Relevant bibliographies by topics / AtGLR3.3 ligand-binding domain structure

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Academic literature on the topic 'AtGLR3.3 ligand-binding domain structure'

Author: Grafiati
Published: 9 March 2023
Last updated: 10 March 2023

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

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Bell, J. K., I. Botos, P. R. Hall, J. Askins, J. Shiloach, D. M. Segal, and D. R. Davies. "The molecular structure of the Toll-like receptor 3 ligand-binding domain." Proceedings of the National Academy of Sciences 102, no. 31 (July 25, 2005): 10976–80. http://dx.doi.org/10.1073/pnas.0505077102.

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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 (September 15, 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 panel anti-chicken beta 1 mAbs. Epitopes were identified by a loss of antibody binding upon substitution of regions of the chicken beta 1 subunit by homologous regions of the mouse beta 1 subunit. The identification of the epitope was confirmed by a reciprocal exchange of chicken and mouse beta 1 domains that resulted in the gain of the ability of the mouse subunit to interact with a particular anti-chicken beta 1 mAb. Using this approach, we found that the epitopes for one set of antibodies that block ligand binding mapped toward the amino terminal region of the beta 1 subunit. This region is homologous to a portion of the ligand-binding domain of the beta 3 subunit. In addition, a second set of antibodies that either block ligand binding, alter ligand specificity, or induce alpha/beta subunit dissociation mapped to the cysteine rich repeats near the transmembrane domain of the molecule. These data are consistent with a model in which a portion of beta 1 ligand binding domain rests within the amino terminal 200 amino acids and a regulatory domain, that affects ligand binding through secondary changes in the structure of the molecule resides in a region of the subunit, possibly including the cysteine-rich repeats, nearer the transmembrane domain. The data also suggest the possibility that the alpha subunit may exert an influence on ligand specificity by interacting with this regulatory domain of the beta 1 subunit.
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Jensen, Maria Risager, Goran Bajic, Xianwei Zhang, Anne Kjær Laustsen, Heidi Koldsø, Katrine Kirkeby Skeby, Birgit Schiøtt, Gregers R. Andersen, and Thomas Vorup-Jensen. "Structural Basis for Simvastatin Competitive Antagonism of Complement Receptor 3." Journal of Biological Chemistry 291, no. 33 (June 23, 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 binding to the complement fragments iC3b and C3d but not to intercellular adhesion molecule-1. By virtue of the I domain's wide distribution in binding kinetics to ligands, it was possible to identify ligand binding kinetics as discriminator for simvastatin antagonism. In static cellular experiments, 15–25 μm simvastatin reduced adhesion by K562 cells expressing recombinant CR3 and by primary human monocytes, with an endogenous expression of this receptor. Application of force to adhering monocytes potentiated the effects of simvastatin where only a 50–100 nm concentration of the drug reduced the adhesion by 20–40% compared with untreated cells. The ability of simvastatin to target CR3 in its ligand binding-activated conformation is a novel mechanism to explain the known anti-inflammatory effects of this compound, in particular because this CR3 conformation is found in pro-inflammatory environments. Our report points to new designs of CR3 antagonists and opens new perspectives and identifies druggable receptors from characterization of the ligand binding kinetics in the presence of antagonists.
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Springer, Timothy A., Junichi Takagi, Barry S. Coller, Jia-Huai Wang, and 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, no. 11 (November 16, 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 (2.7–3.1 and 2.9 Å resolution), respectively. Ca2+ was assigned at the 4 αIIb β-hairpin sites in blades 4–7, and I-like (βA) LIMBS and ADMIDAS; Mg2+ was assigned to MIDAS. The major findings are: 1) As compared to unliganded αVβ3, αIIbβ3 has a ~62° outward pivot of the β3 hybrid domain from the I-like (βA) domain, indicating adoption of an open, high affinity conformation driven by cacodylate or the Asp (D) carboxyl of the drugs binding to MIDAS and acting as activating ligand equivalents. 2) The αIIb ligand binding cleft is rigid and includes αIIb D224 [end-on H bond to ligand Lys (K) or Arg (R)] and hydrophobic residues F160, Y190, and F231, accounting for the selective binding to αIIbβ3 (vs αVβ3) of KGD and homoarginine-GDW peptides, fibrinogen γ-chain peptide, eptifibatide, and tirofiban. 3) 10E5 Fab interacts with a unique “cap” subdomain in αIIb formed by 4 insertions in β-propeller loops in blades 1–3 that form a β-sheet and α-helix structure involved in ligand binding. 4) Comparison of unliganded αVβ3 and liganded αIIbβ3 indicates that receptor activation and ligand binding involves: extensive movement of β3 subunit β1-α1 loop and α1 helix, and β6-α7 loop and α7 helix; alterations in the coordinating residues at the ADMIDAS, MIDAS, and LIMBS; and breaking the ADMIDAS Ca2+ coordination by the M335 backbone carbonyl (providing a mechanism by which Mn2+, which competes with Ca2+ at the ADMIDAS but has a lower propensity for carbonyl coordination than Ca2+, activates integrins). The 62° pivot results from a one-turn piston-like displacement of the α7 helix involving a hydrophobic ratchet of the β6-α7 loop; a ratchet motion of the α1-helix in which L134 moves to the space previously occupied by V340; and complete remodeling at the interface between the β3 I-like (βA) and hybrid domains. 5) The structure of the β3 PSI domain reveals that the long range disulfide is between β3 C13 (rather than C5) and C435, and comparison to the PSI of semaphorin 4D demonstrates that C435 is an integral part of the PSI domain fold. Thus, the I-like (βA) domain appears to be inserted in the hybrid domain, which is inserted in the PSI domain. 6) The structure reveals the location of the Leu/Pro-33 PSI polymorphism responsible for the HPA1 alloantigen. At a rigid interface with the hybrid domain, polymorphism of Arg93 demonstrates the requirement of the hybrid/PSI interface for alloantigenicity at Leu-33. Overall, the structure reveals how allostery regulates ligand binding affinity of αIIbβ3, and how the outward swing of the lever-like hybrid and PSI domains communicates the conformation of the ligand binding site to the α and β leg domains, and to the membrane and cytosol.
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Kolenko, Petr, Daniel Rozbeský, Tereza Skálová, Tomáš Kovaľ, Karla Fejfarová, Jarmila Dušková, Jan Stránský, Jindřich Hašek, and Jan Dohnálek. "Domain swapping in structure of mNKR-P1A: unique feature with unknown function." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 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, observation of domain swapping in crystal structure of mouse (m) NKR-P1A represents an unusual structural feature that might be involved in a new mechanism of ligand binding that would be specific for some members of NKR-P1 family. Nevertheless, our crystal structure of mNKR-P1A represents a unique structural observation that demands careful analysis. Even the latest structural studies do not answer the question of function or role of swapped domain of the receptor in potential ligand binding. We have generated new variants of mNKR-P1A of varied chain length that undergo biochemical and structural analysis including mass spectrometry.
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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 (October 31, 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 bundle domain. AadA crystallizes as a monomer and is a monomer in solution as confirmed by small-angle X-ray scattering, in contrast to structurally similar homodimeric adenylating enzymes such as kanamycin nucleotidyltransferase. Isothermal titration calorimetry experiments show that ATP binding has to occur before binding of the aminoglycoside substrate, and structure analysis suggests that ATP binding repositions the two domains for aminoglycoside binding in the interdomain cleft. Candidate residues for ligand binding and catalysis were subjected to site-directed mutagenesis.In vivoresistance andin vitrobinding assays support the role of Glu87 as the catalytic base in adenylation, while Arg192 and Lys205 are shown to be critical for ATP binding.
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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 (November 9, 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 compact structure versus that in the 3′,3′-cGAMP-bound state. The binding of the 3′,3′-cGAMP molecule to the 3′,3′-cGAMP riboswitch induces the rotation of P1 helix through the allosteric communication from the binding sites pocket containing the J1/2, J1/3 and J2/3 junction to the P1 helix. Simultaneously, these simulations also revealed that the preferential binding of the 3′,3′-cGAMP riboswitch to its cognate ligand, 3′,3′-cGAMP, over its noncognate ligand, c-di-GMP and c-di-AMP. The J1/2 junction in the 3′,3′-cGAMP riboswitch contributing to the specificity of ligand recognition have also been found.
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Rudenko, Gabby, Thai Nguyen, Yogarany Chelliah, Thomas C. Südhof, and Johann Deisenhofer. "Regulation of LNS Domain Function by Alternative Splicing: The Structure of the Ligand-Binding Domain of Neurexin Iβ." Cell 99, no. 1 (October 1999): 93–101. http://dx.doi.org/10.1016/s0092-8674(00)80065-3.

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9

Tamura, Tatsushiro, Jun Yamanouchi, Shigeru Fujita, and Takaaki Hato. "Critical residues for ligand binding in blade 2 of the propeller domain of the integrin αIIb subunit." Thrombosis and Haemostasis 91, no. 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 RGD ligand in the crystal structure of the αV propeller. Replacement by alanine of Q111, H112 or N114 in the loop within the blade 2 (the W2:2-3 loop in the propeller model) abolished binding of a ligand-mimetic antibody and fibrinogen to αIIbβ3 induced by different types of integrin activation including activation of αIIbβ3 by β3 cytoplasmic mutation. CHO cells stably expressing recombinant αIIbβ3 bearing Q111A, H112A or N114A mutation did not exhibit αIIbβ3mediated adhesion to fibrinogen. According to the crystal structure of αVβ3, the αV residue corresponding to αIIbN114 is exposed on the integrin surface and close to the RGD binding site. These results suggest that the Q111, H112 and N114 residues in the loop within blade 2 of the αIIb propeller are critical for ligand binding, possibly because of direct interaction with ligands or modulation of the RGD binding pocket.
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Rossjohn, Jamie, William J. McKinstry, Joanna M. Woodcock, Barbara J. McClure, Timothy R. Hercus, Michael W. Parker, Angel F. Lopez, and Christopher J. Bagley. "Structure of the activation domain of the GM-CSF/IL-3/IL-5 receptor common β-chain bound to an antagonist." Blood 95, no. 8 (April 15, 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-chain (βc) signaling subunit in complex with the Fab fragment of the antagonistic monoclonal antibody, BION-1. This is the first single antagonist of all 3 known eosinophil-producing cytokines, and it is therefore capable of regulating eosinophil-related diseases such as asthma. The structure reveals a fibronectin type III domain, and the antagonist-binding site involves major contributions from the loop between the B and C strands and overlaps the cytokine-binding site. Furthermore, tyrosine421 (Tyr421), a key residue involved in receptor activation, lies in the neighboring loop between the F and G strands, although it is not immediately adjacent to the cytokine-binding residues in the B-C loop. Interestingly, functional experiments using receptors mutated across these loops demonstrate that they are cooperatively involved in full receptor activation. The experiments, however, reveal subtle differences between the B-C loop and Tyr421, which is suggestive of distinct functional roles. The elucidation of the structure of the ligand-binding domain of βc also suggests how different cytokines recognize a single receptor subunit, which may have implications for homologous receptor systems.
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Dissertations / Theses on the topic "AtGLR3.3 ligand-binding domain structure"

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Xue, Yu Lord Susan T. "Study protein-protein interaction in methyl-directed DNA mismatch repair in E. coli exonuclease I Exo I and DNA helicas II UvrD; A minimal exonuclease domain of WRN forms a hexamer on DNA and possesses both 3'-5' exonuclease and 5'-protruding strand endonuclease activities; Solving the structure of the ligand-binding domain of the pregnane-xenobiotic-receptor with 17[beta] estradiol and T1317 /." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2008. http://dc.lib.unc.edu/u?/etd,2015.

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Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2008.
Title from electronic title page (viewed Feb. 17, 2009). "... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Chemistry." Discipline: Chemistry; Department/School: Chemistry.
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Book chapters on the topic "AtGLR3.3 ligand-binding domain structure"

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Gallastegui, Nerea, and Eva Estébanez-Perpiñá. "Thinking Outside the Box: Alternative Binding Sites in the Ligand Binding Domain of Nuclear Receptors." In Nuclear Receptors: From Structure to the Clinic, 179–203. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-18729-7_10.

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Reynaud, J. P., V. Bissery, C. Gaboriaud, T. Ojasoo, G. Teutsch, and J. P. Mornon. "An Analysis of the Steroid Binding Domain of Receptors and of Ligand Structure and Binding Affinity." In The Steroid/Thyroid Hormone Receptor Family and Gene Regulation, 337–66. Basel: Birkhäuser Basel, 1989. http://dx.doi.org/10.1007/978-3-0348-5466-5_24.

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Conference papers on the topic "AtGLR3.3 ligand-binding domain structure"

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Beeler, D., L. Fritze, G. Soff, R. Jackman, and R. Rosenberg. "HUMAN THROMBOMODULIN cDNA:SEQUENCE AND TRANSLATED STRUCTURE." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643967.

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A 750 bp bovine Thrombomodulin (TM) cDNA fragment was used as an hybridization probe to screen an oligo-dT primed Lambda gtll. cDNA library prepared from human umbilical vein endothelial cell mRNA. A 2.4 kb positive human clone was isolated which showed an 80% nucleotide sequence homology with bovine TM cDNA. This clone and a 550 bp fragment from its 5' end were used to further screen the oligo-dT primed library as well as randomly primed library prepared from the same mRNA. The cDNA clones obtained allow us to describe the overall structure of human TM and reveal that it is extremely similar to the structure of bovine TM, especially as the bovine TM is organized like the receptor for low density lipoprotein (LDL R). Both TM and LDL R exhibit short cytoplasmic C-terminal tails which are either neutral or negatively charged. Other coated pit receptors such as the insulin receptor or the epidermal growth factor (EGF) receptor have very large cytoplasmic regions with a complex tyrosine kinase segment as well as multiple sites for phosphorylation. Both TM and LDL R possess a transmembrane region and an immediately adjacent extracellular serine/threonine rich region which in LDL R has been shown to bear 0-1inked sugars. Both TM and LDL R contain a more distal area of cysteine rich repeats, first noted in the EGF precursor and termed EGF type B. However, the TM EGF type B repeats appear to have been duplicated in TM resulting in their being 6 of them rather than the 3 found in LDL R. The N-terminal half of LDL R is thought to contain the ligand binding region of the receptor and is constructed from multiple cysteine rich repeats similar to those of Complement factor C9. The structure of this region of TM is quite different from that of LDL R, possessing few cysteines. We suspect that protein C and/or thrombin may bind to this unique domain of TM.
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