Relevant bibliographies by topics / Structural binding characterization

Academic literature on the topic 'Structural binding characterization'

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Published: 10 December 2022
Last updated: 28 January 2023

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Journal articles on the topic "Structural binding characterization"

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Joseph, Prem Raj B., Ziyan Yuan, Eric A. Kumar, G. L. Lokesh, Smitha Kizhake, Krishna Rajarathnam, and Amarnath Natarajan. "Structural characterization of BRCT–tetrapeptide binding interactions." Biochemical and Biophysical Research Communications 393, no. 2 (March 2010): 207–10. http://dx.doi.org/10.1016/j.bbrc.2010.01.098.

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BRIX, Lulu A., Ronald G. DUGGLEBY, Andrea GAEDIGK, and Michael E. McMANUS. "Structural characterization of human aryl sulphotransferases." Biochemical Journal 337, no. 2 (January 8, 1999): 337–43. http://dx.doi.org/10.1042/bj3370337.

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Human aryl sulphotransferase (HAST) 1, HAST3, HAST4 and HAST4v share greater than 90% sequence identity, but vary markedly in their ability to catalyse the sulphonation of dopamine and p-nitrophenol. In order to investigate the amino acid(s) involved in determining differing substrate specificities of HASTs, a range of chimaeric HAST proteins were constructed. Analysis of chimaeric substrate specificities showed that enzyme affinities are mainly determined within the N-terminal end of each HAST protein, which includes two regions of high sequence divergence, termed Regions A (amino acids 44–107) and B (amino acids 132–164). To investigate the substrate-binding sites of HASTs further, site-directed mutagenesis was performed on HAST1 to change 13 individual residues within these two regions to the HAST3 equivalent. A single amino acid change in HAST1 (A146E) was able to change the specificity for p-nitrophenol to that of HAST3. The substrate specificity of HAST1 towards dopamine could not be converted into that of HAST3 with a single amino acid change. However, compared with wild-type HAST1, a number of the mutations resulted in interference with substrate binding, as shown by elevated Ki values towards the co-substrate 3´-phosphoadenosine 5´-phosphosulphate, and in some cases loss of activity towards dopamine. These findings suggest that a co-ordinated change of multiple amino acids in HAST proteins is needed to alter the substrate specificities of these enzymes towards dopamine, whereas a single amino acid at position 146 determines p-nitrophenol affinity. A HAST1 mutant was constructed to express a protein with four amino acids deleted (P87–P90). These amino acids were hypothesized to correspond to a loop region in close proximity to the substrate-binding pocket. Interestingly, the protein showed substrate specificities more similar to wild-type HAST3 than HAST1 and indicates an important role of these amino acids in substrate binding.
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Miller, Maria. "Structural Characterization of Transcription Factor C/EBPbeta." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1510. http://dx.doi.org/10.1107/s2053273314084897.

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The basic region:leucine zipper (bZIP) DNA-binding protein, C/EBPbeta, plays a central role in many vital cellular processes, but is also implicated in tumorigenesis, tumor progression, as well as viral replication within cells. C/EBPbeta binds to specific DNA sites as homo- or hetero-dimers and interacts with other transcription factors to control the transcription of a number of eukaryotic genes. C/EBPbeta is an intrinsically repressed protein that is activated in response to growth factors. This study employs a variety of techniques such as sequence analysis, molecular modeling, X-ray crystallography, and mutagenesis to provide structural insights into the mechanisms that modulate the biological activities of C/EBPbeta. Analysis of the primary structure indicates that C/EBPbeta is a largely disordered protein that consists of unstructured regions that have the potential to fold upon binding to molecular partners as well as regions that retain irregular conformations regardless of their environment. Here, a model of the auto-inhibited form of C/EBPbeta is presented as well as the structural basis of its specific dimerization, DNA-binding, and interactions with the p300 transcriptional co-activator.
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Culurgioni, Simone, Minzhe Tang, and Martin Austin Walsh. "Structural characterization of theStreptococcus pneumoniaecarbohydrate substrate-binding protein SP0092." Acta Crystallographica Section F Structural Biology Communications 73, no. 1 (January 1, 2017): 54–61. http://dx.doi.org/10.1107/s2053230x16020252.

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Streptococcus pneumoniaeis an opportunistic respiratory pathogen that remains a major cause of morbidity and mortality globally, with infants and the elderly at the highest risk.S. pneumoniaerelies entirely on carbohydrates as a source of carbon and dedicates a third of all uptake systems to carbohydrate import. The structure of the carbohydrate-free substrate-binding protein SP0092 at 1.61 Å resolution reveals it to belong to the newly proposed subclass G of substrate-binding proteins, with a ligand-binding pocket that is large enough to accommodate complex oligosaccharides. SP0092 is a dimer in solution and the crystal structure reveals a domain-swapped dimer with the monomer subunits in a closed conformation but in the absence of carbohydrate ligand. This closed conformation may be induced by dimer formation and could be used as a mechanism to regulate carbohydrate uptake.
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Suda, Yasuo, Dalila Marques, John C. Kermode, Shoichi Kusumoto, and Michael Sobel. "Structural characterization of heparin's binding domain for human platelets." Thrombosis Research 69, no. 6 (March 1993): 501–8. http://dx.doi.org/10.1016/0049-3848(93)90054-r.

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Bassenden, Angelia, Dmitry Rodionov, Nilu Sabet-Kassouf, Tahereh Haji, Kun Shi, and Albert Berghuis. ""Structural characterization of aminoglycoside modifying enzyme ANT(2"")-Ia"." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C702. http://dx.doi.org/10.1107/s2053273314092973.

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Aminoglycosides are a class of broad-spectrum antibiotics used in the treatment of serious Gram-negative bacterial infections, they target the 16S RNA subunit and upon binding cause errors in translation, eventually inducing a bactericidal effect [1]. Aminoglycoside nucleotidyltransferase (2")-Ia (ANT(2")-Ia) is an aminoglycoside modifying enzyme that prevents aminoglycosides from binding to the ribosomal subunit, making this enzyme a principle candidate structure-based drug design [2]. Characterization of ANT(2")-Ia has been proven to be difficult due to the low stability and solubility of overexpressed protein, where 95% of the protein being expressed is in the form of inclusion bodies [3]. We describe a protocol that has lead to successful expression and purification of ANT(2")-Ia. A successful enzymatic assay has also been adapted and the protein is active and stable under these conditions with a specific activity of 0.14 U/mg. Furthermore, nuclear magnetic resonance (NMR) studies have allowed for the assignment of 144 of the 176 non-proline backbone residues. Substrate binding NMR experiments have shown unique global chemical shift perturbations upon binding ATP and tobramycin, suggesting unique binding sites for each substrate. Structural determination of ANT(2")-Ia using NMR in conjunction with x-ray crystallography can be utilized in order to develop small molecules that will act as more effective aminoglycosides in order to inhibit ANT(2")-Ia from binding and modifying these antibiotics.
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Lee, Meng-Hwan, Wen-Lin Lai, Shuen-Fuh Lin, Cheng-Sheng Hsu, Shwu-Huey Liaw, and Ying-Chieh Tsai. "Structural Characterization of Glucooligosaccharide Oxidase from Acremonium strictum." Applied and Environmental Microbiology 71, no. 12 (December 2005): 8881–87. http://dx.doi.org/10.1128/aem.71.12.8881-8887.2005.

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ABSTRACT Glucooligosaccharide oxidase from Acremonium strictum was screened for potential applications in oligosaccharide acid production and carbohydrate detection. This protein is a unique covalent flavoenzyme which catalyzes the oxidation of a variety of carbohydrates with high selectivity for cello- and maltooligosaccharides. Kinetic measurements suggested that this enzyme possesses an open carbohydrate-binding groove, which is mainly composed of two glucosyl-binding subsites. The encoding gene was subsequently cloned, and one intron was detected in the genomic DNA. Large amounts of active enzymes were expressed in Pichia pastoris, with a yield of 300 mg per liter medium. The protein was predicted to share structural homology with plant cytokinin dehydrogenase and related flavoproteins that share a conserved flavin adenine dinucleotide (FAD)-binding domain. The closest sequence matches are those of plant berberine bridge enzyme-like proteins, particularly the characteristic flavinylation site. Unexpectedly, mutation of the putative FAD-attaching residue, H70, to alanine, serine, cysteine, and tyrosine did not abolish the covalent FAD linkage and had little effect on the Km . Instead, the variants displayed k cat values that were 50- to 600-fold lower, indicating that H70 is crucial for efficient redox catalysis, perhaps through modulation of the oxidative power of the flavin.
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Su, Hua-Poo, Keith Rickert, Christine Burlein, Kartik Narayan, Marina Bukhtiyarova, Danielle M. Hurzy, Craig A. Stump, et al. "Structural characterization of nonactive site, TrkA-selective kinase inhibitors." Proceedings of the National Academy of Sciences 114, no. 3 (December 30, 2016): E297—E306. http://dx.doi.org/10.1073/pnas.1611577114.

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Current therapies for chronic pain can have insufficient efficacy and lead to side effects, necessitating research of novel targets against pain. Although originally identified as an oncogene, Tropomyosin-related kinase A (TrkA) is linked to pain and elevated levels of NGF (the ligand for TrkA) are associated with chronic pain. Antibodies that block TrkA interaction with its ligand, NGF, are in clinical trials for pain relief. Here, we describe the identification of TrkA-specific inhibitors and the structural basis for their selectivity over other Trk family kinases. The X-ray structures reveal a binding site outside the kinase active site that uses residues from the kinase domain and the juxtamembrane region. Three modes of binding with the juxtamembrane region are characterized through a series of ligand-bound complexes. The structures indicate a critical pharmacophore on the compounds that leads to the distinct binding modes. The mode of interaction can allow TrkA selectivity over TrkB and TrkC or promiscuous, pan-Trk inhibition. This finding highlights the difficulty in characterizing the structure-activity relationship of a chemical series in the absence of structural information because of substantial differences in the interacting residues. These structures illustrate the flexibility of binding to sequences outside of—but adjacent to—the kinase domain of TrkA. This knowledge allows development of compounds with specificity for TrkA or the family of Trk proteins.
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Gangi Setty, Thanuja, Christine Cho, Sowmya Govindappa, Michael A. Apicella, and S. Ramaswamy. "Bacterial periplasmic sialic acid-binding proteins exhibit a conserved binding site." Acta Crystallographica Section D Biological Crystallography 70, no. 7 (June 24, 2014): 1801–11. http://dx.doi.org/10.1107/s139900471400830x.

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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 bacteriaFusobacterium nucleatum,Pasteurella multocidaandVibrio choleraeand their thermodynamic characterization are reported. The binding affinities of several mutations in the Neu5Ac binding site of theHaemophilus influenzaeprotein 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.
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Ludzia, Patryk, Edward D. Lowe, Gabriele Marcianò, Shabaz Mohammed, Christina Redfield, and Bungo Akiyoshi. "Structural characterization of KKT4, an unconventional microtubule-binding kinetochore protein." Structure 29, no. 9 (September 2021): 1014–28. http://dx.doi.org/10.1016/j.str.2021.04.004.

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Dissertations / Theses on the topic "Structural binding characterization"

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Hoy, Julie Anne. "Structural characterization of ligand binding in hexacoordinate hemoglobins." [Ames, Iowa : Iowa State University], 2006.

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Pang, Bo, and 龐博. "Structural characterization of H1N1 nucleoprotein-nucleozin binding sites." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2013. http://hdl.handle.net/10722/205641.

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Although influenza is usually acute self-limiting respiratory infection, influenza viruses are among the most common pathogens that threaten the health of humans and animals worldwide. Various anti-viral therapeutic agents are currently used for treatment and prophylaxis of influenza virus, but the problem is that the targets of these drugs are easily mutated and result in resistance. Therefore, medications that have broad spectrum coverage are urgently needed to combat with the disease. Since nucleoprotein (NP), which is encoded by influenza virus genome, is regarded as a druggable target due to its conserved sequence and important functions during influenza virus life cycle, numerous studies are focused on this protein in attempts to develop broad-spectrum anti-influenza therapeutics. Recently, Kao et al. found that the addition of a novel small molecule nucleozin could lead to large aggregates of NP, which in turn caused cessation of virus replication. Give that the interaction between NP and nucleozin is still not unveiled, it is crucial to identify the binding sites using X-ray crystallography. The full length influenza A/WSN/33 (H1N1) NP gene was cloned into pET28 vector, with His-tag in its C-terminus and overexpressed in E.coli strain Rosetta 2. Cell culture was purified by HisTrap HP and Superdex-200 16/60 gel filtration columns. Crystals were grown using the vapour diffusion method and the NP-nucleozin complex was prepared by soaking native crystal in solution containing 0.25 mM nucleozin for 2h. Crystals of the complex can diffract to 3.0 Å at the Shanghai Synchrotron Radiation Facility. The structure of NP was determined by molecular replacement and it belongs to space group C121 with two NP trimers per asymmetric unit. After further refinement, two nucleozin molecules were found in each asymmetric unit, and each of them could bind with two NP molecules at the same time. The ligand binding pockets were formed by the combination of Y289/N309 pocket from one NP molecule, and R382 pocket from another NP molecule. Therefore, the function of nucleozin is to bridge two NP molecules and lead to NP aggregation, which are in agreement with functional studies on nucleozin. Furthermore, computational models of the NP-nucleozin binding are provided to reveal the mechanism of nucleozin induced aggregation. In addition, recent work on interaction between NP and another novel molecule named compound A has also been briefly described and compared with NP-nucleozin complex at the end of this thesis. Collectively, this study presents a new paradigm for better understanding of how NP and nucleozin interact with each other and hence result in NP aggregates, which is envisaged to accelerate the development of anti-influenza therapeutic agents.
published_or_final_version
Physiology
Doctoral
Doctor of Philosophy
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Butan, Carmen Crina. "Structural characterization of the RNA binding domain of BTV non-structural protein 2." Thesis, Birkbeck (University of London), 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.414198.

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Santelli, Eugenio. "The binding of MEF2A to DNA : biochemical and structural characterization /." [S.l.] : [s.n.], 2000. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=13752.

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Gilbert, Sunny Deshea. "Biochemical and structural characterization of ligand binding by the purine riboswitch." Connect to online resource, 2007. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3256472.

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Desjardins, Geneviève. "Structural characterization of DNA binding and autoinhibition by the Ets1 transcription factor." Thesis, University of British Columbia, 2015. http://hdl.handle.net/2429/52606.

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Ets1 belongs to the ETS transcription factor family and plays key roles in regulating eukaryotic gene expression. The affinity of the Ets1 for its cognate DNA sites is autoinhibited by an intrinsically disordered serine-rich region (SRR) and an appended helical inhibitory module (IM). Through transient interactions, the SRR both sterically blocks the ETS domain and allosterically stabilizes the IM to modulate DNA-binding affinity. Calmodulin-dependent kinase II phosphorylation of five serines within the SRR progressively reinforces autoinhibition in response to calcium signaling. Using mutagenesis and quantitative DNA-binding measurements, we demonstrate that phosphorylation-enhanced autoinhibition requires the presence of phenylalanine/tyrosine (ϕ) residues adjacent to the SRR phosphoacceptor serines. The introduction of additional phosphorylated Ser-ϕ-Asp, but not Ser-Ala-Asp, repeats within the SRR dramatically reinforces autoinhibition. NMR spectroscopic studies of phosphorylated and mutated SRR variants, both within their native context and as separate trans-acting peptides, confirmed that the aromatic residues and phosphoserines contribute to the formation of a dynamic complex with the ETS domain. Complementary NMR studies also identified the SRR-interacting surface of the ETS domain, which encompasses its positively-charged DNA recognition interface and an adjacent region of neutral polar and nonpolar residues. Collectively, these studies highlight the role of aromatic residues and their synergy with phosphoserines in an intrinsically disordered regulatory sequence that integrates cellular signaling and gene expression. We also investigated by NMR spectroscopy the interaction of Ets1 with specific and nonspecific oligonucleotides. Upon binding DNA, helices HI-1 and HI-2 of the IM unfold. Thus, autoinibition does not impart DNA-binding specificity. Using amide chemical shift perturbation mapping, we also show that Ets1 binds both specific and non-specific oligonucleotides through its canonical ETS domain interface. However, the non-specific complex is formed by weak and dynamic electrostatic interactions, whereas the specific complex involves well-ordered hydrogen bonds and salt bridges. In support of this conclusion, five lysine sidechains are protected from rapid hydrogen exchange upon binding of specific DNA, whereas only one is stabilized in the non-specific complex. Overall, these data are consistent with Ets1 rapidly finding specific DNA sites within the genome via facilitated diffusion (sliding and hopping) within a vast background of non-specific sequences.
Medicine, Faculty of
Biochemistry and Molecular Biology, Department of
Graduate
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Brooksbank, Robert Alan. "Expression, purification and structural characterization of the DNA-binding domain of BZLF1." Thesis, University of Cambridge, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.321537.

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Oke, Muse. "Functional and structural characterization of the transferrin binding protein A from Neisseria meningitidis." Thesis, Birkbeck (University of London), 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.413693.

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Juntunen, K. (Kari). "Functional and structural characterization of nuclear vitamin D receptor and its ligand binding domain." Doctoral thesis, University of Oulu, 2002. http://urn.fi/urn:isbn:9514268784.

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Abstract The hormonally active form of vitamin D, 1,25(OH)2D3, is involved in many biological functions throughout the body, such as regulation of calcium and phosphate homeostasis, bone remodeling and controlling cell proliferation and differentiation. Vitamin D receptor (VDR), a member of the nuclear hormone receptor (NHR) super family, mediates those genomic actions of 1,25 (OH)2D3 by actively repressing or activating its target genes. In the present study recombinant human nuclear VDR and its ligand binding domain (LBD) were expressed in Spodoptera frugiperda (Sf9) insect cells and in E.coli. Recombinant proteins were purified and their biochemical and biophysical properties were characterized. Recombinant VDR was shown to bind to the vitamin D response element (VDRE) of osteopontin and osteocalcin genes as a homodimer or as a heterodimer with the retinoid X receptor (RXR)-αΔAB. Full-length VDR and its LBD were demonstrated to bind natural ligand 1,25 (OH)2D3 with high affinity. The binding affinities of several vitamin D analogs were also determined. Ligand binding induced conformational change within the receptor was studied using several methods such as partial proteolytic digestion, small angle neutron scattering (SANS), native gel electrophoresis and circular dichroism (CD) spectroscopy. Results indicate that ligand binding induces conformational change within VDR and different 1,25(OH)2D3 analogs might induce a somewhat different conformation within the receptor. This is seen as an unequal capacity of analogs to stabilize receptor against proteases or heat and as differences in the promotion of receptor homodimerization. Compared to other nuclear hormone receptors, VDR presents a large insertion region at the N-terminal part of the LBD between helices H1 and H3, encoded by an additional exon. In the present study this additional exon was deleted and the properties of mutated LBD were compared to the wild type LBD. Biochemical analyses indicated that the mutant protein exhibits the same ligand binding, dimerization with RXR and transactivation properties as the wild-type VDR, suggesting that the insertion region does not affect these main functions. Furthermore, solution studies by small angle X-ray scattering indicated that the insertion region in the VDR locates on the surface of molecule and it is not structurally well ordered.
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Sharif, Azar. "Structural characterization of the polycomb repressor complex 1 binding partner ubiquitin specific protease 11." Thesis, Imperial College London, 2013. http://hdl.handle.net/10044/1/39355.

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Ubiquitin Specific Protease 11 (USP11), USP4 and USP15 are highly conserved and are characterised by an N-terminal 'domain present in ubiquitin specific proteases' (DUSP) and 'ubiquitin-like' (UBL) domains. This DUSP-UBL (DU) domain is thought to be involved in substrate recognition. It was shown that USP11 co-purifies with human Polycomb Repressive Complex type 1 (PRC1) and regulates the stability of the E3 ligase component of PRC1 (Maertens et al, 2010). PRC1 repress transcription from the INK4a tumour suppressor locus. Hence knockdown of USP11 in primary human fibroblasts causes de-repression of INK4a, followed by a senescence-like proliferative arrest. In this project we aimed to map the interaction between USP11 and PRC1 components (BMI1, RING2, MEL18 and CBX8). We used two methods to investigate their interactions; yeast two-hybrid and in vitro pull down. Unexpectedly, we could not confirm a direct interaction between USP11 and any PRC1 component. We hypothesize that the lack of post-translation modifications, the presence of fusion tags and/or the need of a multi-subunit PRC1 complex might be needed to observe a high affinity interaction. We also aimed to map the interaction between three PRC1 components; RING2, BMI1 and RYBP, with the ultimate aim of solving the X-ray structure of the complex. The main obstacle in this project was to express, extract and purify these proteins at high levels in bacterial culture. Preliminary data suggests that RYBP and BMI1 do not interact directly. Here we report the 3.6 Å resolution X-ray structure of the human USP11 DU. The sequence linking the DUSP and UBL domains, the DU finger, could not be assigned in the electron density map due to low resolution. Comparison with the related USP4 DU crystal structure reveals that the structures are mostly conserved.
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Books on the topic "Structural binding characterization"

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Doig, Peter Clifford. Characterization of the binding of "Pseudomonas aeruginosa" alginate to human buccal epithelial cells: structural diversity in alginates. 1986.

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Book chapters on the topic "Structural binding characterization"

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Auffinger, Pascal, Benoit Masquida, and Eric Westhof. "Structural and Dynamical Characterization of Nucleic Acid Water and Ion Binding Sites." In Lecture Notes in Computational Science and Engineering, 61–70. Berlin, Heidelberg: Springer Berlin Heidelberg, 2002. http://dx.doi.org/10.1007/978-3-642-56080-4_3.

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Williamson, P. T. F., S. Bains, C. Chung, R. Cooke, B. H. Meier, and A. Watts. "Characterization and assignment of uniformly labeled NT(8–13) at the agonist binding site of the G-protein coupled neurotensin receptor." In Focus on Structural Biology, 191–201. Dordrecht: Springer Netherlands, 2001. http://dx.doi.org/10.1007/978-94-017-2579-8_17.

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Morita, Takashi, and Hideko Atoda. "The Structural Characterization of Coagulation Factor IX/Factor X-Binding Protein Isolated from the Venom of Trimeresurus Flavoviridis." In Current Aspects of Blood Coagulation, Fibrinolysis, and Platelets, 35–40. Tokyo: Springer Japan, 1993. http://dx.doi.org/10.1007/978-4-431-68323-0_6.

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Cernooka, Elina, Janis Rumnieks, and Andris Kazaks. "Structural Characterization of a Single-Stranded DNA-Binding Protein: A Case Study of the ORF6 Protein from Bacteriophage Enc34." In Methods in Molecular Biology, 343–73. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1290-3_23.

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Gerke, Volker. "Structural and Functional Characterization of Protein I (p362p112) and II (p32) - Calcium/Phospholipid Binding Proteins with Homologies to Lipocortin I." In Advances in Experimental Medicine and Biology, 135–38. Boston, MA: Springer US, 1990. http://dx.doi.org/10.1007/978-1-4684-5754-4_21.

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Gualerzi, C. O., M. A. Losso, M. Lammi, K. Friedrich, R. T. Pawlik, M. A. Canonaco, G. Gianfranceschi, A. Pingoud, and C. L. Pon. "Proteins from the Prokaryotic Nucleoid. Structural and Functional Characterization of the Escherichia coli DNA-Binding Proteins NS (HU) and H-NS." In Proceedings in Life Sciences, 101–34. Berlin, Heidelberg: Springer Berlin Heidelberg, 1986. http://dx.doi.org/10.1007/978-3-642-71266-1_10.

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Leighton, Jonathan. "Identification and Characterization of Novel ATP-Binding Cassette Proteins in Saccharomyces Cerevisiae." In Biological Membranes: Structure, Biogenesis and Dynamics, 263–68. Berlin, Heidelberg: Springer Berlin Heidelberg, 1994. http://dx.doi.org/10.1007/978-3-642-78846-8_26.

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Popescu, Andrei. "Rensets and Renaming-Based Recursion for Syntax with Bindings." In Automated Reasoning, 618–39. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-031-10769-6_36.

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AbstractI introduce renaming-enriched sets (rensets for short), which are algebraic structures axiomatizing fundamental properties of renaming (also known as variable-for-variable substitution) on syntax with bindings. Rensets compare favorably in some respects with the well-known foundation based on nominal sets. In particular, renaming is a more fundamental operator than the nominal swapping operator and enjoys a simpler, equationally expressed relationship with the variable-freshness predicate. Together with some natural axioms matching properties of the syntactic constructors, rensets yield a truly minimalistic characterization of $$\lambda $$ λ -calculus terms as an abstract datatype – one involving an infinite set of unconditional equations, referring only to the most fundamental term operators: the constructors and renaming. This characterization yields a recursion principle, which (similarly to the case of nominal sets) can be improved by incorporating Barendregt’s variable convention. When interpreting syntax in semantic domains, my renaming-based recursor is easier to deploy than the nominal recursor. My results have been validated with the proof assistant Isabelle/HOL.
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Litchfield, David W., Denis G. Bosc, David A. Canton, Ronald B. Saulnier, Greg Vilk, and Cunjie Zhang. "Functional specialization of CK2 isoforms and characterization of isoform-specific binding partners." In Protein Kinase CK2 — From Structure to Regulation, 21–29. Boston, MA: Springer US, 2001. http://dx.doi.org/10.1007/978-1-4615-1723-8_3.

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Brandenburg, K., and G. Lehwark-Yvetot. "Characterization of the binding of endogenous proteins to endotoxins: binding stochiometry and protein secondary structure." In Spectroscopy of Biological Molecules: New Directions, 17–18. Dordrecht: Springer Netherlands, 1999. http://dx.doi.org/10.1007/978-94-011-4479-7_6.

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Conference papers on the topic "Structural binding characterization"

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Towfic, Fadi, David C. Gemperline, Cornelia Caragea, Feihong Wu, Drena Dobbs, and Vasant Honavar. "Structural characterization of RNA-binding sites of proteins: Preliminary results." In 2007 IEEE International Conference on Bioinformatics and Biomedicine Workshops. IEEE, 2007. http://dx.doi.org/10.1109/bibmw.2007.4425401.

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Sousa, B. L., J. C. Silva Filho, R. I. Pereira, B. A. M. Rocha, P. Delatorre, G. A. Bezerra, C. S. Nagano, K. Gruber, and B. S. Cavada. "STRUCTURAL CHARACTERIZATION OF A RECOMBINANT TN ANTIGEN-BINDING LECTIN FROM VATAIREA MACROCARPA." In International Symposium on Crystallography. São Paulo: Editora Edgard Blücher, 2015. http://dx.doi.org/10.5151/phypro-sic100-050.

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"Structural and functional characterization of transcription factor binding sites: from bioinformatics to hormone biosensors." In Plant Genetics, Genomics, Bioinformatics, and Biotechnology. Novosibirsk ICG SB RAS 2021, 2021. http://dx.doi.org/10.18699/plantgen2021-038.

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Østergaard, Søren, Szu Wong, Susanne Bang, Jonas Emsley, and Henning Stennicke. "Identification of FXI Binding Peptides by Solid Phase Peptide Library Screening: Structural and Functional Characterization." In The Twenty-Third American and the Sixth International Peptide Symposium. Prompt Scientific Publishing, 2013. http://dx.doi.org/10.17952/23aps.2013.098.

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Tome, Carla M. Lema, Enzo Palma, Jill Wykoski, and Waldemar Debinski. "Abstract 5465: Functional and structural characterization of the high-affinity EphA2-binding site of ephrinA1." In Proceedings: AACR 101st Annual Meeting 2010‐‐ Apr 17‐21, 2010; Washington, DC. American Association for Cancer Research, 2010. http://dx.doi.org/10.1158/1538-7445.am10-5465.

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Krishnan, Srivatsava, Prasant Vijayaraghavan, and Vishnubaba Sundaresan. "Characterization of Mechanoluminescent Composites and Their Applications for SHM of Polymer Composites." In ASME 2015 Conference on Smart Materials, Adaptive Structures and Intelligent Systems. American Society of Mechanical Engineers, 2015. http://dx.doi.org/10.1115/smasis2015-9078.

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Mechanoluminescence (ML) is a property of inorganic and organic materials that describes the emission of light due from the application of force. Inorganic crystals (mostly phosphors) and certain organic macromolecules exhibit elastico-ML and are a natural fit for structural health monitoring (SHM) of composite structures. Composites with particulate ML crystals enable the visualization of stress distribution over a plane and over contoured surfaces in a spatially continuous manner. Imaging ML composites with affordable high-resolution imaging methods further enables the creation of high-resolution validation method for computational methods. Also, with the embedding of suitable photo-detectors for signal detection, the need for additional wiring, sensor electronics and high-level electronics is eliminated. In this conference proceedings technical publication, the application of commercially available ZnS:Cu, Mn phosphors for SHM of polymer composites will be presented via experimental and structural simulation. Results demonstrate the dependence of intensity of elastico-ML (in cd/cm2) on strain rate, strain and composition (w/w of ML particulates). The experiments show methods to fabricate elastic coupons of phosphors in polydimethylsiloxane (PDMS) and subsequent methods for application in SHM. The structures are excited at 5Hz to 17.5Hz to develop empirical relationships between strain rate and EML intensity and it is shown that the intensity increases nonlinearly with the magnitude of stress/strain rate. A range of stresses transferred to the EML particles by the PDMS matrix is also numerically predicted. The numerical simulations show the importance of interfacial binding in the transfer of stress and subsequent EML emission. These results also provided a basis for validation and improvement of structural simulation models.
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Baglia, F. A., D. Sinha, and P. N. Walsh. "STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF DOMAINS IN THE HEAVY CHAIN REGION OF FACTOR XI (XIa) INVOLVED IN BINDING HIGH MOLECULAR WEIGHT KININOGEN AND FACTOR IX." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642804.

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Previous studies from our laboratory (J. Biol. Chem. 260:10714,1985; J. Clin. Invest. 78:1631,1986) provide evidence that a monoclonal antibody (3C1) directed against the heavy chain region of factor XIa (FXIa) recognizes an epitope near a substrate binding site for FIX and a binding site for high molecular weight kininogen (HMWK). The present studies were carried out to determine whether these two sites are identical or different. Another heavy-chain-specific murine monoclonal antibody (5F7) was found to recognize an epitope distinct from that recognized by 3C1 since 3C1 did not compete with 5F7 for binding to FXI in a solid-phase radioimmunoassay. Antibody 3C1 was a competitive inhibitor of F-XIa-catalyzed F-IX activation, assayed by the release of a 3H-labeled activation peptide from FIX, whereas 5F7 had no effect on F—IX activation by FXIa. In contrast, 5F7 (which also inhibited F-XIIa-catalyzed F-XI activation in the presence of HMWK and kaolin) completely blocked FXI binding to immobilized HMWK at concentrations 1,000-fold lower than 3C1. Finally, HMWK had no effect on F-IX activation by FXIa. We therefore conclude that two separate and distinct domains are present in the heavy-chain region of FXI, one of which is a substrate binding site for FIX and the other a binding site for HMWK. A 15,000 Mr peptide containing the HMWK binding site was isolated using cyanogen bromide digests of factor XI which were bound to and eluted from a ,5F7 antibody affinity column and further purified using high performance liquid chromatography. Gas phase sequencing studies are in progress to characterize this peptide and place its sequence within the known structure of the heavy chain of FXIa. In conclusion, our antibodies have defined two domains within the heavy chain region of FXI: one defined by 5F7 is near the HMWK binding site, whereas the other, recognized by 3C1, is a substrate binding site for FIX. Finally, a peptide domain in the heavy chain of FXI that compriaes the HMWK binding site has been identified and isolated.
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Vippola, M., S. Ahmaniemi, P. Vuoristo, T. Lepistö, and T. Mäntylä. "Microstructural Study of Plasma Sprayed Chromium Oxide Coatings: Effect of Aluminum Phosphate Sealing." In ITSC2001, edited by Christopher C. Berndt, Khiam A. Khor, and Erich F. Lugscheider. ASM International, 2001. http://dx.doi.org/10.31399/asm.cp.itsc2001p0607.

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Abstract Microstructural study of plasma sprayed chromia coatings sealed with aluminum phosphate, was carried out for determining strengthening mechanisms of the sealant. Characterization was accomplished by X-ray diffractometry, scanning electron microscopy, and analytical transmission electron microscopy. The main phase in the coating is the eskolaite type α-Cr2O3. The overall structure of the coating is lamellar with columnar grains parallel to the lamella thickness. Amorphous aluminum phosphate sealant has penetrated into the coating filling the structural defects such as cracks, gaps and pores between the lamellas. The average composition of the sealant in the coating is 25 at% aluminum and 75 at% phosphorus giving the molar ratio P/Al of 3, that corresponds to metaphosphates Al(PO3)3. The aluminum phosphate sealing in the chromium oxide coatings is based on adhesive binding due to the attractive forces between the condensed phosphates and the coating. There were no indications about chemical binding due to reactions between the sealant and the coating in the sealing treatment for chromia coatings.
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Bezeaud, A., and M. C. Guillin. "FUNCTIONAL CHARACTERIZATION OF HUMAN β-THROMBIN." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644665.

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Autolysis or tryptic hydrolysis converts β-thrombin (α-T) t β-thrombin ( β -T), and subsequently β-T to y-thrombin (γ-T). Human β-T differs from native α-T by the loss of a unique ll-re-sidues peptide arising from the B chain. Unlike its bovine counterpart, human β-Tisa transient intermediate and its enzymatic properties had not yet been investigated using purified materiaL After 3 min incubation of human β-T with trypsin-sepharose, the resulting β-T was separated from α- and γ-T by chromatography on Biorex 70 with a gradient from 10 mM to 500 mM phosphate at pH 8. No major differences were found between human α- and β-T regarding the kinetic parameters (Km, kcat, kcat/Km) on S 2238, nor the rate of inactivation by TLCK. In contrast, inhibition of β-T by DFP was slower (k = 426 ±[; 10.8 M-1 min−1) compared to α-T (764.5 ± 19.5 M−11min−1and the inhibition constant for benzami-dine was higher with β-T (Ki = 11.2 ± x00B1;.2 10−4 M) compared to α-T (Ki = 2.86± 0,06 10−4 M). The drastic reduction in the clotting activity of β-T (25 u mg−1 versus 3000 u mg−1 for α-T) was further explored by measuring the affinity of β-T for fibrinogen and fibrin. Human fibrinogen was used as a competitor in the inactivation of thrombin by DFP : 10 μM fibrinogen prevented the inhibition of α-T by DFP but failed to modify the inactivation rate of α-T. Binding of thrombin to fibrin was studied using fibrin monomers covalently linked to sepharose 4B, equilibrated in 50mM Tris, pH 7.5, 50 mM NaCl : β -T did not bind to the resin, whereas α-T was retained and eluted upon application of a NaCl gradient.In conclusion, the loss of the peptide extending from lie (63) to Arg (73) in the thrombin B chain is responsiblefor multiple defects in thrombin enzymatic activity. Although, the three active site residues Ser (205), His (43), Asp (99) remain in an active configuration, subtle changes are induced in the microenvironment of the catalytic Ser (205), and in particular, in the primary binding pocket. In addition, the results presented in this study indicate thatthe loss of clotting activity is mainly the result of a decreased affinity for fibrinogen and fibrin, suggesting that the structural changesaffect both the fibrinopeptide groove and the anionic binding site involved in fibrinogen/fibrin recognition.
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Lee, Eric H., Chen-Shing Chen, and Ly Le. "Abstract 3396: Structural modeling and functional characterization of caspase inhibitor and tumor oncogene survivin 2B isoform: Implications in ligand binding and targeted drug design." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.am2019-3396.

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Reports on the topic "Structural binding characterization"

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Nunes, C., and C. Benz. Structural Characterization of a Novel HER2/neu Binding Ets Factor, ESX. Fort Belvoir, VA: Defense Technical Information Center, July 2001. http://dx.doi.org/10.21236/ada398281.

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Gurevitz, Michael, William A. Catterall, and Dalia Gordon. face of interaction of anti-insect selective toxins with receptor site-3 on voltage-gated sodium channels as a platform for design of novel selective insecticides. United States Department of Agriculture, December 2013. http://dx.doi.org/10.32747/2013.7699857.bard.

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Voltage-gated sodium channels (Navs) play a pivotal role in excitability and are a prime target of insecticides like pyrethroids. Yet, these insecticides are non-specific due to conservation of Navs in animals, raising risks to the environment and humans. Moreover, insecticide overuse leads to resistance buildup among insect pests, which increases misuse and risks. This sad reality demands novel, more selective, insect killers whose alternative use would avoid or reduce this pressure. As highly selective insect toxins exist in venomous animals, why not exploit this gift of nature and harness them in insect pest control? Many of these peptide toxins target Navs, and since their direct use via transformed crop plants or mediator microorganisms is problematic in public opinion, we focus on the elucidation of their receptor binding sites with the incentive of raising knowledge for design of toxin peptide mimetics. This approach is preferred nowadays by agro-industries in terms of future production expenses and public concern. However, characterization of a non-continuous epitope, that is the channel receptor binding site for such toxins, requires a suitable experimental system. We have established such a system within more than a decade and reached the stage where we employ a number of different insect-selective toxins for the identification of their receptor sites on Navs. Among these toxins we wish to focus on those that bind at receptor site-3 and inhibit Nav inactivation because: (1) We established efficient experimental systems for production and manipulation of site-3 toxins from scorpions and sea anemones. These peptides vary in size and structure but compete for site-3 on insect Navs. Moreover, these toxins exhibit synergism with pyrethroids and with other channel ligands; (2) We determined their bioactive surfaces towards insect and mammalian receptors (see list of publications); (3) We found that despite the similar mode of action on channel inactivation, the preference of the toxins for insect and mammalian channel subtypes varies greatly, which can direct us to structural features in the basis of selectivity; (4) We have identified by channel loop swapping and point mutagenesis extracellular segments of the Navinvolved with receptor site-3. On this basis and using channel scanning mutagenesis, neurotoxin binding, electrophysiological analyses, and structural data we offer: (i) To identify the residues that form receptor site-3 at insect and mammalian Navs; (ii) To identify by comparative analysis differences at site-3 that dictate selectivity toward various Navs; (iii) To exploit the known toxin structures and bioactive surfaces for modeling their docking at the insect and mammalian channel receptors. The results of this study will enable rational design of novel anti-insect peptide mimetics with minimized risks to human health and to the environment. We anticipate that the release of receptor site-3 molecular details would initiate a worldwide effort to design peptide mimetics for that site. This will establish new strategies in insect pest control using alternative insecticides and the combined use of compounds that interact allosterically leading to increased efficiency and reduced risks to humans or resistance buildup among insect pests.
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Rafaeli, Ada, and Russell Jurenka. Molecular Characterization of PBAN G-protein Coupled Receptors in Moth Pest Species: Design of Antagonists. United States Department of Agriculture, December 2012. http://dx.doi.org/10.32747/2012.7593390.bard.

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The proposed research was directed at determining the activation/binding domains and gene regulation of the PBAN-R’s thereby providing information for the design and screening of potential PBAN-R-blockers and to indicate possible ways of preventing the process from proceeding to its completion. Our specific aims included: (1) The identification of the PBAN-R binding domain by a combination of: (a) in silico modeling studies for identifying specific amino-acid side chains that are likely to be involved in binding PBAN with the receptor and; (b) bioassays to verify the modeling studies using mutant receptors, cell lines and pheromone glands (at tissue and organism levels) against selected, designed compounds to confirm if compounds are agonists or antagonists. (2) The elucidation ofthemolecular regulationmechanisms of PBAN-R by:(a) age-dependence of gene expression; (b) the effect of hormones and; (c) PBAN-R characterization in male hair-pencil complexes. Background to the topic Insects have several closely related G protein-coupled receptors (GPCRs) belonging to the pyrokinin/PBAN family, one with the ligand pheromone biosynthesis activating neuropeptide or pyrokinin-2 and another with diapause hormone or pyrokinin-1 as a ligand. We were unable to identify the diapause hormone receptor from Helicoverpa zea despite considerable effort. A third, related receptor is activated by a product of the capa gene, periviscerokinins. The pyrokinin/PBAN family of GPCRs and their ligands has been identified in various insects, such as Drosophila, several moth species, mosquitoes, Triboliumcastaneum, Apis mellifera, Nasoniavitripennis, and Acyrthosiphon pisum. Physiological functions of pyrokinin peptides include muscle contraction, whereas PBAN regulates pheromone production in moths plus other functions indicating the pleiotropic nature of these ligands. Based on the alignment of annotated genomic sequences, the primary and secondary structures of the pyrokinin/PBAN family of receptors have similarity with the corresponding structures of the capa or periviscerokinin receptors of insects and the neuromedin U receptors found in vertebrates. Major conclusions, solutions, achievements Evolutionary trace analysisof receptor extracellular domains exhibited several class-specific amino acid residues, which could indicate putative domains for activation of these receptors by ligand recognition and binding. Through site-directed point mutations, the 3rd extracellular domain of PBAN-R was shown to be critical for ligand selection. We identified three receptors that belong to the PBAN family of GPCRs and a partial sequence for the periviscerokinin receptor from the European corn borer, Ostrinianubilalis. Functional expression studies confirmed that only the C-variant of the PBAN-R is active. We identified a non-peptide agonist that will activate the PBAN-receptor from H. zea. We determined that there is transcriptional control of the PBAN-R in two moth species during the development of the pupa to adult, and we demonstrated that this transcriptional regulation is independent of juvenile hormone biosynthesis. This transcriptional control also occurs in male hair-pencil gland complexes of both moth species indicating a regulatory role for PBAN in males. Ultimate confirmation for PBAN's function in the male tissue was revealed through knockdown of the PBAN-R using RNAi-mediated gene-silencing. Implications, both scientific and agricultural The identification of a non-peptide agonist can be exploited in the future for the design of additional compounds that will activate the receptor and to elucidate the binding properties of this receptor. The increase in expression levels of the PBAN-R transcript was delineated to occur at a critical period of 5 hours post-eclosion and its regulation can now be studied. The mysterious role of PBAN in the males was elucidated by using a combination of physiological, biochemical and molecular genetics techniques.
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Gurevitz, Michael, Michael Adams, and Eliahu Zlotkin. Insect Specific Alpha Neurotoxins from Scorpion Venoms: Mode of Action and Structure-Function Relationships. United States Department of Agriculture, June 1996. http://dx.doi.org/10.32747/1996.7613029.bard.

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This study was motivated by the need to develop new means and approaches to the design of future, environmentally-safe, insecticides. Utilization of anti-insect selective toxins from scorpion venoms and clarification of the molecular basis for their specificity, are a major focus in this project and may have an applicative value. Our study concentrated on the highly insecticidal toxin, LqhaIT, and was devoted to: (I) Characterization of the neuropharmacological and electrophysiological features of this toxin. (II) Establishment of a genetic system for studying structure/activity relationships of the toxin. (III) Analysis of the insecticidal efficacy of an entomopathogenic baculovirus engineered and expressing LqhaIT. The results obtained in this project suggest that: 1) The receptor binding site of LqhaIT on insect sodium channels differs most likely from its analogous receptor site 3 on vertebrate sodium channels. 2) The effects of LqhaIT are presynaptic. Hyperexcitation at the neuromuscular results from dramatic slowing of sodium channel inactivation and enhanced peak sodium currents causes by LqhaIT. 3) The putative toxic surface of LqhaIT involves aromatic and charged amino acid residues located around the C-terminal region and five-residue-turn of the toxin (unpublished). 4) The anti-insect/anti-mammalian toxicity ratio can be altered by site-directed mutagenesis (publication 8). This effect was partly shown at the level of sodium channel function. 5) The insecticidal efficacy of AcNPV baculovirus increased to a great extent when infection was accompanied by expression of LqhaIT (publication 5).
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Shomer, Ilan, Ruth E. Stark, Victor Gaba, and James D. Batteas. Understanding the hardening syndrome of potato (Solanum tuberosum L.) tuber tissue to eliminate textural defects in fresh and fresh-peeled/cut products. United States Department of Agriculture, November 2002. http://dx.doi.org/10.32747/2002.7587238.bard.

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The project sought to understand factors and mechanisms involved in the hardening of potato tubers. This syndrome inhibits heat softening due to intercellular adhesion (ICA) strengthening, compromising the marketing of industrially processed potatoes, particularly fresh peeled-cut or frozen tubers. However, ICA strengthening occurs under conditions which are inconsistent with the current ideas that relate it to Ca-pectate following pectin methyl esterase (PME) activity or to formation of rhamnogalacturonan (RG)-II-borate. First, it was necessary to induce strengthening of the middle lamellar complex (MLX) and the ICA as a stress response in some plant parenchyma. As normally this syndrome does not occur uniformly enough to study it, we devised an efficient model in which ICA-strengthening is induced consistently under simulated stress by short-chain, linear, mono-carboxylic acid molecules (OAM), at 65 oC [appendix 1 (Shomer&Kaaber, 2006)]. This rapid strengthening was insufficient for allowing the involved agents assembly to be identifiable; but it enabled us to develop an efficient in vitro system on potato tuber parenchyma slices at 25 ºC for 7 days, whereas unified stress was reliably simulated by OAMs in all the tissue cells. Such consistent ICA-strengthening in vitro was found to be induced according to the unique physicochemical features of each OAM as related to its lipophilicity (Ko/w), pKa, protonated proportion, and carbon chain length by the following parameters: OAM dissociation constant (Kdiss), adsorption affinity constant (KA), number of adsorbed OAMs required for ICA response (cooperativity factor) and the water-induced ICA (ICAwater). Notably, ICA-strengthening is accompanied by cell sap leakage, reflecting cell membrane rupture. In vitro, stress simulation by OAMs at pH<pKa facilitated the consistent assembly of ICAstrengthening agents, which we were able to characterize for the first time at the molecular level within purified insoluble cell wall of ICA-strengthened tissue. (a) With solid-state NMR, we established the chemical structure and covalent binding to cell walls of suberin-like agents associated exclusively with ICA strengthening [appendix 3 (Yu et al., 2006)]; (b) Using proteomics, 8 isoforms of cell wall-bound patatin (a soluble vacuolar 42-kDa protein) were identified exclusively in ICA-strengthened tissue; (c) With light/electron microscopy, ultrastructural characterization, histochemistry and immunolabeling, we co-localized patatin and pectin in the primary cell wall and prominently in the MLX; (d) determination of cell wall composition (pectin, neutral sugars, Ca-pectate) yielded similar results in both controls and ICA-strengthened tissue, implicating factors other than PME activity, Ca2+ or borate ions; (e) X-ray powder diffraction experiments revealed that the cellulose crystallinity in the cell wall is masked by pectin and neutral sugars (mainly galactan), whereas heat or enzymatic pectin degradation exposed the crystalline cellulose structure. Thus, we found that exclusively in ICA-strengthened tissue, heat-resistant pectin is evident in the presence of patatin and suberinlike agents, where the cellulose crystallinity was more hidden than in fresh control tissue. Conclusions: Stress response ICA-strengthening is simulated consistently by OAMs at pH< pKa, although PME and formation of Ca-pectate and RG-II-borate are inhibited. By contrast, at pH>pKa and particularly at pH 7, ICA-strengthening is mostly inhibited, although PME activity and formation of Ca-pectate or RG-II-borate are known to be facilitated. We found that upon stress, vacuolar patatin is released with cell sap leakage, allowing the patatin to associate with the pectin in both the primary cell wall and the MLX. The stress response also includes formation of covalently bound suberin-like polyesters within the insoluble cell wall. The experiments validated the hypotheses, thus led to a novel picture of the structural and molecular alterations responsible for the textural behavior of potato tuber. These findings represent a breakthrough towards understanding of the hardening syndrome, laying the groundwork for potato-handling strategies that assure textural quality of industrially processed particularly in fresh peeled cut tubers, ready-to-prepare and frozen preserved products.
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Altstein, Miriam, and Ronald Nachman. Rationally designed insect neuropeptide agonists and antagonists: application for the characterization of the pyrokinin/Pban mechanisms of action in insects. United States Department of Agriculture, October 2006. http://dx.doi.org/10.32747/2006.7587235.bard.

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The general objective of this BARD project focused on rationally designed insect neuropeptide (NP) agonists and antagonists, their application for the characterization of the mechanisms of action of the pyrokinin/PBAN (PK-PBAN) family and the development of biostable, bioavailable versions that can provide the basis for development of novel, environmentally-friendly pest insect control agents. The specific objectives of the study, as originally proposed, were to: (i) Test stimulatory potencies of rationally designed backbone cyclic (BBC) peptides on pheromonotropic, melanotropic, myotropic and pupariation activities; (ii) Test the inhibitory potencies of the BBC compounds on the above activities evoked either by synthetic peptides (PBAN, LPK, myotropin and pheromonotropin) or by the natural endogenous mechanism; (iii) Determine the bioavailability of the most potent BBC compounds that will be found in (ii); (iv) Design, synthesize and examine novel PK/PBAN analogs with enhanced bioavailability and receptor binding; (v) Design and synthesize ‘magic bullet’ analogs and examine their ability to selectively kill cells expressing the PK/PBAN receptor. To achieve these goals the agonistic and antagonistic activities/properties of rationally designed linear and BBC neuropeptide (NP) were thoroughly studied and the information obtained was further used for the design and synthesis of improved compounds toward the design of an insecticide prototype. The study revealed important information on the structure activity relationship (SAR) of agonistic/antagonistic peptides, including definitive identification of the orientation of the Pro residue as trans for agonist activity in 4 PK/PBANbioassays (pheromonotropic, pupariation, melanotropic, & hindgut contractile) and a PK-related CAP₂b bioassay (diuretic); indications that led to the identification of a novel scaffold to develop biostbiostable, bioavailable peptidomimetic PK/PBANagonists/antagonists. The work led to the development of an arsenal of PK/PBAN antagonists with a variety of selectivity profiles; whether between different PKbioassays, or within the same bioassay between different natural elicitors. Examples include selective and non-selective BBC and novel amphiphilic PK pheromonotropic and melanotropic antagonists some of which are capable of penetrating the moth cuticle in efficacious quantities. One of the latter analog group demonstrated unprecedented versatility in its ability to antagonize a broad spectrum of pheromonotropic elicitors. A novel, transPro mimetic motif was proposed & used to develop a strong, selective PK agonist of the melanotropic bioassay in moths. The first antagonist (pure) of PK-related CAP₂b diuresis in flies was developed using a cisPro mimetic motif; an indication that while a transPro orientation is associated with receptor agonism, a cisPro orientation is linked with an antagonist interaction. A novel, biostablePK analog, incorporating β-amino acids at key peptidase-susceptible sites, exhibited in vivo pheromonotropic activity that by far exceeded that of PBAN when applied topically. Direct analysis of neural tissue by state-of-the-art MALDI-TOF/TOF mass spectrometry was used to identify specific PK/PK-related peptides native to eight arthropod pest species [house (M. domestica), stable (S. calcitrans), horn (H. irritans) & flesh (N. bullata) flies; Southern cattle fever tick (B. microplus), European tick (I. ricinus), yellow fever mosquito (A. aegypti), & Southern Green Stink Bug (N. viridula)]; including the unprecedented identification of mass-identical Leu/Ile residues and the first identification of NPs from a tick or the CNS of Hemiptera. Evidence was obtained for the selection of Neb-PK-2 as the primary pupariation factor of the flesh fly (N. bullata) among native PK/PK-related candidates. The peptidomic techniques were also used to map the location of PK/PK-related NP in the nervous system of the model fly D. melanogaster. Knowledge of specific PK sequences can aid in the future design of species specific (or non-specific) NP agonists/antagonists. In addition, the study led to the first cloning of a PK/PBAN receptor from insect larvae (S. littoralis), providing the basis for SAR analysis for the future design of 2ⁿᵈgeneration selective and/or nonselective agonists/antagonists. Development of a microplate ligand binding assay using the PK/PBAN pheromone gland receptor was also carried out. The assay will enable screening, including high throughput, of various libraries (chemical, molecular & natural product) for the discovery of receptor specific agonists/antagonists. In summary, the body of work achieves several key milestones and brings us significantly closer to the development of novel, environmentally friendly pest insect management agents based on insect PK/PBANNPs capable of disrupting critical NP-regulated functions.
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Epel, Bernard, and Roger Beachy. Mechanisms of intra- and intercellular targeting and movement of tobacco mosaic virus. United States Department of Agriculture, November 2005. http://dx.doi.org/10.32747/2005.7695874.bard.

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To cause disease, plant viruses must replicate and spread locally and systemically within the host. Cell-to-cell virus spread is mediated by virus-encoded movement proteins (MPs), which modify the structure and function of plasmodesmata (Pd), trans-wall co-axial membranous tunnels that interconnect the cytoplasm of neighboring cells. Tobacco mosaic virus (TMV) employ a single MP for cell- cell spread and for which CP is not required. The PIs, Beachy (USA) and Epel (Israel) and co-workers, developed new tools and approaches for study of the mechanism of spread of TMV that lead to a partial identification and molecular characterization of the cellular machinery involved in the trafficking process. Original research objectives: Based on our data and those of others, we proposed a working model of plant viral spread. Our model stated that MPᵀᴹⱽ, an integral ER membrane protein with its C-terminus exposed to the cytoplasm (Reichel and Beachy, 1998), alters the Pd SEL, causes the Pd cytoplasmic annulus to dilate (Wolf et al., 1989), allowing ER to glide through Pd and that this gliding is cytoskeleton mediated. The model claimed that in absence of MP, the ER in Pd (the desmotubule) is stationary, i.e. does not move through the Pd. Based on this model we designed a series of experiments to test the following questions: -Does MP potentiate ER movement through the Pd? - In the presence of MP, is there communication between adjacent cells via ER lumen? -Does MP potentiate the movement of cytoskeletal elements cell to cell? -Is MP required for cell-to-cell movement of ER membranes between cells in sink tissue? -Is the binding in situ of MP to RNA specific to vRNA sequences or is it nonspecific as measured in vitro? And if specific: -What sequences of RNA are involved in binding to MP? And finally, what host proteins are associated with MP during intracellular targeting to various subcellular targets and what if any post-translational modifications occur to MP, other than phosphorylation (Kawakami et al., 1999)? Major conclusions, solutions and achievements. A new quantitative tool was developed to measure the "coefficient of conductivity" of Pd to cytoplasmic soluble proteins. Employing this tool, we measured changes in Pd conductivity in epidermal cells of sink and source leaves of wild-type and transgenic Nicotiana benthamiana (N. benthamiana) plants expressing MPᵀᴹⱽ incubated both in dark and light and at 16 and 25 ᵒC (Liarzi and Epel, 2005 (appendix 1). To test our model we measured the effect of the presence of MP on cell-to-cell spread of a cytoplasmic fluorescent probe, of two ER intrinsic membrane protein-probes and two ER lumen protein-probes fused to GFP. The effect of a mutant virus that is incapable of cell-to-cell spread on the spread of these probes was also determined. Our data shows that MP reduces SEL for cytoplasmic molecules, dilates the desmotubule allowing cell-cell diffusion of proteins via the desmotubule lumen and reduces the rate of spread of the ER membrane probes. Replicase was shown to enhance cell-cell spread. The data are not in support of the proposed model and have led us to propose a new model for virus cell-cell spread: this model proposes that MP, an integral ER membrane protein, forms a MP:vRNAER complex and that this ER-membrane complex diffuses in the lipid milieu of the ER into the desmotubule (the ER within the Pd), and spreads cell to cell by simple diffusion in the ER/desmotubule membrane; the driving force for spread is the chemical potential gradient between an infected cell and contingent non-infected neighbors. Our data also suggests that the virus replicase has a function in altering the Pd conductivity. Transgenic plant lines that express the MP gene of the Cg tobamovirus fused to YFP under the control the ecdysone receptor and methoxyfenocide ligand were generated by the Beachy group and the expression pattern and the timing and targeting patterns were determined. A vector expressing this MPs was also developed for use by the Epel lab . The transgenic lines are being used to identify and isolate host genes that are required for cell-to-cell movement of TMV/tobamoviruses. This line is now being grown and to be employed in proteomic studies which will commence November 2005. T-DNA insertion mutagenesis is being developed to identify and isolate host genes required for cell-to-cell movement of TMV.
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