Receptor-ligand interactions

The diversity of objects and concepts in biological chemistry can be reflected in the number of ways used to describe an ‘elementary’ biochemical event such as enzymatic reaction. The terminology used in publications or biological databases is often a mixture of terms borrowed from widely different or even contradictory classifications. The ever-growing knowledge cannot be processed meaningfully (e.g. efficiently and correctly referenced in biological databases) without organisation, from controlled vocabularies to dictionaries and thesauri to taxonomies and formal ontologies. Ontology of some domain of knowledge is a controlled vocabulary of terms with defined logical relationships to each other. The unique types of relationships between terms have to be included in biochemical ontologies. The relevance of chemical thesauri and ontologies to bioinformatics is illustrated by current resources and projects at the European Bioinformatics Institute, such as IntEnz (Enzyme Nomenclature), COMe (the bioinorganic motif database) and the IUPHAR Receptor Database.

The paradigm for how we approach scientific research is rapidly changing and currently reflects not only the advances in equipment but also the interdisciplinary nature of the research itself. With a special focus on immunological research, we demonstrate how this evolution has impacted the life sciences. In particular, we describe the integration and application of two different imaging technologies, the Atomic Force Microscope (AFM) and Laser Scanning Confocal Microscope (LSCM). Interfacing AFM and confocal microscopy makes it possible to directly correlate high-resolution surface features with specific
fluorescently tagged molecules thus, generati ng a better understanding of receptor-ligand interactions as well as surface feature analysis, measurements that can now be made in real-time. Advantages, disadvantages and technological challenges also will be described. We expect the combination of these complementary techniques will continue to advance and provide significant methods to investigate complex biological system in a non-invasive way.

Insulin receptor (IR) and epidermal growth factor receptors (EGFR) are members of the receptor tyrosine kinase super family. The extracellular regions of both IR and EGFR contain two L domains. Many crystal structures of the extracellular regions of the IR and EGFR families have been determined in both the unliganded state and in complexes with ligands. The structures reveal that the L domains consist of four to six leucine rich repeats (LRRs); although, their amino acid sequences are highly variable. The present bioinformatic analysis reveals some features on the LRRs and the structures. We conclude that the LRRs in the L domains belong to a non-canonical motif differing from the known (canonical) motifs; the repeat units consist of two β-strands and the overall shape of the LRRs resembles a prism. To characterize the spatial arrangement of the two L-domains we propose two parameters; the distance between the two L domains (D) and the angle between the two axes showing the direction of the β-sheet stacking of the LRRs in the L domains (Ψ). These two parameters, D and Ψ, describe an essential feature of the structures and ligand induced structural changes.

In this review we discuss the role of protonation states in receptor-ligand interactions, providing experimental evidences and computational predictions that complex formation may involve titratable groups with unusual pKa's and that protonation states frequently change from unbound to bound states. These protonation changes result in proton uptake/release, which in turn causes the pHdependence of the binding. Indeed, experimental data strongly suggest that almost any binding is pH-dependent and to be correctly modeled, the protonation states must be properly assigned prior to and after the binding. One may accurately predict the protonation states when provided with the structures of the unbound proteins and their complex; however, the modeling becomes much more complicated if the bound state has to be predicted in a docking protocol or if the structures of either bound or unbound receptor-ligand are not available. The major challenges that arise in these situations are the coupling between binding and protonation states, and the conformational changes induced by the binding and ionization states of titratable groups. In addition, any assessment of the protonation state, either before or after binding, must refer to the pH of binding, which is frequently unknown. Thus, even if the pKa's of ionizable groups can be correctly assigned for both unbound and bound state, without knowing the experimental pH one cannot assign the corresponding protonation states, and consequently one cannot calculate the resulting proton uptake/release. It is pointed out, that while experimental pH may not be the physiological pH and binding may involve proton uptake/release, there is a tendency that the native receptor-ligand complexes have evolved toward specific either subcellular or tissue characteristic pH at which the proton uptake/release is either minimal or absent.

Fcγ RIIA (CD32A) and their ligands, including the immunoglobulin Fc fragment and pentraxins, are key players in a variety of innate immune responses. Still unclear is whether additional ligands of CD32A do exist. The objective of this study is to demonstrate that CD32A-chimeric receptor (CR) can be utilized for the identification of CD32A cell surface ligand(s). Among fifteen cancer cell lines tested, CD32A-CR T cells recognized three of breast cancer (BC) including the MDA-MB-468 and one colorectal carcinoma (HT29) in the absence of targeting antibodies. Conjugation of sensitive BC cells with CD32A-CR T cells induced CD32A polarization and down-regulation, CD107 release, and mutual cell elimination in vitro. Conversely, normal fibroblasts and myoblasts were not affected while normal HUVEC cells promoted CD32A down-regulation. CD32A-CR T cell activity was not inhibited by human IgGs or human serum, but; it was rather enhanced by cetuximab antibody. RNAseq analysis of sensitive vs resistant BC cells identified a fingerprint of 42 genes predicting the sensitivity of BC cells to CD32A-CR T cells and their association with favorable prognostic significance in advanced BC patients. Our data also identify ICAM 1 as a major regulator of CD32A-CR T cell-mediated cytotoxicity. Finally, CD32A-CR T cell administration protected immunodeficient mice from subcutaneous growth of MDA-MB-468 cells in the absence of tumor-specific antibodies. These data indicate that CD32A-CR can be utilized for the identification of (1) cell surface CD32A ligand(s); (2) rational therapeutic strategies to target BC; and (3) novel transcriptomic signatures prognostically relevant for advanced BC patients.

Cell signaling systems sense and respond to ligands that bind cell surface receptors. These systems often respond to changes in the concentration of extracellular ligand more rapidly than the ligand equilibrates with its receptor. We demonstrate, by modeling and experiment, a general "systems level" mechanism cells use to take advantage of the information present in the early signal, before receptor binding reaches a new steady state. This mechanism, preequilibrium sensing and signaling (PRESS), operates in signaling systems in which the kinetics of ligand-receptor binding are slower than the downstream signaling steps, and it typically involves transient activation of a downstream step. In the systems where it operates, PRESS expands and shifts the input dynamic range, allowing cells to make different responses to ligand concentrations so high as to be otherwise indistinguishable. Specifically, we show that PRESS applies to the yeast directional polarization in response to pheromone gradients. Consideration of preexisting kinetic data for ligand-receptor interactions suggests that PRESS operates in many cell signaling systems throughout biology. The same mechanism may also operate at other levels in signaling systems in which a slow activation step couples to a faster downstream step. cellular signaling | binding kinetics | dose-response

Turing models have been proposed to explain the emergence of digits during limb development. However, so far the molecular components that would give rise to Turing patterns are elusive. We have recently shown that a particular type of receptor-ligand interaction can give rise to Schnakenberg-type Turing patterns, which reproduce patterning during lung and kidney branching morphogenesis. Recent knockout experiments have identified Smad4 as a key protein in digit patterning. We show here that the BMP-receptor interaction meets the conditions for a Schnakenberg-type Turing pattern, and that the resulting model reproduces available wildtype and mutant data on the expression patterns of BMP, its receptor, and Fgfs in the apical ectodermal ridge (AER) when solved on a realistic 2D domain that we extracted from limb bud images of E11.5 mouse embryos. We propose that receptor-ligand-based mechanisms serve as a molecular basis for the emergence of Turing patterns in many developing tissues.