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Journal articles on the topic 'AtGLR3.3 ligand-binding domain structure'

Author: Grafiati

Published: 9 March 2023

Last updated: 31 July 2025

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1

Shih, DT, JM Edelman, AF Horwitz, GB Grunwald, and CA Buck. "Structure/function analysis of the integrin beta 1 subunit by epitope mapping." Journal of Cell Biology 122, no. 6 (1993): 1361–71. http://dx.doi.org/10.1083/jcb.122.6.1361.

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Monoclonal antibodies (mAbs) have been produced against the chicken beta 1 subunit that affect integrin functions, including ligand binding, alpha subunit association, and regulation of ligand specificity. Epitope mapping of these antibodies was used to identify regions of the subunit involved in these functions. To accomplish this, we produced mouse/chicken chimeric beta 1 subunits and expressed them in mouse 3T3 cells. These chimeric subunits were fully functional with respect to heterodimer formation, cell surface expression, and cell adhesion. They differed in their ability to react with a

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2

Jensen, Maria Risager, Goran Bajic, Xianwei Zhang, et al. "Structural Basis for Simvastatin Competitive Antagonism of Complement Receptor 3." Journal of Biological Chemistry 291, no. 33 (2016): 16963–76. http://dx.doi.org/10.1074/jbc.m116.732222.

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The complement system is an important part of the innate immune response to infection but may also cause severe complications during inflammation. Small molecule antagonists to complement receptor 3 (CR3) have been widely sought, but a structural basis for their mode of action is not available. We report here on the structure of the human CR3 ligand-binding I domain in complex with simvastatin. Simvastatin targets the metal ion-dependent adhesion site of the open, ligand-binding conformation of the CR3 I domain by direct contact with the chelated Mg2+ ion. Simvastatin antagonizes I domain bind

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Springer, Timothy A., Junichi Takagi, Barry S. Coller, Jia-Huai Wang та Tsan Xiao. "Crystal Structure of the Integrin αIIBβ3 Headpiece at 2.7–3.1 Å: Structure, Mechanisms of Activation and Ligand Binding, Inhibition by Eptifibatide, Tirofiban, and mAb 10E5, and Structure of the HPA-1 Alloantigen Epitope." Blood 104, № 11 (2004): 327. http://dx.doi.org/10.1182/blood.v104.11.327.327.

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Abstract The αIIbβ3 headpiece (αIIb, 1–621; β3, 1–472) was expressed in CHO cells, purified, digested with chymotrypsin, mixed with either mAb 10E5 Fab (form A) or without (form B), repurified, digested with carboxypeptidase (leaving αIIb, 1–452 and β3, 1–440) and crystallized with PEG, Mg acetate, and Na cacodylate at 4°C. Cocrystallization of αIIbβ3/10E5 (A) with eptifibatide or tirofiban was with imidazole instead of cacodylate. Crystals were diffracted at APS and CHESS and analyzed by HKL2000, AMoRe, O, CNS, and CCP4 software. Crystal forms A and B contain 1 and 3 molecules/asymmetric unit

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4

Bell, J. K., I. Botos, P. R. Hall, et al. "The molecular structure of the Toll-like receptor 3 ligand-binding domain." Proceedings of the National Academy of Sciences 102, no. 31 (2005): 10976–80. http://dx.doi.org/10.1073/pnas.0505077102.

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5

Kolenko, Petr, Daniel Rozbeský, Tereza Skálová, et al. "Domain swapping in structure of mNKR-P1A: unique feature with unknown function." Acta Crystallographica Section A Foundations and Advances 70, a1 (2014): C249. http://dx.doi.org/10.1107/s2053273314097502.

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Natural killer (NK) cells, large granular lymphocytes, play an important role in the innate immune response against viruses, parasites and tumour cells. NK cells use a wide repertoire of surface receptors to modulate their activity [1]. The family of NKR-P1 surface receptors of NK cells belong to proteins with C-type lectin-like (CTL) fold. The overall architecture of other known CTL receptors (e.g. members of Ly49 family, NKG2D, CD94, mouse CLRg) is conserved [2]. The mechanism of ligand binding has been revealed by the crystal structure of Nkp65 bound to its keratinocyte ligand [3]. However,

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Tamura, Tatsushiro, Jun Yamanouchi, Shigeru Fujita та Takaaki Hato. "Critical residues for ligand binding in blade 2 of the propeller domain of the integrin αIIb subunit". Thrombosis and Haemostasis 91, № 01 (2004): 111–18. http://dx.doi.org/10.1160/th03-06-0392.

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SummaryLigand binding to integrin αIIbβ3 is a key event of thrombus formation. The propeller domain of the αIIb subunit has been implicated in ligand binding. Recently, the ligand binding site of the αV propeller was determined by crystal structure analysis. However, the structural basis of ligand recognition by the αIIb propeller remains to be determined. In this study, we conducted site-directed mutagenesis of all residues located in the loops extending above blades 2 and 4 of the αIIb propeller, which are spatially close to, but distinct from, the loops that contain the binding site for an

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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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8

Rossjohn, Jamie, William J. McKinstry, Joanna M. Woodcock та ін. "Structure of the activation domain of the GM-CSF/IL-3/IL-5 receptor common β-chain bound to an antagonist". Blood 95, № 8 (2000): 2491–98. http://dx.doi.org/10.1182/blood.v95.8.2491.

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Abstract Heterodimeric cytokine receptors generally consist of a major cytokine-binding subunit and a signaling subunit. The latter can transduce signals by more than 1 cytokine, as exemplified by the granulocyte-macrophage colony-stimulating factor (GM-CSF), interleukin-2 (IL-2), and IL-6 receptor systems. However, often the signaling subunits in isolation are unable to bind cytokines, a fact that has made it more difficult to obtain structural definition of their ligand-binding sites. This report details the crystal structure of the ligand-binding domain of the GM-CSF/IL-3/IL-5 receptor β-ch

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Rossjohn, Jamie, William J. McKinstry, Joanna M. Woodcock та ін. "Structure of the activation domain of the GM-CSF/IL-3/IL-5 receptor common β-chain bound to an antagonist". Blood 95, № 8 (2000): 2491–98. http://dx.doi.org/10.1182/blood.v95.8.2491.008k06_2491_2498.

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Heterodimeric cytokine receptors generally consist of a major cytokine-binding subunit and a signaling subunit. The latter can transduce signals by more than 1 cytokine, as exemplified by the granulocyte-macrophage colony-stimulating factor (GM-CSF), interleukin-2 (IL-2), and IL-6 receptor systems. However, often the signaling subunits in isolation are unable to bind cytokines, a fact that has made it more difficult to obtain structural definition of their ligand-binding sites. This report details the crystal structure of the ligand-binding domain of the GM-CSF/IL-3/IL-5 receptor β-chain (βc)

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10

Ozheriedov, D. S., and P. A. Karpov. "Structural profile of ligand-based inhibition of bacterial FtsZ." Faktori eksperimental'noi evolucii organizmiv 32 (September 1, 2023): 142–47. http://dx.doi.org/10.7124/feeo.v32.1551.

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Aim. The idea of the study was to compare and generalize RCSB Protein Data Bank and ChEMBL data in order to establish the structural and biological relationship of experimentaly proved effectors of FtsZ with binding sites. Methods. Literature and database search. Comparison of protein and ligand structures. Protein structure modeling, MD, structural superimposition, etc. Results. The experimental protein-ligand complexes structures of bacterial FtsZ were revised. The structural superimposition of experinental PDB and full-atomic AlphaFold2 models of bacterial FtsZs confirmed their significant

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Chen, Yang, Joakim Näsvall, Shiying Wu, Dan I. Andersson, and Maria Selmer. "Structure of AadA fromSalmonella enterica: a monomeric aminoglycoside (3′′)(9) adenyltransferase." Acta Crystallographica Section D Biological Crystallography 71, no. 11 (2015): 2267–77. http://dx.doi.org/10.1107/s1399004715016429.

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Aminoglycoside resistance is commonly conferred by enzymatic modification of drugs by aminoglycoside-modifying enzymes such as aminoglycoside nucleotidyltransferases (ANTs). Here, the first crystal structure of an ANT(3′′)(9) adenyltransferase, AadA fromSalmonella enterica, is presented. AadA catalyses the magnesium-dependent transfer of adenosine monophosphate from ATP to the two chemically dissimilar drugs streptomycin and spectinomycin. The structure was solved using selenium SAD phasing and refined to 2.5 Å resolution. AadA consists of a nucleotidyltransferase domain and an α-helical bundl

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12

Sayre, P. H., R. E. Hussey, H. C. Chang, T. L. Ciardelli, and E. L. Reinherz. "Structural and binding analysis of a two domain extracellular CD2 molecule." Journal of Experimental Medicine 169, no. 3 (1989): 995–1009. http://dx.doi.org/10.1084/jem.169.3.995.

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The 50-kD CD2 (T11) surface glycoprotein on human T lymphocytes and thymocytes plays a critical role in T lineage cell activation and adhesion via its ligand LFA-3. To begin to define structure-function relationships in the extracellular segment of the transmembrane CD2 molecule, we have used a eukaryotic expression system and a CD2 cDNA to produce milligram amounts of recombinant soluble CD2 molecule that corresponds to the two extracellular segment exons. We show that this protein, termed T11ex2, behaves as a monomer in aqueous solution and includes a proteolytically resistant NH2-terminal f

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13

Smaldone, Giovanni, Alessia Ruggiero, Nicole Balasco, and Luigi Vitagliano. "Development of a Protein Scaffold for Arginine Sensing Generated through the Dissection of the Arginine-Binding Protein from Thermotoga maritima." International Journal of Molecular Sciences 21, no. 20 (2020): 7503. http://dx.doi.org/10.3390/ijms21207503.

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Arginine is one of the most important nutrients of living organisms as it plays a major role in important biological pathways. However, the accumulation of arginine as consequence of metabolic defects causes hyperargininemia, an autosomal recessive disorder. Therefore, the efficient detection of the arginine is a field of relevant biomedical/biotechnological interest. Here, we developed protein variants suitable for arginine sensing by mutating and dissecting the multimeric and multidomain structure of Thermotoga maritima arginine-binding protein (TmArgBP). Indeed, previous studies have shown

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14

Akke, Mikael. "Conformational dynamics and thermodynamics of protein–ligand binding studied by NMR relaxation." Biochemical Society Transactions 40, no. 2 (2012): 419–23. http://dx.doi.org/10.1042/bst20110750.

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Protein conformational dynamics can be critical for ligand binding in two ways that relate to kinetics and thermodynamics respectively. First, conformational transitions between different substates can control access to the binding site (kinetics). Secondly, differences between free and ligand-bound states in their conformational fluctuations contribute to the entropy of ligand binding (thermodynamics). In the present paper, I focus on the second topic, summarizing our recent results on the role of conformational entropy in ligand binding to Gal3C (the carbohydrate-recognition domain of galect

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15

Laursen, Louise, Elin Karlsson, Stefano Gianni, and Per Jemth. "Functional interplay between protein domains in a supramodular structure involving the postsynaptic density protein PSD-95." Journal of Biological Chemistry 295, no. 7 (2019): 1992–2000. http://dx.doi.org/10.1074/jbc.ra119.011050.

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Cell scaffolding and signaling are governed by protein–protein interactions. Although a particular interaction is often defined by two specific domains binding to each other, this interaction often occurs in the context of other domains in multidomain proteins. How such adjacent domains form supertertiary structures and modulate protein–protein interactions has only recently been addressed and is incompletely understood. The postsynaptic density protein PSD-95 contains a three-domain supramodule, denoted PSG, which consists of PDZ, Src homology 3 (SH3), and guanylate kinase-like domains. The P

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16

Wright, P. S., V. Saudek, T. J. Owen, S. L. Harbeson, and A. J. Bitonti. "An echistatin C-terminal peptide activates GPIIbIIIa binding to fibrinogen, fibronectin, vitronectin and collagen type I and type IV." Biochemical Journal 293, no. 1 (1993): 263–67. http://dx.doi.org/10.1042/bj2930263.

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Integrin binding to proteins often involves recognition of domains containing the arginine-glycine-aspartate (RGD) motif. Different binding affinities and specificities of the integrin-ligand protein interactions involve additional protein domains. The n.m.r. structure of the snake-venom protein echistatin suggested that the C-terminal portion of the molecule might be important, in addition to the RGD domain, in binding to the integrin glycoprotein IIbIIIa (GPIIbIIIa) [Saudek, Atkinson and Pelton (1991) Biochem. 30, 7369-7372]. The synthetic C-terminal peptide, echistatin-(40-49), PRNPHKGPAT,

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17

Byrne, Lee J., Ateesh Sidhu, A. Katrine Wallis, et al. "Mapping of the ligand-binding site on the b′ domain of human PDI: interaction with peptide ligands and the x-linker region." Biochemical Journal 423, no. 2 (2009): 209–17. http://dx.doi.org/10.1042/bj20090565.

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PDI (protein disulfide-isomerase) catalyses the formation of native disulfide bonds of secretory proteins in the endoplasmic reticulum. PDI consists of four thioredoxin-like domains, of which two contain redox-active catalytic sites (a and a′), and two do not (b and b′). The b′ domain is primarily responsible for substrate binding, although the nature and specificity of the substrate-binding site is still poorly understood. In the present study, we show that the b′ domain of human PDI is in conformational exchange, but that its structure is stabilized by the addition of peptide ligands or by b

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18

Akçeşme, Faruk Berat, Nail Beşli, Jorge Peña-García, and Horacio Pérez-Sánchez. "Assessment of Interaction of Human OCT 1-3 Proteins and Metformin Using Silico Analyses." Acta Chimica Slovenica 67, no. 4 (2020): 1202–15. http://dx.doi.org/10.17344/acsi.2020.6108.

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Metformin, a drug frequently used by diabetic patients as the first-line treatment worldwide, is positively charged and is transported into the cell through human organic cation transporter (hOCT 1-3) proteins. We aimed to mimic the cellular uptake of metformin by hOCT1-3 with various bioinformatics methods and tools. 3D structure of OCT1-3 proteins was predicted by considering the structures and function of these proteins. We predicted functional regions (active and ligand binding sites) of OCT1-3 and performed comparative bioinformatics analysis. The predicted structure of hOCT1-3 was then a

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19

Suino-Powell, Kelly, Yong Xu, Chenghai Zhang, et al. "Doubling the Size of the Glucocorticoid Receptor Ligand Binding Pocket by Deacylcortivazol." Molecular and Cellular Biology 28, no. 6 (2007): 1915–23. http://dx.doi.org/10.1128/mcb.01541-07.

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ABSTRACT A common feature of nuclear receptor ligand binding domains (LBD) is a helical sandwich fold that nests a ligand binding pocket within the bottom half of the domain. Here we report that the ligand pocket of glucocorticoid receptor (GR) can be continuously extended into the top half of the LBD by binding to deacylcortivazol (DAC), an extremely potent glucocorticoid. It has been puzzling for decades why DAC, which contains a phenylpyrazole replacement at the conserved 3-ketone of steroid hormones that are normally required for activation of their cognate receptors, is a potent GR activa

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Rudenko, Gabby, Thai Nguyen, Yogarany Chelliah, Thomas C. Südhof та Johann Deisenhofer. "Regulation of LNS Domain Function by Alternative Splicing: The Structure of the Ligand-Binding Domain of Neurexin Iβ". Cell 99, № 1 (1999): 93–101. http://dx.doi.org/10.1016/s0092-8674(00)80065-3.

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21

Fernandes, Humberto, Honorata Czapinska, Katarzyna Grudziaz, Janusz M. Bujnicki, and Martyna Nowacka. "Crystal structure of human Acinus RNA recognition motif domain." PeerJ 6 (July 4, 2018): e5163. http://dx.doi.org/10.7717/peerj.5163.

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Acinus is an abundant nuclear protein involved in apoptosis and splicing. It has been implicated in inducing apoptotic chromatin condensation and DNA fragmentation during programmed cell death. Acinus undergoes activation by proteolytic cleavage that produces a truncated p17 form that comprises only the RNA recognition motif (RRM) domain. We have determined the crystal structure of the human Acinus RRM domain (AcRRM) at 1.65 Å resolution. It shows a classical four-stranded antiparallel β-sheet fold with two flanking α-helices and an additional, non-classical α-helix at the C-terminus, which ha

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22

Yu, Xinzhe, and Ping Yi. "Structural Insights of Transcriptionally Active, Full-Length Androgen Receptor Coactivator Complexes." Journal of the Endocrine Society 5, Supplement_1 (2021): A817. http://dx.doi.org/10.1210/jendso/bvab048.1665.

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Abstract Steroid hormone receptors activate gene transcription by binding specific DNA sequences and recruiting coactivators to initiate transcription of their target genes. For most nuclear hormone receptors (NRs), the ligand-dependent activation function domain-2 (AF-2), residing in the C-terminal ligand binding domain (LBD), is a primary contributor to the NR transcriptional activity. In contrast to other steroid receptors such as estrogen receptor-α (ERα), the transcriptional activation function of androgen receptor (AR) is thought to be largely dependent on its ligand-independent activati

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Boesen, Christian C., Sergei Radaev, Shawn A. Motyka, Apisit Patamawenu та Peter D. Sun. "The 1.1 Å Crystal Structure of Human TGF-β Type II Receptor Ligand Binding Domain". Structure 10, № 7 (2002): 913–19. http://dx.doi.org/10.1016/s0969-2126(02)00780-3.

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24

Sharma, Tripti. "INSILICO DOCKING APPROACH TO STUDY THE BINDING AFFINITY OF ISOFLAVONES ON THE CRYSTAL STRUCTURE OF ESTROGEN RECEPTOR ALPHA." INDIAN DRUGS 54, no. 10 (2017): 7–15. http://dx.doi.org/10.53879/id.54.10.11152.

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The objective of the study was to carry out docking studies of isoflavone derivatives and examine their binding efficiencies to the ligand binding domain of ERα using Autodock program. A series of isoflavone derivatives were computationally designed and optimized with the AutoDock Vina software to investigate the interactions between the target compounds and the amino acid residues of the ERα.. In silico docking studies were carried out using AutoDock Vina, based on the Lamarckian genetics algorithm principle. The results showed that all the selected isoflavones showed binding energy ranging b

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Slater, Alexandre, Ying Di, Joanne C. Clark, et al. "Structural characterization of a novel GPVI-nanobody complex reveals a biologically active domain-swapped GPVI dimer." Blood 137, no. 24 (2021): 3443–53. http://dx.doi.org/10.1182/blood.2020009440.

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Abstract Glycoprotein VI (GPVI) is the major signaling receptor for collagen on platelets. We have raised 54 nanobodies (Nb), grouped into 33 structural classes based on their complementary determining region 3 loops, against recombinant GPVI-Fc (dimeric GPVI) and have characterized their ability to bind recombinant GPVI, resting and activated platelets, and to inhibit platelet activation by collagen. Nbs from 6 different binding classes showed the strongest binding to recombinant GPVI-Fc, suggesting that there was not a single dominant class. The most potent 3, Nb2, 21, and 35, inhibited coll

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Ramos, Jorge, Wonyong Jung, Josefina Ramos-Franco, Gregory A. Mignery, and Michael Fill. "Single Channel Function of Inositol 1,4,5-trisphosphate Receptor Type-1 and -2 Isoform Domain-Swap Chimeras." Journal of General Physiology 121, no. 5 (2003): 399–411. http://dx.doi.org/10.1085/jgp.200208718.

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The InsP3R proteins have three recognized domains, the InsP3-binding, regulatory/coupling, and channel domains (Mignery, G.A., and T.C. Südhof. 1990. EMBO J. 9:3893–3898). The InsP3 binding domain and the channel-forming domain are at opposite ends of the protein. Ligand regulation of the channel must involve communication between these different regions of the protein. This communication likely involves the interceding sequence (i.e., the regulatory/coupling domain). The single channel functional attributes of the full-length recombinant type-1, -2, and -3 InsP3R channels have been defined.

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Boggon, Titus J. "Jak3 Kinase Domain Crystal Structures and Implications for Jak-Specific Drug Design." Blood 106, no. 11 (2005): 69. http://dx.doi.org/10.1182/blood.v106.11.69.69.

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Abstract Janus (Jak) family non-receptor tyrosine kinases are critical for appropriate signaling of many growth factors and cytokines. The four vertebrate Jak kinase family members demonstrate differential receptor cytoplasmic tail binding associations and transduce discrete signals on extracellular binding of ligand to the transmembrane cytokine or growth factor receptor. On ligand binding, a rapid tyrosine phosphorylation mediated signaling cascade is initiated, culminating in translocation of cytosolic latent transcription factors, signal transducer and activator of transcription (Stat) pro

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28

Oliveira, Laerte, Claudio M. Costa-Neto, Clovis R. Nakaie, Shirley Schreier, Suma I. Shimuta, and Antonio C. M. Paiva. "The Angiotensin II AT1 Receptor Structure-Activity Correlations in the Light of Rhodopsin Structure." Physiological Reviews 87, no. 2 (2007): 565–92. http://dx.doi.org/10.1152/physrev.00040.2005.

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The most prevalent physiological effects of ANG II, the main product of the renin-angiotensin system, are mediated by the AT1 receptor, a rhodopsin-like AGPCR. Numerous studies of the cardiovascular effects of synthetic peptide analogs allowed a detailed mapping of ANG II's structural requirements for receptor binding and activation, which were complemented by site-directed mutagenesis studies on the AT1 receptor to investigate the role of its structure in ligand binding, signal transduction, phosphorylation, binding to arrestins, internalization, desensitization, tachyphylaxis, and other prop

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Sakurai, Shunya, Umeharu Ohto, and Toshiyuki Shimizu. "Structure of human Roquin-2 and its complex with constitutive-decay element RNA." Acta Crystallographica Section F Structural Biology Communications 71, no. 8 (2015): 1048–54. http://dx.doi.org/10.1107/s2053230x15011887.

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Roquin mediates mRNA degradation by recognizing the constitutive-decay element (CDE) in the 3′ untranslated region of the target gene followed by recruitment of the deadenylation machinery. Deficiency or dysfunction of Roquin has been associated with autoimmunity and inflammation. To establish the structural basis for the recognition of CDE RNA by Roquin, the crystal structure of the ROQ domain of human Roquin-2 was determined in ligand-free and CDE-derived RNA-bound forms. The ROQ domain of Roquin-2 folded into a winged-helix structure in which the wing region showed structural flexibility an

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Kiran, K. S., M. K. Kokila, Guruprasad R, and Niranjan M.S. "Crystal Structure Determination and Molecular Docking Studies of 4- (5-Phenyl Pyrazin-2-Yl)-4h-1,2,4 Triazole-3-Thiol with Focal Adhesion Kinase Inhibitors." Open Chemistry Journal 3, no. 1 (2016): 69–74. http://dx.doi.org/10.2174/1874842201603010069.

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The main objective of the present work is to determine crystal structure of the ligand by x-ray methods and to perform molecular docking studies of the ligand 4- Phenyl -5-Pyrazinyl-3-mercapto 1,2,4 Triazole with protein focal adhesion kinase (FAK) domain using the software, Autodock and pymol. Macromolecular modeling by docking studies provides the most detailed view possible of drug receptor interaction. It has created a new rational approach to drug design, where the structure of drug is designed, based on its fit to three dimensional structures of receptor site, rather than basing it on an

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Radaeva, Mariia, Huifang Li, Eric LeBlanc, et al. "Structure-Based Study to Overcome Cross-Reactivity of Novel Androgen Receptor Inhibitors." Cells 11, no. 18 (2022): 2785. http://dx.doi.org/10.3390/cells11182785.

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The mutation-driven transformation of clinical anti-androgen drugs into agonists of the human androgen receptor (AR) represents a major challenge for the treatment of prostate cancer patients. To address this challenge, we have developed a novel class of inhibitors targeting the DNA-binding domain (DBD) of the receptor, which is distanced from the androgen binding site (ABS) targeted by all conventional anti-AR drugs and prone to resistant mutations. While many members of the developed 4-(4-phenylthiazol-2-yl)morpholine series of AR-DBD inhibitors demonstrated the effective suppression of wild

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Mankelow, Tosti J., Nicholas Burton, Fanney O. Stefansdottir, et al. "Characterisation of the Laminin 10/11 Binding Site on the Lutheran Glycoprotein Suggests a Novel Type of Protein-Protein Interaction." Blood 108, no. 11 (2006): 1566. http://dx.doi.org/10.1182/blood.v108.11.1566.1566.

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Abstract The Lutheran glycoprotein is a five domain member of the immunoglobulin superfamily (IgSF) with a wide tissue distribution. It is a ligand for Laminin isoforms containing the alpha5 chain (Laminins 10 and 11). Lutheran glycoprotein on erythrocytes is thought to play a role in vasocclusive events that are a serious cause of morbidity in sickle cell anaemia. We have investigated the molecular basis of the Lutheran:Laminin 10/11 interaction. Lutheran binding to Laminin 10/11 is pH and salt dependent suggesting the interaction is influenced by surface charge. Since Laminins are known to c

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Tweardy, David John, Xu Xuejun, Naijie Jing, and Huang Shao. "Structural Determinants for Signal Transducer and Activator of Transcription (STAT) 3 Recruitment and Activation by the Granulocyte Colony-Stimulating Factor Receptor (G-CSFR) at Phosphotyrosine Ligands 704 and 744." Blood 104, no. 11 (2004): 2169. http://dx.doi.org/10.1182/blood.v104.11.2169.2169.

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Abstract Four tyrosine (Y) residues within the cytoplasmic domain of the G-CSFR (Y704, Y228, Y744 and Y764 in the human receptor; Y703, Y227, Y743 and Y763 in the murine receptor) become phosphorylated by Jak kinases upon ligand binding leading to recruitment of Src homology (SH) 2 domain-containing proteins that link to programs for myeloid cell survival and differentiation (Stat3 recruitment to Y704 and Y744) and proliferation (SHP-2 and PI3K recruitment to Y04; Grb2, Shc and SHP-2 recruitment to Y764). While the preference of SH2 domain binding to specific phospho (p) Y peptide ligands was

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Howard, Barbara-Ann, George Thom, Ian Jeffrey, Dave Colthurst, David Knowles, and Catherine Prescott. "Fragmentation of the ribosome to investigate RNA–ligand interactions." Biochemistry and Cell Biology 73, no. 11-12 (1995): 1161–66. http://dx.doi.org/10.1139/o95-125.

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RNA molecules perform a variety of important and diverse functions and, therefore, an understanding of their structure and interaction with proteins and ligands is essential. Large RNA molecules (for example, the ribosomal RNAs) are complex and hence reports describing their fragmentation into functional subdomains has provided a means for their detailed analysis. We present here an in vivo approach to study RNA–ligand interactions. This is based on the concept that an RNA fragment could mimic a drug-binding site present on the intact molecule. Overexpression of the fragment would sequester th

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COUETTE, Brigitte, Jérôme FAGART, Stéphan JALAGUIER, Marc LOMBES, Anny SOUQUE, and Marie-Edith RAFESTIN-OBLIN. "Ligand-induced conformational change in the human mineralocorticoid receptor occurs within its hetero-oligomeric structure." Biochemical Journal 315, no. 2 (1996): 421–27. http://dx.doi.org/10.1042/bj3150421.

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To determine the first steps involved in the mechanism of action of aldosterone and its antagonists, we analysed the ligand-induced structural changes of the human mineralocorticoid receptor (hMR) translated in vitro. Limited chymotrypsin digestion of the receptor generated a 30 kDa fragment. Following binding of a ligand to hMR, the 30 kDa fragment became resistant to chymotrypsin proteolysis, indicating a change in the receptor conformation. Differences in sensitivity to chymotrypsin of the 30 kDa fragment were observed after binding of agonists and antagonists to hMR, suggesting that these

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Yang, Zhao, Zhi-Li Huang, and Ya-Xiong Tao. "Functions of DPLIY motif and helix 8 of human melanocortin-3 receptor." Journal of Molecular Endocrinology 55, no. 2 (2015): 107–17. http://dx.doi.org/10.1530/jme-15-0116.

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The melanocortin-3 receptor (MC3R) is a member of the family A G protein-coupled receptors (GPCRs). The MC3R remains the most enigmatic of the melanocortin receptors with regard to its physiological functions, especially its role in energy homeostasis. The N/DPxxY motif and the eighth helix (helix 8) in the carboxyl terminus of GPCRs have been identified to be important for receptor expression, ligand binding, signal transduction and internalization. To gain a better understanding of the structure-function relationship of MC3R, we performed a systematic study of all 20 residues in this domain

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Booker, Grant W., Ivan Gout, A. Kristina^Downing та ін. "Solution structure and ligand-binding site of the SH3 domain of the p85α subunit of phosphatidylinositol 3-kinase". Cell 73, № 4 (1993): 813–22. http://dx.doi.org/10.1016/0092-8674(93)90259-s.

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Fujiwara, Yoshie, Natsuko Goda, Tomonari Tamashiro, et al. "Crystal structure of afadin PDZ domain-nectin-3 complex shows the structural plasticity of the ligand-binding site." Protein Science 24, no. 3 (2015): 376–85. http://dx.doi.org/10.1002/pro.2628.

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Cash, Devin R., Nicholas Noinaj, Susan K. Buchanan, and Cynthia Nau Cornelissen. "Beyond the Crystal Structure: Insight into the Function and Vaccine Potential of TbpA Expressed by Neisseria gonorrhoeae." Infection and Immunity 83, no. 11 (2015): 4438–49. http://dx.doi.org/10.1128/iai.00762-15.

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ABSTRACTNeisseria gonorrhoeae, the causative agent of the sexually transmitted infection gonorrhea, is not preventable by vaccination and is rapidly developing resistance to antibiotics. However, the transferrin (Tf) receptor system, composed of TbpA and TbpB, is an ideal target for novel therapeutics and vaccine development. Using a three-dimensional structure of gonococcal TbpA, we investigated two hypotheses, i.e., that loop-derived antibodies can interrupt ligand-receptor interactions in the native bacterium and that the loop 3 helix is a critical functional domain. Preliminary loop-derive

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Gustafsson, Jan-Åke. "Steroids and the Scientist." Molecular Endocrinology 19, no. 6 (2005): 1412–17. http://dx.doi.org/10.1210/me.2004-0479.

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Abstract Our interest in nuclear receptors (NRs) originated from early studies on hepatic steroid metabolism. We discovered a new hypothalamo-pituitary-liver axis, imprinted neonatally by androgens and operating through sexually differentiated GH secretory patterns. Male and female patterns have opposite effects on sexually differentiated hepatic genes, explaining sexually dimorphic liver patterns. To further understand steroid action, we purified the glucocorticoid receptor (GR) leading to our discovery of the NR three-domain structure, with separable DNA binding domain and ligand binding dom

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Yong, E. "Partial androgen insensitivity and correlations with the predicted three dimensional structure of the androgen receptor ligand-binding domain." Molecular and Cellular Endocrinology 137, no. 1 (1998): 41–50. http://dx.doi.org/10.1016/s0303-7207(97)00229-3.

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Wang, Lu, Jihong Li та Barry S. Coller. "Loss of the Interaction Linking the αIIb Thigh Domain K514 to the β3 I-EGF2 Domain E500 Results in Constitutive Fibrinogen Binding to αIIbβ3". Blood 144, Supplement 1 (2024): 5416. https://doi.org/10.1182/blood-2024-205370.

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Introduction: Structure/function studies have shown 3 major conformations of αIIbβ3, bent-closed, extended-closed, and extended-open. We recently noted the interaction of K514 in the thigh domain of αIIb with E500 in the I-EGF2 domain of β3 in the bent, closed conformation because we produced a mAb (R21D10) that 1) disrupts this interaction, 2) traps a semi-extended conformation in which the K514-E500 is lost and a new interaction is created between αIIb R516 and β3 E475, 3) partially inhibits fibrinogen binding and platelet aggregation. The K514-E500 interaction must be broken in order for αI

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Jääskeläinen, J., A. Deeb, J. W. Schwabe, N. P. Mongan, H. Martin, and I. A. Hughes. "Human androgen receptor gene ligand-binding-domain mutations leading to disrupted interaction between the N- and C-terminal domains." Journal of Molecular Endocrinology 36, no. 2 (2006): 361–68. http://dx.doi.org/10.1677/jme.1.01885.

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Most mutations in the androgen receptor (AR) ligand-binding domain (LBD) disrupt binding of the natural ligands: dihydrotestosterone and testosterone. Some AR LBD mutations do not affect ligand binding but they disrupt androgen-induced interaction of the N-terminal motif FXXLF and C-terminal activation function 2 (AF2). As N-/C-terminal interaction requires binding of agonists that have androgen activity in vivo, it correlates well with the phenotype. To study this further, we searched the Cambridge intersex database for patients with a detected missense mutation in the AR LBD presenting with

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Solowska, J., J. M. Edelman, S. M. Albelda, and C. A. Buck. "Cytoplasmic and transmembrane domains of integrin beta 1 and beta 3 subunits are functionally interchangeable." Journal of Cell Biology 114, no. 5 (1991): 1079–88. http://dx.doi.org/10.1083/jcb.114.5.1079.

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Integrin beta subunits combine with specific sets of alpha subunits to form functional adhesion receptors. The structure and binding properties of integrins suggest the presence of domains controlling at least three major functions: subunit association, ligand binding, and cytoskeletal interactions. To more carefully define structure/function relationships, a cDNA construct consisting of the extracellular domain of the avian beta 1 subunit and the cytoplasmic and transmembrane domains of the human beta 3 subunit was prepared and expressed in murine 3T3 cells. The resulting chimeric beta 1/3 su

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Hung, Tzu-Chieh, Tung-Ti Chang, Ming-Jen Fan, Cheng-Chun Lee, and Calvin Yu-Chian Chen. "In SilicoInsight into Potent of Anthocyanin Regulation of FKBP52 to Prevent Alzheimer’s Disease." Evidence-Based Complementary and Alternative Medicine 2014 (2014): 1–20. http://dx.doi.org/10.1155/2014/450592.

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Alzheimer’s disease (AD) is caused by the hyperphosphorylation of Tau protein aggregation. FKBP52 (FK506 binding protein 52) has been found to inhibit Tau protein aggregation. This study found six different kinds of anthocyanins that have high binding potential. After analyzing the docking positions, hydrophobic interactions, and hydrogen bond interactions, several amino acids were identified that play important roles in protein and ligand interaction. The proteins’ variation is described using eigenvectors and the distance between the amino acids during a molecular dynamics simulation (MD). T

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Kristensen, C., A. S. Andersen, M. Hach, F. C. Wiberg, L. Schäffer, and T. Kjeldsen. "A single-chain insulin-like growth factor I/insulin hybrid binds with high affinity to the insulin receptor." Biochemical Journal 305, no. 3 (1995): 981–86. http://dx.doi.org/10.1042/bj3050981.

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1. To investigate the structure/function relationship of the interaction between ligand and receptor in the insulin-like growth factor I (IGF-I) and insulin receptor systems we have prepared and characterized a single-chain insulin/IGF-I hybrid. The single-chain hybrid consists of the insulin molecule combined with the C domain of IGF-I. The single-chain hybrid was found to bind with high affinity to both truncated soluble insulin receptors and membrane-bound holoreceptors. The affinity for interacting with the soluble truncated insulin receptors was 55-94% relative to insulin, and affinity fo

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Babgi, Bandar A., Jalal H. Alsayari, Bambar Davaasuren та ін. "Synthesis, Structural Studies, and Anticancer Properties of [CuBr(PPh3)2(4,6-Dimethyl-2-Thiopyrimidine-κS]". Crystals 11, № 6 (2021): 688. http://dx.doi.org/10.3390/cryst11060688.

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CuBr(PPh3)2(4,6-dimethylpyrimidine-2-thione) (Cu-L) was synthesized by stirring CuBr(PPh3)3 and 4,6-dimethylpyrimidine-2-thione in dichloromethane. The crystal structure of Cu-L was obtained, and indicated that the complex adopts a distorted tetrahedral structure with several intramolecular hydrogen bonds. Moreover, a centrosymmetric dimer is formed by the intermolecular hydrogen bonding of the bromine acceptor created by symmetry operation 1−x, 1−y, 1−z to the methyl group (D3 = C42) of the pyrimidine–thione ligand. HSA-binding of Cu-L and its ligand were evaluated, revealing that Cu-L binds

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Nowicki, B., A. Hart, K. E. Coyne, D. M. Lublin, and S. Nowicki. "Short consensus repeat-3 domain of recombinant decay-accelerating factor is recognized by Escherichia coli recombinant Dr adhesin in a model of a cell-cell interaction." Journal of Experimental Medicine 178, no. 6 (1993): 2115–21. http://dx.doi.org/10.1084/jem.178.6.2115.

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A bacterial pathogen that is important in both urinary tract and intestinal infections is Escherichia coli which expresses Dr or related adhesins. In this report, we present a model for testing cell-cell interaction, using both molecularly characterized laboratory cells that express recombinant molecules of human decay-accelerating factor (DAF), and recombinant bacterial Dr colonization factors. Dr adhesin ligand was identified as DAF (CD55), a membrane protein that protects autologous tissues from damage due to the complement system. Structure-function studies mapped the adhesin-binding site

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Hassan, Mujtaba, Klaveren Sjors van, Maria Hakansson, et al. "Benzimidazole–galactosides bind selectively to the Galectin-8 N-Terminal domain: Structure-based design and optimisation." European Journal of Medicinal Chemistry 223 (June 25, 2021): 113664. https://doi.org/10.1016/j.ejmech.2021.113664.

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We have obtained the X-ray crystal structure of the galectin-8 N-terminal domain (galectin-8N) with a previously reported quinoline–galactoside ligand at a resolution of 1.6 Å. Based on this X-ray structure, a collection of galactosides derivatised at O3 with triazole, benzimidazole, benzothiazole, and benzoxazole moieties were designed and synthesised. This led to the discovery of a 3-<em>O-</em>(N-methylbenzimidazolylmethyl)–galactoside with a K<sub>d</sub> of 1.8 μM for galectin-8N, the most potent selective synthetic galectin-8N

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Gordon, Wendy R., Monideepa Roy, Didem Vardar-Ulu, et al. "Structure of the Notch1-negative regulatory region: implications for normal activation and pathogenic signaling in T-ALL." Blood 113, no. 18 (2009): 4381–90. http://dx.doi.org/10.1182/blood-2008-08-174748.

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Abstract Proteolytic resistance of Notch prior to ligand binding depends on the structural integrity of a negative regulatory region (NRR) of the receptor that immediately precedes the transmembrane segment. The NRR includes the 3 Lin12/Notch repeats and the juxtamembrane heterodimerization domain, the region of Notch1 most frequently mutated in T-cell acute lymphoblastic leukemia lymphoma (T-ALL). Here, we report the x-ray structure of the Notch1 NRR in its autoinhibited conformation. A key feature of the Notch1 structure that maintains its closed conformation is a conserved hydrophobic plug

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