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1
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.
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Wang, Chenguang, Nagarajan Pattabiraman, Jian Nian Zhou, Maofu Fu, Toshiyuki Sakamaki, Chris Albanese, Zhiping Li, et al. "Cyclin D1 Repression of Peroxisome Proliferator-Activated Receptor γ Expression and Transactivation." Molecular and Cellular Biology 23, no. 17 (September 1, 2003): 6159–73. http://dx.doi.org/10.1128/mcb.23.17.6159-6173.2003.
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ABSTRACT The cyclin D1 gene is overexpressed in human breast cancers and is required for oncogene-induced tumorigenesis. Peroxisome proliferator-activated receptor γ (PPARγ) is a nuclear receptor selectively activated by ligands of the thiazolidinedione class. PPARγ induces hepatic steatosis, and liganded PPARγ promotes adipocyte differentiation. Herein, cyclin D1 inhibited ligand-induced PPARγ function, transactivation, expression, and promoter activity. PPARγ transactivation induced by the ligand BRL49653 was inhibited by cyclin D1 through a pRB- and cdk-independent mechanism, requiring a region predicted to form an helix-loop-helix (HLH) structure. The cyclin D1 HLH region was also required for repression of the PPARγ ligand-binding domain linked to a heterologous DNA binding domain. Adipocyte differentiation by PPARγ-specific ligands (BRL49653, troglitazone) was enhanced in cyclin D1−/− fibroblasts and reversed by retroviral expression of cyclin D1. Homozygous deletion of the cyclin D1 gene, enhanced expression by PPARγ ligands of PPARγ and PPARγ-responsive genes, and cyclin D1−/− mice exhibit hepatic steatosis. Finally, reduction of cyclin D1 abundance in vivo using ponasterone-inducible cyclin D1 antisense transgenic mice, increased expression of PPARγ in vivo. The inhibition of PPARγ function by cyclin D1 is a new mechanism of signal transduction cross talk between PPARγ ligands and mitogenic signals that induce cyclin D1.
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Scior, Thomas R. F., and Israel Quiroga. "Induced fit for cytochrome P450 3A4 based on molecular dynamics." ADMET and DMPK 7, no. 4 (December 10, 2019): 252–66. http://dx.doi.org/10.5599/admet.729.
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The present study aims at numerically describing to what extent substrate - enzyme complexes in solution may change over time as a natural process of conformational changes for a liganded enzyme in comparison to those movements which occur independently from substrate interaction, i.e. without a ligand. To this end, we selected structurally known pairs of liganded / unliganded CYP450 3A4 enzymes with different geometries hinting at induced fit events. We carried out molecular dynamics simulations (MD) comparing the trajectories in a “cross-over†protocol: (i) we added the ligand to the unliganded crystal form which should adopt geometries similar to the known geometry of the liganded crystal structure during MD, and – conversely – (ii) we removed the bound ligand form the known liganded complex to test if a geometry similar to the known unliganded (apo-) form can be adopted during MD. To compare continues changes we measured root means square deviations and frequencies. Results for case (i) hint at larger conformational changes required for accepting the substrate during its approach to final position – in contrast to case (ii) when mobility is fairly reduced by ligand binding (strain energy). In conclusion, a larger conformational sampling prior to ligand binding and the freezing-in (rigidity) of conformations for bound ligands can be interpreted as two conditions linked to induced-fit.
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Minucci, S., M. Leid, R. Toyama, J. P. Saint-Jeannet, V. J. Peterson, V. Horn, J. E. Ishmael, et al. "Retinoid X receptor (RXR) within the RXR-retinoic acid receptor heterodimer binds its ligand and enhances retinoid-dependent gene expression." Molecular and Cellular Biology 17, no. 2 (February 1997): 644–55. http://dx.doi.org/10.1128/mcb.17.2.644.
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Retinoic acid receptor (RAR) and retinoid X receptor (RXR) form heterodimers and regulate retinoid-mediated gene expression. We studied binding of RXR- and RAR-selective ligands to the RXR-RAR heterodimer and subsequent transcription. In limited proteolysis analyses, both RXR and RAR in the heterodimer bound their respective ligands and underwent a conformational change in the presence of a retinoic acid-responsive element. In reporter analyses, the RAR ligand (but not the RXR ligand), when added singly, activated transcription, but coaddition of the two ligands led to synergistic activation of transcription. This activation required the AF-2 domain of both RXR and RAR. Genomic footprinting analysis was performed with P19 embryonal carcinoma cells, in which transcription of the RARbeta gene is induced upon retinoid addition. Paralleling the reporter activation data, only the RAR ligand induced in vivo occupancy of the RARbeta2 promoter when added singly. However, at suboptimal concentrations of RAR ligand, coaddition of the RXR ligand increased the stability of promoter occupancy. Thus, liganded RXR and RAR both participate in transcription. Finally, when these ligands were tested for teratogenic effects on zebra fish and Xenopus embryos, we found that coadministration of the RXR and RAR ligands caused more severe abnormalities in these embryos than either ligand alone, providing biological support for the synergistic action of the two ligands.
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Chen, Xun, Steven Stout, Uwe Mueller, George Boykow, Richard Visconti, Phieng Siliphaivanh, Kerrie Spencer, et al. "Label-Free, LC-MS-Based Assays to Quantitate Small-Molecule Antagonist Binding to the Mammalian BLT1 Receptor." SLAS DISCOVERY: Advancing the Science of Drug Discovery 22, no. 9 (August 1, 2017): 1131–41. http://dx.doi.org/10.1177/2472555217719748.
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We have developed and validated label-free, liquid chromatography–mass spectrometry (LC-MS)-based equilibrium direct and competition binding assays to quantitate small-molecule antagonist binding to recombinant human and mouse BLT1 receptors expressed in HEK 293 cell membranes. Procedurally, these binding assays involve (1) equilibration of the BLT1 receptor and probe ligand, with or without a competitor; (2) vacuum filtration through cationic glass fiber filters to separate receptor-bound from free probe ligand; and (3) LC-MS analysis in selected reaction monitoring mode for bound probe ligand quantitation. Two novel, optimized probe ligands, compounds 1 and 2, were identified by screening 20 unlabeled BLT1 antagonists for direct binding. Saturation direct binding studies confirmed the high affinity, and dissociation studies established the rapid binding kinetics of probe ligands 1 and 2. Competition binding assays were established using both probe ligands, and the affinities of structurally diverse BLT1 antagonists were measured. Both binding assay formats can be executed with high specificity and sensitivity and moderate throughput (96-well plate format) using these approaches. This highly versatile, label-free method for studying ligand binding to membrane-associated receptors should find broad application as an alternative to traditional methods using labeled ligands.
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McNeely, Patrick M., Andrea N. Naranjo, Kimberly Forsten-Williams, and Anne Skaja Robinson. "A2AR Binding Kinetics in the Ligand Depletion Regime." SLAS DISCOVERY: Advancing the Science of Drug Discovery 22, no. 2 (September 27, 2016): 166–75. http://dx.doi.org/10.1177/1087057116667256.
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Ligand binding plays a fundamental role in stimulating the downstream signaling of membrane receptors. Here, ligand-binding kinetics of the full-length human adenosine A2A receptor (A2AR) reconstituted in detergent micelles were measured using a fluorescently labeled ligand via fluorescence anisotropy. Importantly, to optimize the signal-to-noise ratio, these experiments were conducted in the ligand depletion regime. In the ligand depletion regime, the assumptions used to determine analytical solutions for one-site binding models for either one or two ligands in competition are no longer valid. We therefore implemented a numerical solution approach to analyze kinetic binding data as experimental conditions approach the ligand depletion regime. By comparing the results from the numerical and the analytical solutions, we highlight the ligand-receptor ratios at which the analytical solution begins to lose predictive accuracy. Using the numerical solution approach, we determined the kinetic rate constants of the fluorescent ligand, FITC-APEC, and those for three unlabeled ligands using competitive association experiments. The association and dissociation rate constants of the unlabeled ligands determined from the competitive association experiments were then independently validated using competitive dissociation data. Based on this study, a numerical solution is recommended to determine kinetic ligand-binding parameters for experiments conducted in the ligand-depletion regime.
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Williams, Mobolaji. "Derangement model of ligand-receptor binding." Computational and Mathematical Biophysics 10, no. 1 (January 1, 2022): 123–66. http://dx.doi.org/10.1515/cmb-2022-0137.
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Abstract We introduce a derangement model of ligand-receptor binding that allows us to quantitatively frame the question “How can ligands seek out and bind to their optimal receptor sites in a sea of other competing ligands and suboptimal receptor sites?” To answer the question, we first derive a formula to count the number of partial generalized derangements in a list, thus extending the derangement result of Gillis and Even. We then compute the general partition function for the ligand-receptor system and derive the equilibrium expressions for the average number of bound ligands and the average number of optimally bound ligands. A visual model of squares assembling onto a grid allows us to easily identify fully optimal bound states. Equilibrium simulations of the system reveal its extremes to be one of two types, qualitatively distinguished by whether optimal ligand-receptor binding is the dominant form of binding at all temperatures and quantitatively distinguished by the relative values of two critical temperatures. One of those system types (termed “search-limited,” as it was in previous work) does not exhibit kinetic traps and we thus infer that biomolecular systems where optimal ligand-receptor binding is functionally important are likely to be search-limited.
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Urien, S., F. Brée, B. Testa, and J. P. Tillement. "pH-dependency of basic ligand binding to α1-acid glycoprotein (orosomucoid)." Biochemical Journal 280, no. 1 (November 15, 1991): 277–80. http://dx.doi.org/10.1042/bj2800277.
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The binding interactions of a series of basic ligands with alpha 1-acid glycoprotein (AAG) were examined as a function of pH. The binding to AAG increased with increasing pH, and the binding data were satisfactorily fitted to a model that incorporates the effect of pH and discriminates the association constants of neutral (non-protonated) and protonated forms of ligands. It was shown that ligands in the neutral form have a markedly higher affinity for AAG than the protonated forms, resulting in a concomitant decrease in the pKa of bound ligands. The u.v.-visible difference spectra generated upon binding of a representative ligand to AAG also showed that there was a contribution to the binding arising from the deprotonation of the ligand. It is suggested that all tested ligands bind similarly to AAG and that hydrophobic interactions dominate high-affinity binding to AAG.
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Han, Ji Ho, and Moon Jung Song. "인간 허피스바이러스에 대한 G-quadruplex 결합 리간드의 항바이러스 효과." Institute of Life Science and Natural Resources 30 (December 31, 2022): 23–31. http://dx.doi.org/10.33147/lsnrr.2022.30.1.23.
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G-quadruplexes (G4s) are noncanonical secondary nucleic acid structures constituted by stacking of guanine rich planar shaped tetrad formations that form a complex. G4s are implicated for various important roles in key cellular processes transcription, translation, telomere maintenance, epigenetic regulation, replication, and recombination. G-quadruplexes were first discovered as important structures in oncology, but for the past decade its relevance in viruses is becoming more evident. Human herpesviruses are DNA viruses of the Herpesviridae family and are unique in characteristic with two types of infection which can be distinguished by lytic and latency establishment in the host. During latency the virus maintains lifelong dormancy and intermittently undergoes reactivation, causing the host medical problems. Recently there are increasing number of reports regarding role of G4s in viral genomes and the potential antiviral efficacy of G4 ligands, including G4s in latency. Many results suggest viral G4s play significant roles in the virus life cycle and treatment of G4 ligands exhibit antiviral activities in both lytic and latent infections. In this review, the importance of G4s in herpesvirus genomes will be introduced with the potent G4 ligands used to study these mechanisms and finally explain the distinct functional properties of each G4 ligands.
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Tozer, Eileen Collins, Paul E. Hughes, and Joseph C. Loftus. "Ligand binding and affinity modulation of integrins." Biochemistry and Cell Biology 74, no. 6 (December 1, 1996): 785–98. http://dx.doi.org/10.1139/o96-085.
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Integrins are cell adhesion receptors that mediate cell–cell and cell–extracellular matrix interactions. The extracellular domains of these receptors possess binding sites for a diverse range of protein ligands. Ligand binding is divalent cation dependent and involves well-defined motifs in the ligand. Integrins can dynamically regulate their affinity for ligands (inside-out signaling). This ability to rapidly modulate their affinity state is key to their involvement in such processes as cell migration and platelet aggregation. This review will focus on two aspects of integrin function: first, on the molecular basis of ligand–integrin interactions and, second, on the underlying mechanisms controlling the affinity state of integrins for their ligands.Key words: integrins, ligand binding, affinity modulation.
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Christensen, U., and L. Mølgaard. "Positive co-operative binding at two weak lysine-binding sites governs the Glu-plasminogen conformational change." Biochemical Journal 285, no. 2 (July 15, 1992): 419–25. http://dx.doi.org/10.1042/bj2850419.
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The kinetics of a series of Glu-plasminogen ligand-binding processes were investigated at pH 7.8 and 25 degrees C (in 0.1 M-NaCl). The ligands include compounds analogous to C-terminal lysine residues and to normal lysine residues. Changes of the Glu-plasminogen protein fluorescence were measured in a stopped-flow instrument as a function of time after rapid mixing of Glu-plasminogen and ligand at various concentrations. Large positive fluorescence changes (approximately 10%) accompany the ligand-induced conformational changes of Glu-plasminogen resulting from binding at weak lysine-binding sites. Detailed studies of the concentration-dependencies of the equilibrium signals and the rate constants of the process induced by various ligands showed the conformational change to involve two sites in a concerted positive co-operative process with three steps: (i) binding of a ligand at a very weak lysine-binding site that preferentially, but not exclusively, binds C-terminal-type lysine ligands, (ii) the rate-determining actual-conformational-change step and (iii) binding of one more lysine ligand at a second weak lysine-binding site that then binds the ligand more tightly. Further, totally independent initial small negative fluorescence changes (approximately 2-4%) corresponding to binding at the strong lysine-binding site of kringle 1 [Sottrup-Jensen, Claeys, Zajdel, Petersen & Magnusson (1978) Prog. Chem. Fibrinolysis Thrombolysis 3, 191-209] were observed for the C-terminal-type ligands. The finding that the conformational change in Glu-plasminogen involves two weak lysine-binding sites indicates that the effect cannot be assigned to any single kringle and that the problem of whether kringle 4 or kringle 5 is responsible for the process resolves itself. Probably kringle 4 and 5 are both participating. The involvement of two lysine binding-sites further makes the high specificity of Glu-plasminogen effectors more conceivable.
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Weatherman, Ross V., Robert J. Fletterick, and Thomas S. Scanlan. "Nuclear-Receptor Ligands and Ligand-Binding Domains." Annual Review of Biochemistry 68, no. 1 (June 1999): 559–81. http://dx.doi.org/10.1146/annurev.biochem.68.1.559.
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Genest, Alexander, Sven Krüger, Alexei B. Gordienko, and Notker Rösch. "Gold-Thiolate Clusters: A Relativistic Density Functional Study of the Model Species Au13(SR)n, R = H, CH3, n = 4, 6, 8." Zeitschrift für Naturforschung B 59, no. 11-12 (December 1, 2004): 1585–99. http://dx.doi.org/10.1515/znb-2004-11-1232.
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The binding of sulfanyl and alkylsulfanyl model ligands to gold clusters was studied for the case of Au13(SR)n with R = H, CH3 and n = 4, 6, 8. Accurate all-electron electronic structure calculations and geometry optimizations of these gold-thiolate clusters have been performed with a scalar relativistic Kohn-Sham procedure as implemented in the density functional program PARAGAUSS. In all structures obtained, bridge coordination was preferred for both types of ligands; no higher coordinated sites where occupied. While in many cases ligand decoration did not change the overall structure of the Au13 core, also more open structures with Au-Au distances elongated beyond the bulk value have been obtained. The effects due to increasing ligand decoration were small: a small decrease of the binding energy per ligand does not exclude higher ligand coverages. The differences between the model ligands SH and SCH3 were consistent in all cases considered: SCH3 exhibits weaker binding and a slightly smaller charge separation between cluster core and ligand shell, which amounts up to about 1.5 e for 8 ligands. Overall, the Au13 core of the clusters was found to be quite flexible. This can be rationalized by the fact that the calculated binding energy per ligand is comparable or even exceeds the binding energy per atom in Au13.
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Zlatovic, Mario, Vladimir Sukalovic, Sladjana Kostic-Rajacic, Deana Andric, and Goran Roglic. "Influence of N-1 substituent properties on binding affinities of arylpiperazines to the binding site of 5-HT1A receptor." Journal of the Serbian Chemical Society 71, no. 11 (2006): 1125–35. http://dx.doi.org/10.2298/jsc0611125z.
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Serotonin receptors (5-HTRs), especially the 5-HT1A subtype, have been the subject of intensive research for the past decade, due to their function in human physiology. Several structurally different classes of ligands are known to bind to the 5-HT1A receptor, but arylpiperazine derivatives are among the most important ligands. In the work, docking analyses were used to explain the binding affinities of a series of ligands with different N-1 substituent. All ligands had in common the arylpiperazine structure, while the N-1 subsistent was modified to investigate the influence of ligand structure on its binding affinity. The shape and size, as well as the rigidity of the subsistents were altered to investigate the possible effects on the formation of the receptor - ligand complex.
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Devgan, Manish. "STRUCTURE PREDICTION AND IN SILICO DESIGNING OF DRUGS AGAINST KALLIKREIN PROTEIN 12." International Journal of Current Pharmaceutical Research 9, no. 2 (March 1, 2017): 64. http://dx.doi.org/10.22159/ijcpr.2017v9i2.17387.
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Objective: Human Kallikrein protein 12 (hK12) might serve as a novel diagnostic and prognostic biomarker, as well as a potential therapeutic target, in gastric cancer.Methods: In this work, a theoretical model of hK12 receptor protein was generated using the concepts of homology modeling and loop modeling. The resulting model was validated with Ramachandran plot analysis. The ligands generated with the help of Drug bank were docked against hK12 receptor protein using AutoDock Vina in PyRx 0.8. The structure of ligand DB04786 (Suramin), with least binding energy, was varied by using ACD/ChemSketch 8.0 and the docking was done for the resulting 16 new ligands.Results: The results indicated that the ligand10 bears the minimum binding energy (-12.3 Kcal/mol) with the target protein and thus the prospects of binding are high. The results also clearly demonstrated that the in silico molecular docking studies of selected ligands, i.e., suramin, ligands 5, 6, 10 and 16 with hK12 protein exhibited favourable binding interactions and warranted.Conclusion: Further studies needed for the development of potent inhibitors for the overexpression of hK12 protein making the management of gastric cancer more efficient.
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Newham, Peter, Sue E. Craig, Katherine Clark, A. Paul Mould, and Martin J. Humphries. "Analysis of Ligand-Induced and Ligand-Attenuated Epitopes on the Leukocyte Integrin α4β1: VCAM-1, Mucosal Addressin Cell Adhesion Molecule-1, and Fibronectin Induce Distinct Conformational Changes." Journal of Immunology 160, no. 9 (May 1, 1998): 4508–17. http://dx.doi.org/10.4049/jimmunol.160.9.4508.
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Abstract The leukocyte integrin α4β1 is a receptor for both cell surface ligands (VCAM-1 and mucosal addressin cell adhesion molecule-1 (MAdCAM-1)) and extracellular matrix components (fibronectin). Through regulated interactions with these molecules, α4β1 mediates leukocyte migration from the vasculature at sites of inflammation. Regulation of integrin activity plays a key role in controlling leukocyte-adhesive events and appears to be partly determined by changes in integrin conformation. Several mAbs that recognize ligand-induced binding site epitopes on integrins have been characterized, and a subset of these mAbs are capable of stimulating integrin-ligand binding. Conversely, some mAbs recognize epitopes that are attenuated by ligand engagement and allosterically inhibit ligand binding. To gain insight into ligand-specific effects on integrin conformation, we have examined the ability of different ligands to modulate the binding of four distinct classes (A, B1, B2, and C) of anti-α4 Abs to α4β1. VCAM-1 attenuated B (antifunctional) class epitopes via an allosteric mechanism and also allosterically inhibited the binding of the function-blocking anti-β1 mAb 13. Additional α4β1 ligands (fibronectin fragments, MAdCAM-1, and the CS1 peptide) also inhibited mAb 13-integrin binding; however, the epitopes of the class B anti-α4 mAbs were attenuated by the fibronectin fragments, but not by MAdCAM-1 or the CS1 peptide. Of the two anti-α4 class A mAbs examined, one recognized an epitope that was induced uniquely by VCAM-1. Taken together, these data suggest that overlapping but distinct binding mechanisms exist for different α4β1 ligands and that distinct conformational changes are induced upon integrin engagement by different ligands.
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Katzenellenbogen, J. A., and R. Muthyala. "Interactions of exogenous endocrine active substances with nuclear receptors." Pure and Applied Chemistry 75, no. 11-12 (January 1, 2003): 1797–817. http://dx.doi.org/10.1351/pac200375111797.
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Nuclear receptors function as ligand-regulated transcription factors and modulate the expression of sets of genes in response to varying concentrations of ligands. The ligand modulators can be endogenous metabolites that function as hormones, or they can be exogenous substances, such as pharmaceutical agents or environmental substances of natural or man-made origin, which in some cases can cause endocrine disruption. Ligands modulate nuclear receptor activity by binding to their ligand-binding domains and stabilizing conformations that lead either to transcriptional activation or repression. The ligand-binding pocket is somewhat flexible, and binding affinities can be measured over a 10-million-fold range (i.e., with equilibrium dissociation constant values ranging from ca. 0.01 nM to 100 μM). Thus, it is not surprising that by binding a large variety of structures, some nuclear receptors can appear to be promiscuous; however, when affinity is considered, the binding patterns are more restricted. The spectrum of ligands that bind to the estrogen receptor has been most thoroughly investigated. Those from natural sources include natural products in food, such as soy isoflavones and whole grain lignans, as well as microbial products and components from wood. Aside from pharmaceuticals, man-made estrogen ligands can be found in industrial products, such as alkyl phenols from nonionic detergents, bisphenols from plastics, indicator dye impurities, polymer chemicals, and chlorinated aromatics and pesticides. Exogenous ligands are also known for the androgen and progesterone receptors. While it is possible that endocrine disruption can result from exogenous chemicals acting directly as ligands for the nuclear receptors, endocrine disruption needs to be considered in the broader context; thus, compounds also need to be assessed for their effects at other levels, such as on endogenous hormone production, transport, metabolism, and clearance, and at points in signal transduction cascades that are beyond the ligand-receptor interaction.
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Chitnis, C. E., A. Chaudhuri, R. Horuk, A. O. Pogo, and L. H. Miller. "The domain on the Duffy blood group antigen for binding Plasmodium vivax and P. knowlesi malarial parasites to erythrocytes." Journal of Experimental Medicine 184, no. 4 (October 1, 1996): 1531–36. http://dx.doi.org/10.1084/jem.184.4.1531.
Full textAbstract:
Plasmodium vivax and the related simian malarial parasite P. knowlesi use the Duffy blood group antigen as a receptor to invade human erythrocytes and region II of the parasite ligands for binding to this erythrocyte receptor. Here, we identify the peptide within the Duffy blood group antigen of human and rhesus erythrocytes to which the P. vivax and P. knowlesi ligands bind. Peptides from the NH2-terminal extracellular region of the Duffy antigen were tested for their ability to block the binding of erythrocytes to transfected Cos cells expressing on their surface region II of the Duffy-binding ligands. The binding site on the human Duffy antigen used by both the P. vivax and P. knowlesi ligands maps to a 35-amino acid region. A 34-amino acid peptide from the equivalent region of the rhesus Duffy antigen blocked the binding of P. vivax to human erythrocytes, although the P. vivax ligand expressed on Cos cells does not bind rhesus erythrocytes. The binding of the rhesus peptide, but not the rhesus erythrocyte, to the P. vivax ligand was explained by interference of carbohydrate with the binding process. Rhesus erythrocytes, treated with N-glycanase, bound specifically to P. vivax region II. Thus, the interaction of P. vivax ligand with human and rhesus erythrocytes appears to be mediated by a peptide-peptide interaction. Glycosylation of the rhesus Duffy antigen appears to block binding of the P. vivax ligand to rhesus erythrocytes.
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Cao, Chen, Lincong Wang, Xiaoyang Chen, Shuxue Zou, Guishen Wang, and Shutan Xu. "Amino Acids in Nine Ligand-Prefer Ramachandran Regions." BioMed Research International 2015 (2015): 1–10. http://dx.doi.org/10.1155/2015/757495.
Full textAbstract:
Several secondary structures, such asπ-helix and left-handed helix, have been frequently identified at protein ligand-binding sites. A secondary structure is considered to be constrained to a specific region of dihedral angles. However, a comprehensive analysis of the correlation between main chain dihedral angles and ligand-binding sites has not been performed. We undertook an extensive analysis of the relationship between dihedral angles in proteins and their distance to ligand-binding sites, frequency of occurrence, molecular potential energy, amino acid composition, van der Waals contacts, and hydrogen bonds with ligands. The results showed that the values of dihedral angles have a strong preference for ligand-binding sites at certain regions in the Ramachandran plot. We discovered that amino acids preceding the ligand-preferϕ/ψbox residues are exposed more to solvents, whereas amino acids following ligand-preferϕ/ψbox residues form more hydrogen bonds and van der Waals contacts with ligands. Our method exhibited a similar performance compared with the program Ligsite-csc for both ligand-bound structures and ligand-free structures when just one ligand-binding site was predicted. These results should be useful for the prediction of protein ligand-binding sites and for analysing the relationship between structure and function.
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Urien, S., P. Nguyen, S. Berlioz, F. Brée, F. Vacherot, and J. P. Tillement. "Characterization of discrete classes of binding sites of human serum albumin by application of thermodynamic principles." Biochemical Journal 302, no. 1 (August 15, 1994): 69–72. http://dx.doi.org/10.1042/bj3020069.
Full textAbstract:
The binding interactions of four ligands differing in acid-base properties with human serum albumin (HSA) were examined as a function of temperature. Binding to HSA decreased with increasing temperature for all four ligands. The bound and free ligand concentrations obtained at different temperatures were satisfactorily fitted to a model that incorporates the effect of temperature as an independent covariable and that directly allows the estimation of the enthalpic and entropic components of the ligand-albumin interaction, along with the precision of this estimation. Using this analysis, the binding of acidic ligands could be resolved into two classes of saturable sites, with the determination of the corresponding number of sites, whereas interpretation of binding data at each isolated temperature allowed only the determination of one saturable plus one non-saturable class of site. The thermodynamic constants indicate that binding of ionizable ligands to HSA involves electrostatic plus hydrophobic interactions, whereas only hydrophobic interactions are involved in binding to a second low-affinity class of site when present. Binding of non-ionizable ligands resembles that of the second class of low-affinity sites of ionizable ligands.
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Fan, Qikui, Hao Yang, Juan Ge, Shumeng Zhang, Zhaojun Liu, Bo Lei, Tao Cheng, Youyong Li, Yadong Yin, and Chuanbo Gao. "Customizable Ligand Exchange for Tailored Surface Property of Noble Metal Nanocrystals." Research 2020 (January 21, 2020): 1–12. http://dx.doi.org/10.34133/2020/2131806.
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It is highly desirable, while still challenging, to obtain noble metal nanocrystals with custom capping ligands, because their colloidal synthesis relies on specific capping ligands for the shape control while conventional ligand exchange processes suffer from “the strong replaces the weak” limitation, which greatly hinders their applications. Herein, we report a general and effective ligand exchange approach that can replace the native capping ligands of noble metal nanocrystals with virtually any type of ligands, producing flexibly tailored surface properties. The key is to use diethylamine with conveniently switchable binding affinity to the metal surface as an intermediate ligand. As a strong ligand, it in its original form can effectively remove the native ligands; while protonated, it loses its binding affinity and facilitates the adsorption of new ligands, especially weak ones, onto the metal surface. By this means, the irreversible order in the conventional ligand exchange processes could be overcome. The efficacy of the strategy is demonstrated by mutual exchange of the capping ligands among cetyltrimethylammonium, citrate, polyvinylpyrrolidone, and oleylamine. This novel strategy significantly expands our ability to manipulate the surface property of noble metal nanocrystals and extends their applicability to a wide range of fields, particularly biomedical applications.
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Mailfait, S., E. Thoreau, D. Belaiche, and P. Formstecher And B Sablonnie. "Critical role of the H6-H7 loop in the conformational adaptation of all-trans retinoic acid and synthetic retinoids within the ligand-binding site of RARalpha." Journal of Molecular Endocrinology 24, no. 3 (June 1, 2000): 353–64. http://dx.doi.org/10.1677/jme.0.0240353.
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The pleiotropic effects of the natural and synthetic retinoids are mediated by the activation of the two subfamilies of nuclear receptors, the retinoic acid receptors (RARs) and the retinoic X receptors (RXRs). At the molecular level, these events begin with the specific ligand recognition by a nuclear receptor subtype. The adaptation of ligands to the receptor binding site leads to an optimal number of interactions for binding and selectivity which justifies elucidation of the structural requirements of the ligand binding pocket. To explore the contribution of H6-H7 loop folding in the ligand-induced conformational changes explained by the mouse-trap model, four RARalpha mutants were constructed. Ligand binding and transactivation studies revealed that three residues from the H6-H7 loop (Gly(301), Phe(302) and Gly(303)) are critical for the conformational adaptation of both synthetic agonists and antagonists. Model building and analysis of both RARalpha-ATRA and RARalpha-CD367 complexes demonstrate that accommodation of CD367 results in a less tight contact of the saturated ring of this ligand with the amino acid side chains of the receptor ligand-binding pocket compared with that of ATRA. According to the flexibility of the agonists tested (ATRA>TTNPB=Am580> CD367), we observed a decrease in binding that was dependent on ligand structure rigidity. In contrast, the binding and transactivating activities of the L266A mutant confirmed the structural constraints imposed by synthetic ligands on binding affinity for the receptor and revealed that subtle local rearrangements induced by specific conformational adaptation changes result in different binding affinities. Our results illustrate the dynamic nature of the interaction between RARalpha and its ligands and demonstrate the critical role of the H6-H7 loop in the binding of both synthetic retinoid agonists and antagonists.
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Zeng, Haoyang, and David K. Gifford. "DeepLigand: accurate prediction of MHC class I ligands using peptide embedding." Bioinformatics 35, no. 14 (July 2019): i278—i283. http://dx.doi.org/10.1093/bioinformatics/btz330.
Full textAbstract:
Abstract Motivation The computational modeling of peptide display by class I major histocompatibility complexes (MHCs) is essential for peptide-based therapeutics design. Existing computational methods for peptide-display focus on modeling the peptide-MHC-binding affinity. However, such models are not able to characterize the sequence features for the other cellular processes in the peptide display pathway that determines MHC ligand selection. Results We introduce a semi-supervised model, DeepLigand that outperforms the state-of-the-art models in MHC Class I ligand prediction. DeepLigand combines a peptide language model and peptide binding affinity prediction to score MHC class I peptide presentation. The peptide language model characterizes sequence features that correspond to secondary factors in MHC ligand selection other than binding affinity. The peptide embedding is learned by pre-training on natural ligands, and can discriminate between ligands and non-ligands in the absence of binding affinity prediction. Although conventional affinity-based models fail to classify peptides with moderate affinities, DeepLigand discriminates ligands from non-ligands with consistently high accuracy. Availability and implementation We make DeepLigand available at https://github.com/gifford-lab/DeepLigand. Supplementary information Supplementary data are available at Bioinformatics online.
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Souza, P. C. T., A. C. Puhl, L. Martínez, R. Aparício, A. S. Nascimento, A. C. M. Figueira, P. Nguyen, P. Webb, M. S. Skaf, and I. Polikarpov. "Identification of a New Hormone-Binding Site on the Surface of Thyroid Hormone Receptor." Molecular Endocrinology 28, no. 4 (April 1, 2014): 534–45. http://dx.doi.org/10.1210/me.2013-1359.
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Abstract Thyroid hormone receptors (TRs) are members of the nuclear receptor superfamily of ligand-activated transcription factors involved in cell differentiation, growth, and homeostasis. Although X-ray structures of many nuclear receptor ligand-binding domains (LBDs) reveal that the ligand binds within the hydrophobic core of the ligand-binding pocket, a few studies suggest the possibility of ligands binding to other sites. Here, we report a new x-ray crystallographic structure of TR-LBD that shows a second binding site for T3 and T4 located between H9, H10, and H11 of the TRα LBD surface. Statistical multiple sequence analysis, site-directed mutagenesis, and cell transactivation assays indicate that residues of the second binding site could be important for the TR function. We also conducted molecular dynamics simulations to investigate ligand mobility and ligand-protein interaction for T3 and T4 bound to this new TR surface-binding site. Extensive molecular dynamics simulations designed to compute ligand-protein dissociation constant indicate that the binding affinities to this surface site are of the order of the plasma and intracellular concentrations of the thyroid hormones, suggesting that ligands may bind to this new binding site under physiological conditions. Therefore, the second binding site could be useful as a new target site for drug design and could modulate selectively TR functions.
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Kim, Hye Yeon, Ae Nim Pae, Yeon Joo Lee, Joon Kyu Park, Dae Sung Kim, Kwang Yeon Hwang, Myeong-Hee Yu, and Eunice EunKyeong Kim. "Structural Comparison of Ligand-Binding Domains in Estrogen-Related Receptors." Key Engineering Materials 277-279 (January 2005): 107–12. http://dx.doi.org/10.4028/www.scientific.net/kem.277-279.107.
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Estrogen-related receptors (ERRs), orphan nuclear receptors, share a significant amino acid sequence homology with estrogen receptors (ERs), yet their ligands do not respond in the same manner. In fact, some of the ligands that are known as agonists of ERs show antagonistic effect in ERRs. Accordingly, the current study investigated the structures of the ligand-binding domains using homology model building and docking studies. The results showed clear differences between the ligand-binding pockets of ERRs and ERs, thereby providing structural insights into the activities related to the ligands.
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Suo, Fengzhi, Xinyu Zhou, Rita Setroikromo, and Wim J. Quax. "Receptor Specificity Engineering of TNF Superfamily Ligands." Pharmaceutics 14, no. 1 (January 13, 2022): 181. http://dx.doi.org/10.3390/pharmaceutics14010181.
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The tumor necrosis factor (TNF) ligand family has nine ligands that show promiscuity in binding multiple receptors. As different receptors transduce into diverse pathways, the study on the functional role of natural ligands is very complex. In this review, we discuss the TNF ligands engineering for receptor specificity and summarize the performance of the ligand variants in vivo and in vitro. Those variants have an increased binding affinity to specific receptors to enhance the cell signal conduction and have reduced side effects due to a lowered binding to untargeted receptors. Refining receptor specificity is a promising research strategy for improving the application of multi-receptor ligands. Further, the settled variants also provide experimental guidance for engineering receptor specificity on other proteins with multiple receptors.
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Fukuzawa, Kaori, Kazuo Kitaura, K. Nakata, Tsuguchika Kaminuma, and T. Nakano. "Fragment molecular orbital study of the binding energy of ligands to the estrogen receptor." Pure and Applied Chemistry 75, no. 11-12 (January 1, 2003): 2405–10. http://dx.doi.org/10.1351/pac200375112405.
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We examined the published data for the binding affinity of typical ligands to the α-subtype of the human estrogen receptor with use of an approximate molecular orbital method applicable to interacting molecular clusters. An ab initio procedure for "molecular fragments" proposed recently to deal with such macromolecules as proteins was applied to the molecular orbital calculations. The receptor protein was primarily modeled using 50 amino acid residues surrounding the ligand. For a few ligand-receptor complexes, the binding energy was also calculated with use of 241 amino acid residues contained in the entire binding domain. No significant difference was found in the calculated binding energy between the complex modeled with ligand-surrounding 50 amino acids and that with residues of the entire domain. The calculated binding energy was correlated very well with the published relative binding affinity for typical ligands.
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Marsh, Lorraine. "Strong Ligand-Protein Interactions Derived from Diffuse Ligand Interactions with Loose Binding Sites." BioMed Research International 2015 (2015): 1–6. http://dx.doi.org/10.1155/2015/746980.
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Many systems in biology rely on binding of ligands to target proteins in a single high-affinity conformation with a favorableΔG. Alternatively, interactions of ligands with protein regions that allow diffuse binding, distributed over multiple sites and conformations, can exhibit favorableΔGbecause of their higher entropy. Diffuse binding may be biologically important for multidrug transporters and carrier proteins. A fine-grained computational method for numerical integration of total bindingΔGarising from diffuse regional interaction of a ligand in multiple conformations using a Markov Chain Monte Carlo (MCMC) approach is presented. This method yields a metric that quantifies the influence on overall ligand affinity of ligand binding to multiple, distinct sites within a protein binding region. This metric is essentially a measure of dispersion in equilibrium ligand binding and depends on both the number of potential sites of interaction and the distribution of their individual predicted affinities. Analysis of test cases indicates that, for some ligand/protein pairs involving transporters and carrier proteins, diffuse binding contributes greatly to total affinity, whereas in other cases the influence is modest. This approach may be useful for studying situations where “nonspecific” interactions contribute to biological function.
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Gascoigne, Nicholas R. J., Tomasz Zal, and S. Munir Alam. "T-cell receptor binding kinetics in T-cell development and activation." Expert Reviews in Molecular Medicine 3, no. 6 (February 12, 2001): 1–17. http://dx.doi.org/10.1017/s1462399401002502.
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T-cell activation is of central importance to the generation of an immune response and is also required as part of the host's ability to recognise self proteins. T cells are activated to differing extents by different ligands. Agonist ligands cause the full range of T-cell activation phenotypes – from activation of signalling cascades, to cytokine secretion or target cell killing, to T-cell proliferation. Partial agonists, which can differ from the agonist by as little as a single amino acid residue, can induce some of these responses but not all. Antagonist ligands can disable the signalling of an agonist ligand. These different types of interaction between ligand and T-cell receptor (TCR) also determine the developmental fate of maturing T cells. Much recent work has focused on how the T cell distinguishes between ligands. At least part of the answer lies in the kinetics of its binding to ligand.
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Beck, Jennifer L. "Developments in Electrospray Ionization Mass Spectrometry of Non-Covalent DNA–Ligand Complexes." Australian Journal of Chemistry 64, no. 6 (2011): 705. http://dx.doi.org/10.1071/ch11046.
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Many anti-cancer drugs function by binding non-covalently to double-stranded (ds) DNA. Electrospray ionization mass spectrometry (ESI-MS) has emerged over the past decade as a sensitive technique for the determination of stoichiometries and relative binding affinities of DNA–ligand interactions. The chromosome contains nucleotide sequences, for example, guanosine-rich regions, that predispose them to the formation of higher order structures such as quadruplex DNA (qDNA). Sequences that form qDNA are found in the telomeres. The proposal that ligands that stabilize qDNA might interfere with the activity of telomerase in cancer cells has stimulated the search for ligands that are selective for qDNA over dsDNA. The insights gained from the development of ESI-MS methods for analysis of non-covalent dsDNA–ligand complexes are now being applied in the search for qDNA-selective ligands. ESI-MS is a useful first-pass screening technique for qDNA-binding ligands. This short review describes some experimental considerations for ESI-MS analysis of DNA–ligand complexes, briefly addresses the question of whether non-covalent DNA–ligand complexes are faithfully transferred from solution to the gas phase, discusses ion mobility mass spectrometry as a technique for probing this issue, and highlights some recent ESI-MS studies of qDNA-selective ligands.
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Kuznetsov, Aleksei, and Jaak Järv. "Ligand structure controlled allostery in cAMP-dependent protein kinase catalytic subunit." Open Life Sciences 4, no. 2 (June 1, 2009): 131–41. http://dx.doi.org/10.2478/s11535-009-0012-6.
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AbstractProtein kinase A (cAMP dependent protein kinase catalytic subunit, EC 2.7.11.11) binds simultaneously ATP and a phosphorylatable peptide. These structurally dissimilar allosteric ligands influence the binding effectiveness of each other. The same situation is observed with substrate congeners, which reversibly inhibit the enzyme. In this review these allosteric effects are quantified using the interaction factor, which compares binding effectiveness of ligands with the free enzyme and the pre-loaded enzyme complex containing another ligand. This analysis revealed that the allosteric effect depends upon structure of the interacting ligands, and the principle “better binding: stronger allostery” observed can be formalized in terms of linear free-energy relationships, which point to similar mechanism of the allosteric interaction between the enzyme-bound substrates and/or inhibitor molecules. On the other hand, the type of effect is governed by ligand binding effectiveness and can be inverted from positive allostery to negative allostery if we move from effectively binding ligands to badly binding compounds. Thus the outcome of the allostery in this monomeric enzyme is the same as defined by classical theories for multimeric enzymes: making the enzyme response more efficient if appropriate ligands bind.
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Sencanski, Milan, Milovan Ivanovic, Sonja Vuckovic, and Ljiljana Dosen-Micovic. "Modeling the ligand specific μ- and δ-opioid receptor conformations." Journal of the Serbian Chemical Society 76, no. 9 (2011): 1247–62. http://dx.doi.org/10.2298/jsc110120110s.
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An automated docking procedure was applied to study the binding of a series of ?- and ?-selective ligands to ligand-specific ?- and ?-opioid receptor models. Short-time molecular dynamic simulations were used to obtain ligand-specific ?- and ?-opioid receptors from arbitrarily chosen models of the active form of these receptors. The quality of receptor model depended on the molecular volume of the ligand in the receptor-ligand complex used in the molecular dynamic simulations. Within a series of ligands of similar size (volume), the results of ligand docking to the obtained ligand-specific receptor conformation were in agreement with point mutation studies. The correlation of the calculated and the experimentally determined binding energies was improved in relation to the initial receptor conformation.
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Linthicum, D. S., M. B. Bolger, P. H. Kussie, G. M. Albright, T. A. Linton, S. Combs, and D. Marchetti. "Analysis of idiotypic and anti-idiotypic antibodies as models of receptor and ligand." Clinical Chemistry 34, no. 9 (September 1, 1988): 1676–80. http://dx.doi.org/10.1093/clinchem/34.9.1676.
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Abstract Antibodies to small bioactive ligands and peptides may mimic the binding characteristics of the natural receptor; in turn, the anti-idiotypic antibodies generated against the binding sites of such anti-ligand antibodies may mimic some aspects of small bioactive ligands and peptides. Among the several levels of investigation of such antibody-receptor networks are (a) the quantitative structure-activity relationships of ligand binding to antibody as compared with natural receptor; (b) the molecular modeling of antibody-receptor binding sites and the genomic basis for such structures; and (c) the characteristics of the molecular mimicry exhibited by "mimetopes" on anti-idiotypic antibodies. To illustrate the analysis encountered at each of these levels, we discuss here antibody and anti-idiotypic systems that are directed to small neuroactive ligands and their receptors.
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Iatmanen-Harbi, Soria, lucile Senicourt, Vassilios Papadopoulos, Olivier Lequin, and Jean-Jacques Lacapere. "Characterization of the High-Affinity Drug Ligand Binding Site of Mouse Recombinant TSPO." International Journal of Molecular Sciences 20, no. 6 (March 21, 2019): 1444. http://dx.doi.org/10.3390/ijms20061444.
Full textAbstract:
The optimization of translocator protein (TSPO) ligands for Positron Emission Tomography as well as for the modulation of neurosteroids is a critical necessity for the development of TSPO-based diagnostics and therapeutics of neuropsychiatrics and neurodegenerative disorders. Structural hints on the interaction site and ligand binding mechanism are essential for the development of efficient TSPO ligands. Recently published atomic structures of recombinant mammalian and bacterial TSPO1, bound with either the high-affinity drug ligand PK 11195 or protoporphyrin IX, have revealed the membrane protein topology and the ligand binding pocket. The ligand is surrounded by amino acids from the five transmembrane helices as well as the cytosolic loops. However, the precise mechanism of ligand binding remains unknown. Previous biochemical studies had suggested that ligand selectivity and binding was governed by these loops. We performed site-directed mutagenesis to further test this hypothesis and measured the binding affinities. We show that aromatic residues (Y34 and F100) from the cytosolic loops contribute to PK 11195 access to its binding site. Limited proteolytic digestion, circular dichroism and solution two-dimensional (2-D) NMR using selective amino acid labelling provide information on the intramolecular flexibility and conformational changes in the TSPO structure upon PK 11195 binding. We also discuss the differences in the PK 11195 binding affinities and the primary structure between TSPO (TSPO1) and its paralogous gene product TSPO2.
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Li, Huiqing, Jing Wei, Youming Dong, and Zhiyue Yu. "Interaction between 2-(p-toluidino)-6-naphthalenesulfonic acid sodium salt (TNS) and β-lactoglobulin." Canadian Journal of Chemistry 94, no. 8 (August 2016): 680–86. http://dx.doi.org/10.1139/cjc-2015-0450.
Full textAbstract:
The major bovine milk protein β-lactoglobulin (β-LG), a member of the lipocalin superfamily, can bind a wide range of ligands and act as a transporter. In the present study, the combination of the hydrophobic molecule 2-(p-toluidino)-6-naphthalenesulfonic acid sodium salt (TNS) with β-LG was analyzed using fluorescence spectroscopy and AutoDock modeling to discern the major binding sites of the protein and to determine the capacity of other small ligands to bind with β-LG by utilizing TNS as a reference. The experimental data indicate that in a neutral pH environment, TNS is located in the hydrophobic domain of the protein, 2.5 nm away from the Trp19 residues of β-LG. The binding constant of the small molecule to β-LG is (3.30 ± 0.32) × 106 (mol L–1)−1. An interaction model between the ligand and β-LG was developed, and AutoDock modeling also demonstrates that the ligand is located in the central hydrophobic calyx of β-LG within the regions covered by the Förster radius of the Trp19–ligand pair. Although the interaction between the ligand and β-LG is affected by increasing ion strength, pH change, and heat treatment, the complex is maintained until the secondary structure of β-LG is destroyed. Additionally, the ligand binding stabilizes the folding of β-LG. The binding constants of sodium dodecyl sulfate (SDS) and sodium dodecylbenzene sulfonate (SDBS) to β-LG were obtained using competitive ligand binding measurements. With a sensitive fluorescence signal and stable complex, the ligand could be utilized as a reference to detect the binding of other small ligands to β-LG.
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Jia, Zhe, Lin Li, Yunhui Peng, Feng Ding, and Emil Alexov. "The capricious electrostatic force: Revealing the signaling pathway in integrin α2-I domain." Journal of Theoretical and Computational Chemistry 17, no. 03 (May 2018): 1840001. http://dx.doi.org/10.1142/s0219633618400011.
Full textAbstract:
Integrins are cellular adhesion proteins located on cell surface. They are known to have open and closed conformations that correspond to high and low binding affinity to ligands, respectively. Integrin [Formula: see text]2 binds to the ligands via the ligand binding domain, [Formula: see text]2-I domain, which also has open and closed conformations. Experimentally, the closed to open conformation change is shown to be triggered by pulling the C-terminal away from the ligand binding site, but how the signal propagates from the distant C-terminal to the binding site is unknown. To explain the mechanisms of the conformation change, we built models of the [Formula: see text]2-I domain open and closed conformations in ligand free and ligand bound states, respectively. We found that the signaling pathway consists of F313-I280-V252 residues that connect the C-terminal and the ligand binding site. The pathway is highly conserved as revealed by a protein sequence analysis among 55 species. Furthermore, MM/PBSA energy calculations on the stabilities and ligand binding affinities of the closed and open conformations are consistent with experimental measurements. The open conformation is more favorable for ligand binding, and the closed conformation is more stable in unbound state. Energy analysis also revealed the “hot spots” for ligand binding, and most residues that contribute strongly to ligand binding free energy are highly conserved in evolution. In addition, the electrostatic analysis showed that the closed conformation has stronger long-range electrostatic attraction to the ligand compared with the open conformation. The difference is caused by the rearrangement of several charged residues during the binding. These observations make us suggest that the integrin [Formula: see text]2-I domain binding process involves the two-step “dock-lock” mechanism. The closed conformation first attracts the ligand from a long distance and afterwards, the open conformation locks the ligand at the binding site with high binding affinity.
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Lee, Simon, Clare Faux, Jennifer Nixon, Daniel Alete, John Chilton, Muhamed Hawadle, and Andrew W. Stoker. "Dimerization of Protein Tyrosine Phosphatase σ Governs both Ligand Binding and Isoform Specificity." Molecular and Cellular Biology 27, no. 5 (December 18, 2006): 1795–808. http://dx.doi.org/10.1128/mcb.00535-06.
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ABSTRACT Signaling through receptor protein tyrosine phosphatases (RPTPs) can influence diverse processes, including axon development, lymphocyte activation, and cell motility. The molecular regulation of these enzymes, however, is still poorly understood. In particular, it is not known if, or how, the dimerization state of RPTPs is related to the binding of extracellular ligands. Protein tyrosine phosphatase σ (PTPσ) is an RPTP with major isoforms that differ in their complements of fibronectin type III domains and in their ligand-binding specificities. In this study, we show that PTPσ forms homodimers in the cell, interacting at least in part through the transmembrane region. Using this knowledge, we provide the first evidence that PTPσ ectodomains must be presented as dimers in order to bind heterophilic ligands. We also provide evidence of how alternative use of fibronectin type III domain complements in two major isoforms of PTPσ can alter the ligand binding specificities of PTPσ ectodomains. The data suggest that the alternative domains function largely to change the rotational conformations of the amino-terminal ligand binding sites of the ectodomain dimers, thus imparting novel ligand binding properties. These findings have important implications for our understanding of how heterophilic ligands interact with, and potentially regulate, RPTPs.
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Obermoeller-McCormick, L. M., Y. Li, H. Osaka, D. J. FitzGerald, A. L. Schwartz, and G. Bu. "Dissection of receptor folding and ligand-binding property with functional minireceptors of LDL receptor-related protein." Journal of Cell Science 114, no. 5 (March 1, 2001): 899–908. http://dx.doi.org/10.1242/jcs.114.5.899.
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The LDL receptor-related protein (LRP) is a large, multifunctional endocytic receptor that binds and endocytoses a variety of structurally and functionally distinct ligands. LRP contains four putative ligand-binding domains. However, only domains II, III and IV, but not domain I, bind the receptor-associated protein (RAP), a molecular chaperone and universal antagonist for LRP. In order to dissect the function of RAP in LRP folding and to examine the ligand-binding properties of LRP, we generated LRP minireceptors that represent each of the four putative ligand-binding domains (termed mLRP1, mLRP2, mLRP3 and mLRP4, respectively). We found that proper folding and trafficking of mLRP2, mLRP3, mLRP4, but not mLRP1, is facilitated by coexpression of RAP. When these mLRPs were stably expressed in Chinese Hamster Ovary cells that lack the endogenous LRP, we found that each of these receptors was processed and traffics through the secretory pathway. Cell surface expression of these minireceptors was quantitatively examined by flow cytometric analyses. Using these minireceptor cell lines to map the ligand-binding domains, we found that although the majority of LRP ligands bind to both domain II and domain IV, Pseudomonas exotoxin A utilizes only domain IV for its binding to LRP. We conclude that while domains II and IV of LRP share many ligand-binding properties, each of the putative ligand-binding domains of LRP is unique in its contribution to ligand binding.
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Zhu, Siyu, Qian Meng, Robert T. Schooley, Jing An, Yan Xu, and Ziwei Huang. "Structural and Biological Characterizations of Novel High-Affinity Fluorescent Probes with Overlapped and Distinctive Binding Regions on CXCR4." Molecules 24, no. 16 (August 13, 2019): 2928. http://dx.doi.org/10.3390/molecules24162928.
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CXC-type chemokine receptor 4 (CXCR4) is well known as a co-receptor for cellular entry and infection of human immunodeficiency virus type 1 (HIV-1). As an important member of the G protein-coupled receptor (GPCR) family, CXCR4 also mediates a variety of cellular processes and functions, such as cell chemotaxis, proliferation, and calcium signal transductions. Identification and characterization of molecular ligands or probes of CXCR4 have been an intensive area of investigations as such ligands or probes are of significant clinical values for the studies and treatments of HIV-1 infection and other human diseases mediated by the receptor. The crystal structures of CXCR4 in complex with different ligands have revealed two distinctive binding regions or subpockets. Thus, understanding the interactions of diverse ligands with these distinctive CXCR4 binding regions has become vital for elucidating the relationship between binding modes and biological mechanisms of ligand actions. Peptidic CVX15 is the only ligand that has been validated to bind one of these distinctive binding regions (or so called the major subpocket) of CXCR4. Therefore, in this study, we developed an efficient probe system including two high-affinity peptidic fluorescent probes, designated as FITC-CVX15 and FITC-DV1, with the aim of targeting distinctive CXCR4 subpockets. We conducted rational design and chemical characterization of the two CXCR4-specific probes and examined their application in biological experiments including competitive binding assays, flow cytometry analysis, and confocal imaging. Especially these two probes were applied in parallel CXCR4 competitive binding assays to detect and analyze potential binding modes of diverse CXCR4 ligands, together with molecular docking and simulations. Our results have indicated that these peptidic fluorescent probe systems provide novel ligand detecting tools, as well as present a new approach for analyzing distinctive binding modes of diverse CXCR4 ligands.
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Klunk, W. E., J. W. Pettegrew, and D. J. Abraham. "Two simple methods for quantifying low-affinity dye-substrate binding." Journal of Histochemistry & Cytochemistry 37, no. 8 (August 1989): 1293–97. http://dx.doi.org/10.1177/37.8.2666512.
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Binding with low-affinity ligands, such as histological dyes, can be difficult to quantitate owing to the dissociation of bound ligand with washing or the retention of nonspecifically bound ligand because of incomplete washing. The present report describes two simple, rapid methods of discriminating bound from free ligand without the need for washing steps. One method is based on the spectral changes induced in a dye ligand, Congo red, on binding to the "receptor" insulin fibrils. This method discriminates spectrophotometrically between bound and free ligand without requiring any physical separation of the two forms. No radioactive ligands are necessary, and, by using disposable cuvettes, the entire binding assay can be done in a single container without the need for transfers. The second method employs a non-traditional filtration approach that avoids the need for a washing step by measuring the decrease in concentration of the dye ligand in the filtrate rather than by applying the usual approach of measuring the absolute amount of ligand bound to the precipitated "receptor." Both methods show saturation of binding sites and give similar values for the KD and Bmax.
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Wang, Chenguang, Maofu Fu, Mark D'Amico, Chris Albanese, Jian-Nian Zhou, Michael Brownlee, Michael P. Lisanti, V. Krishna K. Chatterjee, Mitchell A. Lazar, and Richard G. Pestell. "Inhibition of Cellular Proliferation through IκB Kinase-Independent and Peroxisome Proliferator-Activated Receptor γ-Dependent Repression of Cyclin D1." Molecular and Cellular Biology 21, no. 9 (May 1, 2001): 3057–70. http://dx.doi.org/10.1128/mcb.21.9.3057-3070.2001.
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ABSTRACT The nuclear receptor peroxisome proliferator-activated receptor γ (PPARγ) is a ligand-regulated nuclear receptor superfamily member. Liganded PPARγ exerts diverse biological effects, promoting adipocyte differentiation, inhibiting tumor cellular proliferation, and regulating monocyte/macrophage and anti-inflammatory activities in vitro. In vivo studies with PPARγ ligands showed enhancement of tumor growth, raising the possibility that reduced immune function and tumor surveillance may outweigh the direct inhibitory effects of PPARγ ligands on cellular proliferation. Recent findings that PPARγ ligands convey PPARγ-independent activities through IκB kinase (IKK) raises important questions about the specific mechanisms through which PPARγ ligands inhibit cellular proliferation. We investigated the mechanisms regulating the antiproliferative effect of PPARγ. Herein PPARγ, liganded by either natural (15d-PGJ2 and PGD2) or synthetic ligands (BRL49653 and troglitazone), selectively inhibited expression of the cyclin D1 gene. The inhibition of S-phase entry and activity of the cyclin D1-dependent serine-threonine kinase (Cdk) by 15d-PGJ2 was not observed in PPARγ-deficient cells. Cyclin D1 overexpression reversed the S-phase inhibition by 15d-PGJ2. Cyclin D1 repression was independent of IKK, as prostaglandins (PGs) which bound PPARγ but lacked the IKK interactive cyclopentone ring carbonyl group repressed cyclin D1. Cyclin D1 repression by PPARγ involved competition for limiting abundance of p300, directed through a c-Fos binding site of the cyclin D1 promoter. 15d-PGJ2 enhanced recruitment of p300 to PPARγ but reduced binding to c-Fos. The identification of distinct pathways through which eicosanoids regulate anti-inflammatory and antiproliferative effects may improve the utility of COX2 inhibitors.