Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

2D SIFt: a matrix of ligand-receptor interactions.

ABSTRACT: Depicting a ligand-receptor complex via Interaction Fingerprints has been shown to be both a viable data visualization and an analysis tool. The spectrum of its applications ranges from simple visualization of the binding site through analysis of molecular dynamics runs, to the evaluation of the homology models and virtual screening. Here we present a novel tool derived from the Structural Interaction Fingerprints providing a detailed and unique insight into the interactions between receptor and specific regions of the ligand (grouped into pharmacophore features) in the form of a matrix, a 2D-SIFt descriptor. The provided implementation is easy to use and extends the python library, allowing the generation of interaction matrices and their manipulation (reading and writing as well as producing the average 2D-SIFt). The library for handling the interaction matrices is available via repository http://bitbucket.org/zchl/sift2d .

SUBMITTER: Mordalski S

PROVIDER: S-EPMC8424890 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

2D SIFt: a matrix of ligand-receptor interactions.

Mordalski Stefan S Wojtuch Agnieszka A Podolak Igor I Kurczab Rafał R Bojarski Andrzej J AJ

Journal of cheminformatics 20210908 1

Depicting a ligand-receptor complex via Interaction Fingerprints has been shown to be both a viable data visualization and an analysis tool. The spectrum of its applications ranges from simple visualization of the binding site through analysis of molecular dynamics runs, to the evaluation of the homology models and virtual screening. Here we present a novel tool derived from the Structural Interaction Fingerprints providing a detailed and unique insight into the interactions between receptor and ...[more]

PMID: 34496955

Similar Datasets

Exploiting ligand-protein conjugates to monitor ligand-receptor interactions.

Project description:We introduce three assays for analyzing ligand-receptor interactions based on the specific conjugation of ligands to SNAP-tag fusion proteins. Conjugation of ligands to different SNAP-tag fusions permits the validation of suspected interactions in cell extracts and fixed cells as well as the establishment of high-throughput assays. The different assays allow the analysis of strong and weak interactions. Conversion of ligands into SNAP-tag substrates thus provides access to a powerful toolbox for the analysis of their interactions with proteins.

| S-EPMC3365113 | biostudies-literature

LeView: automatic and interactive generation of 2D diagrams for biomacromolecule/ligand interactions.

Project description:: 2D diagrams are widely used in the scientific literature to represent interactions between ligands and biomacromolecules. Such schematic diagrams are very helpful to better understand the chemical interactions and biological processes in which ligands are involved. Here, a new tool for automatic and interactive generation of 2D diagrams for biomacromolecule/ligand interactions is presented. LeView (Ligand-Environment Viewer) produces customised and high-quality figures, with a good compromise between a faithful representation of the 3D data (structures and interactions) and aesthetic criteria. LeView can be freely downloaded at http://www.pegase-biosciences.com/tools/leview/.

| S-EPMC3765711 | biostudies-literature

Structural Analysis of Chemokine Receptor-Ligand Interactions.

Project description:This review focuses on the construction and application of structural chemokine receptor models for the elucidation of molecular determinants of chemokine receptor modulation and the structure-based discovery and design of chemokine receptor ligands. A comparative analysis of ligand binding pockets in chemokine receptors is presented, including a detailed description of the CXCR4, CCR2, CCR5, CCR9, and US28 X-ray structures, and their implication for modeling molecular interactions of chemokine receptors with small-molecule ligands, peptide ligands, and large antibodies and chemokines. These studies demonstrate how the integration of new structural information on chemokine receptors with extensive structure-activity relationship and site-directed mutagenesis data facilitates the prediction of the structure of chemokine receptor-ligand complexes that have not been crystallized. Finally, a review of structure-based ligand discovery and design studies based on chemokine receptor crystal structures and homology models illustrates the possibilities and challenges to find novel ligands for chemokine receptors.

| S-EPMC5483895 | biostudies-literature

Diversity in Notch ligand-receptor signaling interactions.

Project description:The Notch signaling pathway uses families of ligands and receptors to transmit signals to nearby cells. These components are expressed in diverse combinations in different cell types, interact in a many-to-many fashion, both within the same cell (in cis) and between cells (in trans), and their interactions are modulated by Fringe glycosyltransferases. A fundamental question is how the strength of Notch signaling depends on which pathway components are expressed, at what levels, and in which cells. Here, we used a quantitative, bottom-up, cell-based approach to systematically characterize trans-activation, cis-inhibition, and cis-activation signaling efficiencies across a range of ligand and Fringe expression levels in Chinese hamster and mouse cell lines. Each ligand (Dll1, Dll4, Jag1, and Jag2) and receptor variant (Notch1 and Notch2) analyzed here exhibited a unique profile of interactions, Fringe dependence, and signaling outcomes. All four ligands were able to bind receptors in cis and in trans, and all ligands trans-activated both receptors, although Jag1-Notch1 signaling was substantially weaker than other ligand-receptor combinations. Cis-interactions were predominantly inhibitory, with the exception of the Dll1- and Dll4-Notch2 pairs, which exhibited cis-activation stronger than trans-activation. Lfng strengthened Delta-mediated trans-activation and weakened Jagged-mediated trans-activation for both receptors. Finally, cis-ligands showed diverse cis-inhibition strengths, which depended on the identity of the trans-ligand as well as the receptor. The map of receptor-ligand-Fringe interaction outcomes revealed here should help guide rational perturbation and control of the Notch pathway.

| S-EPMC11698495 | biostudies-literature

Monitoring ligand-receptor interactions by photonic force microscopy.

Project description:We introduce a method for the acquisition of single molecule force measurements of ligand-receptor interactions using the photonic force microscope (PFM). Biotin-functionalized beads, manipulated with an optical trap, and a streptavidin-functionalized coverslip were used to measure the effect of different pulling forces on the lifetime of individual streptavidin-biotin complexes. By optimizing the design of the optical trap and selection of the appropriate bead size, pulling forces in excess of 50 pN were achieved. Based on the amplitude of three-dimensional (3D) thermal position fluctuations of the attached bead, we were able to select for a bead-coverslip interaction that was mediated by a single streptavidin-biotin complex. Moreover, the developed experimental system was greatly accelerated by automation of data acquisition and analysis. In force-dependent kinetic measurements carried out between streptavidin and biotin, we observed that the streptavidin-biotin complex exhibited properties of a catch bond, with the lifetime increasing tenfold when the pulling force increased from 10 to 20 pN. We also show that silica beads were more appropriate than polystyrene beads for the force measurements, as tethers, longer than 200 nm, could be extracted from polystyrene beads.

| S-EPMC3255327 | biostudies-literature

The flexibility-complementarity dichotomy in receptor-ligand interactions.

Project description:Synthetic supramolecular complexes provide an opportunity for quantitative systematic exploration of the relationship between chemical structure and molecular recognition phenomena. A family of closely related zinc porphyrin-pyridine complexes was used to examine the interplay of conformational flexibility and geometric complementarity in determining the selectivity of molecular recognition events. The association constants of 48 zinc porphyrin-pyridine complexes were measured in two different solvents, toluene and 1,1,2,2-tetrachloroethane (TCE). These association constants were used to construct 32 chemical double mutant cycles to dissect the free energy contributions of intramolecular H-bonds between the phenol side arms of the porphyrins and the ester or amide side arms of the pyridine ligands. Effective molarities (EM) for the intramolecular interactions were determined by comparison with the corresponding intermolecular H-bonding interactions. The values of EM do not depend on the solvent and are practically identical for amide and ester H-bond acceptors located at the same site on the ligand framework. However, there are variations of an order of magnitude in EM depending on the flexibility of the linker used to connect the H-bond acceptors to the pyridine ligands. Rigid aromatic linkers give values of EM that are an order of magnitude higher than the values of EM for the corresponding ester linkers, which have one additional torsional degree of freedom. However, the most flexible ether linkers give values of EM that are also higher than the values of EM for the corresponding ester linkers, which have one less torsional degree of freedom. Although the penalty for conformational restriction on binding is higher for the more flexible ether linkers, this flexibility allows optimization of the geometric complementarity of the ligand for the receptor, so there is a trade off between preorganization and fit.

| S-EPMC5811160 | biostudies-literature

Dysregulated ligand-receptor interactions from single-cell transcriptomics.

Project description:MotivationIntracellular communication is crucial to many biological processes, such as differentiation, development, homeostasis and inflammation. Single-cell transcriptomics provides an unprecedented opportunity for studying cell-cell communications mediated by ligand-receptor interactions. Although computational methods have been developed to infer cell type-specific ligand-receptor interactions from one single-cell transcriptomics profile, there is lack of approaches considering ligand and receptor simultaneously to identifying dysregulated interactions across conditions from multiple single-cell profiles.ResultsWe developed scLR, a statistical method for examining dysregulated ligand-receptor interactions between two conditions. scLR models the distribution of the product of ligands and receptors expressions and accounts for inter-sample variances and small sample sizes. scLR achieved high sensitivity and specificity in simulation studies. scLR revealed important cytokine signaling between macrophages and proliferating T cells during severe acute COVID-19 infection, and activated TGF-β signaling from alveolar type II cells in the pathogenesis of pulmonary fibrosis.Availability and implementationscLR is freely available at https://github.com/cyhsuTN/scLR.Supplementary informationSupplementary data are available at Bioinformatics online.

| S-EPMC9191214 | biostudies-literature

Extracellular matrix ligand and stiffness modulate immature nucleus pulposus cell-cell interactions.

Project description:The nucleus pulposus (NP) of the intervertebral disc functions to provide compressive load support in the spine, and contains cells that play a critical role in the generation and maintenance of this tissue. The NP cell population undergoes significant morphological and phenotypic changes during maturation and aging, transitioning from large, vacuolated immature cells arranged in cell clusters to a sparse population of smaller, isolated chondrocyte-like cells. These morphological and organizational changes appear to correlate with the first signs of degenerative changes within the intervertebral disc. The extracellular matrix of the immature NP is a soft, gelatinous material containing multiple laminin isoforms, features that are unique to the NP relative to other regions of the disc and that change with aging and degeneration. Based on this knowledge, we hypothesized that a soft, laminin-rich extracellular matrix environment would promote NP cell-cell interactions and phenotypes similar to those found in immature NP tissues. NP cells were isolated from porcine intervertebral discs and cultured in matrix environments of varying mechanical stiffness that were functionalized with various matrix ligands; cellular responses to periods of culture were assessed using quantitative measures of cell organization and phenotype. Results show that soft (<720 Pa), laminin-containing extracellular matrix substrates promote NP cell morphologies, cell-cell interactions, and proteoglycan production in vitro, and that this behavior is dependent upon both extracellular matrix ligand and substrate mechanical properties. These findings indicate that NP cell organization and phenotype may be highly sensitive to their surrounding extracellular matrix environment.

| S-EPMC3210142 | biostudies-literature

Validation of extracellular ligand-receptor interactions by Flow-TriCEPS.

Project description:ObjectiveThe advent of ligand-based receptor capture methodologies, allows the identification of unknown receptor candidates for orphan extracellular ligands. However, further target validation can be tedious, laborious and time-consuming. Here, we present a methodology that provides a fast and cost-efficient alternative for candidate target verification on living cells.ResultsIn the described methodology a ligand of interest (e.g. transferrin, epidermal growth factor or insulin) was conjugated to a linker (TriCEPS) that carries a biotin. To confirm ligand/receptor interactions, the ligand-TriCEPS conjugates were first added onto living cells and cells were subsequently labeled with a streptavidin-fluorophore and analyzed by flow cytometry (thus referred as Flow-TriCEPS). Flow-TriCEPS was also used to validate identified receptor candidates when combined with a siRNA knock down approach (i.e. reduction of expression levels). This approach is versatile as it can be applied for different classes of ligands (proteins, peptides, antibodies) and different cell lines. Moreover, the method is time-efficient since it takes advantage of the large variety of commercially available (and certified) siRNAs.

| S-EPMC6280402 | biostudies-literature

Chemokine ligand-receptor interactions critically regulate cutaneous wound healing.

Project description:BackgroundWound healing represents a dynamic process involving directional migration of different cell types. Chemokines, a family of chemoattractive proteins, have been suggested to be key players in cell-to-cell communication and essential for directed migration of structural cells. Today, the role of the chemokine network in cutaneous wound healing is not fully understood. Unraveling the chemokine-driven communication pathways in this complex process could possibly lead to new therapeutic strategies in wound healing disorders.MethodsWe performed a systematic, comprehensive time-course analysis of the expression and function of a broad variety of cytokines, growth factors, adhesion molecules, matrixmetalloproteinases and chemokines in a murine cutaneous wound healing model.ResultsStrikingly, chemokines were found to be among the most highly regulated genes and their expression was found to coincide with the expression of their matching receptors. Accordingly, we could show that resting and activated human primary keratinocytes (CCR3, CCR4, CCR6, CXCR1, CXCR3), dermal fibroblasts (CCR3, CCR4, CCR10) and dermal microvascular endothelial cells (CCR3, CCR4, CCR6, CCR8, CCR9, CCR10, CXCR1, CXCR2, CXCR3) express a distinct and functionally active repertoire of chemokine receptors. Furthermore, chemokine ligand-receptor interactions markedly improved the wound repair of structural skin cells in vitro.ConclusionTaken together, we here present the most comprehensive analysis of mediators critically involved in acute cutaneous wound healing. Our findings suggest therapeutic approaches for the management of wound closure by targeting the chemokine network.

| S-EPMC5771017 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data