Relevant bibliographies by topics / Ligand Recognition

Academic literature on the topic 'Ligand Recognition'

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Published: 6 September 2023

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Journal articles on the topic "Ligand Recognition"

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Vijayrajratnam, Sukhithasri, Anju Choorakottayil Pushkaran, Aathira Balakrishnan, Anil Kumar Vasudevan, Raja Biswas, and Chethampadi Gopi Mohan. "Understanding the molecular differential recognition of muramyl peptide ligands by LRR domains of human NOD receptors." Biochemical Journal 474, no. 16 (July 27, 2017): 2691–711. http://dx.doi.org/10.1042/bcj20170220.

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Human nucleotide-binding oligomerization domain proteins, hNOD1 and hNOD2, are host intracellular receptors with C-terminal leucine-rich repeat (LRR) domains, which recognize specific bacterial peptidoglycan (PG) fragments as their ligands. The specificity of this recognition is dependent on the third amino acid of the stem peptide of the PG ligand, which is usually meso-diaminopimelic acid (mesoDAP) or l-lysine (l-Lys). Since the LRR domains of hNOD receptors had been experimentally shown to confer the PG ligand-sensing specificity, we developed three-dimensional structures of hNOD1-LRR and the hNOD2-LRR to understand the mechanism of differential recognition of muramyl peptide ligands by hNOD receptors. The hNOD1-LRR and hNOD2-LRR receptor models exhibited right-handed curved solenoid shape. The hot-spot residues experimentally proved to be critical for ligand recognition were located in the concavity of the NOD-LRR and formed the recognition site. Our molecular docking analyses and molecular electrostatic potential mapping studies explain the activation of hNOD-LRRs, in response to effective molecular interactions of PG ligands at the recognition site; and conversely, the inability of certain PG ligands to activate hNOD-LRRs, by deviations from the recognition site. Based on molecular docking studies using PG ligands, we propose few residues — G825, D826 and N850 in hNOD1-LRR and L904, G905, W931, L932 and S933 in hNOD2-LRR, evolutionarily conserved across different host species, which may play a major role in ligand recognition. Thus, our integrated experimental and computational approach elucidates the molecular basis underlying the differential recognition of PG ligands by hNOD receptors.
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Smyth, Mark J., Jeremy Swann, Janice M. Kelly, Erika Cretney, Wayne M. Yokoyama, Andreas Diefenbach, Thomas J. Sayers, and Yoshihiro Hayakawa. "NKG2D Recognition and Perforin Effector Function Mediate Effective Cytokine Immunotherapy of Cancer." Journal of Experimental Medicine 200, no. 10 (November 15, 2004): 1325–35. http://dx.doi.org/10.1084/jem.20041522.

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Single and combination cytokines offer promise in some patients with advanced cancer. Many spontaneous and experimental cancers naturally express ligands for the lectin-like type-2 transmembrane stimulatory NKG2D immunoreceptor; however, the role this tumor recognition pathway plays in immunotherapy has not been explored to date. Here, we show that natural expression of NKG2D ligands on tumors provides an effective target for some cytokine-stimulated NK cells to recognize and suppress tumor metastases. In particular, interleukin (IL)-2 or IL-12 suppressed tumor metastases largely via NKG2D ligand recognition and perforin-mediated cytotoxicity. By contrast, IL-18 required tumor sensitivity to Fas ligand (FasL) and surprisingly did not depend on the NKG2D–NKG2D ligand pathway. A combination of IL-2 and IL-18 stimulated both perforin and FasL effector mechanisms with very potent effects. Cytokines that stimulated perforin-mediated cytotoxicity appeared relatively more effective against tumor metastases expressing NKG2D ligands. These findings indicate that a rational choice of cytokines can be made given the known sensitivity of tumor cells to perforin, FasL, and tumor necrosis factor–related apoptosis-inducing ligand and the NKG2D ligand status of tumor metastases.
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Gasparri, Federica, Jesper Wengel, Thomas Grutter, and Stephan A. Pless. "Molecular determinants for agonist recognition and discrimination in P2X2 receptors." Journal of General Physiology 151, no. 7 (May 24, 2019): 898–911. http://dx.doi.org/10.1085/jgp.201912347.

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P2X receptors (P2XRs) are trimeric ligand-gated ion channels that open a cation-selective pore in response to ATP binding. P2XRs contribute to synaptic transmission and are involved in pain and inflammation, thus representing valuable drug targets. Recent crystal structures have confirmed the findings of previous studies with regards to the amino acid chains involved in ligand recognition, but they have also suggested that backbone carbonyl atoms contribute to ATP recognition and discrimination. Here we use a combination of site-directed mutagenesis, amide-to-ester substitutions, and a range of ATP analogues with subtle alterations to either base or sugar component to investigate the contributions of backbone carbonyl atoms toward ligand recognition and discrimination in rat P2X2Rs. Our findings demonstrate that while the Lys69 backbone carbonyl makes an important contribution to ligand recognition, the discrimination between different ligands is mediated by both the side chain and the backbone carbonyl oxygen of Thr184. Together, our data demonstrate how conserved elements in P2X2Rs recognize and discriminate agonists.
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Baron, Riccardo, and J. Andrew McCammon. "Molecular Recognition and Ligand Association." Annual Review of Physical Chemistry 64, no. 1 (April 2013): 151–75. http://dx.doi.org/10.1146/annurev-physchem-040412-110047.

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Baron, Riccardo, Piotr Setny, and J. Andrew McCammon. "Water in Cavity−Ligand Recognition." Journal of the American Chemical Society 132, no. 34 (August 9, 2010): 12091–97. http://dx.doi.org/10.1021/ja1050082.

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Anand, Praveen, Deepesh Nagarajan, Sumanta Mukherjee, and Nagasuma Chandra. "ABS–Scan: In silico alanine scanning mutagenesis for binding site residues in protein–ligand complex." F1000Research 3 (September 9, 2014): 214. http://dx.doi.org/10.12688/f1000research.5165.1.

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Most physiological processes in living systems are fundamentally regulated by protein–ligand interactions. Understanding the process of ligand recognition by proteins is a vital activity in molecular biology and biochemistry. It is well known that the residues present at the binding site of the protein form pockets that provide a conducive environment for recognition of specific ligands. In many cases, the boundaries of these sites are not well defined. Here, we provide a web-server to systematically evaluate important residues in the binding site of the protein that contribute towards the ligand recognition through in silico alanine-scanning mutagenesis experiments. Each of the residues present at the binding site is computationally mutated to alanine. The ligand interaction energy is computed for each mutant and the corresponding ΔΔG values are computed by comparing it to the wild type protein, thus evaluating individual residue contributions towards ligand interaction. The server will thus provide clues to researchers about residues to obtain loss-of-function mutations and to understand drug resistant mutations. This web-tool can be freely accessed through the following address: http://proline.biochem.iisc.ernet.in/abscan/.
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Anand, Praveen, Deepesh Nagarajan, Sumanta Mukherjee, and Nagasuma Chandra. "ABS–Scan: In silico alanine scanning mutagenesis for binding site residues in protein–ligand complex." F1000Research 3 (December 1, 2014): 214. http://dx.doi.org/10.12688/f1000research.5165.2.

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Most physiological processes in living systems are fundamentally regulated by protein–ligand interactions. Understanding the process of ligand recognition by proteins is a vital activity in molecular biology and biochemistry. It is well known that the residues present at the binding site of the protein form pockets that provide a conducive environment for recognition of specific ligands. In many cases, the boundaries of these sites are not well defined. Here, we provide a web-server to systematically evaluate important residues in the binding site of the protein that contribute towards the ligand recognition through in silico alanine-scanning mutagenesis experiments. Each of the residues present at the binding site is computationally mutated to alanine. The ligand interaction energy is computed for each mutant and the corresponding ΔΔG values are calculated by comparing it to the wild type protein, thus evaluating individual residue contributions towards ligand interaction. The server will thus provide a ranked list of residues to the user in order to obtain loss-of-function mutations. This web-tool can be freely accessed through the following address: http://proline.biochem.iisc.ernet.in/abscan/.
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McMillan, Jourdan K. P., Patrick O’Donnell, and Sandra P. Chang. "Pattern recognition receptor ligand-induced differentiation of human transitional B cells." PLOS ONE 17, no. 8 (August 30, 2022): e0273810. http://dx.doi.org/10.1371/journal.pone.0273810.

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B cells represent a critical component of the adaptive immune response whose development and differentiation are determined by antigen-dependent and antigen-independent interactions. In this study, we explored the effects of IL-4 and pattern-recognition receptor (PRR) ligands on B cell development and differentiation by investigating their capacity to drive the in vitro maturation of human transitional B cells. In the presence of IL-4, ligands for TLR7/8, TLR9, and NOD1 were effective in driving the in vitro maturation of cord blood transitional B cells into mature, naïve B cells as measured by CD23 expression, ABCB1 transporter activation and upregulation of sIgM and sIgD. In addition, several stimulation conditions, including TLR9 ligand alone, favored an expansion of CD27+ IgM memory B cells. Transitional B cells stimulated with TLR7/8 ligand + IL-4 or TLR9 ligand, with or without IL-4, induced a significant subpopulation of CD23+CD27+ B cells expressing high levels of sIgM and sIgD, a minor B cell subpopulation found in human peripheral blood. These studies illustrate the heterogeneity of the B cell populations induced by cytokine and PRR ligand stimulation. A comparison of transitional and mature, naïve B cells transcriptomes to identify novel genes involved in B cell maturation revealed that mature, naïve B cells were less transcriptionally active than transitional B cells. Nevertheless, a subset of differentially expressed genes in mature, naïve B cells was identified including genes associated with the IL-4 signaling pathway, PI3K signaling in B lymphocytes, the NF-κB signaling pathway, and the TNFR superfamily. When transitional B cells were stimulated in vitro with IL-4 and PRR ligands, gene expression was found to be dependent on the nature of the stimulants, suggesting that exposure to these stimulants may alter the developmental fate of transitional B cells. The influence of IL-4 and PRR signaling on transitional B cell maturation illustrates the potential synergy that may be achieved when certain PRR ligands are incorporated as adjuvants in vaccine formulations and presented to developing B cells in the context of an inflammatory cytokine environment. These studies demonstrate the potential of the PRR ligands to drive transitional B cell differentiation in the periphery during infection or vaccination independently of antigen mediated BCR signaling.
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Leboffe, Loris, Alessandra di Masi, Fabio Polticelli, Viviana Trezza, and Paolo Ascenzi. "Structural Basis of Drug Recognition by Human Serum Albumin." Current Medicinal Chemistry 27, no. 30 (September 8, 2020): 4907–31. http://dx.doi.org/10.2174/0929867326666190320105316.

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Background: Human serum albumin (HSA), the most abundant protein in plasma, is a monomeric multi-domain macromolecule with at least nine binding sites for endogenous and exogenous ligands. HSA displays an extraordinary ligand binding capacity as a depot and carrier for many compounds including most acidic drugs. Consequently, HSA has the potential to influence the pharmacokinetics and pharmacodynamics of drugs. Objective: In this review, the structural determinants of drug binding to the multiple sites of HSA are analyzed and discussed in detail. Moreover, insight into the allosteric and competitive mechanisms underpinning drug recognition, delivery, and efficacy are analyzed and discussed. Conclusion: As several factors can modulate drug binding to HSA (e.g., concurrent administration of drugs competing for the same binding site, ligand binding to allosteric-coupled clefts, genetic inherited diseases, and post-translational modifications), ligand binding to HSA is relevant not only under physiological conditions, but also in the pharmacological therapy management.
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Diamond, M. S., J. Garcia-Aguilar, J. K. Bickford, A. L. Corbi, and T. A. Springer. "The I domain is a major recognition site on the leukocyte integrin Mac-1 (CD11b/CD18) for four distinct adhesion ligands." Journal of Cell Biology 120, no. 4 (February 15, 1993): 1031–43. http://dx.doi.org/10.1083/jcb.120.4.1031.

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Despite the identification and characterization of several distinct ligands for the leukocyte integrin (CD11/CD18) family of adhesion receptors, little is known about the structural regions on these molecules that mediate ligand recognition. In this report, we use alpha subunit chimeras of Mac-1 (CD11b/CD18) and p150,95 (CD11c/CD18), and an extended panel of newly generated and previously characterized mAbs specific to the alpha chain of Mac-1 to map the binding sites for four distinct ligands for Mac-1: iC3b, fibrinogen, ICAM-1, and the as-yet uncharacterized counter-receptor responsible for neutrophil homotypic adhesion. Epitopes of mAbs that blocked ligand binding were mapped with the chimeras and used to localize the ligand recognition sites because the data obtained from functional assays with the Mac-1/p150,95 chimeras were not easily interpreted. Results show that the I domain on the alpha chain of Mac-1 is an important recognition site for all four ligands, and that the NH2-terminal and perhaps divalent cation binding regions but not the COOH-terminal segment may contribute. The recognition sites in the I domain appear overlapping but not identical as individual Mac-1-ligand interactions are distinguished by the discrete patterns of inhibitory mAbs. Additionally, we find that the alpha subunit NH2-terminal region and divalent cation binding region, despite being separated by over 200 amino acids of the I domain, appear structurally apposed because three mAbs require the presence of both of these regions for antigenic reactivity, and chimeras that contain the NH2 terminus of p150,95 require the divalent cation binding region of p150,95 to associate firmly with the beta subunit.
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Dissertations / Theses on the topic "Ligand Recognition"

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Baylies, Christian John. "Synthesis of multidentate pyridyl-thiazole ligands and ligand recognition studies." Thesis, University of Huddersfield, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.399824.

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Hughes, P. J. "Multivalent ligand recognition by pentraxins." Thesis, University College London (University of London), 2016. http://discovery.ucl.ac.uk/1473766/.

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The pentraxins, serum amyloid P component (SAP) and C-reactive protein (CRP) are target proteins for the development of treatments for amyloidosis and ischaemic injury, respectively, in humans. This study reports the first multivalent ligands capable of targeting all five SAP binding sites simultaneously. Ligands presenting five or ten D-proline headgroups and composed of five peptideglycol linkers emanating from ε-N-substituted lysine residues on a central cyclic peptide core were synthesised by solid phase peptide synthesis. The sub-nanomolar, ~250pM, binding affinity approximated by Isothermal Titration Calorimetry (ITC) for one decavalent ligand is the strongest affinity for an SAP binding ligand currently known and stronger than the affinity of SAP binding to amyloid deposits. X-ray crystallography and mass spectrometry shows the decavalent ligands noncovalently cross-linking two SAP pentamers, in the same manner observed for lead drug candidate CPHPC, but with increased affinity. In addition, the binding of SAP with N-acetyl D-proline has been investigated by x-ray crystallography. Using a 1.5Å resolution structure the exact interaction of the headgroup used in CPHPC, penta- and decavalent ligands, was investigated. The results show potential for an electrostatic interaction between the carbonyl oxygen of acetyl from the ligand and the side chain amide of Gln148, which has not previously been considered. Applications of multivalent binding are still emerging; in this study, bivalent ligand BPC8 was used as an additive to crystallise CRP from the Rat (rCRP) in non-covalently cross-linked decameric complexes. Previous x-ray crystallography studies have failed due to extreme radiation sensitivity of the crystals produced. This problem has been overcome with a complete dataset obtained from a single crystal at 3.2Å. No inter-protein contacts are seen between pentamers in the decamer complex, therefore the use of bivalent ligands has facilitated the observed crystal packing. Multivalent ligands are suggested as tools for overcoming difficult crystallisation issues.
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McCleverty, Clare. "Structure-function studies of integrin-ligand recognition." Thesis, University of Leicester, 2001. http://hdl.handle.net/2381/29664.

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Integrins are a large family of αβ heterodimeric cell surface receptors that interact with the extracellular matrix and/or counter-receptors on other cells. These interactions control the adhesion and migration of cells as well as regulating numerous signal transduction pathways. Integrins exist in low and high affinity states, subject to allosteric regulation. Integrin-ligand recognition is divalent cation-dependent and mediated by the α subunit N-terminal repeats, the β subunit I domain and in certain integrins, the α subunit I domain. Two competing models based upon structure predictions, the β-propeller and EF-hand-like models, were tested to determine which model represents the structural components of the ligand binding α subunit N-terminal repeats. Recombinant fragments of α4 repeats IV-V, VI-VII and IV-VII, corresponding to the EF-hand-like model, were insoluble, thus preventing further analysis. A recombinant fragment of all seven α4 repeats contains a predominant secondary structure content of anti-parallel β-sheet, compatible with the β-propeller model. The interactions of the αM I domain with fragment D from fibrinogen and the extracellular domains of ICAM-1 were studied using surface plasmon resonance. Optimal binding conditions and equilibrium dissociation constants were established for these interactions. Co-crystallisation studies were pursued with the αM I domain and its ligands, fragment D and ICAM-1, but a co-crystal was not obtained due to the presence of a subpopulation of low affinity I domain molecules. Disulphide bonds were then introduced to lock the αM I domain in the open and closed conformations, corresponding to the high and low affinity states, respectively. Equilibrium dissociation constants for the open and closed mutants reveal a marked increase and decrease in ligand binding affinity, respectively. Stabilisation of the closed mutant via a disulphide bond is verified in the crystal structure. The affinity state of both mutants is fully reversible by reduction of the disulphide bond. These mutants provide useful tools for future studies to understand integrin allostery and will simplify ligand binding studies in the isolated I domain and intact receptor.
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Roy, Julie. "Ligand recognition by the major urinary protein." Thesis, University of Nottingham, 2012. http://eprints.nottingham.ac.uk/27908/.

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Molecular Dynamics (MD) and Quartz Crystal Microbalance (QCM) techniques can provide unique insights into what drives protein-ligand association. The major urinary protein (MUP) binds small ligands in a deeply buried hydrophobic pocket. Detailed calorimetric studies have shown that ligand binding is driven by enthalpic effects, not entropic effects [1]. Previous studies have shown that this is due to 'dewetting' of the binding site cavity even in the absence of ligands, and have also characterised the complex changes in molecular flexibility that accompany ligand binding-features that may be correlated with NMR data [2]. Recent MD revealed the hydration effects of apo-MUP and also shown where certain regions of MUP become more flexible upon ligand binding. They have also shown a water molecule remains close to the tyrosine in the binding pocket [2]. In our current MD studies and OCM experiments we have used wild type and 2 different mutants of MUP to study the binding effects of the ligand IBM. The first mutant has an OH group removed from the binding site of MUP (i.e. tyrosine to phenylalanine (Y120F)). The second mutant has an extra OH group in the binding site (i.e. alanine to serine (A103S)). For all three systems the hydration and flexibility upon ligand binding has been analysed. The hydration analysis from MD reveal (from radial distribution curves and hydration density maps) there is a small density of water that remains even without the presence of the ligand for the WT MUP whereas a larger density of water remains in the binding cavity of the A103S hydrophilic MUP simulation. The results are based on the average structure generated from the 1 mus simulations. The Y120F MUP simulations reveal that there is no water molecules present in the binding cavity. However, as protein molecules are very dynamic in nature, water molecules are observed to hop in and out of the binding pockets for both mutant MUP (but not WT MUP) simulations over the 1 mus simulations. On the other hand the experimental QCM results reveal that on ligand binding no water loss is observed for Y120F mutant MUP whereas A103S and WT MUP have about 2 water molecules which are lost in the binding cavity. The flexibility results from the MD simulations reveal that WT MUP have some residues which increase in flexibility whilst other residues which decrease in flexibility on ligand binding. However, the Y120F hydrophobic MUP show an overall decrease in flexibility whereas the A103S MUP shows an overall increase in flexibility on ligand binding. In contrast the experimental OCM and AFM results reveal that there is an increase in flexibility on ligand binding to all 3 different types of MUP molecules. The experimental and the simulation data have shown a variation in results but it is to be noted that the results cannot be directly compared as the analytical experiments are a surface based techniques whereas the MD simulations do not involve a surface. However, the contrast observed between computer simulation and experiments has revealed important information on the ligand binding effects on MUP. [1] Bingham, R.J., J.B.C. Findlay, S.Y. Hsieh, A.P. Kalverda, A. Kjeliberg, C. Perazzolo, S.E.V. Phillips, K. Seshadri, C.H. Trinh, W. B. TurnbulI, G. Bodenhausen, and S.W. Homans. 2004. Thermodynamics of binding of 2-methoxy-3-lsopropylpyrazlne and 2- methoxy-3-lsobutylpyrazine to the major urinary protein. J. Am. Chem. Soc. 126:1675-1681. [2] Barratt, E., R.J. Bingham. D.J. Warner, C.A. Laughton, S.E.V. Phillips, and S.W. Homans. 2005. Van der Waals interactions dominate ligand-protein association in a protein binding site occluded from solvent water. J. Am. Chem. Soc. 127:11827-11834.
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Croft, Edward. "Computational analyses of protein-ligand interactions." Thesis, University of York, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.265562.

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Lind, Ulrika. "Functional analysis of ligand recognition by the glucocorticoid receptor /." Stockholm, 2000. http://diss.kib.ki.se/2000/91-628-4116-5/.

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Hatherley, Deborah. "Structural basis of ligand recognition by Myeloid Paired Receptors." Thesis, University of Oxford, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.543484.

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Costanzi, Elisa. "Structural analysis of molecular recognition and ligand association processes." Doctoral thesis, Università degli studi di Padova, 2018. http://hdl.handle.net/11577/3421838.

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Molecular recognition is a fundamental step in essentially any biochemical process. Detailed structural knowledge is crucial to have a better understanding of the processes in which the two interacting molecular partners are involved and can be exploited in several applied fields such as supramolecular design of new molecular assemblies, rational drug design, and enzyme engineering. In the context of molecular recognition, I have investigated (mainly by single crystal x-ray crystallography) some relevant protein-protein and protein-ligand systems in order to gain detailed structural insights on the interactions involved, at atomic level. First, the STAS domain of prestin, an anion-dependent motor protein, and its interaction with monovalent anions and with calmodulin. Second, the interaction between protein kinases (CDK2 and CK2) and BCLXL, and inhibitors, for the rational design of specific drugs targeting these proteins involved in different types of cancer.
Il riconoscimento molecolare è uno step fondamentale nei processi biochimici. Una conoscenza strutturale dettagliata è cruciale per capire meglio i processi in cui sono coinvolti due partner molecolari interagenti e può essere sfruttata in vari campi come il disegno di nuovi assemblamenti sopramolecolari, il disegno razionale di farmaci e l’ingegnerizzazione di enzimi. In questo contesto, ho investigato (prevalentemente tramite cristallografia a raggi x su cristallo singolo) alcuni sistemi proteina-proteina e proteina-ligando per ottenere dettagli strutturali delle interazioni coinvolte, a livello atomico. In primis, il dominio STAS di prestina, una proteina motrice anionidipendente, e la sua interazione con anioni monovalenti e con calmodulina. Poi, l’interazione tra protein chinasi (CDK2 e CK2) e BCL-XL, e inibitori, per il disegno razionale di farmaci specifici nel colpire queste proteine coinvolte in vari tipi di cancro.
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Repicky, Sarah Elizabeth. "The Structural Basis for Ligand Recognition by Mouse Odorant Receptors." Scholarly Repository, 2008. http://scholarlyrepository.miami.edu/oa_dissertations/91.

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Mammalian odorant receptors (ORs) are Class I G-protein coupled receptors (GPCRs) located within the nasal epithelium. Odorant receptors interact with Galpha olfactory, a Galpha S type G-protein. Activated Galpha olfactory stimulates adenylate cyclase and the resulting increase in cAMP concentration opens cyclic nucleotide gated channels allowing Ca2+ to enter the cell. The increased Ca2+ then activates a Ca2+ activated Cl- channel which further depolarizes the cell. This depolarization initiates an action potential that reaches the axon of the olfactory sensory neuron located in the main olfactory bulb. Information from the main olfactory bulb is then transmitted to higher regions of the brain. Olfactory information is initially coded through the interaction of odorant molecules with hundreds of distinct ORs, but difficulty in exogenous expression of odorant receptors has delayed the identification of ligands for individual ORs. However, expression of mouse odorant receptors in Xenopus laevis oocytes allows for a systematic screening for potential ligands, as well as for efficient study of the structure-function relationship of the receptors and their ligands. My screening of odorant receptors using Xenopus oocytes included the coexpression of a signal transduction system and the use of robotic two-electrode voltage clamp electrophysiology. In this study, I investigated the structural basis for ligand recognition in mouse odorant receptors. First, I expanded the molecular receptor ranges of seven Class I odorant receptors. By use of a high throughput assay, I was able to expand upon current knowledge in the field for the mouse odorant receptors 23-1, 31-4, 32-11, 40-4, 42-1, 42-2 and 42-3. I then examined one receptor (MOR23-1) in more detail. I used the substituted cysteine accessibility method to identify residues within transmembrane domain five of this receptor that are accessible from the extracellular space. These residues may line the ligand binding site or the ligand access pathway. Conventional mutations of A205 caused little alteration in the molecular receptive range of the receptor, suggesting that this residue may not play a significant role in ligand interaction within the binding pocket. Mutagenesis of G111, a residue within transmembrane domain three caused significant shifts in the molecular receptive range of the receptor, but the location of this residue within the binding pocket could not be confirmed by the substituted cysteine method. Previous reports had suggested significant similarity between the molecular receptive ranges of the seven mouse odorant receptors that I used in my research. By expanding upon the known aliphatic ligands for each receptor identified new ligands for each receptor, I was able to show that the molecular receptive ranges of these receptors are in fact distinct. The experimental identification of residues located within the binding pocket on transmembrane five of mouse odorant receptor 23-1 provides an improved understanding of ligand recognition by this receptor class and will aid in better computer modeling of these receptors. This increased accuracy of the computer models of these basic Class I GPCRs may aid in future drug discoveries. Since GPCRs constitute a significant fraction of current drug targets, understanding the mechanism of ligand interactions with mouse odorant receptors may aid in the development of more efficacious compounds in the treatment of many common ailments.
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Śledź, Paweł. "Novel biophysical approaches to the study of protein-ligand recognition." Thesis, University of Cambridge, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.610024.

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Books on the topic "Ligand Recognition"

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Neidle, Stephen. DNA structure and recognition. Oxford, Eng: IRL Press at Oxford University Press, 1994.

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Hans-Joachim, Böhm, and Schneider Gisbert 1965-, eds. Protein-ligand interactions from molecular recognition to drug design. Weinheim: Wiley-VCH, 2003.

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Nicolae, Voiculetz, Motoc Ioan 1950-, and Simon Zeno, eds. Specific interactions and biological recognition processes. Boca Raton: CRC Press, 1993.

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Makarem, Rima. Regulation and molecular basis of ligand recognition by the integrin [alpha]4[beta]1. Manchester: University of Manchester, 1993.

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William, Hutchens T., J.T. Baker Chemical Co., and University of California, Los Angeles., eds. Protein recognition of immobilized ligands: Proceedings of a J.T. Baker-UCLA Colloquium, held at Santa Fe, New Mexico, December 2-7, 1987. New York: A.R. Liss, 1989.

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Schneider, Gisbert, Gerd Folkers, Raimund Mannhold, Hugo Kubinyi, and Hans-Joachim B�hm. Protein-Ligand Interactions: From Molecular Recognition to Drug Design. Wiley & Sons, Limited, John, 2005.

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Schneider, Gisbert, Gerd Folkers, Raimund Mannhold, Hugo Kubinyi, and Hans-Joachim B�hm. Protein-Ligand Interactions: From Molecular Recognition to Drug Design. Wiley & Sons, Incorporated, John, 2006.

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Nucleic Acid Structure and Recognition. Oxford University Press, USA, 2002.

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Su, Ruey-Chyi. Major histocompatibility complex class I as a ligand for natural killer cell recognition. 2000.

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DNA Structure and Recognition (IN FOCUS). Oxford University Press, USA, 1994.

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Book chapters on the topic "Ligand Recognition"

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Kühn, Klaus. "Conformation-Dependent Recognition Sites." In Integrin-Ligand Interaction, 141–55. Boston, MA: Springer US, 1997. http://dx.doi.org/10.1007/978-1-4757-4064-6_6.

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Pfaff, Martin. "Recognition Sites of RGD-Dependent Integrins." In Integrin-Ligand Interaction, 101–21. Boston, MA: Springer US, 1997. http://dx.doi.org/10.1007/978-1-4757-4064-6_4.

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Maass, Guenter. "Recognition of DNA Sequences by Restriction Endonucleases." In DNA—Ligand Interactions, 225–37. Boston, MA: Springer US, 1987. http://dx.doi.org/10.1007/978-1-4684-5383-6_16.

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Sharp, Kim A. "Statistical Thermodynamics of Binding and Molecular Recognition Models." In Protein-Ligand Interactions, 1–22. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2012. http://dx.doi.org/10.1002/9783527645947.ch1.

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Luchko, Tyler, and David A. Case. "Implicit Solvent Models and Electrostatics in Molecular Recognition." In Protein-Ligand Interactions, 171–89. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2012. http://dx.doi.org/10.1002/9783527645947.ch9.

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Rosenberg, John M., Judith A. McClarin, Christin A. Frederick, Bi-Cheng Wang, John Grable, Herbert W. Boyer, and Patricia Greene. "Structure of the DNA-EcoRI Endonuclease Recognition Complex." In DNA—Ligand Interactions, 251–56. Boston, MA: Springer US, 1987. http://dx.doi.org/10.1007/978-1-4684-5383-6_18.

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Lehming, Norbert, Juergen Sartorius, Brigitte von Wilcken-Bergmann, and Benno Mueller-Hill. "Searching for the Code of Ideal Protein-DNA-Recognition." In DNA—Ligand Interactions, 173–82. Boston, MA: Springer US, 1987. http://dx.doi.org/10.1007/978-1-4684-5383-6_11.

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Eble, Johannes A. "The Ligand Recognition Motifs of α4-Integrins and Leukocyte Integrins." In Integrin-Ligand Interaction, 123–39. Boston, MA: Springer US, 1997. http://dx.doi.org/10.1007/978-1-4757-4064-6_5.

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Meyerhof, Wolfgang, Alessandro Marchiori, Kristina Lossow, Masataka Narukawa, and Maik Behrens. "Ligand Recognition of Taste Receptors." In ACS Symposium Series, 183–92. Washington, DC: American Chemical Society, 2015. http://dx.doi.org/10.1021/bk-2015-1212.ch013.

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Nolan, Tammy, Nidhi Singh, and Christopher R. McCurdy. "Ligand Macromolecule Interactions: Theoretical Principles of Molecular Recognition." In Ligand-Macromolecular Interactions in Drug Discovery, 13–29. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60761-244-5_2.

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Conference papers on the topic "Ligand Recognition"

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Haller, Andrea, Ulrike Rieder, Marie Souliere, Tobias Santner, Christoph Kreutz, and Ronald Micura. "Ligand recognition of riboswitches." In XVth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2011. http://dx.doi.org/10.1135/css201112230.

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Blackburn, G. Michael, Andrzej Guranowski, and Xiaohai Liu. "Ligand recognition in Fhit binding and cleavage of diadenosine polyphosphates." In XIth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 1999. http://dx.doi.org/10.1135/css199902083.

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Nesamalar, E. Kiruba, and C. P. Chandran. "Genetic clustering with Bee Colony Optimization for flexible protein-ligand docking." In 2012 International Conference on Pattern Recognition, Informatics and Medical Engineering (PRIME). IEEE, 2012. http://dx.doi.org/10.1109/icprime.2012.6208291.

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Xie, Hongzhi, Basil I. Swanson, Hiromi K. Kawaga, Jonathan D. Trent, Mudalige Kumara, Thomas Ippolito, and Mircea Cotlet. "Intrinsic fluorescent recognition ligand scaffold based on chaperonins and water-soluble semiconductor quantum dots." In SPIE BiOS: Biomedical Optics, edited by Alexander N. Cartwright and Dan V. Nicolau. SPIE, 2009. http://dx.doi.org/10.1117/12.809576.

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Robles, Jose, Freedy Sotelo, Carlos Rojas, Jose Hurtado, and Jorge Lopez. "Performance Analysis of XGBoost Models with Ultrafast Shape Recognition Descriptors in Ligand-Based Virtual Screening." In ICBRA 2021: 2021 8th International Conference on Bioinformatics Research and Applications. New York, NY, USA: ACM, 2021. http://dx.doi.org/10.1145/3487027.3487029.

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Al-Lawatia, Najla, Thomas Steinbrecher, and Osama K. Abou-Zied. "Water participation in molecular recognition and protein-ligand association: Probing the drug binding site "Sudlow I" in human serum albumin." In SPIE BiOS, edited by Samuel Achilefu and Ramesh Raghavachari. SPIE, 2012. http://dx.doi.org/10.1117/12.905809.

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Hawiger, J. "PLATELET RECEPTOR RECOGNITION DOMAINS AND THEIR SYNTHETIC PEPTIDE ANALOGS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643726.

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Adhesive molecules and their receptorsplay an essential role in hemostasis and thrombosis. Platelet thrombi are formed through the interaction of cell adhesion molecules (CAMs) with intercellular adhesion molecules (IAMs)and substrate adhesion molecules (SAMs). Platelet CAMs encompass membrane glycoproteins lb, lib, Ilia,and possibly la and IV, which constitutemembrane receptors for IAMs(e.g., fibrinogen) and for SAMs encompassingvon Willebrand Factor (vWF), fibronectin, vitronectin, collagen, and thrcmbospondin. Receptorfunction of platelet CAMs can be specific,i.e., only one adhesive protein among IAMs and SAMs is selected forbinding as exemplified by GPIb and vWF. Alternatively,more than one adhesive protein can interact with platelet CAMs comprising the GPIIb/IIIa complex.This common adhesive receptor mechanism switched on by thrombin, ADP, phorbol ester or ionophore A23187 is turned off by a rise in intraplatelet cyclic AMP which provides a negative control.Fibrinogen, the most abundant adhesiveprotein in plasma, interacts with platelet CAMs via receptor recognition domains on gamma and alpha chains. Pinpointing platelet receptor recognition domain to a carboxy-terminal segment of the gamma chain encompassing residues 400-411gave rise to a series of synthetic peptide analogs which do not interfere with themetabolic pathways of platelets but blockbinding of I fibrinogen to its receptors on stimulated platelets, inhibit their aggregation in vitro, and formation of a platelet thrombus in vivo. The alpha chain of human fibrinogen contains the sequenceRGD (residues 95-97 and 572-574). Synthetpeptide analogs of the RGD sequence, which constitute the "cell adhesion site" of fibronectin, also inhibit binding of 125I-fibrinogen to stimulated platelets. However, these synthetic peptides are not "specific" for fibrinogen chains because thealpha chain of human fibrinogen which hasnosequence homology with gamma 400-411 is prevented by a peptide gamma 400-411 from interaction with platelet receptors. Viceversa, the human gamma chain is blocked by tetrapeptide RGDS not expressed in the human gamma chain. Interaction of human vWF with human platelets is blocked by synthetic peptide analogs of gamma 400-411 (not present in vWF)and of RGD sequence (present in vWF).These synthetic peptides inhibite "common" receptor pathwaystimulated with ADP, thrombin, or phorbolester, but they do not interfere with binding of 125I-vWF via a "specific" pathvoy induced with ristocetin and involving GPIb.The design of synthetic peptide analogs which inhibit platelet receptors for adhesive molecules includes the following considerations: ligand specificity (is thepeptide inhibitory toward binding of one or more adhesive molecules?),cell speciicity (is the peptide specific for platelets or does it perturb the adhesive properties of other cells, e.g.,endothelium?);the hydrophilic character; protection against degradation by peptidases; and a sufficiently long half-life to achieve platelet inhibitory potency in vivo without overloading the blood with excessive amounts of peptide.This is accomplished by constructing a peptide-albumin conjugate with ahalf-life extended at least 30 times.Whenpeptides are modeled with predominantly hydrophilic or hydrophobic residues, only the hydrophilic peptide remained active to block the platelet receptor. This agreed with the general observation that sequences on adhesive molecules that are knownto interact with cellular receptors have a hydrophilic rather than a hydrophobic character. Furthermore, changing the charge of synthetic peptides toward the negative reduced the reactivity, whereas introducing additional arginine residues enhanced the reactivity toward platelet receptors. Localization of the functionally important binding domain in the flexible segment of an adhesive protein increases the likelihood that the synthetic peptide will assume the conformation mimicking such a domain in the native adhesive protein. Structure-function studies of the receptor recognition domains on adhesive molecules led to development of a new class of platelet inhibitors acting at the membranereceptors responsible for anchoring of platelets to the vessel wall and linking them to each other.
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Hantgan, R. R. "LOCALIZATION OF THE DOMAINS OF FIBRIN INVOLVED IN BINDING TO PLATELETS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643773.

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The molecular basis of platelet-fibrin interactions has been investigated by using synthetic peptides as potential inhibitors of binding fibrin protofibrils and fibrinogen to ADP-stimulated platelets, adhesion of fibrin fibers to the platelet surface, and platelet-mediated clot retraction. Synthetic peptides RGDS and HHLGGAKQAGDV, corresponding to regions of the fibrinogen α and γ chains previously identified as platelet recognition sites, inhibited the binding of radiolabelled soluble fibrin oligomers to ADP-stimulated platelets with IC50 values of 12 and 40 μM, respectively. The IC50 values obtained with fibrinogen as the ligand were 3-fold higher. Synthetic GPRP and GHRP, corresponding to the N-terminal sequences of the fibrin α and β chains, were minimally effective in blocking soluble fibrin oligomer binding to ADP-stimulated platelets. The extent of fibrin:platelet adhesion was determined with a microfluorimetric technique which measures the quantity of fluorescein-labelled fibrin attached to the surface of platelets. The signal obtained from the brightly fluorescent platelet:fibrin adducts was time- and concentration-dependent, and was fully inhibited by a monoclonal antibody directed against the glycoprotein II:IIIa complex (HP1-1D, kindly provided by Dr. W. Nichols). Inhibition of fibrin:platelet adhesion by RGDS, HHGGAKQAGDV, and GHRP all exhibited a similar, linear dependence on the peptide concentration, reaching 1/2 maximum at about 200 μM, suggesting nonspecific effects. GPRP inhibited fibrin assembly but did not appear to have specific effects on fibrin:platelet adhesion. The time course of clot retraction was followed by right angle light scattering intensity measurements. Only RGDS affected clot retraction, causing a 4-fold decrease in rate at 230 μM. These results indicate that fibrinogen and fibrin protofibrils, which are obligatory intermediates in the fibrin assembly pathway, share a set of common platelet recognition sites located at specific regions of the α and γ chains of the multinodular fibrin(ogen) molecules. The RGDS site is also involved in mediating interactions between the three dimensional fibrin network and ADP-stimulated platelets.
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Charon, M. H., L. Tranqui, A. Andrieux, G. Hudry-Clergeon, and G. Marguerie. "FIBRINOGEN BINDING TO ENDOTHELIAL CELLS AND INTERFERING PEPTIDES." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644735.

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Fibrinogen interacts with platelets and endothelial cells via specific binding sites. While the platelet fibrinogen receptor has been identified and was found to be associated with GPIIb-IIIa, the binding site on endothelial cells has not been characterized yet. The platelet GPIIb-IIIa belongs to the newly identified cytoadhesin family which includes immunologicaly related receptors interacting with RGD containing proteins. A cytoadhesin has recently been described on endothelial cells and the possibility that fibrinogen might interact with this glycoprotein was examined. Peptides corresponding to γ and α chains sequences were synthesized and their capacity to inhibit fibrinogen binding to endothelial cells and platelets were compared. Analogues of the γ chain from His 400 to Val 411 produced an inhibition similar to that observed for fibrinogen platelet interaction, suggesting that the structure function relationship of γ peptides is identical in both systems. In contrast synthetic analogues corresponding to the a chain and including RGD yielded slightly different results. While RGD alone was inactive on platelet, this tripeptide was active on endothelial cells. RGDS and RGDF corresponding to α 572-575 and α 95-98 partially or fully inhibited fibrinogen binding to endothelial cells but the structure activity relationship was different when compared to that observed for platelets. Addition of the N and C sequences adjacent to RGDS reduced the activity of this peptide whereas the activity of RGDF analogues was not modified by addition of N and C-sequences. In contrast platelet fibrinogen binding decreased with these RGDF analogues. These results suggest that fibrinogen endothelial cell binding is mediated by an RGD adhesion receptor with subtle differences in the recognition selectivity of the ligand, which is controled by the surrounding sequence.
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Lebedeva, Olga. "PATTERN-RECOGNITION RECEPTORS, ACTIVATED BY BACTERIAL LIGANDS, IN PATHOGENESIS OF MISSED AND SPONTANEOUS ABORTIONS." In 4th SGEM International Multidisciplinary Scientific Conferences on SOCIAL SCIENCES and ARTS Proceedings. STEF92 Technology, 2017. http://dx.doi.org/10.5593/sgemsocial2017/33/s12.059.

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Reports on the topic "Ligand Recognition"

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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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Rafaeli, Ada, Russell Jurenka, and Chris Sander. Molecular characterisation of PBAN-receptors: a basis for the development and screening of antagonists against Pheromone biosynthesis in moth pest species. United States Department of Agriculture, January 2008. http://dx.doi.org/10.32747/2008.7695862.bard.

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The original objectives of the approved proposal included: (a) The determination of species- and tissue-specificity of the PBAN-R; (b) the elucidation of the role of juvenile hormone in gene regulation of the PBAN-R; (c) the identificationof the ligand binding domains in the PBAN-R and (d) the development of efficient screening assays in order to screen potential antagonists that will block the PBAN-R. Background to the topic: Moths constitute one of the major groups of pest insects in agriculture and their reproductive behavior is dependent on chemical communication. Sex-pheromone blends are utilised by a variety of moth species to attract conspecific mates. In most of the moth species sex-pheromone biosynthesis is under circadian control by the neurohormone, PBAN (pheromone-biosynthesis-activating neuropeptide). In order to devise ideal strategies for mating disruption/prevention, we proposed to study the interactions between PBAN and its membrane-bound receptor in order to devise potential antagonists. Major conclusions: Within the framework of the planned objectives we have confirmed the similarities between the two Helicoverpa species: armigera and zea. Receptor sequences of the two Helicoverpa spp. are 98% identical with most changes taking place in the C-terminal. Our findings indicate that PBAN or PBAN-like receptors are also present in the neural tissues and may represent a neurotransmitter-like function for PBAN-like peptides. Surprisingly the gene encoding the PBAN-receptor was also present in the male homologous tissue, but it is absent at the protein level. The presence of the receptor (at the gene- and protein-levels), and the subsequent pheromonotropic activity are age-dependent and up-regulated by Juvenile Hormone in pharate females but down-regulated by Juvenile Hormone in adult females. Lower levels of pheromonotropic activity were observed when challenged with pyrokinin-like peptides than with HezPBAN as ligand. A model of the 3D structure of the receptor was created using the X-ray structure of rhodopsin as a template after sequence alignment of the HezPBAN-R with several other GPCRs and computer simulated docking with the model predicted putative binding sites. Using in silico mutagenesis the predicted docking model was validated with experimental data obtained from expressed chimera receptors in Sf9 cells created by exchanging between the three extracellular loops of the HezPBAN-R and the Drosophila Pyrokinin-R (CG9918). The chimera receptors also indicated that the 3ʳᵈ extracellular loop is important for recognition of PBAN or Diapause hormone ligands. Implications: The project has successfully completed all the objectives and we are now in a position to be able to design and screen potential antagonists for pheromone production. The successful docking simulation-experiments encourage the use of in silico experiments for initial (high-throughput) screening of potential antagonists. However, the differential responses between the expressed receptor (Sf9 cells) and the endogenous receptor (pheromone glands) emphasize the importance of assaying lead compounds using several alternative bioassays (at the cellular, tissue and organism levels). The surprising discovery of the presence of the gene encoding the PBAN-R in the male homologous tissue, but its absence at the protein level, launches opportunities for studying molecular regulation pathways and the evolution of these GPCRs. Overall this research will advance research towards the goal of finding antagonists for this important class of receptors that might encompass a variety of essential insect functions.
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Chen, Yona, Jeffrey Buyer, and Yitzhak Hadar. Microbial Activity in the Rhizosphere in Relation to the Iron Nutrition of Plants. United States Department of Agriculture, October 1993. http://dx.doi.org/10.32747/1993.7613020.bard.

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Iron is the fourth most abundant element in the soil, but since it forms insoluble hydroxides at neutral and basic pH, it often falls short of meeting the basic requirements of plants and microorganisms. Most aerobic and facultative aerobic microorganisms possess a high-affinity Fe transport system in which siderophores are excreted and the consequent Fe complex is taken up via a cognate specific receptor and a transport pathway. The role of the siderophore in Fe uptake by plants and microorganisms was the focus of this study. In this research Rhizopus arrhizus was found to produce a novel siderophore named Rhizoferrin when grown under Fe deficiency. This compound was purified and its chemical structure was elucidated. Fe-Rhizoferrin was found to alleviate Fe deficiency when applied to several plants grown in nutrient solutions. It was concluded that Fe-Rhizoferrin is the most efficient Fe source for plants when compared with other among microbial siderophores known to date and its activity equals that of the most efficient synthetic commercial iron fertilizer-Fe EDDHA. Siderophores produced by several rhizosphere organisms including Rhizopus Pseudomonas were purified. Monoclonal antibodies were produced and used to develop a method for detection of the siderophores produced by plant-growth-promoting microorganisms in barley rhizosphere. The presence of an Fe-ferrichrome uptake in fluorescent Pseudomonas spp. was demonstrated, and its structural requirements were mapped in P. putida with the help of biomimetic ferrichrome analogs. Using competition experiments, it was shown that FOB, Cop B and FC share at least one common determinant in their uptake pathway. Since FC analogs did not affect FOB or Cop-mediated 55Fe uptake, it could be concluded that these siderophores make use of a different receptor(s) than FC. Therefore, recognition of Cop, FOB and FC proceeds through different receptors having different structural requirements. On the other hand, the phytosiderophores mugineic acid (MA and DMA), were utilized indirectly via ligand exchange by P. putida. Receptors from different biological systems seem to differ in their structural requirements for siderophore recognition and uptake. The design of genus- or species-specific drugs, probes or chemicals, along with an understanding of plant-microbe and microbe-microbe relationships as well as developing methods to detect siderophores using monoclonal antibodies are useful for manipulating the composition of the rhizosphere microbial population for better plant growth, Fe-nutrition and protection from diseases.
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Eyal, Yoram, and Sheila McCormick. Molecular Mechanisms of Pollen-Pistil Interactions in Interspecific Crossing Barriers in the Tomato Family. United States Department of Agriculture, May 2000. http://dx.doi.org/10.32747/2000.7573076.bard.

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During the evolutionary process of speciation in plants, naturally occurring barriers to reproduction have developed that affect the transfer of genes within and between related species. These barriers can occur at several different levels beginning with pollination-barriers and ending with hybrid-breakdown. The interaction between pollen and pistils presents one of the major barriers to intra- and inter-specific crosses and is the focus of this research project. Our long-term goal in this research proposal was defined to resolve questions on recognition and communication during pollen-pistil interactions in the extended tomato family. In this context, this work was initiated and planned to study the potential involvement of tomato pollen-specific receptor-like kinases (RLK's) in the interaction between pollen and pistils. By special permission from BARD the objectives of this research were extended to include studies on pollen-pistil interactions and pollination barriers in horticultural crops with an emphasis on citrus. Functional characterization of 2 pollen-specific RLK's from tomato was carried out. The data shows that both encode functional kinases that were active as recombinant proteins. One of the kinases was shown to accumulate mainly after pollen germination and to be phosphorylated in-vitro in pollen membranes as well as in-vivo. The presence of style extract resulted in dephosphorylation of the RLK, although no species specificity was observed. This data implies a role for at least one RLK in pollination events following pollen germination. However, a transgenic plant analysis of the RLK's comprising overexpression, dominant-negative and anti-sense constructs failed to provide answers on their role in pollination. While genetic effects on some of the plants were observed in both the Israeli and American labs, no clear functional answers were obtained. An alternative approach to addressing function was pursued by screening for an artificial ligand for the receptor domain using a peptide phage display library. An enriched peptide sequence was obtained and will be used to design a peptide-ligand to be tested for its effect o pollen germination and tube growth. Self-incompatibility (SI) in citrus was studied on 3 varieties of pummelo. SI was observed using fluorescence microscopy in each of the 3 varieties and compatibility relations between varieties was determined. An initial screen for an S-RNase SI mechanism yielded only a cDNA homologous to the group of S-like RNases, suggesting that SI results from an as yet unknown mechanism. 2D gel electrophoresis was applied to compare pollen and style profiles of different compatibility groups. A "polymorphic" protein band from style extracts was observed, isolated and micro-sequenced. Degenerate primers designed based on the peptide sequence date will be used to isolate the relevant genes i order to study their potential involvement in SI. A study on SI in the apple cultivar Top red was initiated. SI was found, as previously shown, to be complete thus requiring a compatible pollinator variety. A new S-RNase allele was discovered fro Top red styles and was found to be highly homologous to pear S-RNases, suggesting that evolution of these genes pre-dated speciation into apples and pears but not to other Rosaceae species. The new allele provides molecular-genetic tools to determine potential pollinators for the variety Top red as well as a tool to break-down SI in this important variety.
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Bradshaw, J. S., F. Huszthy, C. W. McDaniel, M. Oue, and C. Y. Zhu. Enantiomeric Recognition of Organic Ammonium Salts by Chiral Pyridino- 18-Crown-6 Ligands: A Short Review. Fort Belvoir, VA: Defense Technical Information Center, October 1990. http://dx.doi.org/10.21236/ada228546.

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Huszthy, P., J. S. Bradshaw, C. Y. Zhu, T. Wang, and R. M. Izatt. Recognition of the Enantiomers of Chiral Organic Ammonium Salts by Chiral Dibenzyl- and Diphenyl-Substituted Diamido-or Dithionoamidopyridino-18- crown-6 Ligands. Fort Belvoir, VA: Defense Technical Information Center, March 1992. http://dx.doi.org/10.21236/ada248026.

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Gordon, Dalia, Ke Dong, and Michael Gurevitz. Unexpected Specificity of a Sea Anemone Small Toxin for Insect Na-channels and its Synergic Effects with Various Insecticidal Ligands: A New Model to Mimic. United States Department of Agriculture, November 2010. http://dx.doi.org/10.32747/2010.7697114.bard.

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Motivated by the high risks to the environment and human health imposed by the current overuse of chemical insecticides we offer an alternative approach for the design of highly active insect-selective compounds that will be based on the ability of natural toxins to differentiate between insect and mammalian targets. We wish to unravel the interacting surfaces of insect selective toxins with their receptor sites on voltage-gated sodium channels. In this proposal we put forward two recent observations that may expedite the development of a new generation of insect killers that mimic the highly selective insecticidal toxins: (i) A small (27aa) highly insecticidal sea anemone toxin, Av3, whose toxicity to mammals is negligible; (ii) The prominent positive cooperativity between distinct channel ligands, such as the strong enhancement of pyrethroids effects by anti-insect selective scorpion depressant toxins. We possess a repertoire of insecticidal toxins and sodium channel subtypes all available in recombinant form for mutagenesis followed by analysis of various pharmacological, electrophysiological, and structural methods. Our recent success to express Av3 provides for the first time a selective toxin for receptor site-3 on insect sodium channels. In parallel, our recent success to determine the structures and bioactive surfaces of insecticidal site-3 and site-4 toxins establishes a suitable system for elucidation of toxin-receptor interacting faces. This is corroborated by our recent identification of channel residues involved with these two receptor sites. Our specific aims in this proposal are to (i) Determine the bioactive surface of Av3 toward insect Na-channels; (ii) Identify channel residues involved in binding or activity of the insecticidal toxins Av3 and LqhaIT, which differ substantially in their potency on mammals; (iii) Illuminate channel residues involved in recognition by the anti-insect depressant toxins; (iv) Determine the face of interaction of both site-3 (Av3) and site-4 (LqhIT2) toxins with insect sodium channels using thermodynamic mutant cycle analysis; and, (v) Examine whether Av3, LqhIT2, pyrethroids, and indoxacarb (belongs to a new generation of insecticides), enhance allosterically the action of one another on the fruit fly and cockroach paraNa-channels and on their kdr and super-kdr mutants. This research establishes the grounds for rational design of novel anti-insect peptidomimetics with minimal impact on human health, and offers a new approach in insect pest control, whereby a combination of allosterically interacting compounds increases insecticidal action and reduces risks of resistance buildup.
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