Relevant bibliographies by topics / Decoy molecules

Academic literature on the topic 'Decoy molecules'

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Published: 10 December 2022
Last updated: 29 January 2023

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Journal articles on the topic "Decoy molecules"

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Imrie, Fergus, Anthony R. Bradley, and Charlotte M. Deane. "Generating property-matched decoy molecules using deep learning." Bioinformatics 37, no. 15 (February 3, 2021): 2134–41. http://dx.doi.org/10.1093/bioinformatics/btab080.

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Abstract Motivation An essential step in the development of virtual screening methods is the use of established sets of actives and decoys for benchmarking and training. However, the decoy molecules in commonly used sets are biased meaning that methods often exploit these biases to separate actives and decoys, and do not necessarily learn to perform molecular recognition. This fundamental issue prevents generalization and hinders virtual screening method development. Results We have developed a deep learning method (DeepCoy) that generates decoys to a user’s preferred specification in order to remove such biases or construct sets with a defined bias. We validated DeepCoy using two established benchmarks, DUD-E and DEKOIS 2.0. For all 102 DUD-E targets and 80 of the 81 DEKOIS 2.0 targets, our generated decoy molecules more closely matched the active molecules’ physicochemical properties while introducing no discernible additional risk of false negatives. The DeepCoy decoys improved the Deviation from Optimal Embedding (DOE) score by an average of 81% and 66%, respectively, decreasing from 0.166 to 0.032 for DUD-E and from 0.109 to 0.038 for DEKOIS 2.0. Further, the generated decoys are harder to distinguish than the original decoy molecules via docking with Autodock Vina, with virtual screening performance falling from an AUC ROC of 0.70 to 0.63. Availability and implementation The code is available at https://github.com/oxpig/DeepCoy. Generated molecules can be downloaded from http://opig.stats.ox.ac.uk/resources. Supplementary information Supplementary data are available at Bioinformatics online.
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Alam, Fardina Fathmiul, and Amarda Shehu. "Unsupervised multi-instance learning for protein structure determination." Journal of Bioinformatics and Computational Biology 19, no. 01 (February 2021): 2140002. http://dx.doi.org/10.1142/s0219720021400023.

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Many regions of the protein universe remain inaccessible by wet-laboratory or computational structure determination methods. A significant challenge in elucidating these dark regions in silico relates to the ability to discriminate relevant structure(s) among many structures/decoys computed for a protein of interest, a problem known as decoy selection. Clustering decoys based on geometric similarity remains popular. However, it is unclear how exactly to exploit the groups of decoys revealed via clustering to select individual structures for prediction. In this paper, we provide an intuitive formulation of the decoy selection problem as an instance of unsupervised multi-instance learning. We address the problem in three stages, first organizing given decoys of a protein molecule into bags, then identifying relevant bags, and finally drawing individual instances from these bags to offer as prediction. We propose both non-parametric and parametric algorithms for drawing individual instances. Our evaluation utilizes two datasets, one benchmark dataset of ensembles of decoys for a varied list of protein molecules, and a dataset of decoy ensembles for targets drawn from recent CASP competitions. A comparative analysis with state-of-the-art methods reveals that the proposed approach outperforms existing methods, thus warranting further investigation of multi-instance learning to advance our treatment of decoy selection.
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Alvarez-de Miranda, Francisco Javier, Isabel Alonso-Sánchez, Antonio Alcamí, and Bruno Hernaez. "TNF Decoy Receptors Encoded by Poxviruses." Pathogens 10, no. 8 (August 22, 2021): 1065. http://dx.doi.org/10.3390/pathogens10081065.

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Tumour necrosis factor (TNF) is an inflammatory cytokine produced in response to viral infections that promotes the recruitment and activation of leukocytes to sites of infection. This TNF-based host response is essential to limit virus spreading, thus poxviruses have evolutionarily adopted diverse molecular mechanisms to counteract TNF antiviral action. These include the expression of poxvirus-encoded soluble receptors or proteins able to bind and neutralize TNF and other members of the TNF ligand superfamily, acting as decoy receptors. This article reviews in detail the various TNF decoy receptors identified to date in the genomes from different poxvirus species, with a special focus on their impact on poxvirus pathogenesis and their potential use as therapeutic molecules.
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Panneerselvam, Mathivadhani, Piyush M. Patel, David M. Roth, Michael W. Kidd, Blake Chin-Lee, Brian P. Head, Ingrid R. Niesman, Satoki Inoue, Hemal H. Patel, and Daniel P. Davis. "Role of decoy molecules in neuronal ischemic preconditioning." Life Sciences 88, no. 15-16 (April 2011): 670–74. http://dx.doi.org/10.1016/j.lfs.2011.02.004.

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TOMITA, NARUYA, RYUICHI MORISHITA, HUI Y. LAN, KEI YAMAMOTO, MASAHIDE HASHIZUME, MITSUE NOTAKE, KAORU TOYOSAWA, et al. "In VivoAdministration of a Nuclear Transcription Factor-κB Decoy Suppresses Experimental Crescentic Glomerulonephritis." Journal of the American Society of Nephrology 11, no. 7 (July 2000): 1244–52. http://dx.doi.org/10.1681/asn.v1171244.

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Abstract. Glomerular expression of cytokines, interleukin-1 (IL-1), and tumor necrosis factor-α (TNF-α), together with leukocytic infiltration, are prominent features in crescentic glomerulonephritis. Because these cytokines are targets for nuclear transcription factor-κB (NF-κB), the use of NF-κB decoy oligodeoxynucleotide (ODN) treatment was evaluated in an experimental disease model. Crescentic glomerulonephritis was induced in primed Wistar rats by injection of sheep antiglomerular basement membrane serum. Thirty minutes after injection, rats were anesthetized and the left kidney was perfused with NF-κB decoy ODN or scrambled ODN control mixed with a virus-liposome complex, and then killed 7 d later. Animals given the scrambled control ODN developed severe glomerulonephritis by day 7 with heavy proteinuria, glomerular crescents and interstitial lesions, marked leukocytic infiltration, and upregulated renal expression of cytokines (IL-1 and TNF-α) and adhesion molecules (intercellular adhesion molecule-1). In contrast, NF-κB decoy ODN treatment substantially inhibited the disease with a 50% reduction in proteinuria, a threefold reduction in histologic damage, a 50% reduction in leukocytic infiltration, and a 50 to 80% reduction in the renal expression of cytokines and leukocyte adhesion molecules. In conclusion, this study has demonstrated that NF-κB plays a key role in cytokine-mediated renal injury and that NF-κB decoy ODN treatment has clear therapeutic potential in rapidly progressive glomerulonephritis.
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Lohan, Fiona, and Karen Keeshan. "The functionally diverse roles of tribbles." Biochemical Society Transactions 41, no. 4 (July 18, 2013): 1096–100. http://dx.doi.org/10.1042/bst20130105.

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Tribbles are members of the pseudokinase family of proteins, with no associated kinase activity detectable to date. As tribbles appear not to function as kinases, there has been debate surrounding their functional classification. Tribbles have been proposed to function as adaptor molecules facilitating degradation of their target proteins. Tribbles have also been proposed to mediate signalling changes to MAPK (mitogen-activated protein kinase) cascades and also to function as decoy kinases interfering with the activity of known kinases. The present review discusses the functionally divergent roles of tribbles as molecular adaptors mediating degradation, changes to signalling cascades and action as decoy kinases.
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Davis, D. P. "The Role of Decoy Molecules in Neuronal Ischemic Preconditioning." Academic Emergency Medicine 10, no. 5 (May 1, 2003): 438—a—438. http://dx.doi.org/10.1197/aemj.10.5.438-a.

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Suzuki, Kazuto, Yuma Shisaka, Joshua Kyle Stanfield, Yoshihito Watanabe, and Osami Shoji. "Enhanced cis- and enantioselective cyclopropanation of styrene catalysed by cytochrome P450BM3 using decoy molecules." Chemical Communications 56, no. 75 (2020): 11026–29. http://dx.doi.org/10.1039/d0cc04883f.

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Colotta, F., S. Saccani, J. G. Giri, S. K. Dower, J. E. Sims, M. Introna, and A. Mantovani. "Regulated expression and release of the IL-1 decoy receptor in human mononuclear phagocytes." Journal of Immunology 156, no. 7 (April 1, 1996): 2534–41. http://dx.doi.org/10.4049/jimmunol.156.7.2534.

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Abstract The aim of this study was to investigate the expression and release of the IL-1 type II decoy receptor (R) in mononuclear phagocytes, which play a central role in immune and chronic inflammatory reactions. Human monocytes expressed both type I and type II R transcripts, the latter being two- to threefold more represented. By cross-linking and Ab blocking, the predominant surface IL-1-binding molecule was the decoy RII. IL-4, IL-13, and dexamethasone induced RI and RII transcripts and augmented the number of IL-1-binding sites with no modification of Kd values. The induced surface receptor was identified as the decoy RII. These stimuli induced the release of a soluble R with a m.w. of approximately 60 kDa, of which N-glycosylation contributed 22 kDa compared with 45 kDa released from polymorphonuclear leukocytes, of which N-glycosylation contributed 15 kDa. IL-13 and dexamethasone induced a release of 24 ng/ml/2 x 10(7) cells (from 8.7 to 43.2 ng/ml) and 25.6 ng/ml/2 x 10(7) cells (from 9.7 to 36.8 ng/ml) of decoy RII in 18 h, respectively (six donors). Thus, for instance, IL-13-treated (18 h) cells expressed 3.5 x 10(3) sites/cell and released 12 x 10(3) decoy RII/cell. The released decoy RII from monocytes bound IL-1apha and IL-1 receptor antagonist 30- and 2-fold less avidly than IL-1beta, respectively. In vitro-matured, monocyte-derived macrophages showed higher levels of surface expression and release of the IL-1 decoy RII. The results show that, on exposure to diverse molecules with anti-inflammatory properties, mononuclear phagocytes express and release copious amounts of a novel version of the soluble IL-1 decoy RII.
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Kobayashi, Yuichiro, Kenji Kohara, Yusuke Kiuchi, Hiroki Onoda, Osami Shoji, and Hiroyasu Yamaguchi. "Control of microenvironment around enzymes by hydrogels." Chemical Communications 56, no. 49 (2020): 6723–26. http://dx.doi.org/10.1039/d0cc01332c.

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Dissertations / Theses on the topic "Decoy molecules"

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Bryant, William Barton. "Caspases and caspase regulators in Lepidoptera and Diptera." Diss., Manhattan, Kan. : Kansas State University, 2009. http://hdl.handle.net/2097/2612.

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Howle, Christopher Roy. "Decay processes of photoexcited molecules in the VUV : comparison with ion/molecule reactions." Thesis, University of Birmingham, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.421712.

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Rennie, Emma E. "Decay mechanisms of photoexcited molecular ions." Thesis, Heriot-Watt University, 1997. http://hdl.handle.net/10399/658.

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Mendive, Tapia David. "Computational modelling of excited state decay in polyatomic molecules." Thesis, Imperial College London, 2013. http://hdl.handle.net/10044/1/11149.

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The introduction of general numerical methods in the form of widely available software can have a dramatic effect on the development of a scientific field. In electronic structure theory, for example, general-purpose programs (such as Gaussian, ADF, MOLPRO,. . . ) combined with better computational resources have in part led to molecular electronic structure calculations becoming a ubiquitous tool in chemical research. Similarly, quantum dynamics methods based on coupled time-evolving Gaussian basis sets and molecular potential energy surfaces calculated on-the-fly hold out similar promise in the study of non-adiabatic processes, because of their generality and freedom from ad hoc assumptions. Therefore, the aim of this thesis is to investigate the convergence and applicability of quantum dynamics calculations with a fully variational coupled Gaussian basis set description, termed variational Multi-Con guration Gaussian (vMCG). It is suggested that the vMCG approach provides a way to balance accuracy against computational cost for molecules of comparable size by choosing the number of coupled Gaussian product basis functions and a middle way forward between grid-based and trajectory surface hopping approaches to non-adiabatic molecular quantum dynamics calculations. In order to prove the suitability of vMCG we show its application to three problems of chemical interest: the study of fulvene excited state decay, the prediction of a coherent control mechanism for the same system and the benchmarking of an electronic population dynamics model for electronic transitions when occurring through a conical intersection. In the long term, the development of vMCG is expected to have a major impact, allowing nonadiabatic dynamics simulations to be made not only by theoreticians, but also by non-specialists and experimentalists in both industry and academia.Chapter 1: Modelling Excited State Decay [Diagrams appear here. To view, please open pdf attachment] This chapter introduces and reviews the current state-of-the-art modelling of non-adiabatic processes in molecular systems. This is a challenging topic since the simulation must treat simultaneously the motion of the nuclei and the electrons, which are coupled together. It is concluded that a wide range of methodologies are available. However, when looking for a general tool for the study of non-adiabatic processes, quantum dynamics methods based on coupled time-evolving Gaussian basis sets such as the Direct Dynamics variational Multi-Con guration Gaussian (DD-vMCG) wavepacket method, as well as to other related methods - such as Ab Initio Multiple Spawning (AIMS, FMS)[1, 2] and Multi-Con gurational Ehrenfest (MCE)[3, 4] - seem to be an especially suitable choice because of their generality and freedom from ad hoc assumptions. Chapter 2: variational Gaussian nuclear wavepackets [Diagrams appear here. To view, please open pdf attachment] This chapter describes three possible time-evolving Gaussian basis sets for use in non-adiabatic quantum dynamics based on the Direct Dynamics variational Multi-Con guration Gaussian (DD-vMCG) wavepacket method. These general model representations are compared using model calculations in a simple harmonic oscillator and describing their connections to other work. It is suggested that the fully variational nuclear wavefunction, termed vMCG (variational Multi-Con guration Gaussian) is a very convenient formulation leading towards a realistic sampling of the phase space without the initial conditions (i.e. initial disposition and momentum) being so important when using a su cient amount of coupled Gaussian basis functions. Chapter 3: Fulvene S1/S0 Excited State Decay [Diagrams appear here. To view, please open pdf attachment] The vMCG (variational Multi-Con guration Gaussian) approach described in Chapter 2 is benchmarked in a realistic system by modelling the radiationless decay from an electronic excited state through an extended conical intersection seam. As a benchmark system, we model the radiationless decay of fulvene from its rst electronic excited state and monitor two associated properties: the spatial extent to which the conical intersection seam is sampled and the timescale and stepwise nature of the population transfer. We illustrate how the use of a fully variational nuclear wavefunction provides a way to balance accuracy against computational cost for molecules of comparable size by choosing the number of coupled Gaussian product basis functions. Chapter 4: Controlling Fulvene S1/S0 Decay [Diagrams appear here. To view, please open pdf attachment] Direct quantum dynamics simulations using the vMCG (variational Multi- Con guration Gaussian) approach were performed in order to model the control of the stepwise population transfer in fulvene. As shown in Chapter 3, ultra-fast internal conversion takes place centred on the higher-energy planar/sloped region of the S1/S0 conical intersection seam. Therefore, two possible schemes for controlling whether stepwise population transfer occurs or not | either altering the initial geometry distribution or the initial momentum composition of the photo-excited wavepacket - were explored. In both cases, decay took place instead in the lower-energy twisted/peaked region of the crossing seam, switching o the stepwise population transfer. This absence of re-crossing is a direct consequence of the change in the position on the intersection at which decay occurs and its consequences should provide an experimentally observable fingerprint of this system. Chapter 5: A population transfer model for intramolecular electron transfer [Diagrams appear here. To view, please open pdf attachment] The aim of this chapter is to further prove the applicability of the vMCG (variational Multi-Con guration Gaussian) approach by benchmarking an approximate population dynamics model in Jahn-Teller systems. The socalled Density Matrix Non-Equilibrium Fermi Golden Rule (DM-NFGR) can be seen as a simpli ed version of vMCG, in which the nite Gaussian basis set and on-the-fly evaluation of the nuclear Hamiltonian are eliminated via use of the density matrix formalism and a perturbational treatment of the equations. This has three clear advantages: firstly, it allows us to extend the maximum molecular size considerably; secondly, we can relate the population dynamics to an analytical time-dependent rate expression; and finally, temperature effects can be included in the simulations. Benchmark calculations for the 2,6-bis(methylene) adamantyl (BMA) radical cation support the reliability of the results.
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Xiong, Ting. "Modeling of Decay Rate for Molecules at an Island Surface." PDXScholar, 1995. https://pdxscholar.library.pdx.edu/open_access_etds/5198.

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The decay rates for molecules at rough surfaces are studied via an island surface model, with particular emphasis on the effect due to the distribution of surface roughness. Two extreme cases are studied when the surface islands distribute themselves evenly and when they coalesce to form local clusters at the molecule-substrate interface. The optical properties of the interfacial layer in these two cases are described by the Maxwell-Garnett and the fractal-cluster models, respectively. Among other results, it is found that both enhancement and suppression of the surface-induced decay rates are possible due to the presence of roughness, with more dramatic suppression taking place when the surface islands coalesce to form clusters.
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Beelman, Clare Ann 1969. "The control ofmRNA decay in Saccharomyces cerevisiae." Diss., The University of Arizona, 1996. http://hdl.handle.net/10150/289588.

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Control of mRNA degradation is an important step in the regulation of gene expression. In Saccharomyces cerevisiae, pathways of mRNA decay have been determined and have provided a framework for understanding how mRNA decay is controlled. I have studied how the process of translation affects the decay mechanism of a yeast transcript and I have isolated and characterized yeast mutants that exhibit reduced rates of mRNA decay. The process of translation has been shown to affect mRNA decay rates in eukaryotes. However, using a MFA2 mRNA that cannot be translated due to insertion of secondary structure in its 5' untranslated region, I have determined that translation of the MFA2 mRNA is not required for its degradation. This observation demonstrates that translation of an mRNA, per se, is not required for the normal kinetics or mechanism of mRNA decay. Additionally, I have demonstrated that the translational inhibitor, cycloheximide, reduces the rate at which the MFA2 transcript is decapped. Inhibition of decapping occurs even on MFA2 transcripts that cannot be translated due to insertion of secondary structure. This result suggests that the general stabilizing effects of translational inhibitors on mRNAs may not be due to the inhibition of translation of these transcripts. The identification of mRNA decay pathways in yeast, deadenylation-dependent decapping and deadenylation-independent decapping, provided a basis by which gene products required for mRNA decay through these pathways could be identified. To this end, a screen of mutant yeast strains was undertaken. I have isolated and characterized two mutants, mrt1 and mrt3, that exhibit reduced rates of deadenylation-dependent decapping on several yeast transcripts. This result suggests that the MRT1 and MRT3 gene products promote deadenylation-dependent mRNA decapping. A third mutant, dcp1, was also isolated, and the wild-type DCP1 gene was identified. Characterization of dcp1/ mutants by myself and others revealed that the DCP1 gene encodes the decapping enzyme, or an essential component of the decapping enzyme, required for both deadenylation-dependent and deadenylation-independent mRNA decapping. This result demonstrates that the DCP1 gene product, Dcp1p, is required for all known mRNA decapping in yeast.
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Tucker, Morgan Dean. "Deadenylation and mRNA decay in Saccharomyces cerevisiae." Diss., The University of Arizona, 2001. http://hdl.handle.net/10150/289856.

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The process of mRNA turnover is a critical component of the regulation of gene expression. In the past few years, a discrete set of pathways for the degradation of polyadenylated mRNAs, in eukaryotic cells have been described. The major pathway of mRNA degradation in yeast occurs by deadenylation of the mRNA, which primarily leads to a decapping reaction, thereby exposing the mRNA to rapid 5' to 3' exonucleolytic degradation. A critical step in the primary pathway is decapping, since it effectively terminates the mRNA's existence and is the site of numerous control inputs. I discuss the properties of the decapping enzyme and how its activity is regulated to give rise to differential mRNA turnover. The major pathways of mRNA turnover in eukaryotic cells are initiated by shortening of the poly(A) tail. In this work, I demonstrate by several criteria that CCR4 and CAF1 encode critical components of the major cytoplasmic deadenylase in yeast. First, both Ccr4p and Caf1p are required for normal mRNA deadenylation in vivo. Second, both proteins localize to the cytoplasm. Third, Caf1p co-purifies with poly(A) specific exonuclease activity, and this activity is dependent on the presence of Ccr4p. Interestingly, because Ccr4p and Caf1p have been shown previously to interact with transcription factors, these results suggest an unexpected link between mRNA synthesis and turnover. Both the Ccr4 and Caf1 proteins have significant homology to known exonucleases, in this work I demonstrate by several criteria that CCR4 encodes the catalytic subunit of the deadenylase. First, over-expression of Ccr4p rescues the deadenylation defects of a caf1Δ strain, indicating that Caf1p is not essential for deadenylation. Second, purification of Ccr4p co-purifies with poly(A) specific exonuclease activity, and this activity is not dependent on the presence of Caf1p. Third, point mutants in predicted catalytic residues of the Ccr4p exonuclease domain result in deadenylation defects in vivo and in vitro. The strong conservation of Ccr4p and Caf1p in other eukaryotes suggests that they will function in the process of deadenylation in other organisms.
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Vigrow, Anne. "Molecular analysis of the dry rot fungus Serpula lacrymans." Thesis, University of Abertay Dundee, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.306791.

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Ferraiuolo, Maria A. "The role of eIF4AIII and 4E-T in mRNA decay /." Thesis, McGill University, 2006. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=103156.

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Translational control is crucial to balancing the cell's protein output and genetic expression. The substrate of the translational machinery---messenger RNA (mRNA)---is itself subject to regulation. The lifetime of an mRNA is limited and therefore mRNA decay is a critical step in the regulation of gene expression. Translation and mRNA decay are intimately related processes as they both handle the cell economy. mRNAs are generally in a balancing act between the translational and the repression/decay machinery, which ultimately decides the fate of an mRNA and its protein expression rate. In fact, translation affects the rate of mRNA decay. For instance, aberrant messages which contain a premature-termination codon (PTC) require ribosome scanning in order to read the message, discover the mistake, and essentially prompt its destruction. Here, a relationship between the nuclear translation-like factor---eIF4AIII, the nuclear import factor of cIF4E---4E-T, and mRNA decay was discovered. eIF4AIII is a nuclear protein that interacts physically or functionally with translation initiation factors eIF4G and eIF4B, respectively, and shares strikingly high identity with the initiation factors eIF4AI/II. This work demonstrates that eIF4AIII but not eIF4AI is required for nonsense-mediated decay (NMD). NMD is a surveillance mechanism in eukaryotes which degrades the mRNA when a PTC is present. NMD is a splicing and translation-dependent event in mammalians. We show eIF4AIII is deposited at the exon-exon junction during splicing, is a shuttling protein, and is necessary for NMD. At steady state, 4E-T is predominantly cytoplasmic and is concentrated in bodies that conspicuously resemble the recently described Processing bodies (P-bodies), which are sites of mRNA decay. We demonstrate that 4E-T colocalizes with mRNA decapping factors in bona fide P-bodies and that its binding partner, eIF4E, is tethered to P-bodies in a 4E-T dependent manner. Moreover, 4E-T controls mRNA half life. We demonstrate that 4E-T interaction with eIF4E represses translation, which is thought to be a prerequisite for targeting of mRNAs to P-bodies. Hence, analysis of prospective translation factors has led to elucidation of mRNA decay pathways.
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Dougherty, Julie Ann. "Decay of Beta-Globin mRNA in Erythroid Cells." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1397499022.

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Books on the topic "Decoy molecules"

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Lock, G. S. H. The growth and decay of ice. Cambridge [England]: Cambridge University Press, 1990.

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Jones, H. M. The spectroscopy and dynamic decay properties of molecular ions. Birmingham: University of Birmingham, 1992.

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Lambert, Ian Robert. The spectroscopy and dynamic decay properties of some highly symmetric polyatomic molecular ions. Birmingham: University of Birmingham, 1991.

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Sokell, Emma Jane. A study of decay route selectivity in atomic and molecular autoionisation using two-dimensional photoelectron spectroscopy. Manchester: University of Manchester, 1995.

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service), ScienceDirect (Online, ed. RNA turnover in eukaryotes: Nucleases, pathways and analysis of mRNA decay. San Diego, Calif: Academic, 2008.

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Larissa, Chernysheva, Yarzhemsky Victor, and SpringerLink (Online service), eds. Handbook of Theoretical Atomic Physics: Data for Photon Absorption, Electron Scattering, and Vacancies Decay. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012.

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Bensimon, David, Vincent Croquette, Jean-François Allemand, Xavier Michalet, and Terence Strick. Single-Molecule Studies of Nucleic Acids and Their Proteins. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198530923.001.0001.

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This book presents a comprehensive overview of the foundations of single-molecule studies, based on manipulation of the molecules and observation of these with fluorescent probes. It first discusses the forces present at the single-molecule scale, the methods to manipulate them, and their pros and cons. It goes on to present an introduction to single-molecule fluorescent studies based on a quantum description of absorption and emission of radiation due to Einstein. Various considerations in the study of single molecules are introduced (including signal to noise, non-radiative decay, triplet states, etc.) and some novel super-resolution methods are sketched. The elastic and dynamic properties of polymers, their relation to experiments on DNA and RNA, and the structural transitions observed in those molecules upon stretching, twisting, and unzipping are presented. The use of these single-molecule approaches for the investigation of DNA–protein interactions is highlighted via the study of DNA and RNA polymerases, helicases, and topoisomerases. Beyond the confirmation of expected mechanisms (e.g., the relaxation of DNA torsion by topoisomerases in quantized steps) and the discovery of unexpected ones (e.g., strand-switching by helicases, DNA scrunching by RNA polymerases, and chiral discrimination by bacterial topoII), these approaches have also fostered novel (third generation) sequencing technologies.
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The Growth and Decay of Ice. Cambridge University Press, 2005.

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Schnorr, Kirsten. XUV Pump-Probe Experiments on Diatomic Molecules: Tracing the Dynamics of Electron Rearrangement and Interatomic Coulombic Decay. Springer, 2014.

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Schnorr, Kirsten. XUV Pump-Probe Experiments on Diatomic Molecules: Tracing the Dynamics of Electron Rearrangement and Interatomic Coulombic Decay. Springer International Publishing AG, 2016.

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Book chapters on the topic "Decoy molecules"

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Koch, Christiane P. "Quantum Effects in Cold and Controlled Molecular Dynamics." In Molecular Beams in Physics and Chemistry, 477–90. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-63963-1_21.

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AbstractThis chapter discusses three examples of quantum effects that can be observed in state-of-the-art experiments with molecular beams—scattering resonances as a probe of interparticle interactions in cold collisions, the protection of Fano-Feshbach resonances against decay despite resonant coupling to a scattering continuum, and a circular dichroism in photoelectron angular distributions arising in the photoionization of randomly oriented chiral molecules. The molecular beam setup provides molecules in well-defined quantum states. This, together with a theoretical description based on first principles, allows for excellent agreement between theoretical prediction and experimental observation and thus a rigorous understanding of the observed quantum effects.
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Trcek, Tatjana, Samir Rahman, and Daniel Zenklusen. "Measuring mRNA Decay in Budding Yeast Using Single Molecule FISH." In mRNA Decay, 35–54. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7540-2_4.

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Bruder, Lukas, Markus Koch, Marcel Mudrich, and Frank Stienkemeier. "Ultrafast Dynamics in Helium Droplets." In Topics in Applied Physics, 447–511. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-94896-2_10.

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Abstract Helium nanodroplets are peculiar systems, as condensed superfluid entities on the nanoscale, and as vessels for studies of molecules and molecular aggregates and their quantum properties at very low temperature. For both aspects, the dynamics upon the interaction with light is fundamental for understanding the properties of the systems. In this chapter we focus on time-resolved experiments in order to study ultrafast dynamics in neat as well as doped helium nanodroplets. Recent experimental approaches are reviewed, ranging from time-correlated photon detection to femtosecond pump-probe photoelectron and photoion spectroscopy, coherent multidimensional spectroscopy as well as applications of strong laser fields and novel, extreme ultraviolet light sources. The experiments examined in more detail investigate the dynamics of atomic and molecular dopants, including coherent wave packet dynamics and long-lived vibrational coherences of molecules attached to and immersed inside helium droplets. Furthermore, the dynamics of highly-excited helium droplets including interatomic Coulombic decay and nanoplasma states are discussed. Finally, an outlook concludes on the perspectives of time-resolved experiments with helium droplets, including recent options provided by new radiation sources of femto- or even attosecond laser pulses up to the soft X-ray range.
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Lane, A. M. "Decay Modes of Meso-Molecules." In Muon-Catalyzed Fusion and Fusion with Polarized Nuclei, 67–72. Boston, MA: Springer US, 1987. http://dx.doi.org/10.1007/978-1-4757-5930-3_5.

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Raj, Satish R., S. R. Wayne Chen, Robert S. Sheldon, Arti N. Shah, Bharat K. Kantharia, Ulrich Salzer, Bodo Grimbacher, et al. "Tooth Decay." In Encyclopedia of Molecular Mechanisms of Disease, 2084. Berlin, Heidelberg: Springer Berlin Heidelberg, 2009. http://dx.doi.org/10.1007/978-3-540-29676-8_7410.

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Sun, Xiaoxia, and Jian Zhang. "STAT3 Decoy ODN Therapy for Cancer." In Methods in Molecular Biology, 167–83. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2727-2_11.

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Kho, Changwon. "Tough Decoy-Mediated Cardiac Gene Suppression." In Methods in Molecular Biology, 13–30. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2707-5_2.

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Gupta, Neal S. "Molecular Decay of Plant Biopolymers." In Topics in Geobiology, 1–16. Dordrecht: Springer Netherlands, 2013. http://dx.doi.org/10.1007/978-94-007-7936-5_1.

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Schnorr, Kirsten. "Photoionization and Interatomic Coulombic Decay." In XUV Pump-Probe Experiments on Diatomic Molecules, 9–44. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-12139-0_2.

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Elias, Joshua E., and Steven P. Gygi. "Target-Decoy Search Strategy for Mass Spectrometry-Based Proteomics." In Methods in Molecular Biology, 55–71. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60761-444-9_5.

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Conference papers on the topic "Decoy molecules"

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Sapsaman, Temsiri, and Harvey Lipkin. "Improving the Efficiency of Protein Conformation Prediction With Energy Landscape Modification." In ASME 2009 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2009. http://dx.doi.org/10.1115/detc2009-86863.

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Since the native conformation or the natural shape of a protein largely determines its function, a prediction of protein conformation can shorten the process of drug discovery. This prediction is an optimization search to locate a configuration associated with the global minimum energy for the molecule. Due to the complexity of the multidimensional energy landscape, the prediction process can be extensive, which leads to very long simulation run times. For example, a high-resolution structure prediction algorithm [1] refining 20,000 to 30,000 models of several 49 to 88 residue long molecules takes about 150 CPU days per molecule. This paper presents the method of modified energy landscape (MEL) that improves the efficiency of the Broyden–Fletcher–Goldfarb–Shanno (BFGS) method by 12.8% on average, and more than 30% in some cases for a representative sample of cases. Since the efficiency improvement allows the probabilistic search to cover more areas of the energy landscape, locating the global minimum is more likely. Also, in a practical protein prediction running coarse refinements on more decoys is more preferable than comprehensively refining few decoys because of the low accuracy of energy functions. Therefore, the MEL can significantly improve the protein prediction simulation even though it yields less average score improvement. The MEL is implemented in a refinement protocol in Rosetta [2].
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Courtin, S. "Decay Modes of Narrow Molecular Resonances." In FUSION06: Reaction Mechanisms and Nuclear Structure at the Coulomb Barrier. AIP, 2006. http://dx.doi.org/10.1063/1.2338367.

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Müller, U. "Three-body decay of laser-excited triatomic hydrogen molecules." In The 21st international conference on the physics of electronic and atomic collisions (21 IPEAC). AIP, 2000. http://dx.doi.org/10.1063/1.1302657.

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Van Labeke, Daniel, Philippe Grossel, and Jean-Marie Vigoureux. "Decay Of An Excited Molecule Near Small Roughness." In 1989 Intl Congress on Optical Science and Engineering, edited by Tony Wilson. SPIE, 1989. http://dx.doi.org/10.1117/12.961776.

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Feifel, Raimund. "ULTRAFAST MOLECULAR THREE-ELECTRON COLLECTIVE AUGER DECAY." In 71st International Symposium on Molecular Spectroscopy. Urbana, Illinois: University of Illinois at Urbana-Champaign, 2016. http://dx.doi.org/10.15278/isms.2016.fe07.

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Vostrikova, Liubov I., and Vitaly A. Smirnov. "Decay of photoinduced susceptibility under red light." In Laser Physics, Photonic Technologies, and Molecular Modeling, edited by Vladimir L. Derbov. SPIE, 2022. http://dx.doi.org/10.1117/12.2626307.

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Froufe-Perez, L. S., J. J. Saenz, and R. Carminati. "Single molecule fluorescence decay rate fluctuations in complex media." In 2007 Quantum Electronics and Laser Science Conference. IEEE, 2007. http://dx.doi.org/10.1109/qels.2007.4431770.

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Xu, Kaiwen, Takashi Mukaiyama, Jamil R. Abo-Shaeer, Jit Kee Chin, Daniel E. Miller, and Wolfgang Ketterle. "Studying ultra-cold molecules formation and decay via a Feshbach resonance." In International Quantum Electronics Conference. Washington, D.C.: OSA, 2004. http://dx.doi.org/10.1364/iqec.2004.imi1.

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BARANOV, D. S., and O. D. BARANOVA. "EVIDENCE OF THE FORMATION AND DECAY OF GIANT LONG-LIVED NUCLEAR MOLECULES." In Proceedings of the International Symposium. WORLD SCIENTIFIC, 2013. http://dx.doi.org/10.1142/9789814508865_0029.

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Inci, M. Naci, Bukem Bilen, and Sabriye Acikgoz. "Decay rate measurement of perylene dye molecules attached to porous silicon nanostructures." In Photonics, Devices, and Systems IV, edited by Pavel Tománek, Dagmar Senderáková, and Miroslav Hrabovský. SPIE, 2008. http://dx.doi.org/10.1117/12.818073.

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Reports on the topic "Decoy molecules"

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Leung, P. T., Young S. Kim, and Thomas F. George. Decay of Molecules at Corrugated Thin Metal Films. Fort Belvoir, VA: Defense Technical Information Center, February 1989. http://dx.doi.org/10.21236/ada205487.

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Xiong, Ting. Modeling of Decay Rate for Molecules at an Island Surface. Portland State University Library, January 2000. http://dx.doi.org/10.15760/etd.7074.

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Wilkerson, J. F., T. J. Bowles, D. A. Knapp, M. P. Maley, and J. F. Robertson. Los Alamos free molecular and atomic tritium beta decay experiment. Office of Scientific and Technical Information (OSTI), January 1986. http://dx.doi.org/10.2172/6005230.

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Kim, Young S., P. T. Leung, and Thomas F. George. Classical Decay Rates for Molecules in the Presence of a Spherical Surface: A Complete Treatment,. Fort Belvoir, VA: Defense Technical Information Center, October 1987. http://dx.doi.org/10.21236/ada185754.

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Kim, Young S., P. T. Leung, and Thomas F. George. Remark on the Morphology-Dependent Resonance in the Decay Rate Spectrum for Molecules near a Spherical Surface. Fort Belvoir, VA: Defense Technical Information Center, September 1988. http://dx.doi.org/10.21236/ada199417.

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Pipkin, F. M. Study of Energy Levels and Decay Mechanisms for Singlet Rydberg States of Molecular Nitrogen. Fort Belvoir, VA: Defense Technical Information Center, September 1987. http://dx.doi.org/10.21236/ada192505.

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Wisniewski, Michael E., Samir Droby, John L. Norelli, Noa Sela, and Elena Levin. Genetic and transcriptomic analysis of postharvest decay resistance in Malus sieversii and the characterization of pathogenicity effectors in Penicillium expansum. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7600013.bard.

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Blue mold of apple caused by Penicilliumexpansumis a major postharvest disease. Selection for postharvest disease resistance in breeding programs has been ignored in favor of fruit quality traits such as size, color, taste, etc. The identification of postharvest disease resistance as a heritable trait would represent a significant accomplishment and has not been attempted in apple. Furthermore, insight into the biology of the pathogenicity of P. expansumin apple could provide new approaches to postharvest decay management. Hypothesis: Postharvest resistance of apple to P. expansumcan be mapped to specific genetic loci and significant quantitative-trait-loci (QTLs) can be identified that account for a major portion of the population variance. Susceptibility of apple fruit to P. expansumis dependent on the ability of the pathogen to produce LysM effectors that actively suppress primary and/or secondary resistance mechanisms in the fruit. Objectives: 1) Identify QTL(s) and molecular markers for blue mold resistance in GMAL4593 mapping population (‘Royal Gala’ X MalussieversiiPI613981), 2) Characterize the transcriptome of the host and pathogen (P. expansum) during the infection process 3) Determine the function of LysM genes in pathogenicity of P. expansum. Methods: A phenotypic evaluation of blue mold resistance in the GMAL4593 mapping population, conducted in several different years, will be used for QTL analysis (using MapQTL 6.0) to identify loci associated with blue mold resistance. Molecular markers will be developed for the resistance loci. Transcriptomic analysis by RNA-seq will be used to conduct a time course study of gene expression in resistant and susceptible apple GMAL4593 genotypes in response to P. expansum, as well as fungal responses to both genotypes. Candidate resistance genes identified in the transcriptomic study and or bioinformatic analysis will be positioned in the ‘Golden Delicious’ genome to identify markers that co-locate with the identified QTL(s). A functional analysis of LysM genes on pathogenicity will be conducted by eliminating or reducing the expression of individual effectors by heterologous recombination and silencing technologies. LysMeffector genes will also be expressed in a yeast expression system to study protein function. Expected Results: Identification of postharvest disease resistance QTLs and tightly-linked genetic markers. Increased knowledge of the role of effectors in blue mold pathogenic
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Chalutz, Edo, Charles Wilson, Samir Droby, Victor Gaba, Clauzell Stevens, Robert Fluhr, and Y. Lu. Induction of Resistance to Postharvest Diseases and Extension of Shelf-Life of Fruits and Vegetables by Ultra-Violet Light. United States Department of Agriculture, February 1994. http://dx.doi.org/10.32747/1994.7568093.bard.

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Following preliminary observations by one of the collaborating scientists on this project and the completion of a 1-year, BARD-supported feasibility study (IS-1908-90F), this 3-year BARD project has been executed. The main objectives of the research were to elucidate biochemical and pathological aspects of UV-induced resistance in fruits and vegetables, to characterize physical and biological variables of induced resistance and delay of ripening, and to explore the application of the treatment as a control practice of postharvest diseases and shelf-life extension of fruits and vegetables. Our findings, which are detailed in numerous joint publications, have shown that the effect of UV-C light on induction of resistance and delay of ripening is a general one and of wide oddurrence. Apart from surface sterilization of the commodity, the reduction of decay of different fungi has been associated with and induced resistance phenomenon which gradually builds up within 24 to 48 hours after the UV treatment and can be reversed by visible light. In citrus, induced resistance has been associated with increased activity of the enzymes phenylalanine ammonia-lyase and peroxidase, and with the levels of endglucanase and chitinase. In tomato, resistance was correlated with the production of high levels of tomatine. Our study of some molecular aspects of the induced resistance in grapefruit has revealed the induction of a cDNA which represents a gene encoding for an isoflavone reductase-like protein that, in legumes, has been associated with phytoalexin biosynthesis. This gene was cloned and sequenced. Delay of ripening was associated in tomato with inhibition of ethylene production, carotenoid synthesis, and chlorophyll degradation and with the presence of high levels of polyamines. In peach fruit epiphytic populations of a yeast increased following the UV treatment. Pilot-size treatment and packing lines were constructed in the US and Israel to test the application of the UV treatment on a semi-commercial scale. Although effective in reduction of decay and delay of ripening, a number of problems will have to be addressed before practical application of this methodology can be realized. The main issues are associated with the temporal and variable response to the treatment, and its relationship to the maturity and date of harvest of the commodity.
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Wisniewski, Michael, Samir Droby, John Norelli, Dov Prusky, and Vera Hershkovitz. Genetic and transcriptomic analysis of postharvest decay resistance in Malus sieversii and the identification of pathogenicity effectors in Penicillium expansum. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597928.bard.

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Use of Lqh2 mutants (produced at TAU) and rNav1.2a mutants (produced at the US side) for identifying receptor site-3: Based on the fact that binding of scorpion alpha-toxins is voltage-dependent, which suggests toxin binding at the mobile voltage-sensing region, we analyzed which of the toxin bioactive domains (Core-domain or NC-domain) interacts with the DIV Gating-module of rNav1.2a. This analysis was based on the assumption that the dissociation of toxin mutants upon depolarization would vary from that of the unmodified toxin should the substitutions affect a site of interaction with the channel Gating-module. Using a series of toxin mutants (mutations at both domains) and two channel mutants that were shown to reduce the sensitivity to scorpion alpha-toxins, and by comparison of depolarization-driven dissociation of Lqh2 derivatives off their binding site at rNav1.2a mutant channels we found that the toxin Core-domain interacts with the Gating-module of DIV. Details of the experiments and results appear in Guret al (2011). Mapping receptor site 3 at Nav1.2a by extensive channel mutagenesis (Seattle): Since previous studies with photoaffinity labeling and antibody mapping implicated domains I and IV in scorpion alpha-toxin binding, Nav1.2 channel mutants containing substitutions at these extracellular regions were expressed and tested for receptor function by whole-cell voltage clamp. Of a large number of channel mutants, T1560A, F1610A, and E1613A in domain IV had ~5.9-, ~10.7-, and ~3.9-fold lower affinities for the scorpion toxin Lqh2, respectively, and mutant E1613R had 73-fold lower affinity. Toxin dissociation was accelerated by depolarization for both wild-type and mutants, and the rates of dissociation were also increased by mutations T1560A, F1610A and E1613A. In contrast, association rates for these three mutant channels at negative membrane potentials were not significantly changed and were not voltage-dependent. These results indicated that Thr1560 in the S1-S2 loop, Phe1610 in the S3 segment, and Glu1613 in the S3-S4 loop in domain IV participate in toxin binding. T393A in the SS2-S6 loop in domain I also showed a ~3.4-fold lower affinity for Lqh2, indicating that this extracellular loop may form a secondary component of the toxin binding site. Analysis with the Rosetta-Membrane algorithm revealed a three-dimensional model of Lqh2 binding to the voltage sensor in a resting state. In this model, amino acid residues in an extracellular cleft formed by the S1-S2 and S3-S4 loops in domain IV that are important for toxin binding interact with amino acid residues on two faces of the wedge-shaped Lqh2 molecule that are important for toxin action. The conserved gating charges in the S4 transmembrane segment are in an inward position and likely form ion pairs with negatively charged amino acid residues in the S2 and S3 segments (Wang et al 2011; Gurevitz 2012; Gurevitzet al 2013).
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Gurevitz, Michael, Michael E. Adams, Boaz Shaanan, Oren Froy, Dalia Gordon, Daewoo Lee, and Yong Zhao. Interacting Domains of Anti-Insect Scorpion Toxins and their Sodium Channel Binding Sites: Structure, Cooperative Interactions with Agrochemicals, and Application. United States Department of Agriculture, December 2001. http://dx.doi.org/10.32747/2001.7585190.bard.

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Integrated pest management in modern crop protection may combine chemical and biological insecticides, particularly due to the risks to the environment and livestock arising from the massive use of non-selective chemicals. Thus, there is a need for safer alternatives, which target insects more specifically. Scorpions produce anti-insect selective polypeptide toxins that are biodegradable and non-toxic to warm-blooded animals. Therefore, integration of these substances into insect pest control strategies is of major importance. Moreover, clarification of the molecular basis of this selectivity may provide valuable information pertinent to their receptor sites and to the future design of peptidomimetic anti-insect specific substances. These toxins may also be important for reducing the current overuse of chemical insecticides if they produce a synergistic effect with conventional pesticides. Based on these considerations, our major objectives were: 1) To elucidate the three-dimensional structure and toxic-site of scorpion excitatory, "depressant, and anti-insect alpha toxins. 2) To obtain an initial view to the sodium channel recognition sites of the above toxins by generating peptide decoys through a phage display system. 3) To investigate the synergism between toxins and chemical insecticides. Our approach was to develop a suitable expression system for toxin production in a recombinant form and for elucidation of toxin bioactive sites via mutagenesis. In parallel, the mode of action and synergistic effects of scorpion insecticidal toxins with pyrethroids were studied at the sodium channel level using electrophysiological methods. Objective 1 was achieved for the alpha toxin, LqhaIT Zilberberg et al., 1996, 1997; Tugarinov et al., 1997; Froy et al., 2002), and the excitatory toxin, Bj-xtrIT (Oren et al., 1998; Froy et al., 1999; unpublished data). The bioactive surface of the depressant toxin, LqhIT2, has been clarified and a crystal of the toxin is now being analyzed (unpublished). Objective 2 was not successful thus far as no phages that recognize the toxins were obtained. We therefore initiated recently an alternative approach, which is introduction of mutations into recombinant channels and creation of channel chimeras. Objective 3 was undertaken at Riverside and the results demonstrated synergism between LqhaIT or AaIT and pyrethroids (Lee et al., 2002). Furthermore, negative cross-resistance between pyrethroids and scorpion toxins (LqhaIT and AaIT) was demonstrated at the molecular level. Although our study did not yield a product, it paves the way for future design of selective pesticides by capitalizing on the natural competence of scorpion toxins to distinguish between sodium channels of insects and vertebrates. We also show that future application of anti-insect toxins may enable to decrease the amounts of chemical pesticides due to their synergism.
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