DAT interacting ligands.

  18. Studies on the binding of amylopectin sulfate with gastric mucin.

    Science.gov (United States)

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

    1975-07-01

    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.

  19. Topological Analyses of Protein-Ligand Binding: a Network Approach.

    Science.gov (United States)

    Costanzi, Stefano

    2016-01-01

    Proteins can be conveniently represented as networks of interacting residues, thus allowing the study of several network parameters that can shed light onto several of their structural and functional aspects. With respect to the binding of ligands, which are central for the function of many proteins, network analysis may constitute a possible route to assist the identification of binding sites. As the bulk of this review illustrates, this has generally been easier for enzymes than for non-enzyme proteins, perhaps due to the different topological nature of the binding sites of the former over those of the latter. The article also illustrates how network representations of binding sites can be used to search PDB structures in order to identify proteins that bind similar molecules and, lastly, how codifying proteins as networks can assist the analysis of the conformational changes consequent to ligand binding.

  20. TALE proteins bind to both active and inactive chromatin.

    Science.gov (United States)

    Scott, James N F; Kupinski, Adam P; Kirkham, Christopher M; Tuma, Roman; Boyes, Joan

    2014-02-15

    TALE (transcription activator-like effector) proteins can be tailored to bind to any DNA sequence of choice and thus are of immense utility for genome editing and the specific delivery of transcription activators. However, to perform these functions, they need to occupy their sites in chromatin. In the present study, we have systematically assessed TALE binding to chromatin substrates and find that in vitro TALEs bind to their target site on nucleosomes at the more accessible entry/exit sites, but not at the nucleosome dyad. We show further that in vivo TALEs bind to transcriptionally repressed chromatin and that transcription increases binding by only 2-fold. These data therefore imply that TALEs are likely to bind to their target in vivo even at inactive loci.

  1. Rapid identification of DNA-binding proteins by mass spectrometry

    DEFF Research Database (Denmark)

    Nordhoff, E; Krogsdam, A M; Jorgensen, H F

    1999-01-01

    We report a protocol for the rapid identification of DNA-binding proteins. Immobilized DNA probes harboring a specific sequence motif are incubated with cell or nuclear extract. Proteins are analyzed directly off the solid support by matrix-assisted laser desorption/ionization time-of-flight mass...... was validated by the identification of known prokaryotic and eukaryotic DNA-binding proteins, and its use provided evidence that poly(ADP-ribose) polymerase exhibits DNA sequence-specific binding to DNA....

  2. Diversity of Cyclic Di-GMP-Binding Proteins and Mechanisms.

    Science.gov (United States)

    Chou, Shan-Ho; Galperin, Michael Y

    2016-01-01

    Cyclic di-GMP (c-di-GMP) synthetases and hydrolases (GGDEF, EAL, and HD-GYP domains) can be readily identified in bacterial genome sequences by using standard bioinformatic tools. In contrast, identification of c-di-GMP receptors remains a difficult task, and the current list of experimentally characterized c-di-GMP-binding proteins is likely incomplete. Several classes of c-di-GMP-binding proteins have been structurally characterized; for some others, the binding sites have been identified; and for several potential c-di-GMP receptors, the binding sites remain to be determined. We present here a comparative structural analysis of c-di-GMP-protein complexes that aims to discern the common themes in the binding mechanisms that allow c-di-GMP receptors to bind it with (sub)micromolar affinities despite the 1,000-fold excess of GTP. The available structures show that most receptors use their Arg and Asp/Glu residues to bind c-di-GMP monomers, dimers, or tetramers with stacked guanine bases. The only exception is the EAL domains that bind c-di-GMP monomers in an extended conformation. We show that in c-di-GMP-binding signature motifs, Arg residues bind to the O-6 and N-7 atoms at the Hoogsteen edge of the guanine base, while Asp/Glu residues bind the N-1 and N-2 atoms at its Watson-Crick edge. In addition, Arg residues participate in stacking interactions with the guanine bases of c-di-GMP and the aromatic rings of Tyr and Phe residues. This may account for the presence of Arg residues in the active sites of every receptor protein that binds stacked c-di-GMP. We also discuss the implications of these structural data for the improved understanding of the c-di-GMP signaling mechanisms.

  3. AFM studies of nonspecific binding of enzyme on DNA

    Institute of Scientific and Technical Information of China (English)

    张益; 谢恒月; 等

    1996-01-01

    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.

  4. Microfluidic Screening of Electrophoretic Mobility Shifts Elucidates Riboswitch Binding Function

    OpenAIRE

    Karns, Kelly; Vogan, Jacob M.; Qin, Qian; Hickey, Scott F.; Wilson, Stephen C.; Hammond, Ming C.; Herr, Amy E.

    2013-01-01

    Riboswitches are RNA sensors that change conformation upon binding small molecule metabolites, in turn modulating gene expression. Our understanding of riboswitch regulatory function would be accelerated by a high throughput, quantitative screening tool capable of measuring riboswitch-ligand binding. We introduce a microfluidic mobility shift assay that enables precise and rapid quantitation of ligand binding and subsequent riboswitch conformational change. In 0.3% of the time required for be...

  5. Periplasmic binding proteins: a versatile superfamily for protein engineering.

    Science.gov (United States)

    Dwyer, Mary A; Hellinga, Homme W

    2004-08-01

    The diversity of biological function, ligand binding, conformational changes and structural adaptability of the periplasmic binding protein superfamily have been exploited to engineer biosensors, allosteric control elements, biologically active receptors and enzymes using a combination of techniques, including computational design. Extensively redesigned periplasmic binding proteins have been re-introduced into bacteria to function in synthetic signal transduction pathways that respond to extracellular ligands and as biologically active enzymes.

  6. Thermodynamics of sequence-specific binding of PNA to DNA

    DEFF Research Database (Denmark)

    Ratilainen, T; Holmén, A; Tuite, E

    2000-01-01

    For further characterization of the hybridization properties of peptide nucleic acids (PNAs), the thermodynamics of hybridization of mixed sequence PNA-DNA duplexes have been studied. We have characterized the binding of PNA to DNA in terms of binding affinity (perfectly matched duplexes) and seq......For further characterization of the hybridization properties of peptide nucleic acids (PNAs), the thermodynamics of hybridization of mixed sequence PNA-DNA duplexes have been studied. We have characterized the binding of PNA to DNA in terms of binding affinity (perfectly matched duplexes...

  7. Discodermolide interferes with the binding of tau protein to microtubules.

    Science.gov (United States)

    Kar, Santwana; Florence, Gordon J; Paterson, Ian; Amos, Linda A

    2003-03-27

    We investigated whether discodermolide, a novel antimitotic agent, affects the binding to microtubules of tau protein repeat motifs. Like taxol, the new drug reduces the proportion of tau that pellets with microtubules. Despite their differing structures, discodermolide, taxol and tau repeats all bind to a site on beta-tubulin that lies within the microtubule lumen and is crucial in controlling microtubule assembly. Low concentrations of tau still bind strongly to the outer surfaces of preformed microtubules when the acidic C-terminal regions of at least six tubulin dimers are available for interaction with each tau molecule; otherwise binding is very weak.

  8. Penicillin-binding site on the Escherichia coli cell envelope.

    OpenAIRE

    Amaral, L; Lee, Y.; Schwarz, U.; Lorian, V

    1986-01-01

    The binding of 35S-labeled penicillin to distinct penicillin-binding proteins (PBPs) of the "cell envelope" obtained from the sonication of Escherichia coli was studied at different pHs ranging from 4 to 11. At low pH, PBPs 1b, 1c, 2, and 3 demonstrated the greatest amount of binding. At high pH, these PBPs bound the least amount of penicillin. PBPs 1a and 5/6 exhibited the greatest amount of binding at pH 10 and the least amount at pH 4. With the exception of PBP 5/6, the effect of pH on the...

  9. The enigmatic drug binding site for sodium channel inhibitors.

    Science.gov (United States)

    Mike, Arpad; Lukacs, Peter

    2010-11-01

    Local anesthetics have been in clinical use since 1884, and different aspects of the local anesthetic binding site have been studied in enormous detail. In spite of all these efforts, some of the most fundamental questions--such as which exact residues constitute the binding site, how many binding sites exist, do local anesthetics share their binding site(s) with other sodium channel inhibitors, and what are the mechanisms of inhibition--are still largely unanswered. We review accumulated data on the "local anesthetic receptor"and discuss controversial points, such as possible mechanisms of inhibition, the possibility of additional binding sites, the orientation of S6 helices, and the internal vs. external position of the anticonvulsant binding site. We describe the four following specific groups of functionally important residues: i) conserved asparagines six residues below the hinge residues; we propose that they are oriented toward the external surface of S6 helices, and have a critical role in the coupling of voltage sensors to gating, ii) residues lining the inner vestibule and constructing the "orthodox" binding site, iii) residues around the outer vestibule, which have been proposed to constitute an alternative external binding site, and iv) residues determining external access for quaternary amine inhibitors, such as QX314. We conclude that sodium channel inhibitors must be heterogenous in terms of binding sites and inhibition mechanisms, and propose that this heterogeneity should be taken into consideration during drug development.

  10. Oligosaccharide binding to barley alpha-amylase 1

    DEFF Research Database (Denmark)

    Robert, X.; Haser, R.; Mori, H.

    2005-01-01

    Enzymatic subsite mapping earlier predicted 10 binding subsites in the active site substrate binding cleft of barley alpha-amylase isozymes. The three-dimensional structures of the oligosaccharide complexes with barley alpha-amylase isozyme 1 (AMY1) described here give for the first time a thorough...... in barley alpha-amylase isozyme 2 (AMY2), and the sugar binding modes are compared between the two isozymes. The "sugar tongs" surface binding site discovered in the AMY1-thio-DP4 complex is confirmed in the present work. A site that putatively serves as an entrance for the substrate to the active site...

  11. Distinct binding properties of TIAR RRMs and linker region.

    Science.gov (United States)

    Kim, Henry S; Headey, Stephen J; Yoga, Yano M K; Scanlon, Martin J; Gorospe, Myriam; Wilce, Matthew C J; Wilce, Jacqueline A

    2013-04-01

    The RNA-binding protein TIAR is an mRNA-binding protein that acts as a translational repressor, particularly important under conditions of cellular stress. It binds to target mRNA and DNA via its RNA recognition motif (RRM) domains and is involved in both splicing regulation and translational repression via the formation of "stress granules." TIAR has also been shown to bind ssDNA and play a role in the regulation of transcription. Here we show, using surface plasmon resonance and nuclear magnetic resonance spectroscopy, specific roles of individual TIAR domains for high-affinity binding to RNA and DNA targets. We confirm that RRM2 of TIAR is the major RNA- and DNA-binding domain. However, the strong nanomolar affinity binding to U-rich RNA and T-rich DNA depends on the presence of the six amino acid residues found in the linker region C-terminal to RRM2. On its own, RRM1 shows preferred binding to DNA over RNA. We further characterize the interaction between RRM2 with the C-terminal extension and an AU-rich target RNA sequence using NMR spectroscopy to identify the amino acid residues involved in binding. We demonstrate that TIAR RRM2, together with its C-terminal extension, is the major contributor for the high-affinity (nM) interactions of TIAR with target RNA sequences.

  12. High-Fidelity DNA Sensing by Protein Binding Fluctuations

    CERN Document Server

    Tlusty, Tsvi; Libchaber, Albert; 10.1103/PhysRevLett.93.258103

    2010-01-01

    One of the major functions of RecA protein in the cell is to bind single-stranded DNA exposed upon damage, thereby triggering the SOS repair response.We present fluorescence anisotropy measurements at the binding onset, showing enhanced DNA length discrimination induced by adenosine triphosphate consumption. Our model explains the observed DNA length sensing as an outcome of out-of equilibrium binding fluctuations, reminiscent of microtubule dynamic instability. The cascade architecture of the binding fluctuations is a generalization of the kinetic proofreading mechanism. Enhancement of precision by an irreversible multistage pathway is a possible design principle in the noisy biological environment.

  13. In vitro auxin binding to cellular membranes of cucumber fruits.

    Science.gov (United States)

    Narayanan, K R; Mudge, K W; Poovaiah, B W

    1981-04-01

    Specific binding of 1-naphthaleneacetic acid (NAA) to crude membrane preparations from cucumber (Cucumis sativus L.) was demonstrated. This in vitro binding had a pH optimum of 3.75 and an equilibrium dissociation constant of 10 to 20 micromolar with 1250 picomoles binding sites per gram fresh weight. The NAA-binding sites were pronase sensitive. The supernatant from the fruit partially inhibited the in vitro NAA binding to fruit membranes. NAA, 2-naphthoxyacetic acid, 3-indoleacetic acid, 2-4-dichlorophenoxyacetic acid, and 2,3,5-triiodobenzoic acid, which are reported to be very good inducers of parthenocarpy in cucumber, showed a high degree of specific binding to cucumber fruit membranes. In comparison, 2-naphthaleneacetic acid and indolepropionic acid, which are reported to be very weak auxins in corn coleoptile, pea stem, and strawberry fruit growth bioassays, did not bind efficiently to cucumber fruit membranes. In vitro binding studies with fruit membranes suggest that auxin stimulated fruit growth may be mediated by membrane-associated, auxin-binding protein(s).

  14. Regulation of inositol phospholipid binding and signaling through syndecan-4

    DEFF Research Database (Denmark)

    Couchman, John R; Vogt, Susan; Lim, Ssang-Taek

    2002-01-01

    inositol phospholipids. In turn, lipid binding stabilizes the syndecan in oligomeric form, with subsequent binding and activation of protein kinase C. The specificity of phospholipid binding and its potential regulation are investigated here. Highest affinity of the syndecan-4 cytoplasmic domain was seen......-regulator of syndecan-4 signaling. Similarly, phosphorylation of serine 183 in syndecan-4 cytoplasmic domain reduced PtdIns(4,5)P(2) binding affinity by over 100-fold, although interaction could still be detected by nuclear magnetic resonance spectroscopy. Only protein kinase Calpha was up-regulated in activity...

  15. Comparative binding energy COMBINE analysis for understanding the binding determinants of type II dehydroquinase inhibitors.

    Science.gov (United States)

    Peón, Antonio; Coderch, Claire; Gago, Federico; González-Bello, Concepción

    2013-05-01

    Herein we report comparative binding energy (COMBINE) analyses to derive quantitative structure-activity relationship (QSAR) models that help rationalize the determinants of binding affinity for inhibitors of type II dehydroquinase (DHQ2), the third enzyme of the shikimic acid pathway. Independent COMBINE models were derived for Helicobacter pylori and Mycobacterium tuberculosis DHQ2, which is an essential enzyme in both these pathogenic bacteria that has no counterpart in human cells. These studies quantify the importance of the hydrogen bonding interactions between the ligands and the water molecule involved in the DHQ2 reaction mechanism. They also highlight important differences in the ligand interactions with the interface pocket close to the active site that could provide guides for future inhibitor design.

  16. Cortisol levels, binding, and properties of corticosteroid-binding globulin in the serum of primates.

    Science.gov (United States)

    Klosterman, L L; Murai, J T; Siiteri, P K

    1986-01-01

    New World primates have exceptionally high plasma levels of cortisol and other steroid hormones when compared with humans and other primates. It has been suggested that this difference can be explained by either low affinity or concentration of cellular steroid receptors. We have assessed cortisol availability in serum from several species of New and Old World primates under physiological conditions (whole serum at 37 degrees C). Measurements were made of total and free cortisol, corticosteroid-binding globulin (CBG) binding capacity and affinity for cortisol, distribution of cortisol in serum, and its binding to albumin. In agreement with earlier reports, plasma free cortisol levels in Old World primates, prosimians, and humans range from 10-300 nM. However, very high total plasma cortisol together with low CBG binding capacity and affinity result in free cortisol concentrations of 1-4 microM in some New World primates (squirrel monkey and marmosets) but not in others such as the titi and capuchin. In squirrel monkeys, free cortisol levels are far greater than might be predicted from the affinity of the glucocorticoid receptor estimated in cultured skin fibroblasts. In addition to low affinity, CBG from squirrel monkeys and other New World primates exhibits differences in electrophoretic mobility and sedimentation behavior in sucrose density ultracentrifugation, suggestive of a molecular weight that is approximately twice that of CBG from other species. Together with other data these results indicate that the apparent glucocorticoid resistance found in New World primates is a complex phenomenon that is not easily explained by present concepts of glucocorticoid action.

  17. Comprehensive human transcription factor binding site map for combinatory binding motifs discovery.

    Directory of Open Access Journals (Sweden)

    Arnoldo J Müller-Molina

    Full Text Available To know the map between transcription factors (TFs and their binding sites is essential to reverse engineer the regulation process. Only about 10%-20% of the transcription factor binding motifs (TFBMs have been reported. This lack of data hinders understanding gene regulation. To address this drawback, we propose a computational method that exploits never used TF properties to discover the missing TFBMs and their sites in all human gene promoters. The method starts by predicting a dictionary of regulatory "DNA words." From this dictionary, it distills 4098 novel predictions. To disclose the crosstalk between motifs, an additional algorithm extracts TF combinatorial binding patterns creating a collection of TF regulatory syntactic rules. Using these rules, we narrowed down a list of 504 novel motifs that appear frequently in syntax patterns. We tested the predictions against 509 known motifs confirming that our system can reliably predict ab initio motifs with an accuracy of 81%-far higher than previous approaches. We found that on average, 90% of the discovered combinatorial binding patterns target at least 10 genes, suggesting that to control in an independent manner smaller gene sets, supplementary regulatory mechanisms are required. Additionally, we discovered that the new TFBMs and their combinatorial patterns convey biological meaning, targeting TFs and genes related to developmental functions. Thus, among all the possible available targets in the genome, the TFs tend to regulate other TFs and genes involved in developmental functions. We provide a comprehensive resource for regulation analysis that includes a dictionary of "DNA words," newly predicted motifs and their corresponding combinatorial patterns. Combinatorial patterns are a useful filter to discover TFBMs that play a major role in orchestrating other factors and thus, are likely to lock/unlock cellular functional clusters.

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

    OpenAIRE

    Olberg, Dag Erlend

    2004-01-01

    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...

  19. Lectin binding patterns and carbohydrate mediation of sperm binding to llama oviductal cells in vitro.

    Science.gov (United States)

    Apichela, Silvana A; Valz-Gianinet, Jorge N; Schuster, Stefanie; Jiménez-Díaz, María A; Roldán-Olarte, Eugenia M; Miceli, Dora C

    2010-04-01

    Sperm binding to oviductal epithelium would be involved in sperm reservoir formation in the utero tubal junction (UTJ). Although in other mammals sperm-oviduct interaction has been proved to be mediated by carbohydrate-recognition mechanisms, the factors implicated in the sperm adhesion to oviductal epithelium of llama are still unknown. In order to assess the role of carbohydrates present in the mucosa surface, we examined the distribution of glycoconjugates in the llama oviduct by confocal lectin-histochemistry. Mannosyl, glucosyl, N-acetylglucosaminyl, galactosyl, N-acetylgalactosaminyl and sialic acid residues were detected in the oviductal mucose glycocalyx. By incubation of UTJ oviductal explants with LCA, DBA, UEA-1 or PNA lectin previous to co-culture with sperm, we observed a significant decrease in sperm binding only with LCA lectin. In the mucosa surface there were numerous d-glucosyl and D-manosyl residues, which were spotted by this lectin. Probably, this fact promotes the whole covering of the oviduct luminal surface by the sugar-lectin complex, preventing sperm access and adhesion of further residues. However, sperm incubation with mannose or glucose does not significantly prevent binding, which means that glucose and mannose would not be involved in a specific sperm-oviduct interaction. On the other hand, we observed a high reduction in sperm binding to UTJ explants with N-acetylgalactosamine and galactose (pllama sperm have lectin-like molecules in their surface, as is the case in other mammals. Probably, these lectin-like molecules, by means of N-acetylgalactosamine and galactose recognition, could link the sperm to the oviductal mucosa with the purpose of forming storing sites in the UTJ. Our results support the idea that more than one carbohydrate could participate in sperm reservoir formation in the llama UTJ oviductal segment.

  20. The Relationship between Albumin-Binding Capacity of Recombinant Polypeptide and Changes in the Structure of Albumin-Binding Domain.

    Science.gov (United States)

    Bormotova, E A; Gupalova, T V

    2015-07-01

    Many bacteria express surface proteins interacting with human serum albumin (HSA). One of these proteins, PAB from anaerobic bacteria, contains an albumin-binding domain consisting of 45 amino acid residues known as GA domain. GA domains are also found in G proteins isolated from human streptococcal strains (groups C and G) and of albumin-binding protein isolated from group G streptococcal strains of animal origin. The GA domain is a left-handed three-helix bundle structure in which amino acid residues of the second and third helixes are involved in albumin binding. We studied the relationship between HSA-binding activity of the recombinant polypeptide isolated from group G streptococcus of animal origin and structure of the GA domain is studied. Structural changes in GA domain significantly attenuated HAS-binding capacity of the recombinant polypeptide. Hence, affinity HSA-binding polypeptide depends on stability of GA domain structure.

  1. The binding cavity of mouse major urinary protein is optimised for a variety of ligand binding modes

    Energy Technology Data Exchange (ETDEWEB)

    Pertinhez, Thelma A.; Ferrari, Elena; Casali, Emanuela [Department of Experimental Medicine, University of Parma, Via Volturno, 39, 43100 Parma (Italy); Patel, Jital A. [Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR (United Kingdom); Spisni, Alberto, E-mail: alberto.spisni@unipr.it [Department of Experimental Medicine, University of Parma, Via Volturno, 39, 43100 Parma (Italy); Smith, Lorna J., E-mail: lorna.smith@chem.ox.ac.uk [Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR (United Kingdom)

    2009-12-25

    {sup 15}N and {sup 1}HN chemical shift data and {sup 15}N relaxation studies have been used to characterise the binding of N-phenyl-naphthylamine (NPN) to mouse major urinary protein (MUP). NPN binds in the {beta}-barrel cavity of MUP, hydrogen bonding to Tyr120 and making extensive non-bonded contacts with hydrophobic side chains. In contrast to the natural pheromone 2-sec-butyl-4,5-dihydrothiazole, NPN binding gives no change to the overall mobility of the protein backbone of MUP. Comparison with 11 different ligands that bind to MUP shows a range of binding modes involving 16 different residues in the {beta}-barrel cavity. These finding justify why MUP is able to adapt to allow for many successful binding partners.

  2. Discover binding pathways using the sliding binding-box docking approach: application to binding pathways of oseltamivir to avian influenza H5N1 neuraminidase

    Science.gov (United States)

    Tran, Diem-Trang T.; Le, Ly T.; Truong, Thanh N.

    2013-08-01

    Drug binding and unbinding are transient processes which are hardly observed by experiment and difficult to analyze by computational techniques. In this paper, we employed a cost-effective method called "pathway docking" in which molecular docking was used to screen ligand-receptor binding free energy surface to reveal possible paths of ligand approaching protein binding pocket. A case study was applied on oseltamivir, the key drug against influenza a virus. The equilibrium pathways identified by this method are found to be similar to those identified in prior studies using highly expensive computational approaches.

  3. Synthesis, characterization, DNA binding, DNA cleavage, protein binding and cytotoxic activities of Ru(II) complexes.

    Science.gov (United States)

    Thota, Sreekanth; Vallala, Srujana; Yerra, Rajeshwar; Rodrigues, Daniel Alencar; Raghavendra, Nulgumnalli Manjunathaiah; Barreiro, Eliezer J

    2016-01-01

    We report on the synthesis of novel Ru(II) compounds (Ru-1 to Ru-8) bearing R-pdc, 4-Cl-pbinh ligands (where R=4-CF3, 4-F, 4-OH pdc=3-phenyl-5-(1H-pyrrol-2-yl)-4,5-dihydro-1H-pyrazole-1-carbothioamide, pbinh=phenoxybenzylidene isonicotinyl hydrazides) and their in vitro antitumor activity toward the cell lines murine leukemia L1210, human lymphocyte CEM, human epithelial cervical carcinoma HeLa, BEL-7402 and Molt4/C8. Some of the complexes exhibited more potent antiproliferative activity against cell lines than the standard drug cisplatin. Ruthenium complex Ru-2 displayed potent cytotoxicity with than that of cisplatin. DNA-binding, DNA cleavage and protein binding properties of ruthenium complexes with these ligands are reported. Interactions of these ruthenium complexes with DNA revealed an intercalative mode of binding between them. Synchronous fluorescence spectra proved that the interaction of ruthenium complexes with bovine serum albumin (BSA) resulted in a conformational change of the latter.

  4. 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

    2007-01-01

    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.

  5. Dynamics of biomolecules, ligand binding & biological functions

    Science.gov (United States)

    Yi, Myunggi

    Proteins are flexible and dynamic. One static structure alone does not often completely explain biological functions of the protein, and some proteins do not even have high resolution structures. In order to provide better understanding to the biological functions of nicotinic acetylcholine receptor, Diphtheria toxin repressor and M2 proton channel, the dynamics of these proteins are investigated using molecular modeling and molecular dynamics (MD) simulations. With absence of high resolution structure of alpha7 receptor, the homology models of apo and cobra toxin bound forms have been built. From the MD simulations of these model structures, we observed one subunit of apo simulation moved away from other four subunits. With local movement of flexible loop regions, the whole subunit tilted clockwise. These conformational changes occurred spontaneously, and were strongly correlated with the conformational change when the channel is activated by agonists. Unlike other computational studies, we directly compared our model of open conformation with the experimental data. However, the subunits of toxin bound form were stable, and conformational change is restricted by the bound cobra toxin. These results provide activation and inhibition mechanisms of alpha7 receptors and a possible explanation for intermediate conductance of the channel. Intramolecular complex of SH3-like domain with a proline-rich (Pr) peptide segment in Diphtheria toxin repressor (DtxR) is stabilized in inactive state. Upon activation of DtxR by transition metal binding, this intramolecular complex should be dissociated. The dynamics of this intramolecular complex is investigated using MD simulations and NMR spectroscopy. We observed spontaneous opening and closing motions of the Pr segment binding pockets in both Pr-SH3 and SH3 simulations. The MD simulation results and NMR relaxation data suggest that the Pr segment exhibits a binding ↔ unbinding equilibrium. Despite a wealth of experimental

  6. Structures and binding specificity of galactose- and mannose-binding lectins from champedak: differences from jackfruit lectins.

    Science.gov (United States)

    Gabrielsen, Mads; Abdul-Rahman, Puteri Shafinaz; Othman, Shatrah; Hashim, Onn H; Cogdell, Richard J

    2014-06-01

    Galactose-binding and mannose-binding lectins from the champedak fruit, which is native to South-east Asia, exhibit useful potential clinical applications. The specificity of the two lectins for their respective ligands allows the detection of potential cancer biomarkers and monitoring of the glycosylated state of proteins in human serum and/or urine. To fully understand and expand the use of these natural proteins, their complete sequences and crystal structures are presented here, together with details of sugar binding.

  7. The Plasminogen-Binding Group A Streptococcal M Protein-Related Protein Prp Binds Plasminogen via Arginine and Histidine Residues▿

    OpenAIRE

    Martina L. Sanderson-Smith; Dowton, Mark; Ranson, Marie; Walker, Mark J.

    2006-01-01

    The migration of the human pathogen Streptococcus pyogenes (group A streptococcus) from localized to deep tissue sites may result in severe invasive disease, and sequestration of the host zymogen plasminogen appears crucial for virulence. Here, we describe a novel plasminogen-binding M protein, the plasminogen-binding group A streptococcal M protein (PAM)-related protein (Prp). Prp is phylogenetically distinct from previously described plasminogen-binding M proteins of group A, C, and G strep...

  8. Identification and characterisation of a novel adhesin Ifp in Yersinia pseudotuberculosis

    Directory of Open Access Journals (Sweden)

    Champion Olivia L

    2011-04-01

    Full Text Available Abstract Background In order to identify new virulence determinants in Y. pseudotuberculosis a comparison between its genome and that of Yersinia pestis was undertaken. This reveals dozens of pseudogenes in Y. pestis, which are still putatively functional in Y. pseudotuberculosis and may be important in the enteric lifestyle. One such gene, YPTB1572 in the Y. pseudotuberculosis IP32953 genome sequence, encodes a protein with similarity to invasin, a classic adhesion/invasion protein, and to intimin, the attaching and effacing protein from enteropathogenic (EPEC and enterohaemorraghic (EHEC Escherichia coli. Results We termed YPTB1572 Ifp (Intimin family protein and show that it is able to bind directly to human HEp-2 epithelial cells. Cysteine and tryptophan residues in the C-terminal region of intimin that are essential for function in EPEC and EHEC are conserved in Ifp. Protein binding occurred at distinct foci on the HEp-2 cell surface and can be disrupted by mutation of a single cysteine residue at the C-terminus of the protein. Temporal expression analysis using lux reporter constructs revealed that ifp is expressed at late log phase at 37°C in contrast to invasin, suggesting that Ifp is a late stage adhesin. An ifp defined mutant showed a reduction in adhesion to HEp-2 cells and was attenuated in the Galleria mellonella infection model. Conclusion A new Y. pseudotuberculosis adhesin has been identified and characterised. This Ifp is a new member in the family of invasin/intimin outer membrane adhesins.

  9. Isothermal titration calorimetry and surface plasmon resonance allow quantifying substrate binding to different binding sites of Bacillus subtilis xylanase

    DEFF Research Database (Denmark)

    Cuyvers, Sven; Dornez, Emmie; Abou Hachem, Maher

    2012-01-01

    Isothermal titration calorimetry and surface plasmon resonance were tested for their ability to study substrate binding to the active site (AS) and to the secondary binding site (SBS) of Bacillus subtilis xylanase A separately. To this end, three enzyme variants were compared. The first was a cat......Isothermal titration calorimetry and surface plasmon resonance were tested for their ability to study substrate binding to the active site (AS) and to the secondary binding site (SBS) of Bacillus subtilis xylanase A separately. To this end, three enzyme variants were compared. The first...

  10. Predicting DNA-binding proteins and binding residues by complex structure prediction and application to human proteome.

    Directory of Open Access Journals (Sweden)

    Huiying Zhao

    Full Text Available As more and more protein sequences are uncovered from increasingly inexpensive sequencing techniques, an urgent task is to find their functions. This work presents a highly reliable computational technique for predicting DNA-binding function at the level of protein-DNA complex structures, rather than low-resolution two-state prediction of DNA-binding as most existing techniques do. The method first predicts protein-DNA complex structure by utilizing the template-based structure prediction technique HHblits, followed by binding affinity prediction based on a knowledge-based energy function (Distance-scaled finite ideal-gas reference state for protein-DNA interactions. A leave-one-out cross validation of the method based on 179 DNA-binding and 3797 non-binding protein domains achieves a Matthews correlation coefficient (MCC of 0.77 with high precision (94% and high sensitivity (65%. We further found 51% sensitivity for 82 newly determined structures of DNA-binding proteins and 56% sensitivity for the human proteome. In addition, the method provides a reasonably accurate prediction of DNA-binding residues in proteins based on predicted DNA-binding complex structures. Its application to human proteome leads to more than 300 novel DNA-binding proteins; some of these predicted structures were validated by known structures of homologous proteins in APO forms. The method [SPOT-Seq (DNA] is available as an on-line server at http://sparks-lab.org.

  11. The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes

    OpenAIRE

    Neugebauer, Karla M.; Änkö, Minna-Liisa; Müller-McNicoll, Michaela; Brandl, Holger; Henry, Ian; Gorup, Črtomir; Curk, Tomaž; Ule, Jernej

    2015-01-01

    Background The SR proteins comprise a family of essential, structurally related RNA binding proteins. The complexity of their RNA targets and specificity of RNA recognition in vivo is not well understood. Here we use iCLIP to globally analyze and compare the RNA binding properties of two SR proteins, SRSF3 and SRSF4, in murine cells. Results SRSF3 and SRSF4 binding sites mapped to largely non-overlapping target genes, and in vivo consensus binding motifs were distinct. Interactions with intro...

  12. Allostery between two binding sites in the ion channel subunit TRIP8b confers binding specificity to HCN channels.

    Science.gov (United States)

    Lyman, Kyle A; Han, Ye; Heuermann, Robert J; Cheng, Xiangying; Kurz, Jonathan E; Lyman, Reagan E; Van Veldhoven, Paul P; Chetkovich, Dane M

    2017-09-08

    Tetratricopeptide repeat (TPR) domains are ubiquitous structural motifs that mediate protein-protein interactions. For example, the TPR domains in the peroxisomal import receptor PEX5 enable binding to a range of type 1 peroxisomal targeting signal (PTS1) motifs. A homolog of PEX5, tetratricopeptide repeat-containing Rab8b interacting protein (TRIP8b), binds to and functions as an auxiliary subunit of hyperpolarization-activated cyclic nucleotide-gated (HCN) channels. Given the similarity between TRIP8b and PEX5, this difference in function raises the question of what mechanism accounts for their binding specificity. In this report, we found that the cyclic nucleotide-binding domain (CNBD) and the C-terminus of the HCN channel are critical for conferring specificity to TRIP8b binding. We show that TRIP8b binds the HCN CNBD through a 37-residue domain and the HCN C-terminus through the TPR domains. Using a combination of fluorescence polarization and co-immunoprecipitation based assays, we establish that binding at either site increases affinity at the other. Thus, allosteric coupling of the TRIP8b TPR domains both promotes binding to HCN channels and limits binding to PTS1 substrates. These results raise the possibility that other TPR domains may similarly be influenced by allosteric mechanisms as a general feature of protein-protein interactions. Copyright © 2017, The American Society for Biochemistry and Molecular Biology.

  13. In vitro characterization of cocaine binding sites in human hair.

    Science.gov (United States)

    Joseph, R E; Tsai, W J; Tsao, L I; Su, T P; Cone, E J

    1997-09-01

    In vitro studies were performed to characterize [3H]cocaine binding to dark and light ethnic hair types. In vitro binding to hair was selective, was reversible and increased linearly with increasing hair concentration. Scatchard analyses revealed high-affinity (6-112 nM) and low-affinity (906-4433 nM) binding in hair. Competition studies demonstrated that the potencies of 3beta-(4-bromophenyl)tropane-2beta-carboxylic acid methyl ester, and 5-(4-chlorophenyl)-2,5-dihydro-3H-imidazol[2,1-alpha]isoindole-5-ol and 2beta-carbomethoxy-3beta-(4-fluorophenyl)tropane were similar to or less than that of (-)-cocaine. The potency of (-)-cocaine was 10-fold greater than that of (+)-cocaine at inhibiting radioligand specific binding to hair. Multivariate analysis indicated that significantly greater nonspecific and specific radioligand binding occurred in dark hair than in light hair. Multivariate analysis also demonstrated a significant ethnicity x sex effect on specific and nonspecific binding to hair. Greater radioligand binding occurred in male Africoid hair than in female Africoid hair and in all Caucasoid hair types. Melanin was considered the most likely binding site for cocaine in hair. Typically, the concentration of melanin is much greater in dark than in light hair. Scatchard analysis indicated that dark hair had a 5- to 43-fold greater binding capacity than light hair. Differences in radioligand binding between hair types appeared to be due to differences in the density of binding sites formed by melanin in hair.

  14. Nuclear Binding Near a Quantum Phase Transition

    Science.gov (United States)

    Elhatisari, Serdar; Li, Ning; Rokash, Alexander; Alarcón, Jose Manuel; Du, Dechuan; Klein, Nico; Lu, Bing-nan; Meißner, Ulf-G.; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A.; Lee, Dean; Rupak, Gautam

    2016-09-01

    How do protons and neutrons bind to form nuclei? This is the central question of ab initio nuclear structure theory. While the answer may seem as simple as the fact that nuclear forces are attractive, the full story is more complex and interesting. In this work we present numerical evidence from ab initio lattice simulations showing that nature is near a quantum phase transition, a zero-temperature transition driven by quantum fluctuations. Using lattice effective field theory, we perform Monte Carlo simulations for systems with up to twenty nucleons. For even and equal numbers of protons and neutrons, we discover a first-order transition at zero temperature from a Bose-condensed gas of alpha particles (4He nuclei) to a nuclear liquid. Whether one has an alpha-particle gas or nuclear liquid is determined by the strength of the alpha-alpha interactions, and we show that the alpha-alpha interactions depend on the strength and locality of the nucleon-nucleon interactions. This insight should be useful in improving calculations of nuclear structure and important astrophysical reactions involving alpha capture on nuclei. Our findings also provide a tool to probe the structure of alpha cluster states such as the Hoyle state responsible for the production of carbon in red giant stars and point to a connection between nuclear states and the universal physics of bosons at large scattering length.

  15. Expanding sapphyrin: towards selective phosphate binding.

    Science.gov (United States)

    Katayev, Evgeny A; Boev, Nikolay V; Myshkovskaya, Ekaterina; Khrustalev, Victor N; Ustynyuk, Yu A

    2008-01-01

    The anion-templated syntheses and binding properties of novel macrocyclic oligopyrrole receptors in which pyrrole rings are linked through amide or imine bonds are described. The efficient synthesis was accomplished by anion-templated [1+1] Schiff-base condensation and acylation macrocyclization reactions. Free receptors and their host-guest complexes with hydrochloric acid, acetic acid, tetrabutylammonium chloride, and hydrogen sulfate were analyzed by single-crystal X-ray diffraction analysis. Stability constants with different tetrabutylammonium salts of inorganic acids were determined by standard 1H NMR and UV/Vis titration techniques in [D6]DMSO/0.5% water solution. According to the titration data, receptors containing three pyrrole rings (10 and 12) exhibit high affinity (log Ka=5-7) for bifluoride, acetate, and dihydrogen phosphate, and interact weakly with chloride and hydrogen sulfate. The amido-bipyrrole receptors 11 and 13 with four pyrrole rings exhibit 10(4)- and 10(2)-fold selectivity for dihydrogen phosphate, respectively, as inferred from competitive titrations in the presence of tetrabutylammonium acetate.

  16. Binding of Sulpiride to Seric Albumins.

    Science.gov (United States)

    da Silva Fragoso, Viviane Muniz; de Morais Coura, Carla Patrícia; Hoppe, Luanda Yanaan; Soares, Marília Amável Gomes; Silva, Dilson; Cortez, Celia Martins

    2016-01-04

    The aim of this work was to study the interaction of sulpiride with human serum albumin (HSA) and bovine serum albumin (BSA) through the fluorescence quenching technique. As sulpiride molecules emit fluorescence, we have developed a simple mathematical model to discriminate the quencher fluorescence from the albumin fluorescence in the solution where they interact. Sulpiride is an antipsychotic used in the treatment of several psychiatric disorders. We selectively excited the fluorescence of tryptophan residues with 290 nm wavelength and observed the quenching by titrating HSA and BSA solutions with sulpiride. Stern-Volmer graphs were plotted and quenching constants were estimated. Results showed that sulpiride form complexes with both albumins. Estimated association constants for the interaction sulpiride-HSA were 2.20 (±0.08) × 10⁴ M(-1), at 37 °C, and 5.46 (±0.20) × 10⁴ M(-1), at 25 °C. Those for the interaction sulpiride-BSA are 0.44 (±0.01) × 10⁴ M(-1), at 37 °C and 2.17 (±0.04) × 10⁴ M(-1), at 25 °C. The quenching intensity of BSA, which contains two tryptophan residues in the peptide chain, was found to be higher than that of HSA, what suggests that the primary binding site for sulpiride in albumin should be located next to the sub domain IB of the protein structure.

  17. Binding of Sulpiride to Seric Albumins

    Directory of Open Access Journals (Sweden)

    Viviane Muniz da Silva Fragoso

    2016-01-01

    Full Text Available The aim of this work was to study the interaction of sulpiride with human serum albumin (HSA and bovine serum albumin (BSA through the fluorescence quenching technique. As sulpiride molecules emit fluorescence, we have developed a simple mathematical model to discriminate the quencher fluorescence from the albumin fluorescence in the solution where they interact. Sulpiride is an antipsychotic used in the treatment of several psychiatric disorders. We selectively excited the fluorescence of tryptophan residues with 290 nm wavelength and observed the quenching by titrating HSA and BSA solutions with sulpiride. Stern-Volmer graphs were plotted and quenching constants were estimated. Results showed that sulpiride form complexes with both albumins. Estimated association constants for the interaction sulpiride–HSA were 2.20 (±0.08 × 104 M−1, at 37 °C, and 5.46 (±0.20 × 104 M−1, at 25 °C. Those for the interaction sulpiride-BSA are 0.44 (±0.01 × 104 M−1, at 37 °C and 2.17 (±0.04 × 104 M−1, at 25 °C. The quenching intensity of BSA, which contains two tryptophan residues in the peptide chain, was found to be higher than that of HSA, what suggests that the primary binding site for sulpiride in albumin should be located next to the sub domain IB of the protein structure.

  18. Vitamin D Binding Protein and Bone Health

    Directory of Open Access Journals (Sweden)

    Ishir Bhan

    2014-01-01

    Full Text Available Vitamin D binding protein (DBP is the major carrier protein of 25-hydroxyvitamin D (25(OH D in the circulation, where it may serve roles in maintaining stable levels during times of decreased 25(OH availability and in regulating delivery of 25(OH D to target tissues. Several genetic polymorphisms of DBP have been described that lead to phenotypic changes in the protein that may affect affinity, activity, and concentration. These polymorphisms have been linked with alterations in bone density in several populations. One of the mechanisms by which DBP may alter bone health involves regulating vitamin D bioavailability. DBP-bound vitamin is thought to be relatively unavailable to target tissues, and thus alterations in DBP levels or affinity could lead to changes in vitamin D bioactivity. As a result, functional vitamin D status may differ greatly between individuals with similar total 25(OH D levels. Additionally, DBP may have independent roles on macrophage and osteoclast activation. This review will summarize recent findings about DBP with respect to measures of bone density and health.

  19. Bilirubin Binding to PPARα Inhibits Lipid Accumulation.

    Science.gov (United States)

    Stec, David E; John, Kezia; Trabbic, Christopher J; Luniwal, Amarjit; Hankins, Michael W; Baum, Justin; Hinds, Terry D

    2016-01-01

    Numerous clinical and population studies have demonstrated that increased serum bilirubin levels protect against cardiovascular and metabolic diseases such as obesity and diabetes. Bilirubin is a potent antioxidant, and the beneficial actions of moderate increases in plasma bilirubin have been thought to be due to the antioxidant effects of this bile pigment. In the present study, we found that bilirubin has a new function as a ligand for PPARα. We show that bilirubin can bind directly to PPARα and increase transcriptional activity. When we compared biliverdin, the precursor to bilirubin, on PPARα transcriptional activation to known PPARα ligands, WY 14,643 and fenofibrate, it showed that fenofibrate and biliverdin have similar activation properties. Treatment of 3T3-L1 adipocytes with biliverdin suppressed lipid accumulation and upregulated PPARα target genes. We treated wild-type and PPARα KO mice on a high fat diet with fenofibrate or bilirubin for seven days and found that both signal through PPARα dependent mechanisms. Furthermore, the effect of bilirubin on lowering glucose and reducing body fat percentage was blunted in PPARα KO mice. These data demonstrate a new function for bilirubin as an agonist of PPARα, which mediates the protection from adiposity afforded by moderate increases in bilirubin.

  20. Mannan-Binding Lectin in Cardiovascular Disease

    Directory of Open Access Journals (Sweden)

    Izabela Pągowska-Klimek

    2014-01-01

    Full Text Available Cardiovascular disease remains the leading cause of mortality and morbidity worldwide so research continues into underlying mechanisms. Since innate immunity and its potent component mannan-binding lectin have been proven to play an important role in the inflammatory response during infection and ischaemia-reperfusion injury, attention has been paid to its role in the development of cardiovascular complications as well. This review provides a general outline of the structure and genetic polymorphism of MBL and its role in inflammation/tissue injury with emphasis on associations with cardiovascular disease. MBL appears to be involved in the pathogenesis of atherosclerosis and, in consequence, coronary artery disease and also inflammation and tissue injury after myocardial infarction and heart transplantation. The relationship between MBL and disease is rather complex and depends on different genetic and environmental factors. That could be why the data obtained from animal and clinical studies are sometimes contradictory proving not for the first time that innate immunity is a “double-edge sword,” sometimes beneficial and, at other times disastrous for the host.

  1. Neptunium Binding Kinetics with Arsenazo(III)

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Leigh R. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Johnson, Aaron T. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Mezyk, Stephen P. [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2014-08-01

    This document has been prepared to meet FCR&D level 2 milestone M2FT-14IN0304021, “Report on the results of actinide binding kinetics with aqueous phase complexants” This work was carried out under the auspices of the Thermodynamics and Kinetics of Advanced Separations Systems FCR&D work package. The report details kinetics experiments that were performed to measure rates of aqueous phase complexation for pentavalent neptunium with the chromotropic dye Arsenazo III (AAIII). The studies performed were designed to determine how pH, ionic strength and AAIII concentration may affect the rate of the reaction. A brief comparison with hexavalent neptunium is also made. It was identified that as pH was increased the rate of reaction also increased, however increasing the ionic strength and concentration of AAIII had the opposite effect. Interestingly, the rate of reaction of Np(VI) with AAIII was found to be slower than that of the Np(V) reaction.

  2. Matrix binding of ochratoxin A during roasting.

    Science.gov (United States)

    Bittner, Andrea; Cramer, Benedikt; Humpf, Hans-Ulrich

    2013-12-26

    The mycotoxin ochratoxin A is degraded during coffee roasting by up to 90%. During this process, the two known degradation products, 14R-ochratoxin A and 14-decarboxy-ochratoxin A are formed. However, there is still an unexplained loss of more than 50% ochratoxin A. Here, we describe the binding of ochratoxin A to coffee polysaccharides via esterification as a further thermal reaction. This ester formation was studied by heating ochratoxin A with methyl α-d-glucopyranoside, a model compound to mimic polysaccharides. From this experiment, (22 → 6') ochratoxin A-methyl-α-d-glucopyranoside ester was isolated and characterized as a reaction product, showing the general ability of ochratoxin A for esterification with carbohydrates at roasting temperatures. Subsequently, a sample preparation protocol for the detection of ochratoxin A saccharide esters based on an enzymatic cleavage and purification using immunoaffinity chromatography was developed and applied. The detection was carried out by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). Using this method, it was possible to detect ochratoxin A polysaccharide esters formed during roasting of artificially contaminated coffee, confirming the results of the previous model experiments. Thus, the formation of ochratoxin A esters is a further explanation for the loss of ochratoxin A during coffee roasting.

  3. Neuronal calcium-binding proteins and schizophrenia.

    Science.gov (United States)

    Eyles, D W; McGrath, J J; Reynolds, G P

    2002-09-01

    Calcium-binding proteins (CBPs) such as calbindin, parvalbumin and calretinin are used as immunohistochemical markers for discrete neuronal subpopulations. They are particularly useful in identifying the various subpopulations of GABAergic interneurons that control output from prefrontal and cingulate cortices as well as from the hippocampus. The strategic role these interneurons play in regulating output from these three crucial brain regions has made them a focus for neuropathological investigation in schizophrenia. The number of pathological reports detailing subtle changes in these CBP-containing interneurons in patients with schizophrenia is rapidly growing. These proteins however are more than convenient neuronal markers. They confer survival advantages to neurons and can increase the neuron's ability to sustain firing. These properties may be important in the subtle pathophysiology of nondegenerative phenomena such as schizophrenia. The aim of this review is to introduce the reader to the functional properties of CBPs and to examine the emerging literature reporting alterations in these proteins in schizophrenia as well as draw some conclusions about the significance of these findings.

  4. Defining the bacteroides ribosomal binding site.

    Science.gov (United States)

    Wegmann, Udo; Horn, Nikki; Carding, Simon R

    2013-03-01

    The human gastrointestinal tract, in particular the colon, hosts a vast number of commensal microorganisms. Representatives of the genus Bacteroides are among the most abundant bacterial species in the human colon. Bacteroidetes diverged from the common line of eubacterial descent before other eubacterial groups. As a result, they employ unique transcription initiation signals and, because of this uniqueness, they require specific genetic tools. Although some tools exist, they are not optimal for studying the roles and functions of these bacteria in the human gastrointestinal tract. Focusing on translation initiation signals in Bacteroides, we created a series of expression vectors allowing for different levels of protein expression in this genus, and we describe the use of pepI from Lactobacillus delbrueckii subsp. lactis as a novel reporter gene for Bacteroides. Furthermore, we report the identification of the 3' end of the 16S rRNA of Bacteroides ovatus and analyze in detail its ribosomal binding site, thus defining a core region necessary for efficient translation, which we have incorporated into the design of our expression vectors. Based on the sequence logo information from the 5' untranslated region of other Bacteroidales ribosomal protein genes, we conclude that our findings are relevant to all members of this order.

  5. Assessment Criteria of Bentonite Binding Properties

    Directory of Open Access Journals (Sweden)

    S. Żymankowska-Kumon

    2012-09-01

    Full Text Available The criteria, with which one should be guided at the assessment of the binding properties of bentonites used for moulding sands, areproposed in the paper. Apart from the standard parameter which is the active bentonite content, the unrestrained growth indicator should be taken into account since it seems to be more adequate in the estimation of the sand compression strength. The investigations performed for three kinds of bentonites, applied in the Polish foundry plants, subjected to a high temperature influences indicate, that the pathway of changes of the unrestrained growth indicator is very similar to the pathway of changes of the sand compression strength. Instead, the character of changes of the montmorillonite content in the sand in dependence of the temperature is quite different. The sand exhibits the significant active bentonite content, and the sand compression strength decreases rapidly. The montmorillonite content in bentonite samples was determined by the modern copper complex method of triethylenetetraamine (Cu(II-TET. Tests were performed for bentonites and for sands with those bentonites subjected to high temperatures influences in a range: 100-700ºC.

  6. Lipopolysaccharide binding protein in preterm infants

    Science.gov (United States)

    Behrendt, D; Dembinski, J; Heep, A; Bartmann, P

    2004-01-01

    Objective: To assess serum concentrations of lipopolysaccharide binding protein (LBP) in preterm infants with neonatal bacterial infection (NBI). Methods: Blood samples were analysed of 57 preterm (28+1 to 36+6, median 33+2 weeks gestation) and 17 term infants admitted to the neonatal intensive care unit within the first 72 hours of life with suspicion of NBI. Samples were obtained at first suspicion of sepsis and after 12 and 24 hours. Diagnosis of NBI was confirmed by raised concentrations of C reactive protein and/or interleukin 6. The influence of gestational age and labour was analysed. Results: Maximum LBP concentrations in infants with NBI were greatly increased compared with infants without NBI (13.0–46.0 µg/ml (median 20.0 µg/ml) v 0.6–17.4 µg/ml (median 4.2 µg/ml)). LBP concentrations in infected infants were not yet significantly raised when NBI was first suspected. The LBP concentrations of preterm infants were comparable to those of term infants. Regression analysis revealed no significant effect of labour or gestational age on LBP. Conclusions: Raised LBP concentrations indicate NBI in preterm and term infants. Preterm infants of > 28 weeks gestation seem to be capable of producing LBP as efficiently as term infants. Neonatal LBP concentrations are not influenced by labour. LBP may be a useful diagnostic marker of NBI in preterm infants. PMID:15499153

  7. Nuclear binding near a quantum phase transition

    CERN Document Server

    Elhatisari, Serdar; Rokash, Alexander; Alarcón, Jose Manuel; Du, Dechuan; Klein, Nico; Lu, Bing-nan; Meißner, Ulf-G; Epelbaum, Evgeny; Krebs, Hermann; Lähde, Timo A; Lee, Dean; Rupak, Gautam

    2016-01-01

    How do protons and neutrons bind to form nuclei? This is the central question of ab initio nuclear structure theory. While the answer may seem as simple as the fact that nuclear forces are attractive, the full story is more complex and interesting. In this work we present numerical evidence from ab initio lattice simulations showing that nature is near a quantum phase transition, a zero-temperature transition driven by quantum fluctuations. Using lattice effective field theory, we perform Monte Carlo simulations for systems with up to twenty nucleons. For even and equal numbers of protons and neutrons, we discover a first-order transition at zero temperature from a Bose-condensed gas of alpha particles (4He nuclei) to a nuclear liquid. Whether one has an alpha-particle gas or nuclear liquid is determined by the strength of the alpha-alpha interactions, and we show that the alpha-alpha interactions depend on the strength and locality of the nucleon-nucleon interactions. The existence of the nearby first-order ...

  8. Multisensory Illusions and the Temporal Binding Window

    Directory of Open Access Journals (Sweden)

    Ryan A Stevenson

    2011-10-01

    Full Text Available The ability of our sensory systems to merge sensory information from distinct modalities is remarkable. One stimulus characteristic utilized in this operation is temporal coincidence. Auditory and visual information are integrated within a narrow range of temporal offsets, known as the temporal binding window (TBW, which varies between individuals, stimulus type, and task. In this series of experiments, we assessed the relationship within individuals between the width of their TBW and their ability to integrate audiovisual information. The TBW was measured through a perceived subjective simultaneity task. In conjunction with this, we measured each individual's ability to integrate auditory and visual information with two multisensory illusions, the McGurk effect and Flashbeep illusion. The results from these studies demonstrate that the TBW is highly correlated with the individual's ability to integrate. These relationships were seen in only the right TBW, in which visual presentations preceded auditory presentations, a finding that is ecologically logical. However, differences were seen between the two illusory conditions, where the McGurk effect was stronger in individuals with narrow TBWs, again, an ecologically logical finding. The opposite relationship was seen with flashbeep illusion, possibly due to inherent asynchronies in the illusion.

  9. Dying or living?: The double bind.

    Science.gov (United States)

    Longhofer, J

    1980-06-01

    Describing the behaviors of terminally ill patients, their families and those charged with their care has received considerable attention during the past decade. This study of comprehensive cancer treatment and research facility indicates that the prevailing theory is limited to explanation at the intra-psychic level. In her work with hundreds of terminal cases, Dr. Elizabeth Kubler-Ross found that patients typically progress through five stages: 1) denial, 2) anger, 3) bargaining, 4) depression, and 5) acceptance. She concludes that the majority of her patients die in a stage of acceptance--a state of equanimity. Recently, scholars have claimed that this five stage scheme has limited applicability and may in fact contribute to the formalization of a dying person's behavior. This preliminary report proposes that the stage theory, if it has any descriptive validity, becomes meaningful only when used to describe behaviors occurring among patients, families, and medical practitioners. A plausible explanation of these behaviors is accomplished by examination of communication patterns containing the structure of paradox or double bind. Patients are forced to perceive realities about their physical conditions not as they appear to them, but as they are defined by those in their environment. This paper explores these communication patterns in relation to the structure of social relationships and the specific contents of messages being transmitted and received.

  10. Unique cell adhesion and invasion properties of Yersinia enterocolitica O:3, the most frequent cause of human Yersiniosis.

    Science.gov (United States)

    Uliczka, Frank; Pisano, Fabio; Schaake, Julia; Stolz, Tatjana; Rohde, Manfred; Fruth, Angelika; Strauch, Eckhard; Skurnik, Mikael; Batzilla, Julia; Rakin, Alexander; Heesemann, Jürgen; Dersch, Petra

    2011-07-01

    Many enteric pathogens are equipped with multiple cell adhesion factors which are important for host tissue colonization and virulence. Y. enterocolitica, a common food-borne pathogen with invasive properties, uses the surface proteins invasin and YadA for host cell binding and entry. In this study, we demonstrate unique cell adhesion and invasion properties of Y. enterocolitica serotype O:3 strains, the most frequent cause of human yersiniosis, and show that these differences are mainly attributable to variations affecting the function and expression of invasin in response to temperature. In contrast to other enteric Yersinia strains, invasin production in O:3 strains is constitutive and largely enhanced compared to other Y. enterocolitica serotypes, in which invA expression is temperature-regulated and significantly reduced at 37°C. Increase of invasin levels is caused by (i) an IS1667 insertion into the invA promoter region, which includes an additional promoter and RovA and H-NS binding sites, and (ii) a P98S substitution in the invA activator protein RovA rendering the regulator less susceptible to proteolysis. Both variations were shown to influence bacterial colonization in a murine infection model. Furthermore, we found that co-expression of YadA and down-regulation of the O-antigen at 37°C is required to allow efficient internalization by the InvA protein. We conclude that even small variations in the expression of virulence factors can provoke a major difference in the virulence properties of closely related pathogens which may confer better survival or a higher pathogenic potential in a certain host or host environment.

  11. Unique cell adhesion and invasion properties of Yersinia enterocolitica O:3, the most frequent cause of human Yersiniosis.

    Directory of Open Access Journals (Sweden)

    Frank Uliczka

    2011-07-01

    Full Text Available Many enteric pathogens are equipped with multiple cell adhesion factors which are important for host tissue colonization and virulence. Y. enterocolitica, a common food-borne pathogen with invasive properties, uses the surface proteins invasin and YadA for host cell binding and entry. In this study, we demonstrate unique cell adhesion and invasion properties of Y. enterocolitica serotype O:3 strains, the most frequent cause of human yersiniosis, and show that these differences are mainly attributable to variations affecting the function and expression of invasin in response to temperature. In contrast to other enteric Yersinia strains, invasin production in O:3 strains is constitutive and largely enhanced compared to other Y. enterocolitica serotypes, in which invA expression is temperature-regulated and significantly reduced at 37°C. Increase of invasin levels is caused by (i an IS1667 insertion into the invA promoter region, which includes an additional promoter and RovA and H-NS binding sites, and (ii a P98S substitution in the invA activator protein RovA rendering the regulator less susceptible to proteolysis. Both variations were shown to influence bacterial colonization in a murine infection model. Furthermore, we found that co-expression of YadA and down-regulation of the O-antigen at 37°C is required to allow efficient internalization by the InvA protein. We conclude that even small variations in the expression of virulence factors can provoke a major difference in the virulence properties of closely related pathogens which may confer better survival or a higher pathogenic potential in a certain host or host environment.

  12. Helical propensity in an intrinsically disordered protein accelerates ligand binding

    DEFF Research Database (Denmark)

    Iesmantavicius, Vytautas; Dogan, Jakob; Jemth, Per;

    2014-01-01

    Many intrinsically disordered proteins fold upon binding to other macromolecules. The secondary structure present in the well-ordered complex is often formed transiently in the unbound state. The consequence of such transient structure for the binding process is, however, not clear. The activatio...

  13. Binding-Induced Fluorescence of Serotonin Transporter Ligands

    DEFF Research Database (Denmark)

    Wilson, James; Ladefoged, Lucy Kate; Babinchak, Michael

    2014-01-01

    The binding-induced fluorescence of 4-(4-(dimethylamino)-phenyl)-1-methylpyridinium (APP(+)) and two new serotonin transporter (SERT)-binding fluorescent analogues, 1-butyl-4-[4-(1-dimethylamino)phenyl]-pyridinium bromide (BPP(+)) and 1-methyl-4-[4-(1-piperidinyl)phenyl]-pyridinium (PPP(+)), has...

  14. Cooperative binding interaction of ethidium with allosteric DNA.

    Science.gov (United States)

    Suh, D

    1999-09-30

    The specific association of drugs with deoxyoligonucleotides, containing a B-Z junction between left-handed Z-DNA and right-handed B-DNA, was examined by fluorescence and circular dichroism (CD) technique. Ethidium was chosen for a simple DNA binding compound because it binds to right-handed DNA and hybrid B-Z forms containing a B-Z junction in a highly cooperative manner. The binding isotherms were analyzed by an allosteric model in order to describe the cooperativity of association. Binding of ethidium to the DNA that are initially in the hybrid B-Z forms showed over an order of magnitude higher affinity than other DNA which were entirely in the B-form. The conformational transitions of deoxyoligonucleotides containing a B-Z junction as a result of ethidium binding were monitored by CD and the influence of NaCl on the complex formation was also determined by the CD spectra. The singular value decomposition (SVD) analysis was used to characterize a family of CD spectra of the species in binding equilibria. The results of SVD analysis showed a strikingly complex thermodynamic equilibria of cooperative binding of drugs to the allosterically converted DNA forms. The results also showed that these DNA forms in low- and high-salt were different in the absence or presence of drug. These results demonstrate that DNA-binding-drugs can preferentially interact with specific DNA structures and that these interactions are accompanied by allosteric changes of DNA conformations.

  15. Hereditary spherocytosis diagnosed with the eosin-5'-maleimide binding test.

    Science.gov (United States)

    Watanabe, Toru; Ono, Hiroyuki; Tajima, Iwao; Ishigaki, Hidetoshi; Hakamata, Akio; Shirai, Masami; Endoh, Akira; Hongo, Teruaki

    2014-06-01

    We describe three cases of hereditary spherocytosis (HS) diagnosed using the eosin-5'-maleimide (EMA) binding test and discuss the relevance of the EMA binding test. In Japan, this test is not widely used because the prevalence of HS is low. This test is a valuable screening test for the diagnosis of HS.

  16. Characterization of the Binding Properties of Molecularly Imprinted Polymers.

    Science.gov (United States)

    Ansell, Richard J

    2015-01-01

    The defining characteristic of the binding sites of any particular molecularly imprinted material is heterogeneity: that is, they are not all identical. Nonetheless, it is useful to study their fundamental binding properties, and to obtain average properties. In particular, it has been instructive to compare the binding properties of imprinted and non-imprinted materials. This chapter begins by considering the origins of this site heterogeneity. Next, the properties of interest of imprinted binding sites are described in brief: affinity, selectivity, and kinetics. The binding/adsorption isotherm, the graph of concentration of analyte bound to a MIP versus concentration of free analyte at equilibrium, over a range of total concentrations, is described in some detail. Following this, the techniques for studying the imprinted sites are described (batch-binding assays, radioligand binding assays, zonal chromatography, frontal chromatography, calorimetry, and others). Thereafter, the parameters that influence affinity, selectivity and kinetics are discussed (solvent, modifiers of organic solvents, pH of aqueous solvents, temperature). Finally, mathematical attempts to fit the adsorption isotherms for imprinted materials, so as to obtain information about the range of binding affinities characterizing the imprinted sites, are summarized.

  17. Measuring Multivalent Binding Interactions by Isothermal Titration Calorimetry.

    Science.gov (United States)

    Dam, Tarun K; Talaga, Melanie L; Fan, Ni; Brewer, Curtis F

    2016-01-01

    Multivalent glycoconjugate-protein interactions are central to many important biological processes. Isothermal titration calorimetry (ITC) can potentially reveal the molecular and thermodynamic basis of such interactions. However, calorimetric investigation of multivalency is challenging. Binding of multivalent glycoconjugates to proteins (lectins) often leads to a stoichiometry-dependent precipitation process due to noncovalent cross-linking between the reactants. Precipitation during ITC titration severely affects the quality of the baseline as well as the signals. Hence, the resulting thermodynamic data are not dependable. We have made some modifications to address this problem and successfully studied multivalent glycoconjugate binding to lectins. We have also modified the Hill plot equation to analyze high quality ITC raw data obtained from multivalent binding. As described in this chapter, ITC-driven thermodynamic parameters and Hill plot analysis of ITC raw data can provide valuable information about the molecular mechanism of multivalent lectin-glycoconjugate interactions. The methods described herein revealed (i) the importance of functional valence of multivalent glycoconjugates, (ii) that favorable entropic effects contribute to the enhanced affinities associated with multivalent binding, (iii) that with the progression of lectin binding, the microscopic affinities of the glycan epitopes of a multivalent glycoconjugate decrease (negative cooperativity), (iv) that lectin binding to multivalent glycoconjugates, especially to mucins, involves internal diffusion jumps, (bind and jump) and (v) that scaffolds of glycoconjugates influence their entropy of binding. © 2016 Elsevier Inc. All rights reserved.

  18. ANDROGEN REGULATION OF PROSTATIC STEROID BINDING PROTEIN GENE TRANSCRIPTION

    Institute of Scientific and Technical Information of China (English)

    ZHANGYong-Lian; ZHOUZong-Xun; ZHANGYou-Duan; PARKERMalcolmG

    1989-01-01

    Prostatic steroid binding protein (PSBP) is a major protein secreted in the rat ventral prostate (V.P.) and also one of the components in seminal fluid, The potential importance of this protein in male fertility emerged from its ability of binding cholesterol which might modulate the proportion of phospholipids and cholesterol in sperm making it suitable

  19. Noncovalent Interactions within a Synthetic Receptor Can Reinforce Guest Binding

    NARCIS (Netherlands)

    Rodriguez-Docampo, Zaida; Pascu, Sofia I.; Kubik, Stefan; Otto, Sijbren

    2006-01-01

    Structural and thermodynamic data are presented on the binding properties of anion receptors containing two covalently linked cyclopeptide subunits that bind sulfate and iodide anions with micromolar affinity in aqueous solution. A synchrotron X-ray crystal structure of the sulfate complex of one

  20. Predictive model of cationic surfactant binding to humic substances

    NARCIS (Netherlands)

    Ishiguro, M.; Koopal, L.K.

    2011-01-01

    The humic substances (HS) have a high reactivity with other components in the natural environment. An important factor for the reactivity of HS is their negative charge. Cationic surfactants bind strongly to HS by electrostatic and specific interaction. Therefore, a surfactant binding model is devel