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Journal articles on the topic 'Ligand Recognition'

Author: Grafiati

Published: 6 September 2023

Last updated: 31 July 2025

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1

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

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Human nucleotide-binding oligomerization domain proteins, hNOD1 and hNOD2, are host intracellular receptors with C-terminal leucine-rich repeat (LRR) domains, which recognize specific bacterial peptidoglycan (PG) fragments as their ligands. The specificity of this recognition is dependent on the third amino acid of the stem peptide of the PG ligand, which is usually meso-diaminopimelic acid (mesoDAP) or l-lysine (l-Lys). Since the LRR domains of hNOD receptors had been experimentally shown to confer the PG ligand-sensing specificity, we developed three-dimensional structures of hNOD1-LRR and t

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Smyth, Mark J., Jeremy Swann, Janice M. Kelly, et al. "NKG2D Recognition and Perforin Effector Function Mediate Effective Cytokine Immunotherapy of Cancer." Journal of Experimental Medicine 200, no. 10 (2004): 1325–35. http://dx.doi.org/10.1084/jem.20041522.

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Single and combination cytokines offer promise in some patients with advanced cancer. Many spontaneous and experimental cancers naturally express ligands for the lectin-like type-2 transmembrane stimulatory NKG2D immunoreceptor; however, the role this tumor recognition pathway plays in immunotherapy has not been explored to date. Here, we show that natural expression of NKG2D ligands on tumors provides an effective target for some cytokine-stimulated NK cells to recognize and suppress tumor metastases. In particular, interleukin (IL)-2 or IL-12 suppressed tumor metastases largely via NKG2D lig

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Gasparri, Federica, Jesper Wengel, Thomas Grutter, and Stephan A. Pless. "Molecular determinants for agonist recognition and discrimination in P2X2 receptors." Journal of General Physiology 151, no. 7 (2019): 898–911. http://dx.doi.org/10.1085/jgp.201912347.

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P2X receptors (P2XRs) are trimeric ligand-gated ion channels that open a cation-selective pore in response to ATP binding. P2XRs contribute to synaptic transmission and are involved in pain and inflammation, thus representing valuable drug targets. Recent crystal structures have confirmed the findings of previous studies with regards to the amino acid chains involved in ligand recognition, but they have also suggested that backbone carbonyl atoms contribute to ATP recognition and discrimination. Here we use a combination of site-directed mutagenesis, amide-to-ester substitutions, and a range o

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

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Most physiological processes in living systems are fundamentally regulated by protein–ligand interactions. Understanding the process of ligand recognition by proteins is a vital activity in molecular biology and biochemistry. It is well known that the residues present at the binding site of the protein form pockets that provide a conducive environment for recognition of specific ligands. In many cases, the boundaries of these sites are not well defined. Here, we provide a web-server to systematically evaluate important residues in the binding site of the protein that contribute towards the lig

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Anand, Praveen, Deepesh Nagarajan, Sumanta Mukherjee, and Nagasuma Chandra. "ABS–Scan: In silico alanine scanning mutagenesis for binding site residues in protein–ligand complex." F1000Research 3 (December 1, 2014): 214. http://dx.doi.org/10.12688/f1000research.5165.2.

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Most physiological processes in living systems are fundamentally regulated by protein–ligand interactions. Understanding the process of ligand recognition by proteins is a vital activity in molecular biology and biochemistry. It is well known that the residues present at the binding site of the protein form pockets that provide a conducive environment for recognition of specific ligands. In many cases, the boundaries of these sites are not well defined. Here, we provide a web-server to systematically evaluate important residues in the binding site of the protein that contribute towards the lig

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Galano-Frutos, Juan J., M. Carmen Morón, and Javier Sancho. "The mechanism of water/ion exchange at a protein surface: a weakly bound chloride in Helicobacter pylori apoflavodoxin." Physical Chemistry Chemical Physics 17, no. 43 (2015): 28635–46. http://dx.doi.org/10.1039/c5cp04504e.

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7

Diamond, M. S., J. Garcia-Aguilar, J. K. Bickford, A. L. Corbi, and T. A. Springer. "The I domain is a major recognition site on the leukocyte integrin Mac-1 (CD11b/CD18) for four distinct adhesion ligands." Journal of Cell Biology 120, no. 4 (1993): 1031–43. http://dx.doi.org/10.1083/jcb.120.4.1031.

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Despite the identification and characterization of several distinct ligands for the leukocyte integrin (CD11/CD18) family of adhesion receptors, little is known about the structural regions on these molecules that mediate ligand recognition. In this report, we use alpha subunit chimeras of Mac-1 (CD11b/CD18) and p150,95 (CD11c/CD18), and an extended panel of newly generated and previously characterized mAbs specific to the alpha chain of Mac-1 to map the binding sites for four distinct ligands for Mac-1: iC3b, fibrinogen, ICAM-1, and the as-yet uncharacterized counter-receptor responsible for

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8

Koehler, Melanie, Anny Fis, Hermann J. Gruber, and Peter Hinterdorfer. "AFM-Based Force Spectroscopy Guided by Recognition Imaging: A New Mode for Mapping and Studying Interaction Sites at Low Lateral Density." Methods and Protocols 2, no. 1 (2019): 6. http://dx.doi.org/10.3390/mps2010006.

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Ligand binding to receptors is one of the most important regulatory elements in biology as it is the initiating step in signaling pathways and cascades. Thus, precisely localizing binding sites and measuring interaction forces between cognate receptor–ligand pairs leads to new insights into the molecular recognition involved in these processes. Here we present a detailed protocol about applying a technique, which combines atomic force microscopy (AFM)-based recognition imaging and force spectroscopy for studying the interaction between (membrane) receptors and ligands on the single molecule le

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9

Gil, Diana, Adam G. Schrum, Balbino Alarcón, and Ed Palmer. "T cell receptor engagement by peptide–MHC ligands induces a conformational change in the CD3 complex of thymocytes." Journal of Experimental Medicine 201, no. 4 (2005): 517–22. http://dx.doi.org/10.1084/jem.20042036.

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The T cell receptor (TCR) can recognize a variety of cognate peptide/major histocompatibility complex (pMHC) ligands and translate their affinity into distinct cellular responses. To achieve this, the nonsignaling αβ heterodimer communicates ligand recognition to the CD3 signaling subunits by an unknown mechanism. In thymocytes, we found that both positive- and negative-selecting pMHC ligands expose a cryptic epitope in the CD3 complex upon TCR engagement. This conformational change is induced in vivo and requires the expression of cognate MHC. We conclude that TCR engagement with a cognate pM

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10

Baron, Riccardo, and J. Andrew McCammon. "Molecular Recognition and Ligand Association." Annual Review of Physical Chemistry 64, no. 1 (2013): 151–75. http://dx.doi.org/10.1146/annurev-physchem-040412-110047.

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11

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

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12

Leboffe, Loris, Alessandra di Masi, Fabio Polticelli, Viviana Trezza, and Paolo Ascenzi. "Structural Basis of Drug Recognition by Human Serum Albumin." Current Medicinal Chemistry 27, no. 30 (2020): 4907–31. http://dx.doi.org/10.2174/0929867326666190320105316.

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Background: Human serum albumin (HSA), the most abundant protein in plasma, is a monomeric multi-domain macromolecule with at least nine binding sites for endogenous and exogenous ligands. HSA displays an extraordinary ligand binding capacity as a depot and carrier for many compounds including most acidic drugs. Consequently, HSA has the potential to influence the pharmacokinetics and pharmacodynamics of drugs. Objective: In this review, the structural determinants of drug binding to the multiple sites of HSA are analyzed and discussed in detail. Moreover, insight into the allosteric and compe

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13

Vivat, V., D. Gofflo, T. Garcia, et al. "Sequences in the ligand-binding domains of the human androgen and progesterone receptors which determine their distinct ligand identities." Journal of Molecular Endocrinology 18, no. 2 (1997): 147–60. http://dx.doi.org/10.1677/jme.0.0180147.

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ABSTRACT The natural ligands of the progesterone (PR) and androgen (AR) receptors, progesterone and testosterone, differ only by their 17β-substitution. To identify within the AR and PR ligand-binding domains (LBDs) the sequences responsible for the differential recognition of these ligands, chimeric LBDs assembled from five homologous AR/PR 'cassettes' linked to the GAL4-DNA binding domain were constructed, and their ligand binding and transactivation characteristics were determined. Replacing the central cassette 3 of PR by that of AR generated a progesterone- and testosterone-responsive PR

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14

Negi, Ajay Singh, and Ajay Kumar Sood. "Electric Field–Enhanced Sensitivity of Grafted Ligands and Receptors." Clinical Chemistry 54, no. 2 (2008): 366–70. http://dx.doi.org/10.1373/clinchem.2007.094417.

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Abstract Background: Particle-based agglutination tests consisting of receptors grafted to colloidal microparticles are useful for detecting small quantities of corresponding ligands of interest in fluid test samples, but detection limits of such tests are limited to a certain concentration and it is most desirable to lower the detection limits and to enhance the rate of recognition of ligands. Methods: A mixture of receptor-coated colloidal microparticles and corresponding ligand was sandwiched between 2 indium tin oxide–coated glass plates. Electrohydrodynamic drag from an alternating-curren

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McMillan, Jourdan K. P., Patrick O’Donnell, and Sandra P. Chang. "Pattern recognition receptor ligand-induced differentiation of human transitional B cells." PLOS ONE 17, no. 8 (2022): e0273810. http://dx.doi.org/10.1371/journal.pone.0273810.

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B cells represent a critical component of the adaptive immune response whose development and differentiation are determined by antigen-dependent and antigen-independent interactions. In this study, we explored the effects of IL-4 and pattern-recognition receptor (PRR) ligands on B cell development and differentiation by investigating their capacity to drive the in vitro maturation of human transitional B cells. In the presence of IL-4, ligands for TLR7/8, TLR9, and NOD1 were effective in driving the in vitro maturation of cord blood transitional B cells into mature, naïve B cells as measured b

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16

Yuan, Xiaojing, and Yechun Xu. "Recent Trends and Applications of Molecular Modeling in GPCR–Ligand Recognition and Structure-Based Drug Design." International Journal of Molecular Sciences 19, no. 7 (2018): 2105. http://dx.doi.org/10.3390/ijms19072105.

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G protein-coupled receptors represent the largest family of human membrane proteins and are modulated by a variety of drugs and endogenous ligands. Molecular modeling techniques, especially enhanced sampling methods, have provided significant insight into the mechanism of GPCR–ligand recognition. Notably, the crucial role of the membrane in the ligand-receptor association process has earned much attention. Additionally, docking, together with more accurate free energy calculation methods, is playing an important role in the design of novel compounds targeting GPCRs. Here, we summarize the rece

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17

Cao, Ruyin, Alejandro Giorgetti, Andreas Bauer, Bernd Neumaier, Giulia Rossetti, and Paolo Carloni. "Role of Extracellular Loops and Membrane Lipids for Ligand Recognition in the Neuronal Adenosine Receptor Type 2A: An Enhanced Sampling Simulation Study." Molecules 23, no. 10 (2018): 2616. http://dx.doi.org/10.3390/molecules23102616.

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Human G-protein coupled receptors (GPCRs) are important targets for pharmaceutical intervention against neurological diseases. Here, we use molecular simulation to investigate the key step in ligand recognition governed by the extracellular domains in the neuronal adenosine receptor type 2A (hA2AR), a target for neuroprotective compounds. The ligand is the high-affinity antagonist (4-(2-(7-amino-2-(furan-2-yl)-[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-ylamino)ethyl)phenol), embedded in a neuronal membrane mimic environment. Free energy calculations, based on well-tempered metadynamics, reproduce

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18

Hutchens, T. W., and J. O. Porath. "Protein recognition of immobilized ligands: promotion of selective adsorption." Clinical Chemistry 33, no. 9 (1987): 1502–8. http://dx.doi.org/10.1093/clinchem/33.9.1502.

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Abstract We are using simple immobilized ligands to evaluate the biochemistry and mechanisms of selective, high-affinity, protein adsorption events. Several specific means have recently been developed to more selectively utilize the favorable entropy changes associated with the displacement of protein-bound water during the formation and stabilization of protein-ligand recognition events. For protein and peptide immobilization these include, besides hydrophobic interaction, for example, metal ion, pi-electron-mediated, and thiophilic interactions. This latter type of protein-ligand recognition

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19

Andersen-Nissen, Erica, Kelly D. Smith, Richard Bonneau, Roland K. Strong, and Alan Aderem. "A conserved surface on Toll-like receptor 5 recognizes bacterial flagellin." Journal of Experimental Medicine 204, no. 2 (2007): 393–403. http://dx.doi.org/10.1084/jem.20061400.

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The molecular basis for Toll-like receptor (TLR) recognition of microbial ligands is unknown. We demonstrate that mouse and human TLR5 discriminate between different flagellins, and we use this difference to map the flagellin recognition site on TLR5 to 228 amino acids of the extracellular domain. Through molecular modeling of the TLR5 ectodomain, we identify two conserved surface-exposed regions. Mutagenesis studies demonstrate that naturally occurring amino acid variation in TLR5 residue 268 is responsible for human and mouse discrimination between flagellin molecules. Mutations within one c

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20

Li, Chaoqun, Xiaojia Zhao, Xiaomin Zhu, Pengtao Xie, and Guangju Chen. "Structural Studies of the 3′,3′-cGAMP Riboswitch Induced by Cognate and Noncognate Ligands Using Molecular Dynamics Simulation." International Journal of Molecular Sciences 19, no. 11 (2018): 3527. http://dx.doi.org/10.3390/ijms19113527.

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Riboswtich RNAs can control gene expression through the structural change induced by the corresponding small-molecule ligands. Molecular dynamics simulations and free energy calculations on the aptamer domain of the 3′,3′-cGAMP riboswitch in the ligand-free, cognate-bound and noncognate-bound states were performed to investigate the structural features of the 3′,3′-cGAMP riboswitch induced by the 3′,3′-cGAMP ligand and the specificity of ligand recognition. The results revealed that the aptamer of the 3′,3′-cGAMP riboswitch in the ligand-free state has a smaller binding pocket and a relatively

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21

Takagi, J. "Structural basis for ligand recognition by RGD (Arg-Gly-Asp)-dependent integrins." Biochemical Society Transactions 32, no. 3 (2004): 403–6. http://dx.doi.org/10.1042/bst0320403.

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Since the discovery of the RGD sequence motif as the essential cell attachment site in Fn (fibronectin), RGD-dependent ligand recognition by integrins has been the major focus of many integrin researches. Although many integrins recognize RGD-containing ligands, it is believed that residues outside the RGD motif provide specificity as well as high affinity for each integrin–ligand pair. These ‘secondary’ sites are generally assumed to interact directly with the α subunit of integrin, whereas the RGD motif binds primarily to the β subunit. This necessitates that the integrin–ligand interface co

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22

Ginsberg, M. H., J. C. Loftus, S. D'Souza, and E. F. Plow. "Ligand binding to integrins: Common and ligand specific recognition mechanisms." Cell Differentiation and Development 32, no. 3 (1990): 203–13. http://dx.doi.org/10.1016/0922-3371(90)90033-s.

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23

Wu, Yiran, Liting Zeng, and Suwen Zhao. "Ligands of Adrenergic Receptors: A Structural Point of View." Biomolecules 11, no. 7 (2021): 936. http://dx.doi.org/10.3390/biom11070936.

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Adrenergic receptors are G protein-coupled receptors for epinephrine and norepinephrine. They are targets of many drugs for various conditions, including treatment of hypertension, hypotension, and asthma. Adrenergic receptors are intensively studied in structural biology, displayed for binding poses of different types of ligands. Here, we summarized molecular mechanisms of ligand recognition and receptor activation exhibited by structure. We also reviewed recent advances in structure-based ligand discovery against adrenergic receptors.

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24

MATSUI, Masakazu. "Ligand design for ion size recognition." Bunseki kagaku 45, no. 3 (1996): 209–23. http://dx.doi.org/10.2116/bunsekikagaku.45.209.

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25

Suehiro, Kazuhisa, Jeffrey W. Smith, and Edward F. Plow. "The Ligand Recognition Specificity of Integrins." Journal of Biological Chemistry 271, no. 17 (1996): 10365–71. http://dx.doi.org/10.1074/jbc.271.17.10365.

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26

Suehiro, Kazuhisa, and Edward F. Plow. "Ligand Recognition by .BETA.3 Integrins." Keio Journal of Medicine 46, no. 3 (1997): 111–14. http://dx.doi.org/10.2302/kjm.46.111.

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27

Mulhbacher, Jérôme, and Daniel A. Lafontaine. "Ligand recognition determinants of guanine riboswitches." Nucleic Acids Research 35, no. 16 (2007): 5568–80. http://dx.doi.org/10.1093/nar/gkm572.

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28

Springer, Barry A., Stephen G. Sligar, John S. Olson, and George N. Jr Phillips. "Mechanisms of Ligand Recognition in Myoglobin." Chemical Reviews 94, no. 3 (1994): 699–714. http://dx.doi.org/10.1021/cr00027a007.

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29

Stephanos, Joseph J., Scott A. Farina, and Anthony W. Addison. "Iron ligand recognition by monomeric hemoglobins." Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology 1295, no. 2 (1996): 209–21. http://dx.doi.org/10.1016/0167-4838(96)00041-6.

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30

Kaur, Punit, Pradeep Sharma, Shavait Yamini, et al. "Molecular Basis of Ligand Recognition by Mammalian Peptidoglycan Recognition Protein." Biophysical Journal 104, no. 2 (2013): 547a. http://dx.doi.org/10.1016/j.bpj.2012.11.3034.

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31

Masson, Thibaut, Corinne Landras Guetta, Eugénie Laigre, et al. "BrdU immuno-tagged G-quadruplex ligands: a new ligand-guided immunofluorescence approach for tracking G-quadruplexes in cells." Nucleic Acids Research 49, no. 22 (2021): 12644–60. http://dx.doi.org/10.1093/nar/gkab1166.

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Abstract G-quadruplexes (G4s) are secondary structures forming in G-rich nucleic acids. G4s are assumed to play critical roles in biology, nonetheless their detection in cells is still challenging. For tracking G4s, synthetic molecules (G4 ligands) can be used as reporters and have found wide application for this purpose through chemical functionalization with a fluorescent tag. However, this approach is limited by a low-labeling degree impeding precise visualization in specific subcellular regions. Herein, we present a new visualization strategy based on the immuno-recognition of 5-bromo-2′-d

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Guzelj, Samo, Tihomir Tomašič, and Žiga Jakopin. "Novel Scaffolds for Modulation of NOD2 Identified by Pharmacophore-Based Virtual Screening." Biomolecules 12, no. 8 (2022): 1054. http://dx.doi.org/10.3390/biom12081054.

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Nucleotide-binding oligomerization domain-containing protein 2 (NOD2) is an innate immune pattern recognition receptor responsible for the recognition of bacterial peptidoglycan fragments. Given its central role in the formation of innate and adaptive immune responses, NOD2 represents a valuable target for modulation with agonists and antagonists. A major challenge in the discovery of novel small-molecule NOD2 modulators is the lack of a co-crystallized complex with a ligand, which has limited previous progress to ligand-based design approaches and high-throughput screening campaigns. To that

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Spassov, Danislav S. "Binding Affinity Determination in Drug Design: Insights from Lock and Key, Induced Fit, Conformational Selection, and Inhibitor Trapping Models." International Journal of Molecular Sciences 25, no. 13 (2024): 7124. http://dx.doi.org/10.3390/ijms25137124.

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Binding affinity is a fundamental parameter in drug design, describing the strength of the interaction between a molecule and its target protein. Accurately predicting binding affinity is crucial for the rapid development of novel therapeutics, the prioritization of promising candidates, and the optimization of their properties through rational design strategies. Binding affinity is determined by the mechanism of recognition between proteins and ligands. Various models, including the lock and key, induced fit, and conformational selection, have been proposed to explain this recognition process

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Tateing, Suriya, and Nuttee Suree. "Decoding molecular recognition of inhibitors targeting HDAC2 via molecular dynamics simulations and configurational entropy estimation." PLOS ONE 17, no. 8 (2022): e0273265. http://dx.doi.org/10.1371/journal.pone.0273265.

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Molecular recognition by enzymes is a complicated process involving thermodynamic energies governing protein-ligand interactions. In order to aid the estimation of inhibitory activity of compounds targeting an enzyme, several computational methods can be employed to dissect this intermolecular contact. Herein, we report a structural dynamics investigation of an epigenetic enzyme HDAC2 in differentiating its binding to various inhibitors within the sub-sites of its active site. Molecular dynamics (MD) simulation was employed to elucidate the intermolecular interactions as well as the dynamics b

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HOWL, John, and Mark WHEATLEY. "Molecular recognition of peptide and non-peptide ligands by the extracellular domains of neurohypophysial hormone receptors." Biochemical Journal 317, no. 2 (1996): 577–82. http://dx.doi.org/10.1042/bj3170577.

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This study was designed to ascertain whether the extracellular loops of vasopressin/oxytocin receptors bind ligands and, if so, to locate the molecular determinants of this ligand–receptor interaction. Ligand-binding studies were employed using a rat liver V1a vasopressin receptor preparation and both peptide and non-peptide receptor ligands. Synthetic peptides corresponding to defined regions of the extracellular surface of the neurohypophysial hormone receptors recognized radioligands. These receptor mimetics inhibited the binding of radioligands to the V1a receptor with apparent affinities

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Nowbakht, Pegah, Mihai-Constantin S. Ionescu, Andreas Rohner, et al. "Ligands for natural killer cell–activating receptors are expressed upon the maturation of normal myelomonocytic cells but at low levels in acute myeloid leukemias." Blood 105, no. 9 (2005): 3615–22. http://dx.doi.org/10.1182/blood-2004-07-2585.

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AbstractNatural killer (NK) cell–mediated cytolytic activity against tumors requires the engagement of activating NK receptors by the tumor-associated ligands. Here, we have studied the role of NKG2D and natural cytotoxicity receptors (NCRs) in the recognition of human leukemia. To detect as-yet-unknown cell-surface molecules recognized by NCRs, we developed soluble forms of NKp30, NKp44, and NKp46 as staining reagents binding the putative cognate ligands. Analysis of UL16-binding protein-1 (ULBP1), ULBP2, and ULBP3 ligands for NKG2D and of potential ligands for NKp30, NKp44, and NKp46 in heal

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Kaiser, Anette, and Irene Coin. "Capturing Peptide–GPCR Interactions and Their Dynamics." Molecules 25, no. 20 (2020): 4724. http://dx.doi.org/10.3390/molecules25204724.

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Many biological functions of peptides are mediated through G protein-coupled receptors (GPCRs). Upon ligand binding, GPCRs undergo conformational changes that facilitate the binding and activation of multiple effectors. GPCRs regulate nearly all physiological processes and are a favorite pharmacological target. In particular, drugs are sought after that elicit the recruitment of selected effectors only (biased ligands). Understanding how ligands bind to GPCRs and which conformational changes they induce is a fundamental step toward the development of more efficient and specific drugs. Moreover

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38

Byzova, Tatiana V., та Edward F. Plow. "Activation of αVβ3 on Vascular Cells Controls Recognition of Prothrombin". Journal of Cell Biology 143, № 7 (1998): 2081–92. http://dx.doi.org/10.1083/jcb.143.7.2081.

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Regulation of vascular homeostasis depends upon collaboration between cells of the vessel wall and blood coagulation system. A direct interaction between integrin αVβ3 on endothelial cells and smooth muscle cells and prothrombin, the pivotal proenzyme of the blood coagulation system, is demonstrated and activation of the integrin is required for receptor engagement. Evidence that prothrombin is a ligand for αVβ3 on these cells include: (a) prothrombin binds to purified αVβ3 via a RGD recognition specificity; (b) prothrombin supports αVβ3-mediated adhesion of stimulated endothelial cells and sm

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Abe, R., O. Kanagawa, M. A. Sheard, B. Malissen, and M. Foo-Phillips. "Characterization of a new minor lymphocyte stimulatory system. I. Cluster of self antigens recognized by "I-E-reactive" V beta s, V beta 5, V beta 11, and V beta 12 T cell receptors for antigen." Journal of Immunology 147, no. 3 (1991): 739–49. http://dx.doi.org/10.4049/jimmunol.147.3.739.

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Abstract In the mouse, two sets of V beta gene products have been shown to be associated with T cell recognition of endogenous self Ag. One of these is the set of V beta associated with T cell reactivities to stimulatory Mls gene products, Mlsa (V beta 6, V beta 8.1, V beta 9) or Mlsc (V beta 3); another is the set of V beta, such as V beta 5, V beta 11, V beta 12, or V beta 17a, which were originally found to be related to I-E recognition. Although the Mls system has been well characterized, little is known about the nature of the ligands for the second set of V beta. In this work, we describ

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Lecut, Christelle, Véronique Arocas, Hans Ulrichts, et al. "Identification of Residues within Human Glycoprotein VI Involved in the Binding to Collagen." Journal of Biological Chemistry 279, no. 50 (2004): 52293–99. http://dx.doi.org/10.1074/jbc.m406342200.

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Glycoprotein VI (GPVI) has a crucial role in platelet responses to collagen. Still, little is known about its interaction with its ligands. In binding assays using soluble or cell-expressed human GPVI, we observed that (i) collagen, and the GPVI-specific ligands collagen-related peptides (CRP) and convulxin, competed with one another for the binding to GPVI and (ii) monoclonal antibodies directed against the extracellular part of the human receptor displayed selective inhibitory properties on GPVI interaction with its ligands. Monoclonal antibody 9E18 strongly reduced the binding of GPVI to co

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Kessler, Benedikt, Denis Hudrisier, Jean-Charles Cerottini, and Immanuel F. Luescher. "Role of CD8 in Aberrant Function of Cytotoxic T Lymphocytes." Journal of Experimental Medicine 186, no. 12 (1997): 2033–38. http://dx.doi.org/10.1084/jem.186.12.2033.

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Using H-2Kd-restricted photoprobe-specific cytotoxic T lymphocyte (CTL) clones, which permit assessment of T cell receptor (TCR)-ligand interactions by TCR photoaffinity labeling, we observed that the efficiency of antigen recognition by CTL was critically dependent on the half-life of TCR-ligand complexes. We show here that antigen recognition by CTL is essentially determined by the frequency of serial TCR engagement, except for very rapid dissociations, which resulted in aberrant TCR signaling and antagonism. Thus agonists that were efficiently recognized exhibited rapid TCR–ligand complex d

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Graham, Kate L., Fiona E. Fleming, Peter Halasz та ін. "Rotaviruses interact with α4β7 and α4β1 integrins by binding the same integrin domains as natural ligands". Journal of General Virology 86, № 12 (2005): 3397–408. http://dx.doi.org/10.1099/vir.0.81102-0.

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Group A rotaviruses are major intestinal pathogens that express potential α4β1 and α4β7 integrin ligand sequences Leu–Asp–Val and Leu–Asp–Ile in their outer capsid protein VP7, and Ile–Asp–Ala in their spike protein VP4. Monkey rotavirus SA11 can use recombinant α4β1 as a cellular receptor. In this study a new potential α4β1, α4β7 and α9β1 integrin ligand sequence, Tyr–Gly–Leu, was identified in VP4. It was shown that several human and monkey rotaviruses bound α4β1 and α4β7, but not α9β1. Binding to α4β1 mediated the infectivity and growth of monkey rotaviruses, and binding to α4β7 mediated th

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Mondoro, TH, CD Wall, MM White, and LK Jennings. "Selective induction of a glycoprotein IIIa ligand-induced binding site by fibrinogen and von Willebrand factor." Blood 88, no. 10 (1996): 3824–30. http://dx.doi.org/10.1182/blood.v88.10.3824.bloodjournal88103824.

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Ligand-induced binding sites (LIBS) are neoantigenic regions of glycoprotein (GP)IIb-IIIa that are exposed upon interaction of the receptor with the ligand fibrinogen or the ligand recognition sequence (RGDS). LIBS have been suggested to contribute to postreceptor occupancy events such as full-scale platelet aggregation, adhesion to collagen, and clot retraction. This study examined the induction requirements of a GPIIIa LIBS with regard to ligand specificity. Through the use of the anti-LIBS D3, we report that this complex- activating antibody induces fibrinogen-and von Willebrand factor-bind

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Kim, Hokyung, Hayeon Choi, Yoonji Heo, Cheoljae Kim, Min Kim, and Ki Tae Kim. "Biosensors Based on Bivalent and Multivalent Recognition by Nucleic Acid Scaffolds." Applied Sciences 12, no. 3 (2022): 1717. http://dx.doi.org/10.3390/app12031717.

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Several biological macromolecules adopt bivalent or multivalent interactions to perform various cellular processes. In this regard, the development of molecular constructs presenting multiple ligands in a specific manner is becoming crucial for the understanding of multivalent interactions and for the detection of target macromolecules. Nucleic acids are attractive molecules to achieve this goal because they are capable of forming various, structurally well-defined 2D or 3D nanostructures and can bear multiple ligands on their structures with precisely controlled ligand–ligand distances. Thank

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Calderone, Richard A. "Recognition of endothelial cells byCandida albicans: role of complement-binding proteins." Canadian Journal of Botany 73, S1 (1995): 1154–59. http://dx.doi.org/10.1139/b95-372.

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Candida albicans, a commensal of humans, can cause either mucosal or systemic infections. The virulence properties of the organism include cell-surface adhesins that recognize ligands of host cells. Hyphal forms of the organism possess a 60-kDa mannoprotein that recognizes a variety of host-cell ligands including the complement C3 conversion products, C3bi and C3d. In addition, a protein of similar molecular mass also binds to endothelial extracellular matrix proteins such as laminin and fibronectin. While the 60-kDa protein is associated with the cell surface of hyphal forms of the organism,

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Omahdi, Zakaria, Yuto Horikawa, Masamichi Nagae, et al. "Structural insight into the recognition of pathogen-derived phosphoglycolipids by C-type lectin receptor DCAR." Journal of Biological Chemistry 295, no. 17 (2020): 5807–17. http://dx.doi.org/10.1074/jbc.ra120.012491.

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The C-type lectin receptors (CLRs) form a family of pattern recognition receptors that recognize numerous pathogens, such as bacteria and fungi, and trigger innate immune responses. The extracellular carbohydrate-recognition domain (CRD) of CLRs forms a globular structure that can coordinate a Ca2+ ion, allowing receptor interactions with sugar-containing ligands. Although well-conserved, the CRD fold can also display differences that directly affect the specificity of the receptors for their ligands. Here, we report crystal structures at 1.8–2.3 Å resolutions of the CRD of murine dendritic ce

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Robertson, Michael J., Justin G. Meyerowitz, Ouliana Panova, Kenneth Borrelli, and Georgios Skiniotis. "Plasticity in ligand recognition at somatostatin receptors." Nature Structural & Molecular Biology 29, no. 3 (2022): 210–17. http://dx.doi.org/10.1038/s41594-022-00727-5.

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Ishiguro, M. "ligand Recognition and Structural Change of GPCR." Seibutsu Butsuri 41, supplement (2001): S20. http://dx.doi.org/10.2142/biophys.41.s20_3.

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CIERNIEWSKI, Czeslaw S., and Jolanta NIEWIAROWSKA. "Ligand Recognition by Cytoadhesins in Vascular Biology." Journal of Clinical Biochemistry and Nutrition 28, no. 3 (2000): 201–15. http://dx.doi.org/10.3164/jcbn.28.201.

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Verdino, P., C. Aldag, D. Hilvert, and I. A. Wilson. "Antibodies: specificity and promiscuity of ligand recognition." Acta Crystallographica Section A Foundations of Crystallography 62, a1 (2006): s38. http://dx.doi.org/10.1107/s0108767306099247.

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