CLiBE: a database of computed ligand binding energy for ligand–receptor complexes

2002 ◽  
Vol 26 (6) ◽  
pp. 661-666 ◽  
Author(s):  
X. Chen ◽  
Z.L. Ji ◽  
D.G. Zhi ◽  
Y.Z. Chen
Keyword(s):  
Binding Energy ◽  
Ligand Binding ◽  
Receptor Complexes

Search for approaches to improving the calculation accuracy of the protein—ligand binding energy by docking

2017 ◽  
Vol 66 (10) ◽  
pp. 1913-1924 ◽  
Author(s):  
A. V. Sulimov ◽  
D. C. Kutov ◽  
E. V. Katkova ◽  
O. A. Kondakova ◽  
V. B. Sulimov
Keyword(s):  
Binding Energy ◽  
Ligand Binding

scholarly journals Dap10 and Dap12 Form Distinct, but Functionally Cooperative, Receptor Complexes in Natural Killer Cells

2000 ◽  
Vol 192 (7) ◽  
pp. 1059-1068 ◽  
Author(s):  
Jun Wu ◽  
Holly Cherwinski ◽  
Thomas Spies ◽  
Joseph H. Phillips ◽  
Lewis L. Lanier
Keyword(s):  
Ligand Binding ◽  
Nk Cells ◽  
Natural Killer ◽  
Tyrosine Kinases ◽  
Nk Cell ◽  
Adaptor Proteins ◽  
Transmembrane Segments ◽  
Receptor Complexes ◽  
Activating Receptors ◽  
Specific Association

Many of the activating receptors on natural killer (NK) cells are multisubunit complexes composed of ligand-binding receptors that are noncovalently associated with membrane-bound signaling adaptor proteins, including CD3ζ, FcεRIγ, DAP12, and DAP10. Because the DAP10 and DAP12 genes are closely linked, expressed in NK cells, and have remarkably similar transmembrane segments, it was of interest to determine the specificity of their interactions with ligand-binding receptors and to examine their signaling properties. Despite their similarities, DAP10, DAP12, FcεRIγ, and CD3ζ form specific receptor complexes with their ligand-binding partners in NK cells and transfectants. The transmembrane regions of DAP10 and DAP12 are sufficient to confer specific association with their partners. Although cross-linking of either DAP10- or DAP12-associated receptors has been shown to be sufficient to trigger NK cell–mediated cytotoxicity against Fc receptor–bearing cells, substantial synergy was observed in the induction of cytokine production when both receptors were engaged. Activation of the Syk/ZAP70 tyrosine kinases by the immunoreceptor tyrosine-based activation motif–containing DAP12 adaptor and of the phosphatidylinositol 3-kinase pathway by the YxNM-containing DAP10 adaptor may play an important role in the stimulation of NK cells and T cells.

scholarly journals Noncontiguous regions in the extracellular domain of EGF receptor define ligand-binding specificity.

1991 ◽  
Vol 2 (5) ◽  
pp. 337-345 ◽  
Author(s):  
I Lax ◽  
R Fischer ◽  
C Ng ◽  
J Segre ◽  
A Ullrich ◽  
...  
Keyword(s):  
Binding Energy ◽  
Ligand Binding ◽  
Binding Site ◽  
Binding Affinity ◽  
Egf Receptor ◽  
Binding Properties ◽  
Amino Terminal ◽  
High Affinity ◽  
Domain Iii ◽  
Domain I

Murine epidermal growth factor (EGF) binds with approximately 250-fold higher binding affinity to the human EGF receptor (EGFR) than to the chicken EGFR. This difference in binding affinity enabled the identification of a major ligand-binding domain for EGF by studying the binding properties of various chicken/human EGFR chimera expressed in transfected cells lacking endogenous EGFR. It was shown that domain III of EGFR is a major ligand-binding region. Here, we analyze the binding properties of novel chicken/human chimera to further delineate the contact sequences in domain III and to assess the role of other regions of EGFR for their contribution to the display of high-affinity EGF binding. The chimeric receptors include chicken EGFR containing domain I of the human EGFR, chicken receptor containing domain I and III of the human EGFR, and two chimeric chicken EGFR containing either the amino terminal or the carboxy terminal halves of domain III of human EGFR, respectively. In addition, the binding of various human-specific anti-EGFR monoclonal antibodies that interfere with EGF binding is also compared. It is concluded that noncontiguous regions of the EGFR contribute additively to the binding of EGF. Each of the two halves of domain III has a similar contribution to the binding energy, and the sum of both is close to that of the entire domain III. This suggests that the folding of domain III juxtaposes sequences that together constitute the ligand-binding site. Domain I also provides a contribution to the binding energy, and the added contributions of both domain I and III to the binding energy generate the high-affinity binding site typical of human EGFR.

Regulation of interacting populations during endocytosis: models of growth factor-tumor promoter dynamics

1986 ◽  
Vol 250 (6) ◽  
pp. R1123-R1132
Author(s):  
M. Gex-Fabry ◽  
C. DeLisi
Keyword(s):  
Growth Factor ◽  
Ligand Binding ◽  
Phorbol Ester ◽  
Egf Receptor ◽  
Phorbol Esters ◽  
Time Lag ◽  
Tumor Promoter ◽  
Necessary Condition ◽  
Coated Pits ◽  
Receptor Complexes

A model of growth factor-cell receptor interactions, including internalization, sorting, recycling, and degradation and their modulation by tumor promoters, is developed, analyzed, and tested. In keeping with data and concepts based on a large number of systems, the main assumption is that after receptor-ligand binding the complex associates with a second membrane protein, localized in coated pits, and that this event is a necessary condition for receptor-mediated endocytosis and subsequent intracellular processes. As a consequence of the model, ligands having distinct receptors interfere at the cell surface through competition between their receptor complexes for a limited pool of coated pit proteins. The utility of the model is illustrated by a detailed analysis of binding, endocytosis, and degradation of epidermal growth factor (EGF) and their modulation by phorbol esters. The analysis permits quantitative characterization of the dynamics of the endocytic processes and leads to the following conclusions. The Scatchard plot changes from linear to nonlinear as the ratio of the number of coated pit proteins to the number of receptors decreases. Competition between phorbol ester and EGF-bound receptors for coated pit proteins predicts, in agreement with observation, conversion of nonlinear EGF Scatchard plots to linear plots subsequent to reincubation with phorbol esters. The postulated competition suggests a local homology between the phorbol ester receptor and the EGF receptor. Homologous and heterologous downregulations observed in numerous systems are natural consequences of the model. Preincubation with the heterologous ligand increases the time lag between ligand binding and lysosomal degradation and alters intracellular sorting.

scholarly journals Architecture and subunit arrangement of native AMPA receptors elucidated by cryo-EM

Science ◽  
2019 ◽  
Vol 364 (6438) ◽  
pp. 355-362 ◽  
Author(s):  
Yan Zhao ◽  
Shanshuang Chen ◽  
Adam C. Swensen ◽  
Wei-Jun Qian ◽  
Eric Gouaux
Keyword(s):  
Molecular Structure ◽  
Electron Microscopy ◽  
Signal Transduction ◽  
Ligand Binding ◽  
Ampa Receptor ◽  
Ampa Receptors ◽  
Mammalian Brain ◽  
Receptor Complexes ◽  
Cryo Electron Microscopy ◽  
Chemical Synapses

Glutamate-gated AMPA receptors mediate the fast component of excitatory signal transduction at chemical synapses throughout all regions of the mammalian brain. AMPA receptors are tetrameric assemblies composed of four subunits, GluA1–GluA4. Despite decades of study, the subunit composition, subunit arrangement, and molecular structure of native AMPA receptors remain unknown. Here we elucidate the structures of 10 distinct native AMPA receptor complexes by single-particle cryo–electron microscopy (cryo-EM). We find that receptor subunits are arranged nonstochastically, with the GluA2 subunit preferentially occupying the B and D positions of the tetramer and with triheteromeric assemblies comprising a major population of native AMPA receptors. Cryo-EM maps define the structure for S2-M4 linkers between the ligand-binding and transmembrane domains, suggesting how neurotransmitter binding is coupled to ion channel gating.

scholarly journals In silico approach of receptor-ligand binding and interaction: Established phytoligands from Tagetes errecta Linn. against bacterial β-glucosidase receptor

2019 ◽  
Vol 9 (1-s) ◽  
pp. 125-131
Author(s):  
Madhumita Lahiri ◽  
Partha Talukdar ◽  
Soumendra Nath Talapatra
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Ligand Binding ◽  
Antimicrobial Agents ◽  
Volatile Oil ◽  
Competitive Inhibitor ◽  
Ornamental Plant ◽  
Binding Interaction ◽  
Receptor Ligand ◽  
Energy Value

The medicinal plant, Tagetes errecta Linn. is a common ornamental plant and leaves of this plant are containing phytochemicals (volatile oil) that inhibit the growth of bacteria, fungi and known natural antimicrobial agents. The objective of the present study was to detect receptor-ligand binding energy and interaction through molecular docking for phytoligands established in the leaves of T. errecta against β-glucosidase receptor (PDB ID: 3AHZ). Molecular docking was performed by using PyRx (Version 0.8) for the structure-based virtual screening and visualized the interaction in the molecular graphic laboratory (MGL) tool (Version 1.5.6). Among 25 phytochemicals and 2 synthetic compounds (Carbendazim and 2-Amino-2-hydroxymethyl-propane-1,3-diol), binding energy value was obtained highest in Bicyclogermacrene (-6.4 Kcal/mol) and lowest in Octanol (-4.4 Kcal/mol) and Carbendazim and 2-Amino-2-hydroxymethyl-propane-1,3-diol showed -6.7 Kcal/mol and -3.5 Kcal/mol all of these showed no hydrogen bonding. The binding interaction of target protein with this phytocompound found binding at the mouth of the active site may be treated as competitive inhibitor. In conclusion, phytocompound Bicyclogermacrene can be alternative of synthetic fungicide as per binding energy value and interaction. It is suggesting further pharmacological and toxicological assay with this phytocompound after isolation from ornamental plant (T. errecta).

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