Academic literature on the topic 'Binding ligandi'
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Journal articles on the topic "Binding ligandi"
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Sunkara, Mallikarjuna Rao, Tina Schwabe, Gunter Ehrlich, Jana Kusch, and Klaus Benndorf. "All four subunits of HCN2 channels contribute to the activation gating in an additive but intricate manner." Journal of General Physiology 150, no. 9 (June 29, 2018): 1261–71. http://dx.doi.org/10.1085/jgp.201711935.
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Hyperpolarization-activated cyclic nucleotide–modulated (HCN) channels are tetramers that elicit electrical rhythmicity in specialized brain neurons and cardiomyocytes. The channels are dually activated by voltage and binding of cyclic adenosine monophosphate (cAMP) to their four cyclic nucleotide-binding domains (CNBDs). Here we analyze the effects of cAMP binding to different concatemers of HCN2 channel subunits, each having a defined number of functional CNBDs. We show that each liganded CNBD promotes channel activation in an additive manner and that, in the special case of two functional CNBDs, functionality does not depend on the arrangement of the subunits. Correspondingly, the reverse process of deactivation is slowed by progressive liganding, but only if four and three ligands as well as two ligands in trans position (opposite to each other) are bound. In contrast, two ligands bound in cis positions (adjacent to each other) and a single bound ligand do not affect channel deactivation. These results support an activation mechanism in which each single liganded CNBD causes a turning momentum on the tetrameric ring-like structure formed by all four CNBDs and that at least two liganded subunits in trans positions are required to maintain activation.
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Seo, Sangmin, Jonghwan Choi, Soon Kil Ahn, Kil Won Kim, Jaekwang Kim, Jaehyuck Choi, Jinho Kim, and Jaegyoon Ahn. "Prediction of GPCR-Ligand Binding Using Machine Learning Algorithms." Computational and Mathematical Methods in Medicine 2018 (2018): 1–5. http://dx.doi.org/10.1155/2018/6565241.
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We propose a novel method that predicts binding of G-protein coupled receptors (GPCRs) and ligands. The proposed method uses hub and cycle structures of ligands and amino acid motif sequences of GPCRs, rather than the 3D structure of a receptor or similarity of receptors or ligands. The experimental results show that these new features can be effective in predicting GPCR-ligand binding (average area under the curve [AUC] of 0.944), because they are thought to include hidden properties of good ligand-receptor binding. Using the proposed method, we were able to identify novel ligand-GPCR bindings, some of which are supported by several studies.
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Féau, Clémentine, Leggy A. Arnold, Aaron Kosinski, and R. Kiplin Guy. "A High-Throughput Ligand Competition Binding Assay for the Androgen Receptor and Other Nuclear Receptors." Journal of Biomolecular Screening 14, no. 1 (November 21, 2008): 43–48. http://dx.doi.org/10.1177/1087057108326662.
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Standardized, automated ligand-binding assays facilitate evaluation of endocrine activities of environmental chemicals and identification of antagonists of nuclear receptor ligands. Many current assays rely on fluorescently labeled ligands that are significantly different from the native ligands. The authors describe a radiolabeled ligand competition scintillation proximity assay (SPA) for the androgen receptor (AR) using Ni-coated 384-well FlashPlates® and liganded AR-LBD protein. This highly reproducible, low-cost assay is well suited for automated high-throughput screening. In addition, the authors show that this assay can be adapted to measure ligand affinities for other nuclear receptors (peroxisome proliferation-activated receptor γ, thyroid receptors α and β). ( Journal of Biomolecular Screening 2009:43-48)
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Kohn, MC, and RL Melnick. "Biochemical origins of the non-monotonic receptor-mediated dose-response." Journal of Molecular Endocrinology 29, no. 1 (August 1, 2002): 113–23. http://dx.doi.org/10.1677/jme.0.0290113.
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A mathematical model was created to examine how xenobiotic ligands that bind to nuclear receptor proteins may affect transcriptional activation of hormone-regulated genes. The model included binding of the natural ligand (e.g. hormone) and xenobiotic ligands to the receptor, binding of the liganded receptor to receptor-specific DNA response sequences, binding of co-activator or co-repressor proteins (Rp) to the resulting complex, and the consequent transcriptional rate relative to that in the absence of the xenobiotic agent. The model predicted that the xenobiotic could act as a pure agonist, a pure antagonist, or a mixed agonist whose dose-response curve exhibits a local maximum. The response to the agent depends on the affinity of the liganded receptor-DNA complex for binding additional transcription factors (e.g. co-activator proteins). An inverted U-shaped dose-response occurred when basal levels of the natural ligand did not saturate receptor binding sites and the affinity for co-activator is weaker when the xenobiotic ligand is bound to the receptor than when the endogenous ligand is bound. The dose-response curve shape was not dependent on the affinity of the receptor for the xenobiotic agent; alteration of this value merely shifted the curve along the concentration axis. The amount of receptor, the density of DNA response sequences, and the affinity of the DNA-bound receptor for Rp determine the amplitude of the computed response with little overall change in curve shape. This model indicates that a non-monotonic dose-response is a plausible outcome for xenobiotic agents that activate nuclear receptors in the same manner as natural ligands.
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Ruiz, MariaLuisa, and Jeffrey W. Karpen. "Opening Mechanism of a Cyclic Nucleotide–gated Channel Based on Analysis of Single Channels Locked in Each Liganded State." Journal of General Physiology 113, no. 6 (June 1, 1999): 873–95. http://dx.doi.org/10.1085/jgp.113.6.873.
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Cyclic nucleotide–gated channels contain four subunits, each with a binding site for cGMP or cAMP in the cytoplasmic COOH-terminal domain. Previous studies of the kinetic mechanism of activation have been hampered by the complication that ligands are continuously binding and unbinding at each of these sites. Thus, even at the single channel level, it has been difficult to distinguish changes in behavior that arise from a channel with a fixed number of ligands bound from those that occur upon the binding and unbinding of ligands. For example, it is often assumed that complex behaviors like multiple conductance levels and bursting occur only as a consequence of changes in the number of bound ligands. We have overcome these ambiguities by covalently tethering one ligand at a time to single rod cyclic nucleotide–gated channels (Ruiz, ML., and J.W. Karpen. 1997. Nature. 389:389–392). We find that with a fixed number of ligands locked in place the channel freely moves between three conductance states and undergoes bursting behavior. Furthermore, a thorough kinetic analysis of channels locked in doubly, triply, and fully liganded states reveals more than one kinetically distinguishable state at each conductance level. Thus, even when the channel contains a fixed number of bound ligands, it can assume at least nine distinct states. Such complex behavior is inconsistent with simple concerted or sequential allosteric models. The data at each level of liganding can be successfully described by the same connected state model (with different rate constants), suggesting that the channel undergoes the same set of conformational changes regardless of the number of bound ligands. A general allosteric model, which postulates one conformational change per subunit in both the absence and presence of ligand, comes close to providing enough kinetically distinct states. We propose an extension of this model, in which more than one conformational change per subunit can occur during the process of channel activation.
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Takahashi, Masaki, Ryo Amano, Michiru Ozawa, Anna Martinez, Kazumasa Akita, and Yoshikazu Nakamura. "Nucleic acid ligands act as a PAM and agonist depending on the intrinsic ligand binding state of P2RY2." Proceedings of the National Academy of Sciences 118, no. 18 (April 28, 2021): e2019497118. http://dx.doi.org/10.1073/pnas.2019497118.
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G protein–coupled receptors (GPCRs) play diverse roles in physiological processes, and hence the ligands to modulate GPCRs have served as important molecules in biological and pharmacological approaches. However, the exploration of novel ligands for GPCR still remains an arduous challenge. In this study, we report a method for the discovery of nucleic acid ligands against GPCRs by an advanced RNA aptamer screening technology that employs a virus-like particle (VLP), exposing the GPCR of interest. An array of biochemical analyses coupled with a cell-based assay revealed that one of the aptamers raised against purinergic receptor P2Y2 (P2RY2), a GPCR, exhibits an activation potency to unliganded receptor and prohibits a further receptor activation by endogenous ligand, behaving like a partial agonist. However, the aptamer enhances the activity of intrinsic ligand-binding P2RY2, thereby acting as a positive allosteric modulator (PAM) to liganded receptor. Our findings demonstrate that the nucleic acid aptamer conditionally exerts PAM and agonist effects on GPCRs, depending on their intrinsic ligand binding state. These results indicate the validity of our VLP-based aptamer screening targeting GPCR and reemphasize the great potential of nucleic acid ligands for exploring the GPCR activation mechanism and therapeutic applications.
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SAYED, Yasien, Judith A. T. HORNBY, Marimar LOPEZ, and Heini DIRR. "Thermodynamics of the ligandin function of human class Alpha glutathione transferase A1-1: energetics of organic anion ligand binding." Biochemical Journal 363, no. 2 (April 8, 2002): 341–46. http://dx.doi.org/10.1042/bj3630341.
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In addition to their catalytic functions, cytosolic glutathioneS-transferases (GSTs) are a major reserve of high-capacity binding proteins for a large variety of physiological and exogenous non-substrate compounds. This ligandin function has implicated GSTs in numerous ligand-uptake, -transport and -storage processes. The binding of non-substrate ligands to GSTs can inhibit catalysis. In the present study, the energetics of the binding of the non-substrate ligand 8-anilino-1-naphthalene sulphonate (ANS) to wild-type human class Alpha GST with two type-1 subunits (hGSTA1-1) and its ΔPhe-222 deletion mutant were studied by isothermal titration calorimetry. The stoichiometry of binding to both proteins is one ANS molecule per GST subunit with a greater affinity for the wild-type (Kd=65μM) than for the ΔPhe-222 mutant (Kd=105μM). ANS binding to the wild-type protein is enthalpically driven and it is characterized by a large negative heat-capacity change, ΔCp. The negative ΔCp value for ANS binding indicates a specific interface with a significant hydrophobic component in the protein—ligand complex. The negatively charged sulphonate group of the anionic ligand is apparently not a major determinant of its binding. Phe-222 contributes to the binding affinity for ANS and the hydrophobicity of the binding site.
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Mendoza, A., P. Navarrete-Ramírez, G. Hernández-Puga, P. Villalobos, G. Holzer, J. P. Renaud, V. Laudet, and A. Orozco. "3,5-T2 Is an Alternative Ligand for the Thyroid Hormone Receptor β1." Endocrinology 154, no. 8 (August 1, 2013): 2948–58. http://dx.doi.org/10.1210/en.2013-1030.
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Abstract Several liganded nuclear receptors have alternative ligands acting in a tissue-specific fashion and playing important biological roles. We present evidence that 3,5-diiodothyronine (T2), a naturally occurring iodothyronine that results from T3 outer-ring deiodination, is an alternative ligand for thyroid hormone receptor β1 (TRβ1). In tilapia, 2 TRβ isoforms differing by 9 amino acids in the ligand-binding domain were cloned. Binding and transactivation studies showed that T2 activates the human and the long tilapia TRβ1 isoform, but not the short one. A chimeric human TRβ1 (hTRβ1) that contained the 9–amino-acid insert showed no response to T2, suggesting that the conformation of the hTRβ1 naturally allows T2 binding and that other regions of the receptor are implicated in TR activation by T2. Indeed, further analysis showed that the N terminus is essential for T2-mediated transactivation but not for that by T3 in the long and hTRβ1, suggesting a functional interaction between the N-terminal domain and the insertion in the ligand-binding domain. To establish the functional relevance of T2-mediated TRβ1 binding and activation, mRNA expression and its regulation by T2 and T3 was evaluated for both isoforms. Our data show that long TRβ1expression is 106-fold higher than that of the short isoform, and T3 and T2 differentially regulate the expression of these 2 TRβ1 isoforms in vivo. Taken together, our results prompted a reevaluation of the role and mechanism of action of thyroid hormone metabolites previously believed to be inactive. More generally, we propose that classical liganded receptors are only partially locked to very specific ligands and that alternative ligands may play a role in the tissue-specific action of receptors.
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Suzuki, Sadako, Shigekazu Sasaki, Hiroshi Morita, Yutaka Oki, Daisuke Turiya, Takeshi Ito, Hiroko Misawa, Keiko Ishizuka, and Hirotoshi Nakamura. "The role of the amino-terminal domain in the interaction of unliganded peroxisome proliferator-activated receptor γ-2 with nuclear receptor co-repressor." Journal of Molecular Endocrinology 45, no. 3 (June 29, 2010): 133–45. http://dx.doi.org/10.1677/jme-10-0007.
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Peroxisome proliferator-activated receptor γ-2 (PPARG2) is a ligand-dependent transcriptional factor involved in the pathogenesis of insulin resistance. In the presence of a ligand, PPARG2 associates with co-activators, while it recruits co-repressors (CoRs) in the absence of a ligand. It has been reported that the interaction of liganded PPARG2 with co-activators is regulated by the amino-terminal A/B domain (NTD) via inter-domain communication. However, the role of the NTD is unknown in the case of the interaction between unliganded PPARG2 and CoRs. To elucidate this, total elimination of the influence of ligands is required, but the endogenous ligands of PPARG2 have not been fully defined. PPARG1-P467L, a naturally occurring mutant of PPARG1, was identified in a patient with severe insulin resistance. Reflecting its very low affinity for various ligands, this mutant does not have transcriptional activity in the PPAR response element, but exhibits dominant negative effects (DNEs) on liganded wild-type PPARG2-mediated transactivation. Using the corresponding PPARG2 mutant, PPARG2-P495L, we evaluated the role of the NTD in the interaction between unliganded PPARG2 and CoRs. Interestingly, the DNE of PPARG2-P495L was increased by the truncation of its NTD. NTD deletion also enhanced the DNE of a chimeric receptor, PT, in which the ligand-binding domain of PPARG2 was replaced with that of thyroid hormone receptor β-1. Moreover, NTD deletion facilitated the in vitro binding of nuclear receptor CoR with wild-type PPARG2, mutant P495L, and the PT chimera (PPARG2-THRB). Inter-domain communication in PPARG2 regulates not only ligand-dependent transactivation but also ligand-independent silencing.
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Micovic, Vuk, Milovan Ivanovic, and Ljiljana Dosen-Micovic. "Structural requirements for ligands of the δ-opioid receptor." Journal of the Serbian Chemical Society 74, no. 11 (2009): 1207–17. http://dx.doi.org/10.2298/jsc0911207m.
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The ?-opioid receptor is sensitive to ligand geometry. In order to assist the synthesis of new ?-selective opioid ligands, the structure elements of ?-selective opioid ligands necessary for their effective binding were investigated. The automated docking procedure with a flexible ligand was used to simulate the binding of 17 ?-selective ligands to the ?-receptor. It was found that voluminous N-alkyl groups reduce the binding potency of naltrindole derivatives by preventing the ligands from adopting the preferred conformation in the receptor. This was confirmed by enantiospecific binding of chiral compounds where only one enantiomer adopts the naltrindole-like preferred conformation in the binding pocket. Voluminous groups replacing the hydroxyl group in the 3-hydroxybenzyl fragment of naltrindole analogs reduce the binding potency due to unfavorable steric interactions with the receptor. The two diastereoisomers of the potent ?-opioid ligand SNC80 confirmed the preferred binding conformation and the major receptor-ligand interactions.
Dissertations / Theses on the topic "Binding ligandi"
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CALLEA, LARA. "MODELING OF LIGAND-PROTEIN BINDING WITH ADVANCED MOLECULAR DYNAMICS METHODS." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2022. http://hdl.handle.net/10281/374733.
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Questa tesi è incentrata sulla modellazione del binding ligando-proteina con metodi computazionali basati sulla dinamica molecolare. La comprensione di questo processo è fondamentale per la progettazione e la scoperta di nuovi farmaci e l'uso di metodi computazionali per supportare la ricerca sperimentale in questo campo è in costante crescita. Oggi, grazie alla crescente potenza dei computer, è possibile studiare l'intero processo di binding/unbinding del ligando e ottenere stime sulle proprietà termodinamiche e cinetiche.
Alla luce di ciò, durante il mio dottorato, diversi metodi avanzati di dinamica molecolare classica (MD) sono stati impiegati e confrontati per identificare un approccio computazionale efficace per studiare i processi di binding/unbinding dei ligandi. In particolare, è stato sviluppato un protocollo basato sulla combinazione degli approcci steered MD (sMD) e Metadinamica (MetaD) con Path Collective Variables (PCVs) con lo scopo di utilizzare i vantaggi di entrambi i metodi per ottenere una descrizione completa del processo. Mentre il metodo SMD è stato impiegato per studiare diversi percorsi di disassociazione e identificare quello preferito, la MetaD con le PCVs è stato utilizzato per determinare più accuratamente l'energia libera di legame. Il protocollo proposto è stato applicato con successo per studiare il legame del ligando al fattore inducibile dell'ipossia (HIF-2α) e ha dimostrato di essere efficace per le simulazioni effettuate sia su una struttura a raggi X nota del ligando-proteina che su una posa di docking.
D'altra parte, la maggior parte dei metodi MD richiede la produzione di diverse repliche o lunghe simulazioni per campionare più volte l'evento di binding/unbinding al fine di ottenere una statistica affidabile del processo. Questo produce la necessità di metodi in grado di analizzare tutti gli eventi simulati in una sola volta e di fornire un quadro chiaramente interpretabile delle differenze nei pathway campionati. Per questo motivo, è stato sviluppato un tool basato sulle mappe auto-organizzanti (SOM). Lo strumento PathDetect-SOM (Pathway Detection on SOM), sfruttando i vantaggi dell'ordinamento topologico della SOM, permette di rappresentare visivamente i percorsi di legame campionati durante diversi eventi/repliche MD in una chiara rappresentazione bidimensionale. Inoltre, possono essere derivati suggerimenti sulle proprietà cinetiche e termodinamiche del processo. Lo strumento è stato applicato con successo a diversi casi di studio per dimostrare la sua applicabilità generale.
Inoltre, come parte di un progetto eseguito presso il centro di ricerca Jülich (Istituto di Simulazioni Avanzate e Istituto di Neuroscienze e Medicina) sotto la supervisione del Prof. Paolo Carloni, è stata testata una nuova interfaccia ibrida di meccanica quantistica/meccanica molecolare (QM/MM) (MiMiC). Il codice, che permette simulazioni di dinamica molecolare QM/MM di sistemi biomolecolari, è stato applicato alla proteina chinasi mitogeno-attivata p38 in complesso con il ligando 2g per studiare il processo di unbinding del ligando. L'attenzione si è concentrata sulla prima fase del processo che coinvolge la dinamica del ligando nel suo stato legato. Le simulazioni MD QM/MM sono state efficaci nel descrivere accuratamente le interazioni ligando-proteina. In particolare, monitorando il cambiamento delle cariche atomiche durante la simulazione e calcolando la differenza di densità elettronica tra il ligando nel suo stato legato e nel vuoto, sono stati ottenuti approfondimenti sugli effetti di polarizzazione del campo elettrico della proteina sul ligando. Ci si aspetta che questi effetti, anche se piccoli nello stato legato, diventino molto importanti nelle fasi successive del processo di unbinding.This thesis focused on modeling of ligand-protein binding with computational methods based on molecular dynamics. Understanding this process is crucial for the design and discovery of new drugs and the use of computational methods to support experimental research in this field is constantly growing. Nowadays, thanks to the increasing computer power, it is possible to study the complete ligand binding/unbinding process and obtain estimate on thermodynamic and kinetic properties. In view of this, during my PhD, different advanced classical molecular dynamics (MD) methods were employed and compared to identify an effective computational approach for studying ligand binding/unbinding processes. Specifically, a protocol based on combination of the steered MD (sMD) and the Metadynamics (MetaD) with Path Collective Variables (PCVs) approaches was developed with the aim of using the advantages of both methods to obtain a complete description of the process. While the sMD method was employed to investigate different unbinding pathways and identify the preferred one, MetaD with PCVs was used to determine more accurately the binding free energy. The proposed protocol was successfully applied to study ligand binding to the Hypoxia Inducible Factor (HIF-2α) and it demonstrated to be effective for simulations performed both on a known ligand-protein X-ray structure and on a docking pose. On the other hand, most of the MD methods requires the production of several replicas or long simulations to sample the binding/unbinding event several times in order to obtain a reliable statistics of the process. This produces the need of methods able to analyze all the simulated events at once and to provide a clearly interpretable picture of the differences in the sampled pathways. For this reason, a tool based on the self-organizing maps (SOMs) was developed. The PathDetect-SOM (Pathway Detection on SOM) tool, exploiting the advantages of the topological ordering of the SOM, allowing to visually represent the binding paths sampled during different MD events/replicas in a clear bidimensional representation. In addition, hints on the kinetic and thermodynamic properties of the process can be derived. The tool was successfully applied to different study-cases to demonstrate its general applicability. Furthermore, as part of a project performed at the Jülich research center (Institute of Advanced Simulations and Institute for Neuroscience and Medicine) under the supervision of Prof. Paolo Carloni, a novel hybrid quantum mechanics/molecular mechanics (QM/MM) interface (MiMiC) was tested. The code, that allows QM/MM molecular dynamics simulations of biomolecular systems, was applied to the mitogen-activated protein kinase p38 in complex with the 2g ligand to investigate the ligand unbinding process. The focus was on the first step of the process involving the dynamics of the ligand in its bound state. QM/MM MD simulations were effective in describing ligand-protein interactions accurately. In particular, by monitoring the change of the atomic charges during the simulation and calculating the electronic density difference between the ligand in its bound state and in vacuum, insights into the polarization effects of the protein electric field onto the ligand were obtained. It is expected that these effects, albeit small in the bound state, become very important in the following steps of the unbinding process.
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Schinina', Barbara. "Progettazione, sintesi e valutazione farmacologica di derivati del 4-nitro-7-piperazin-1-il-2,1,3-benzossadiazolo come nuovi ligandi sigma fluorescenti." Doctoral thesis, Università di Catania, 2012. http://hdl.handle.net/10761/1173.
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Da sempre biologi e biochimici hanno focalizzato la loro attenzione in numerosi studi volti a chiarire i processi e le strutture molecolari fondamentali per la vita. Tra le tecnologie utilizzate allo scopo di conoscere la struttura di una biomolecola e la sua interazione con altre strutture, la diffrazione a raggi X, la risonanza magnetica nucleare ela microscopia elettronica permettono misure che richiedono grandi quantit¨¤ di composti purificati, sono spesso eseguite in condizioni non-fisiologiche e sono raramente adatte per osservare le reazioni molecolari in tempo reale.
Recenti sviluppi sono stati mostrati sia nel campo dellafluorescenza che in numerosi metodi che consentono la selettivit¨¤ e l¡¯analisi delle interazioni molecolari in condizioni fisiologiche, come nelle cellule vive.
L'analisi si concentra sulle interazioni ligando-recettore e sul processo successivo di trasduzione del segnale, che determina la risposta finale cellulare. Generalmente questi processi sono mediati, attraverso le membrane cellulari,da proteine canale o recettori accoppiati a proteina G. I nuovi saggi di fluorescenza sono importanti per spiegarela funzione dei recettori e i processi di trasduzione del segnale, cos¨¬ come per lo screening di nuovi composti terapeutici.
In particolare, il metodo della fluorescenza polarizzata (FP), della fluorescenza di risonanza a trasferimento di energia (FRET) e della fluorescenza a tempo risolto (TRFS), sono emersi come soluzione agli high-throughput screening assays(HTS), in quanto pi¨´ rapidi, con minor impatto ambientale e minori costi. Sebbene siano stati riscontrati alcuni problemi analitici, i ligandi fluorescenti sono stati proposti come alternativa ai radioligandi per gli studi di binding sui recettori. Tali composti possono anche dare informazioni sulle caratteristiche bio-fisiche del sito di legame del ligando poich¨¦ alcuni fluorofori mostrano una resa quantica che dipende dalla lipofilicit¨¤ o dal pH dell¡¯ambiente.Inoltre potrebbero essere in grado di chiarire la localizzazione e le funzioni biologiche di alcuni tipi di recettore. Per esempio ligandi fluorescenti hanno permesso la localizzazione dei recettori ¦Á1 adrenergici, dei trasportatori della dopamina, dei recettori A1 adenosinici e dei recettori periferici delle benzodiazepine. Sempre attraverso l¡¯uso di tali composti ¨¨ stato possibile lo studio dell¡¯espressione e del clustering del recettore ionotropico 5-HT3, la visualizzazione in tempo reale del trafficking cellulare e dell¡¯internalizzazione del complesso del ligando con i recettori oppioidi ¦Ì e ¦Ä e infine l¡¯oligomerizzazione dei recettori della somatostatina regolata dal legame con il ligando. Sono stati inoltre sintetizzati composti fluorescenti attivi sui recettori sigma (¦Ò) che potrebbero essere in grado di fornire nuove informazioni e chiarimenti sul loro ruolo fisio-patologico. Tali recettori sono presenti a livello del sistema nervoso centrale (SNC), del fegato, del rene, del sistema immunitario e del tessuto endocrino e le loro funzioni fisiologiche sono ancora oggetto di studio. In particolare, nel SNC i recettori ¦Ò1 sono coinvolti nella modulazione dei canali del potassio e del calcio e nella neurotrasmissione glutammatergica, serotoninergica, dopaminergica e muscarinica, suggerendo un loro potenziale ruolo terapeutico nel trattamento di disturbi cognitivi, depressione e schizofrenia. I recettori ¦Ò2, invece, sono overespressi in linee cellulari tumorali e per questo motivo ligandi ¦Ò fluorescenti potrebbero essere utili alla diagnosi tumorale. Inoltre per meglio chiarire il coinvolgimento fisiologico e patologico dei recettori ¦Ò1 e ¦Ò2 nella crescita delle cellule tumorali, un ligando fluorescente potrebbe rappresentare un potenziale tool molecolare per lo studio della vitalit¨¤ cellulare.
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Kandala, Srikanth. "Diphosphine Ligand Substitution in H4Ru4(CO)12: X-ray Diffraction Structures and Reactivity Studies of the Diphosphine Substituted Cluster Products." Thesis, University of North Texas, 2006. https://digital.library.unt.edu/ark:/67531/metadc5410/.
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The tetraruthenium cluster H4Ru4(CO)12 has been studied for its reactivity with the unsaturated diphosphine ligands (Z)-Ph2PCH=CHPPh2, 4,5-bis (diphenylphosphino)-4-cyclopenten-1,3-dione, bis(diphenyphosphino)benzene and 1,8- bis(diphenyl phosphino)naphthalene under thermal, near-UV photolysis, and Me3NO-assisted activation. All three cluster activation methods promote loss of CO and furnish the anticipated substitution products that possess a chelating diphosphine ligand. Clusters 1, 2, 3 and 4 have been characterized in solution by IR and NMR spectroscopies, and these data are discussed with respect to the crystallographically determined structures for all new cluster compounds. The 31P NMR spectral data and the solid-state structures confirm the presence of a chelating diphosphine ligand in all four new clusters. Sealed NMR tubes containing clusters 1, 2, 3 and 4 were found to be exceeding stable towards near-UV light and temperatures up to ca. 100°C. The surprisingly robust behavior of the new clusters is contrasted with the related cluster Ru3(CO)10(bpcd) that undergoes fragmentation to the donor-acceptor compound Ru2(CO)6(bpcd) and the phosphido-bridged compound Ru2(CO)6 (µ-PPh2)[µ-C=C(PPh2)C(O)CH2C(O)] under mild conditions. The electrochemical properties have been investigated in the case of clusters 1 and 2 by cyclic voltammetry, and the findings are discussed with respect to the reported electrochemical data on the parent cluster H4Ru4(CO)12.
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Schechner-Resom, Martina Gabriele. "Ligand binding and molecular flexibility : Studies on DNA gyrase B." Université Louis Pasteur (Strasbourg) (1971-2008), 2005. http://www.theses.fr/2005STR1A001.
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L’ADN gyrase est une enzyme vitale pour la bactérie grâce à sa capacité de manipuler les molécules d’ADN dans la cellule vivante. Cette capacité fait de l’ADN gyrase une cible idéale pour des composés anti-infectieux. Dans ce travail, l’ADN gyrase a été étudié par des méthodes de modélisatoin moléculaire. Une approche de conception de ligands basée sur la structure a été entreprise sur le sous-domaine N-terminal de 24 kDa de l’ADN gyrase B (domaine GHKL). La flexibilité de deux boucles du site actif du domaine GHKL a été étudiée par des simulations de dynamiques moléculaires en présence de différents ligands. Dans une dernière partie, une analyse des modes normaux du dimère du domaine N-terminal de 43 kDa a été entrepriseDNA gyrase is a vital bacterial enzyme necessary for the handling of the large DNA molecules in the living cell. Therefore DNA gyrase is an ideal target enzyme for anti-infectious compounds. In this work DNA gyrase has been studied by molecular modelling methods. A computational structure-based ligand design approach has been carried out on the N-terminal 24 kDa subdomain of DNA gyrase B (GHKL domain). To further examine the flexibility of two active site loops, molecular dynamics simulations have been carried out on the GHKL domain in different ligand binding conditions. In a final part, normal mode analysis has been carried out on the dimer of the 43 kDa domain of DNA gyrase B
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Wade, R. C. "Ligand-macromolecule interactions." Thesis, University of Oxford, 1988. http://ora.ox.ac.uk/objects/uuid:576ce119-6a93-4eb0-a7e4-1f2513736dbd.
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The optimisation of ligand-macromolecule interactions is fundamental to the design of therapeutic agents. The GRID method is a procedure for determining energetically favourable ligand binding sites on molecules of known structure using an empirical energy potential. In this thesis, it has been extended, tested, and then applied to the design of anti-influenza agents. In the GRID method, the energy of a hydrogen-bond is determined by a function which is dependent on the length of the hydrogen-bond, its orientation at the hydrogen-bond donor and acceptor atoms, and the chemical nature of these atoms. This function has been formulated in order to reproduce experimental observations of hydrogen-bond geometries. The reorientation of hydrogen atoms and lone-pair orbitals on the formation of hydrogen-bonds is calculated analytically. The experimentally observed water structures of crystals of four biological molecules have been used as model systems for testing the GRID method. It has been shown that the location of well-ordered waters can be predicted accurately. The ability of the GRID method to assist in the assignment of water sites during crystallographic refinement has been demonstrated. It has also been shown that waters in the active site of an enzyme may be both stabilized and displaced by a bound substrate. Ligands have been designed to block the highly conserved host cell receptor site of the influenza virus haemagglutinin in order to prevent the attachment of the virus to the host cells. The protein was mapped energetically by program GRID and specific ligand binding sites were identified. Ligands, which exploited these binding sites, were then designed using computer graphics and energy minimization techniques. Some of the designed ligands were peptides and these were synthesised and assayed. Preliminary results indicate that they may possess anti-influenza activity.
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Teng, Su Fern. "Immunoglobulins binding ligands." Thesis, University of Cambridge, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.627345.
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Yamamoto, Izumi. "Structure-function studies of GABA-C receptor ligands." Thesis, The University of Sydney, 2012. https://hdl.handle.net/2123/28927.
Full textAbstract:
Throughout the central nervous system (CNS), the Cys-loop superfamily of ligand-gated ion channels {LGICs), including nicotinic acetylcholine, serotonin type-3A, strychnine-sensitive glycine and y-aminobutyric acid A/C receptors, play important roles in synaptic transmission by converting chemical signals into electric signals. Designing potent and subtype-selective ligands with therapeutic value requires knowledge about how ligands interact with their binding sites.
y-Aminobutyric acid (GABA) is the predominant inhibitory neurotransmitter in the mammalian CNS and its binding modes at GABA receptors have not been fully elucidated. GABAc receptors consist of p subunits (p1-p3) and they are known to form homomeric receptors. The five subunits are arranged around a central chloride selective ion channel pore. Each subunit contains a large extracellular N-terminal domain, four transmembrane domains {Ml-M4) of which the second (M2) lines the channel pore and a large M3-M4 intracellular loop. The orthosteric binding site is located at the interface between two subunits in the N-terminal domain and the key residues for ligand binding are found at the five discontinuous loops (A-E).
This thesis describes how ligand binding and receptor gating are closely related and explores the effect of receptor conformational changes upon ligand binding. A series of point mutations in the N-terminal domain of the GABAc p1 receptor were created and expressed in Xenopus oocytes. The mutant receptors were then examined using a range of pharmacological tools to probe function which was measured using the two-electrode voltage clamp method.
The GABA binding mode was explored at GABA receptors using the enantiomers of 3-fluoro-y-aminobutyric acid (3F-GABA) and stereoisomers of 2,3-difluoro-4-aminobutyric acids as conformational probes. Both enantiomers of 3FGABA were full agonists, with the R-3F-GABA being approximately 3-fold more potent than 5-3F-GABA at GABAc receptors. In contrast, both enantiomers were partial agonists with similar efficacy and potency at GABAA receptors. These results suggest a different GABA binding mode at GABAc receptors to that found in the related but pharmacologically distinct GABAA receptors. The effect of the different stereoisomers of 2,3-difluoro-4-aminobutyric acids were also examined at GABAA, GABA8 and GABAc receptors. In the study, two enantiomeric GABAc receptor ligands were identified, one of which is an agonist (25,35-2,3-difluoro-4-aminobutyric acid) while the other is an antagonist (2R,3R-2,3-difluoro-4-aminobutyric acid).
4-Amino-3-hydroxybutanoic acid (GABOB) is an endogenous ligand found in the CNS in mammals and a metabolite of GABA. Homology modeling of the GABAc Pi receptor revealed a potential hydrogen (H-bond) interaction between the hydroxyl group of GABOB and threonine 244 (T244) located on loop C of the ligand binding site. Using site-directed mutagenesis, the effect of mutating T244 on the efficacy and pharmacology of GABOB and various ligands were examined. It was found that mutating T244 to amino acids that lacked a hydroxyl group in the side chain produced GABA insensitive receptors. Only by mutating PiT244 to serine (PiT2445) produced a GABA responsive receptor, albeit 39-fold less sensitive to GABA than Pi wild-type. It was also found that this mutation also changed the activity of GABAc receptor partial agonists, muscimol and imidazole-4-acetic acid (I4AA). At the concentrations tested, both muscimol and I4AA antagonized the currents produced by GABA at PiT2445 mutant receptors (Muscimol: PiWild-type, EC50 = 1.4 µM; PiT2445, IC50 = 32.8 µM. I4AA: Pi wild-type, EC50 = 8.6 µM; PiT2445, IC50 = 21.4 µM). This indicates that T244 is predominantly involved in channel gating.
R-(-)-GABOB and 5-(+)-GABOB are full agonists at Pi wild-type receptors. In contrast, R-(-)-GABOB was a weak partial agonist at PiT2445 (lmM activates 26 % of the current produced by GABA ECso versus Pi wild-type, EC50 = 19 µM; lmax 100%), and 5-(+)-GABOB was a competitive antagonist at PiT2445 receptors (Pi wild-type, EC50 = 45 µM versus PiT2445, IC50 = 417.4 µM, Ks = 204 µM). This highlights that the interaction of GABOB with T244 is enantioselective.
In contrast, the potencies of a range of antagonists tested, 3-aminopropyl(methyl)phosphinic acid (3-APMPA), 3-aminopropylphosphonic acid (3-APA), 5- and R-(3-amino-2-hydroxypropyl)methylphosphinic acid (5-(-)-CGP44532 and R-(+)-CGP44533), were not altered. This suggests that T244 is not critical for antagonist binding. Receptor gating is dynamic and this study highlights the role of loop C in agonist-evoked receptor activation, coupling agonist binding to channel gating.
Ligands acting on receptors are considered to induce a conformational change within the ligand-binding site by interacting with specific amino acids. In this study, tyrosine 102 (Y102) located in the GABA binding site of the Pi subunit of the GABAc receptor was mutated to alanine (piY102A), serine (piY102S) and cysteine (piY102C) to assess the role of this amino acid plays on the action of 12 known and 2 novel antagonists. Of the mutated receptors, piY102S was constitutively active providing an opportunity to assess the activity of the antagonists on Pi receptors with a proportion of receptors existing in the open conformational state compared to those existing predominantly in the closed conformational state (pi wild-type, PiY102C and PiY102A).
It was found that the majority of antagonists studied were able to inhibit the constitutive activity displayed by PiY1025, thus displaying inverse agonist activity. The exception was (±)-4-aminocyclopent-1-enecarboxamide ((±)-4-ACPAM) not exhibiting any inverse agonist activity, but acting explicitly on the closed conformational state of Pi receptors.
It was also found that GABA antagonists were more potent at the closed compared to the open conformational states of Pi receptors suggesting that they may act by stabilizing the closed conformational state and thus reducing activation by agonists. Furthermore, of the antagonists tested, Y102 was found to have the greatest influence on the antagonist activity of gabazine (SR-95531) and its analogue (SR-95813).
Our GABAc Pi receptor homology model identified a novel cavity, which extended beyond the GABA binding site. The model predicted phenylalanine 124(F124), one of the residues lining the cavity, was pointing towards the orthosteric binding site. In this study, F124 was mutated to various amino acids and only a modest effect on receptor pharmacology was observed. However, the mutations had a significant effect on the channel deactivation rate ('toeactivation)- This finding suggests that F124 may play a role in channel gating or stabilizing the open conformation of the receptor.
Designing potent selective agents are the key for the further understanding of the physiological roles of GABAc receptors. Gabazine (SR-95531) is a potent GABAA receptor competitive antagonist. In this study, a series of novel gabazine analogues were tested at GABAA and GABAc receptors. Of the compounds studied, (p)-methoxy analogue without the butyric acid side-chain was 20-fold more potent at GABAc over GABAA receptors. As there was no butyric acid side chain, it is suggested that the carboxylic acid is not important for gabazine activity at this receptor. Establishing the structure-activity relationship based on this analogue will facilitate the development of selective GABAc receptor antagonists with possible physiological effects including memory-enhancement.
Overall, our studies describe agonist and GABAc receptor antagonist induced conformational changes within the ligand binding site. Our findings also highlight the dynamic nature of receptor gating, initiated by ligand binding at a site physically distinct from the ion channel.
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Duraj-Thatte, Anna. "Fluorescent GFP chromophores as potential ligands for various nuclear receptors." Diss., Georgia Institute of Technology, 2012. http://hdl.handle.net/1853/44764.
Full textAbstract:
Nuclear receptors are ligand activated transcription factors, where upon binding
with small molecule ligands, these proteins are involved in the regulation of gene
expression. To date there are approximately 48 human nuclear receptors known, involved
in multiple biological and cellular processes, ranging from differentiation to maintenance
of homeostasis. Due to their critical role in transcriptional regulation, these receptors are
implicated in several diseases. Currently, 13% of prescribed drugs in the market are NR
ligands for diseases such as cancer, diabetes and osteoporosis. In addition to drug discovery, the mechanism of function, mobility and trafficking of these receptors is poorly understood. Gaining insight into the relationship between the function and /or
dysfunction of these receptors and their mobility will aid in a better understanding of the
role of these receptors.
The green fluorescent protein (GFP) has revolutionized molecular biology by
providing the ability to monitor protein function and structure via fluorescence. The
fluorescence contribution from this biological marker is the chromophore, formed from
the polypeptide backbone of three amino acid residues, buried inside 11-stranded â-barrel
protein. Synthesis of GFP derivatives of is based on the structure of the
arylmethyleneimidazolidinone (AMI), creating a molecule that is only weakly fluorescent.
Characterizing these AMI derivatives for other proteins can provide a powerful
visualization tool for analysis of protein function and structure. This development could
provide a very powerful method for protein analysis in vitro and in vivo.
Development of such fluorescent ligands will prove beneficial for the nuclear
receptors.
In this work, libraries of AMIs derviatives were synthesized by manipulating
various R groups around the core structure, and tested for their ability to serve as nuclear
receptor ligands with the ability to fluoresce upon binding. The fluorogens are developed
for steroidal and non-steroidal receptors, two general classes of nuclear receptors.
Specific AMIs were designed and developed for steroid receptor estrogen receptor á
(ERá). These ligands are showed to activate the receptor with an EC50 of value 3 ìM and the 10-fold activation with AMI 1 and AMI 2 in comparison to the 21-fold activation
observed with natural ERá ligand, 17â-estradiol. These novel ligands were not able to
display the fluorescence upon binding the receptor. However, fluorescence localized in
nucleus was observed in case of another AMI derivative, AMI 10, which does not
activate the receptor. Such ligands open new avenues for developing fluorescent probes
for ERá that do not involve fluorescent conjugates attached to a known ERá ligand core.
AMIs were also characterized for non-steroidal receptors,specifically the pregnane x receptor (PXR) and retinoic acid receptor á (RARá). To date, fluorogens which turn fluorescence upon binding and activate the receptor have not been developed for these receptors. With respect to PXR, several AMI derivatives were discovered to bind and activate this receptor with a fold-activation better than the known agonist, rifampicin. The best characterized AMI derivative, AMI 4, activates the receptor with an EC50 of value 6.3 ìM and the 154-fold activation in comparison to the 90-fold activation and an EC50 value of 1.3 ìM seen with rifamipicin. This ligand is not only able to activate PXR but also displays fluorescence upon binding to the receptor. The fluroscence pattern was observed around the nucleus. Besides AMI 4, 16 other AMI derivatives are identified that activate PXR with different activation profiles. Thus, a novel class of PXR ligands with fluorescence ability has been developed. The AMI derivatives able to bind and activate RAR, also displayed activation profiles that were comparable to the wild-type ligand, all trans retinoic acid. These ligands activated the receptor with an EC50 value of 220 nM with AMI 109 in comparison to an EC50 value of 0.8 nM with the natural ligand for RARá. When these ligands were tested for fluorescence in yeast, the yeast were able to fluoresce only in the presence of the receptor and the AMI derivative, indicating that these agonists also have the ability to fluoresce.
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Mikolajek, Halina. "Ligand binding to pentraxins." Thesis, University of Southampton, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.486591.
Full textAbstract:
The human pentraxin proteins, serum amyloid P component (SAP) and C-reactive protein (CRP) have emerged as potentially important targets in the treatment of amyloidosis and cardiovascular diseases respectively, although their normal physiological functions are unclear. Structurally highly conserved homologous proteins are present in common experimental animals such as the rat, mouse, rabbit and hamster but there are major differences from the human p,entraxins in their normal behaviour as acute phase proteins, fine ligand specificity and capacity to activate the complement system. . SAP binds to amyloid fibrils ofall types and may contribute to their formation, stabilisation and persistence. In order to extend our current knowledge ofligand recognition by SAP, the crystal structures ofSAP complexed to two ligands, Methylmalonic acid and Phosphatidylethanolamine, have been solved to 1.6 Aand 1.4Aresolution respectively. Since important biological functions ofproteins are often conserved among species, the structural differences between the rat and human pentraxins were investigated. The crystal structure ofrat SAP was solved to 2.2 Aresolution by molecular replacement. This pentameric structure displayed subtle differences in the electrostatic properties. It remains to be determined whether this has an effect on avid binding of SAP to DNA, a functional property ofh~manSAP still poorly understood. CRP, a pentraxin traditionally defined by its binding affinity for PC, was studied in complex with PE. The crystal structure ofthe CRP-PE complex at 2.7 Aresolution revealed that the nitrogen end ofPE dips further downwards into the hydrophobic pocket ofCRP than PC. CRP-mediated complement activation can exacerbate ischemic tissue injury in the heart as well as in the brain. Therefore, knowledge ofthe exact stoichiometry and the protein-protein interactions between CRP and C1q may aid the development ofsmall molecules capable ofdisrupting such protein-protein interactions. Purification of C1q has been achieved by ion-exchange chromatography and gel filtration from BPL paste. Crystallisation trials have been performed, however no crystals have been observed that contain the protein-protein complex.
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Kolstoe, Simon Erik. "Ligand binding to pentraxins." Thesis, University of Southampton, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.416900.
Full textBooks on the topic "Binding ligandi"
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H, Sawyer William, ed. Quantitative characterization of ligand binding. New York: Wiley-Liss, 1995.
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Bellelli, Andrea, and Jannette Carey. Reversible Ligand Binding. Chichester, UK: John Wiley & Sons, Ltd, 2017. http://dx.doi.org/10.1002/9781119238508.
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Khan, Masood N., and John W. A. Findlay, eds. Ligand-Binding Assays. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2009. http://dx.doi.org/10.1002/9780470541517.
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Woodbury, Charles P. Introduction to macromolecular binding equilibria. Boca Raton: CRC Press, 2008.
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Thermodynamic theory of site-specific binding processes in biological macromolecules. Cambridge, [Eng.]: Cambridge University Press, 1995.
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E, Harding S., and Chowdhry Babur Z, eds. Protein-ligand interactions, structure and spectroscopy: A practical approach. Oxford: Oxford University Press, 2001.
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1961-, Keen Mary, ed. Receptor binding techniques. Totowa, N.J: Humana Press, 1999.
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Stoddard, Barry L., ed. Computational Design of Ligand Binding Proteins. New York, NY: Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3569-7.
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Krishna, Mallia A., and Smith Paul K, eds. Immobilized affinity ligand techniques. San Diego: Academic Press, 1992.
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(Firm), Knovel, ed. Engineering biosensors: Kinetics and design applications. San Diego: Academic Press, 2002.
Find full textBook chapters on the topic "Binding ligandi"
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Prakash, Om, and Feroz Khan. "CoSSDb: A Database of Co-crystallized Ligand Sub-structures for Anticancer Lead Designing & Optimization." In Proceedings of the Conference BioSangam 2022: Emerging Trends in Biotechnology (BIOSANGAM 2022), 133–41. Dordrecht: Atlantis Press International BV, 2022. http://dx.doi.org/10.2991/978-94-6463-020-6_14.
Full textAbstract:
AbstractThe Discovery of the novel optimized structures of small molecules for selective targeting is one of the challenging tasks in drug designing. Bioisosteres are the key components of the lead compound, which provide hidden power to the compound scaffold for selective targeting. We are presenting a database, named CoSSDb which stands for Co-crystallized Sub-Structure Database. The CoSSDb contains ligand sub-structures as possible bioisosteres. extracted from PDB files, available in Protein Data Bank. Sub-structures were extracted through an algorithm, which utilizes the location of atoms in the 3D domain of the complex ligand & protein. It processes the relative positioning of atoms for demarcation of the influential part of the ligand, which interacts with macromolecule and provides potency to that ligand for binding with a specific binding pocket of the protein. The algorithm was used to extract sub-structures from the ligands co-crystallized with proteins involved in cancer. About 7721 x-ray crystallography PDB files were processed, and 654 non-redundant substructures were identified. These sub-structures will be useful during designing & optimization of novel ligands for selective targets. The database is freely accessible at ‘https://opticket49.wixsite.com/substructdb’.
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Fischer, Gabriele, Annemarie Unger, W. Wolfgang Fleischhacker, Cécile Viollet, Jacques Epelbaum, Daniel Hoyer, Ina Weiner, et al. "Ligand Binding." In Encyclopedia of Psychopharmacology, 709. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-540-68706-1_3350.
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Bonomo, R. P., D. Grasso, G. Grasso, V. Guantieri, G. Impellizzeri, C. Rosa, D. Milardi, G. Pappalardo, G. Tabbì, and E. Rizzarelli. "Metal Binding to Prion Protein." In Metal-Ligand Interactions, 21–39. Dordrecht: Springer Netherlands, 2003. http://dx.doi.org/10.1007/978-94-010-0191-5_2.
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Lambert, Bernard, and Jean-Bernard Le Pecq. "Pharmacology of DNA Binding Drugs." In DNA—Ligand Interactions, 141–57. Boston, MA: Springer US, 1987. http://dx.doi.org/10.1007/978-1-4684-5383-6_9.
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Rana, Brinda K., Philip E. Bourne, and Paul A. Insel. "Receptor Databases and Computational Websites for Ligand Binding." In Receptor Binding Techniques, 1–13. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-61779-909-9_1.
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Fischer, Gabriele, Annemarie Unger, W. Wolfgang Fleischhacker, Cécile Viollet, Jacques Epelbaum, Daniel Hoyer, Ina Weiner, et al. "Labeled Ligand Binding." In Encyclopedia of Psychopharmacology, 685. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-540-68706-1_3342.
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Tuckwell, Danny S., and Martin J. Humphries. "Ligand Binding Sites Within the Integrins." In Integrin-Ligand Interaction, 199–217. Boston, MA: Springer US, 1997. http://dx.doi.org/10.1007/978-1-4757-4064-6_9.
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Holdgate, Geoffrey A., and Paul E. Hemsley. "Ligand Discovery: High-Throughput Binding: Fluorescence ()." In Protein-Ligand Interactions, 231–46. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1197-5_10.
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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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Tangemann, Kirsten, and Jürgen Engel. "Binding Studies of Integrins with Their Respective Ligands." In Integrin-Ligand Interaction, 85–100. Boston, MA: Springer US, 1997. http://dx.doi.org/10.1007/978-1-4757-4064-6_3.
Full textConference papers on the topic "Binding ligandi"
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Dzichenka, Yaraslau, Michail Shapira, Sergei Usanov, Marina Savić, Ljubica Grbović, Jovana Ajduković, and Suzana Jovanović-Šanta. "NOVEL LIGANDS OF HUMAN CYP7 ENZYMES – POSSIBLE MODULATORS OF CHOLESTEROL BLOOD LEVEL: COMPUTER SIMULATION STUDIES." In 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac, 2021. http://dx.doi.org/10.46793/iccbi21.435d.
Full textAbstract:
Our in vitro studies showed that a couple of perspective steroidal derivatives showed previously biomedical potential via enzyme inhibition, receptor binding or antiproliferative effect against the cancer cells of reproductive tissues are able to bind to human CYP7 enzymes – key enzymes taking part in hydroxylation of cholesterol, 25-, 27-hydroxycholesterol and a number of steroidal hormones. In silico screening of binding affinity of the modified steroids toward CYP7 enzymes showed that interaction energy for the new ligands is comparable with consequent values, calculated for the ‘essential’ substrates of the enzymes – cholestenone (CYP7A1) and DHEA (CYP7B1). However, no correlation between binding energy and the affinity of the ligand was found. Novel ligands interact with conserved amino acids taking part in stabilization of natural substrates of CYP7 enzymes. A couple of structural features, governing ligand binding, were identified. Among which are planar structure of A-ring for CYP7A1 ligands, absence of many polar fragments in side-chain and presence of polar group at C3 position. Analysis of the docking results showed that CYP7B1 higher selectivity in comparison with CYP7A1 is connected by the structure of the cavity formed by α-helices I and B`. The data obtained will be used for the explanation of ligand specificity of human sterol- hydroxylases.
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Christensen, Ulla. "Kinetics of piasminogen-activation. Effects of ligands binding to the AH-site of plasminogen." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644420.
Full textAbstract:
Detailed kinetic studies of the urokinase catalysed conversion of Lys-77- and Val-440-plasminogens in the presence and absence of ligands binding to the AH-site of the plasminogens shows that the effects of such ligand-binding correspond with a model of the activation reaction in which the effective Km and kc decreases, but kc/Km increases when the ligands bind. Apparently plasminogen with a free AH-site is a less specific substrate for urokinase, than is plasminogen with an AH-site-bound ligand.The AH-site is a weak lysine binding site of plasminogen located in the mini plasminogen part (Val-440-Asn-790) of plasminogen and is suggested to participate in the binding of the plasminogens to undegraded fibrin.
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Sigurdson, M., C. Meinhart, D. Wang, X. Liu, J. J. Feng, S. Krishnamoorthy, and S. Sundaram. "AC Electrokinetics for Microfluidic Immunosensors." In ASME 2003 International Mechanical Engineering Congress and Exposition. ASMEDC, 2003. http://dx.doi.org/10.1115/imece2003-41442.
Full textAbstract:
A technique is proposed to enhance microfluidic immuno-sensors, specifically, sensors in which a ligand immobilized within a microchannel binds analyte flowing through the channel for the purpose of detection of that analyte. These sensors can be limited in both response time and sensitivity by the diffusion of analyte to the sensing surface. The sensitivity and response of these heterogeneous immunoassays may be improved by using AC electrokinetically-driven microscale fluid motion to enhance antigen motion towards immobilized ligands. Specifically, electrothermal effects can produce swirling flow patterns that carry sample past the binding surface. Numerical simulations of antigen in a microchannel flow subjected to the electrothermal effect suggest that 14 V rms applied to electrodes strategically placed opposite a narrow binding region can increase binding in the first few minutes by a factor of five. Optimization of the electrode geometry and placement can render this technique useful for a large variety of microfluidic sensors.
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Solis-Calero, C., PA Morais, FF Maia Jr, VN Freire, and HF Carvalho. "Explaining SARS-CoV-2 3CL Mpro binding to peptidyl Michael acceptor and a ketone-based inhibitors using Molecular fractionation with conjugate caps method." In VIII Simpósio de Estrutura Eletrônica e Dinâmica Molecular. Universidade de Brasília, 2020. http://dx.doi.org/10.21826/viiiseedmol2020185.
Full textAbstract:
The main protease SARS-CoV-2 3CL Mpro (3CL-Mpro) is an attractive target for developing antiviral inhibitors due to its essential role in processing the polyproteins translated from viral coronavirus RNA. In this work, it was obtained non-covalent complexes of this protease with two distinct ligands, a peptidyl Michael acceptor (N3) and a ketone-based compound (V2M). The complexes were modeled from processed crystallographic data (PDB id: 6LU7 and 6XHM respectively) using combined quantum mechanics/molecular mechanics (QM/MM) calculations. The QM region was treated at the PBE-def2-SV(P) level, while the Amber-ff19SB force field was used to describe the MM region. The obtained models were used to perform calculations for describing the protease/ligand binding, based in the framework of the Density Functional Theory (DFT) and within the Molecular Fractionation with Conjugated Caps (MFCC) scheme. Our results have shown values for the total interaction energies of -111.84 and -111.64 kcal mol-1 having as ligands a N3 and V2M, respectively. Most importantly, it was possible to assess the relative individual amino acid energy contribution for the binding of both ligands considering residues around them up to 10 Å of radial distance. Residues Gln189, Met165, Glu166, His164, and Asn142 were identified as main interacting amino acid residues for both complexes, being their negative interaction energy contributions higher than -5.0 kcal mol-1. In the case of 3CL-Mpro/ V2M complex, we should add His41, Ser144, and Cys145 as main contributing residues. Our data also have shown that interactions of type π-amide, π-alkyl and alkyl-alkyl and carbon hydrogen bonds should be also considered in order to explain the binding of 3CL-Mpro with the selected inhibitors. Our results also determined that the carbonyl-L-leucinamide scaffold of both inhibitors is its main determinant of binding with a contribution to the energy of interaction of 54.51 and 50.69 kcal mol-1 for N3 and V2M, respectively.
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Lim, Manko, Timothy A. Jackson, and Philip A. Anfinrud. "Ultrafast Near-IR Spectroscopy of Carbonmonoxymyoglobin: the Dynamics of Protein Relaxation." In International Conference on Ultrafast Phenomena. Washington, D.C.: Optica Publishing Group, 1992. http://dx.doi.org/10.1364/up.1992.thb3.
Full textAbstract:
The conformation of a protein often influences its activity, yielding a structure-function relationship. X-ray diffraction studies have shown that the tertiary structures of ligated and deligated myoglobin (Mb) are somewhat different1. Consequently, dissociation of a ligand from Mb triggers a transition between the two tertiary conformations. The potential energy gradient causing this change is developed at the heme; the iron prefers to be in the plane of the porphyrin in ligated Mb but is displaced 0.5 Å from the plane of the porphyrin in deoxy Mb. The dynamics of this conformational transition may influence the dynamics of rebinding ligands, implying that protein dynamics are also functionally important. For example, the dynamics of ligand recombination with Mb following photolysis of MbCO or MbO2 in low-temperature glasses are similar2. In contrast, Mb expurgates CO with far greater efficiency than O2 when photolysis is carried out at biologically important temperatures3. Since protein motion is inhibited at low temperatures, protein relaxation likely accounts for the temperature-dependent difference in the quantum yield of photodissociation. The ability to discriminate against the binding and storage of CO is functionally important as endogenously produced CO would otherwise compete effectively with O2 for binding sites. A steric mechanism for discriminating against the binding of CO, involving the distal histidine, is well known. The dynamics of protein relaxation evidently provide a mechanism for discriminating against the storage of CO. We have investigated the dynamics of protein relaxation in order to probe this mechanism and thereby elucidate the relation between protein dynamics and function.
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Jovanović-Šanta, Suzana S., Aleksandar M. Oklješa, Antos B. Sachanka, Yaraslau U. Dzichenka, and Sergei A. Usanov. "17-SUBSTITUTED STEROIDAL TETRAZOLES – NOVEL LIGANDS FOR HUMAN STEROID-CONVERTING CYP ENZYMES." In 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac, 2021. http://dx.doi.org/10.46793/iccbi21.336js.
Full textAbstract:
In animal and human organisms, there are many enzymes, members of the family of heme- containing proteins, cytochromes P450 (CYPs), included in the biosynthesis and metabolism of many biomolecules, as cholesterol, bile acids, sex, and corticosteroid hormones, as well as in metabolism of drugs and xenobiotics. It is also well-known that different imidazole and triazole derivatives are efficient inhibitors of CYPs activity. In this study, we present in vitro screening of binding of novel androstane derivatives with tetrazole- containing substituents in position 17 to human recombinant steroid-converting CYP enzymes: CYP7A1, CYP7B1, CYP17A1, CYP19, and CYP21. Initial screening was performed using a high throughput screening approach, while the affinity of the ligands was analyzed using spectrophotometric titration. For some among tested compounds type I spectral response (substrate-like binding) for CYP7A1 selectively, while for one compound type II spectral response (inhibitor-like binding) for CYP21 were detected, with micromolar values of Kds. Interestingly, one compound with mixed spectral response was found to bind for CYP7B1, which means that there are two optimal positions of the ligand inside the protein active site. Such results could be useful in CYP-inhibiting drug development, during a fast, high-throughput screening of pharmacological potential of novel compounds, as well as in side- effects recognizing.
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Lim, Manho, Timothy A. Jackson, and Philip A. Anfinrud. "Ultrafast Mid-IR Spectroscopy of Carbonmonoxymyoglobin: The Dynamics of Ligand Motion." In International Conference on Ultrafast Phenomena. Washington, D.C.: Optica Publishing Group, 1994. http://dx.doi.org/10.1364/up.1994.fb.4.
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Myoglobin (Mb) is an oxygen-binding protein found in muscle. The active binding site is an iron-II-containing porphyrin (heme) that is located within the hydrophobic interior of the protein. The X-ray structure of Mb reveals a distal cavity large enough to accommodate a ligand the size of O2, but no channel large enough for the ligand to diffuse between the heme pocket and the surrounding solvent. Clearly, structural fluctuations of the protein are required to open channels for ligand transport to and from the binding site. What is the functional role of the heme pocket and the residues that circumscribe it? What pathways exist for ligand transport between the heme pocket and the solvent? On what time scale does the ligand escape into the surrounding solvent? We have sought to answer these questions by probing the time-resolved vibrational spectrum of CO, a ligand similar in size to O2, following photodissociation of MbCO at physiological temperatures. We have developed a femtosecond time-resolved mid-IR spectrometer with the sensitivity required to measure the “free” CO absorbance. Ultrafast diffusion to a “docking” site has been observed, the orientation of the docked CO relative to the plane of the heme has been measured, and the rate of escape from the heme pocket has been determined. Additional studies with mutants of Mb are being conducted to probe the location of the docking site within the heme pocket and the pathways for ligand escape from the heme pocket.
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Hsu, Kai-Cheng, Yen-Fu Chen, and Jinn-Moon Yang. "Binding Affinity Analysis of Protein-Ligand Complexes." In 2008 2nd International Conference on Bioinformatics and Biomedical Engineering. IEEE, 2008. http://dx.doi.org/10.1109/icbbe.2008.46.
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Gupta, Vijay K., and Charles D. Eggleton. "A 3-D Computational Model of L-Selectin-PSGL-1 Dependent Homotypic Leukocyte Binding and Rupture in Shear Flow." In ASME 2012 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/sbc2012-80862.
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Cell adhesion plays a pivotal role in diverse biological processes, including inflammation, tumor metastasis, arteriosclerosis, and thrombosis. Changes in cell adhesion can be the defining event in a wide range of diseases, including cancer, atherosclerosis, osteoporosis, and arthritis. Cells are exposed constantly to hemodynamic/hydrodynamic forces and the balance between the dispersive hydrodynamic forces and the adhesive forces generated by the interactions of membrane-bound receptors and their ligands determines cell adhesion. Therefore to develop novel tissue engineering based approaches for therapeutic interventions in thrombotic disorders, inflammatory, and a wide range of other diseases, it is crucial to understand the complex interplay among blood flow, cell adhesion, and vascular biology at the molecular level. In response to tissue injury or infection, polymorphonuclear (PMN) leukocytes are recruited from the bloodstream to the site of inflammation through interactions between cell surface receptors and complementary ligands expressed on the surface of the endothelium [1]. PMN-PMN interactions also contribute to the process of recruitment. It has been shown that PMNs rolling on activated endothelium cells can mediate secondary capture of PMNs flowing in the free blood stream through homotypic interactions [2]. This is mediated by L-selectin (ligand) binding to PSGL-1 (receptor) between a free-stream PMN and one already adherent to the endothelium cells [3]. Both PSGL-1 and L-selectin adhesion molecules are concentrated on tips of PMN microvilli [4]. Homotypic PMN aggregation in vivo or in vitro is supported by multiple L-selectin–PSGL-1 bondings between pairs of microvilli. The ultimate objective of our work is to develop software that can simulate the adhesion of cells colliding under hydrodynamic forces that can be used to investigate the complex interplay among the physical mechanisms and scales involved in the adhesion process. However, cell-cell adhesion is a complex phenomenon involving the interplay of bond kinetics and hydrodynamics. Hence, as a first step we recently developed a 3-D computational model based on the Immersed Boundary Method to simulate adhesion-detachment of two PMN cells in quiescent conditions and the exposing the cells to external pulling forces and shear flow in order to investigate the behavior of the nano-scale molecular bonds to forces applied at the cellular scale [5]. Our simulations predicted that the total number of bonds formed is dependent on the number of available receptors (PSGL-1) when ligands (L-selectin) are in excess, while the excess amount of ligands controls the rate of bond formation [5]. Increasing equilibrium bond length causes an increased intercellular contact area hence results in a higher number of receptor-ligand bonds [5]. Off-rates control the average number of bonds by modulating bond lifetimes while On-rate constants determine the rate of bond formation [5]. An applied external pulling force leads to time-dependent on- and off-rates and causes bond rupture [5]. It was shown that the time required for bond rupture in response to an applied external force is inversely proportional to the applied external force and decreases with increasing offrate [5]. Fig. 1 shows the time evolution of the total number of bonds formed for various values of NRmv (number of receptor) and NLmv (number of ligand). As expected, the total number of bonds formed at equilibrium is dependent on NRmv when NLmv is in excess. In this particular case study since two pairs (or four) microvilli each with NRmv are involved in adhesion hence the equilibrium bond number is approximately 4NRmv. It is noticed that for NRmv = 50, as we vary NLmv the mean value of the total number of bonds at equilibrium does not change appreciably. However, it can be noticed from Fig. 1 that for NRmv = 50, as the excess number of ligands (NLmv) increases there is a slight increase in the rate of bond formation due to the increase in probability of bond formation. Having developed confidence in the ability of the numerical method to simulate the adhesion of two cells that can form up to 200 bonds, we apply the method to study the effect of shear rate on the detachment of two cells. In particular, we first would like to establish the minimum shear rate needed for the two cells to detach for a given number of bonds between them. Fig. 2 shows the variation of force per bond at no rupture with number of bonds for various shear rates indicated. It is seen that at a given shear rate as the number of bonds increases the force per bond at no rupture decreases. This is attributed to the fact that force caused by shear flow is shared equally among the existing bonds. Further, it is seen that a given number of bonds as the shear rate increases the force per bond at no rupture increases. This is due to the fact that at a given number of bonds between the cells as we increase the shear rate the force caused by the flow increases hence the force per bond increases. We further notice that at shear rate = 3000 s−1 cells attached either by a single bond or by two bonds detach while they don’t for higher (> 2) number of bonds. This clearly demonstrate that there is a minimum shear rate needed to detach cells adhered by a given number of bonds. The higher the number of bonds, the higher the minimum shear rate for complete detachment of cells. For example, from Fig. 2 is it clear that for the cells adhered by two and five bonds the minimum shear rate needed for complete detachment of these two cells are 3000 s−1 and 6000 s−1, respectively.
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Nechipurenko, Y. D., A. S. Buchelnikov, and I. A. Lavrinenko. "COOPERATIVE EFFECTS IN BINDING OF LIGANDS TO BIOPOLYMERS." In NOVEL TECHNOLOGIES IN MEDICINE, BIOLOGY, PHARMACOLOGY AND ECOLOGY. Institute of information technology, 2022. http://dx.doi.org/10.47501/978-5-6044060-2-1.257-261.
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Models and methods of statistical thermodynamics and physical adsorption theory allow us to quantitate cooperative interactions between ligand molecules adsorbed on a macromol-ecule, in particular allosteric effects described in detail in oxygen binding to hemoglobin. We show how the Hill equation can be modified and how the Hill coefficient can be interpreted. On the other hand, the entropy of the adsorption system allows us to visualize cooperative binding processes. Cooperative interactions lead to a decrease in the entropy of the system and an increase in the information it contains.
Reports on the topic "Binding ligandi"
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Henderson, Terry J., and Rossitza K. Gitti. Conformational Changes in Small Ligands Upon Tetanus Toxin Binding. Fort Belvoir, VA: Defense Technical Information Center, June 2008. http://dx.doi.org/10.21236/ada485632.
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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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Chung, Arthur. Development of Novel Ligand Binding Assay for Estrogen Receptor. Fort Belvoir, VA: Defense Technical Information Center, April 2000. http://dx.doi.org/10.21236/ada390487.
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Chung, Arthur C. Development of a Novel Ligand Binding Assay for Estrogen Receptor. Fort Belvoir, VA: Defense Technical Information Center, April 2002. http://dx.doi.org/10.21236/ada421346.
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Arnold, John. Potential New Ligand Systems for Binding Uranyl Ions in Seawater Environments. Office of Scientific and Technical Information (OSTI), December 2014. http://dx.doi.org/10.2172/1166963.
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Trewhella, J. The role of low frequency collective modes in biological function: Ligand binding and cooperativity in calcium-binding proteins. Office of Scientific and Technical Information (OSTI), November 2000. http://dx.doi.org/10.2172/768788.
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Fagan, Patricia A. NMR studies of DNA oligomers and their interactions with minor groove binding ligands. Office of Scientific and Technical Information (OSTI), May 1996. http://dx.doi.org/10.2172/373863.
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Ontko, Alyn. Equilibrium binding studies of mono, di and triisocyanide ligands on Au powder surfaces. Office of Scientific and Technical Information (OSTI), October 1997. http://dx.doi.org/10.2172/587882.
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Arnold, John. Selectivity in ligand binding to uranyl compounds: A synthetic, structural, thermodynamic and computational study. Office of Scientific and Technical Information (OSTI), January 2015. http://dx.doi.org/10.2172/1183657.
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Arnold, John. Selectivity in Ligand Binding to Uranyl Compounds: A Synthetic, Structural, Thermodynamic and Computational Study. Office of Scientific and Technical Information (OSTI), December 2017. http://dx.doi.org/10.2172/1414423.
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