ligand clustering
Dotaz
Zobrazit nápovědu
Signaling by the human C-type lectin-like receptor, natural killer (NK) cell inhibitory receptor NKR-P1, has a critical role in many immune-related diseases and cancer. C-type lectin-like receptors have weak affinities to their ligands; therefore, setting up a comprehensive model of NKR-P1-LLT1 interactions that considers the natural state of the receptor on the cell surface is necessary to understand its functions. Here we report the crystal structures of the NKR-P1 and NKR-P1:LLT1 complexes, which provides evidence that NKR-P1 forms homodimers in an unexpected arrangement to enable LLT1 binding in two modes, bridging two LLT1 molecules. These interaction clusters are suggestive of an inhibitory immune synapse. By observing the formation of these clusters in solution using SEC-SAXS analysis, by dSTORM super-resolution microscopy on the cell surface, and by following their role in receptor signaling with freshly isolated NK cells, we show that only the ligation of both LLT1 binding interfaces leads to effective NKR-P1 inhibitory signaling. In summary, our findings collectively support a model of NKR-P1:LLT1 clustering, which allows the interacting proteins to overcome weak ligand-receptor affinity and to trigger signal transduction upon cellular contact in the immune synapse.
- MeSH
- antigeny povrchové MeSH
- buňky NK * MeSH
- difrakce rentgenového záření MeSH
- lektinové receptory NK-buněk - podrodina B MeSH
- lektiny typu C MeSH
- lidé MeSH
- ligandy MeSH
- maloúhlový rozptyl MeSH
- receptory buněčného povrchu * MeSH
- shluková analýza MeSH
- synapse MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
PrankWeb is an online resource providing an interface to P2Rank, a state-of-the-art method for ligand binding site prediction. P2Rank is a template-free machine learning method based on the prediction of local chemical neighborhood ligandability centered on points placed on a solvent-accessible protein surface. Points with a high ligandability score are then clustered to form the resulting ligand binding sites. In addition, PrankWeb provides a web interface enabling users to easily carry out the prediction and visually inspect the predicted binding sites via an integrated sequence-structure view. Moreover, PrankWeb can determine sequence conservation for the input molecule and use this in both the prediction and result visualization steps. Alongside its online visualization options, PrankWeb also offers the possibility of exporting the results as a PyMOL script for offline visualization. The web frontend communicates with the server side via a REST API. In high-throughput scenarios, therefore, users can utilize the server API directly, bypassing the need for a web-based frontend or installation of the P2Rank application. PrankWeb is available at http://prankweb.cz/, while the web application source code and the P2Rank method can be accessed at https://github.com/jendelel/PrankWebApp and https://github.com/rdk/p2rank, respectively.
- MeSH
- benchmarking MeSH
- datové soubory jako téma MeSH
- interakční proteinové domény a motivy MeSH
- internet MeSH
- konformace proteinů, alfa-helix MeSH
- konformace proteinů, beta-řetězec MeSH
- lidé MeSH
- ligandy MeSH
- proteiny chemie metabolismus MeSH
- sekvence aminokyselin MeSH
- software * MeSH
- strojové učení * MeSH
- termodynamika MeSH
- vazba proteinů MeSH
- vazebná místa MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Interactions between C-type lectin-like NK cell receptors and their protein ligands form one of the key recognition mechanisms of the innate immune system that is involved in the elimination of cells that have been malignantly transformed, virally infected, or stressed by chemotherapy or other factors. We determined an x-ray structure for the extracellular domain of mouse C-type lectin related (Clr) protein g, a ligand for the activation receptor NKR-P1F. Clr-g forms dimers in the crystal structure resembling those of human CD69. This newly reported structure, together with the previously determined structure of mouse receptor NKR-P1A, allowed the modeling and calculations of electrostatic profiles for other closely related receptors and ligands. Despite the high similarity among Clr-g, Clr-b, and human CD69, these molecules have fundamentally different electrostatics, with distinct polarization of Clr-g. The electrostatic profile of NKR-P1F is complementary to that of Clr-g, which suggests a plausible interaction mechanism based on contacts between surface sites of opposite potential.
- MeSH
- CD antigeny chemie imunologie MeSH
- diferenciační antigeny T-lymfocytů chemie imunologie MeSH
- krystalografie rentgenová MeSH
- lektiny typu C chemie imunologie MeSH
- lidé MeSH
- ligandy MeSH
- membránové proteiny chemie imunologie MeSH
- myši MeSH
- receptory imunologické chemie imunologie MeSH
- statická elektřina MeSH
- strukturní homologie proteinů MeSH
- terciární struktura proteinů MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Using the protein-protein docking program, this study investigates the relationship between TRAF2 and its related proteins and the diversity within the 3D structures of TRAF2s. TRAF2 exists in monomer, trimer, and hexamer forms and it can combine with a number of proteins. Through comparative analysis we found that TRAF2(122), TRAF2(22), TRAF2(21740), TRAF2(2), TRAF2( 22ABC), and TRAF2(Phyre) perform very close homoousia in docking with the same group of ligands, though these TRAF2s come from different sources. The TRAF2-related proteins of cluster 1 change docking values strongly from top to bottom. The TRAF2- related proteins of clusters 2 and 3 have acceptable variation of the docking values. In consideration of the amino acid percentage, TRAF2-related proteins of cluster 2 represent appropriate docking values.
MOTIVATION: Proteins often recognize their interaction partners on the basis of short linear motifs located in disordered regions on proteins' surface. Experimental techniques that study such motifs use short peptides to mimic the structural properties of interacting proteins. Continued development of these methods allows for large-scale screening, resulting in vast amounts of peptide sequences, potentially containing information on multiple protein-protein interactions. Processing of such datasets is a complex but essential task for large-scale studies investigating protein-protein interactions. RESULTS: The software tool presented in this article is able to rapidly identify multiple clusters of sequences carrying shared specificity motifs in massive datasets from various sources and generate multiple sequence alignments of identified clusters. The method was applied on a previously published smaller dataset containing distinct classes of ligands for SH3 domains, as well as on a new, an order of magnitude larger dataset containing epitopes for several monoclonal antibodies. The software successfully identified clusters of sequences mimicking epitopes of antibody targets, as well as secondary clusters revealing that the antibodies accept some deviations from original epitope sequences. Another test indicates that processing of even much larger datasets is computationally feasible. AVAILABILITY AND IMPLEMENTATION: Hammock is published under GNU GPL v. 3 license and is freely available as a standalone program (from http://www.recamo.cz/en/software/hammock-cluster-peptides/) or as a tool for the Galaxy toolbox (from https://toolshed.g2.bx.psu.edu/view/hammock/hammock). The source code can be downloaded from https://github.com/hammock-dev/hammock/releases. CONTACT: muller@mou.cz SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
- MeSH
- algoritmy * MeSH
- databáze proteinů * MeSH
- epitopy chemie MeSH
- interakční proteinové domény a motivy * MeSH
- lidé MeSH
- Markovovy řetězce MeSH
- molekulární sekvence - údaje MeSH
- monoklonální protilátky chemie MeSH
- peptidy chemie MeSH
- sekvence aminokyselin MeSH
- sekvenční seřazení MeSH
- shluková analýza MeSH
- software MeSH
- src homologní domény MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The mechanism of oxidative coupling of two naphthol molecules to form binaphthol catalyzed by Cu(OH)ClTMEDA (TMEDA=N,N,N',N'-tetramethylethylenediamine) was approached by means of a gas-phase model system. Concise evidence is provided that the coupling reaction proceeds in clusters with two Cu(II) centers, whereby the intermediacy of free naphthoxy radicals in the coupling step is avoided. In the absence of TMEDA, the cluster is bound via a bridging counterion and the coupling reaction is followed by cluster cleavage. The coordination of one or two TMEDA molecules to the reactive complex results in more efficient coupling of naphthol molecules, and moreover, the binuclear cluster is also conserved after the reaction is completed. The effect of TMEDA is twofold: First, it supports clustering of copper and, second, as a ligand bound to a copper center in the reactive complex, it weakens the bond between copper and the naphtholato ligand such that the naphtholato unit is more prone to undergo C--C coupling. Furthermore, a pronounced counterion effect is found that correlates well with condensed-phase data: weakly bridging counterions (e.g., NO3(-)) yield less stable dicopper clusters and the coupling reaction hardly occurs, whereas better bridging counterions (e.g., Cl(-) or Br(-)) provide more stable clusters that make the coupling reaction more efficient.
Gangliosides located at the outer leaflet of plasma membrane are molecules that either participate in recognizing of exogenous ligand molecules or exhibit their own receptor activity, which are both essential phenomena for cell communication and signaling as well as for virus and toxin entry. Regulatory mechanisms of lipid-mediated recognition are primarily subjected to the physical status of the membrane in close vicinity of the receptor. Concerning the multivalent receptor activity of the ganglioside GM1, several regulatory strategies dealing with GM1 clustering and cholesterol involvement have been proposed. So far however, merely the isolated issues were addressed and no interplay between them investigated. In this work, several advanced fluorescence techniques such as Z-scan fluorescence correlation spectroscopy, Förster resonance energy transfer combined with Monte Carlo simulations, and a newly developed fluorescence antibunching assay were employed to give a more complex portrait of clustering and cholesterol involvement in multivalent ligand recognition of GM1. Our results indicate that membrane properties have an impact on a fraction of GM1 molecules that is not available for the ligand binding. While at low GM1 densities (~1 %) it is the cholesterol that turns GM1 headgroups invisible, at higher GM1 level (~4 %) it is purely the local density of GM1 molecules that inhibits the recognition. At medium GM1 content, cooperation of the two phenomena occurs. This article is part of a Special Issue entitled: Nanoscale membrane organisation and signalling.
- MeSH
- buněčná membrána metabolismus MeSH
- cholesterol MeSH
- difuze MeSH
- G(M1) gangliosid chemie metabolismus MeSH
- hydraziny metabolismus MeSH
- ligandy MeSH
- metoda Monte Carlo MeSH
- ovce MeSH
- počítačová simulace MeSH
- receptory buněčného povrchu metabolismus MeSH
- rezonanční přenos fluorescenční energie MeSH
- shluková analýza MeSH
- titrace MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
T cell activation is initiated when ligand binding to the T cell receptor (TCR) triggers intracellular phosphorylation of the TCR-CD3 complex. However, it remains unknown how biophysical properties of TCR engagement result in biochemical phosphorylation events. Here, we constructed an optogenetic tool that induces spatial clustering of ζ-chain in a light controlled manner. We showed that spatial clustering of the ζ-chain intracellular tail alone was sufficient to initialize T cell triggering including phosphorylation of ζ-chain, Zap70, PLCγ, ERK and initiated Ca2+ flux. In reconstituted COS-7 cells, only Lck expression was required to initiate ζ-chain phosphorylation upon ζ-chain clustering, which leads to the recruitment of tandem SH2 domain of Zap70 from cell cytosol to the newly formed ζ-chain clusters at the plasma membrane. Taken together, our data demonstrated the biophysical relevance of receptor clustering in TCR signaling.
- MeSH
- aminokyselinové motivy MeSH
- buněčná membrána metabolismus MeSH
- Cercopithecus aethiops MeSH
- COS buňky MeSH
- cytosol metabolismus MeSH
- difuze MeSH
- fluorescenční spektrometrie MeSH
- fosforylace MeSH
- Jurkat buňky MeSH
- lidé MeSH
- optogenetika MeSH
- receptory antigenů T-buněk chemie metabolismus MeSH
- shluková analýza MeSH
- signální transdukce * MeSH
- světlo MeSH
- tyrosinkinasa p56(lck), specifická pro lymfocyty metabolismus MeSH
- vápník metabolismus MeSH
- zelené fluorescenční proteiny metabolismus MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
On the basis of the highly branched ovomucoid-type undecasaccharide that had been shown previously to be an endogenous ligand for CD69 leukocyte receptor, a systematic investigation of smaller oligosaccharide mimetics was performed based on linear and branched N-acetyl-d-hexosamine homooligomers prepared synthetically using hitherto unexplored reaction schemes. The systematic structure-activity studies revealed the tetrasaccharide GlcNAcbeta1-3(GlcNAcbeta1-4)(GlcNAcbeta1-6)GlcNAc (compound 52) and its alpha-benzyl derivative 49 as the best ligand for CD69 with IC(50) as high as 10(-9) M. This compound thus approaches the affinity of the classical high-affinity neoglycoprotein ligand GlcNAc(23)BSA. Compound 68, GlcNAc tetrasaccharide 52 dimerized through a hydrophilic flexible linker, turned out to be effective in activating CD69(+) lymphocytes. It also proved efficient in enhancing natural killing in vitro, decreasing the growth of tumors in vivo, and activating the CD69(+) tumor infiltrating lymphocytes examined ex vivo. This compound is thus a candidate for carbohydrate-based immunomodulators with promising antitumor potential.
- MeSH
- acetylglukosamin analogy a deriváty chemická syntéza chemie farmakologie MeSH
- aktivace lymfocytů MeSH
- buňky NK účinky léků imunologie metabolismus MeSH
- CD antigeny metabolismus MeSH
- diferenciační antigeny T-lymfocytů metabolismus MeSH
- dimerizace MeSH
- imunologické faktory chemická syntéza chemie farmakologie MeSH
- krysa rodu rattus MeSH
- lektinové receptory NK-buněk - podrodina B metabolismus MeSH
- lektiny typu C metabolismus MeSH
- lidé MeSH
- ligandy MeSH
- melanom experimentální imunologie patologie MeSH
- molekulární mimikry MeSH
- molekulární modely MeSH
- molekulární sekvence - údaje MeSH
- myši inbrední C57BL MeSH
- myši MeSH
- nádorové buněčné linie MeSH
- oligosacharidy chemická syntéza chemie farmakologie MeSH
- protinádorové látky chemická syntéza chemie farmakologie MeSH
- rekombinantní proteiny chemie MeSH
- sacharidové sekvence MeSH
- screeningové testy protinádorových léčiv MeSH
- techniky in vitro MeSH
- zvířata MeSH
- Check Tag
- krysa rodu rattus MeSH
- lidé MeSH
- myši MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- odvolaná publikace MeSH
- práce podpořená grantem MeSH
