The benefits of clustering in TNF receptor superfamily signaling

The tumor necrosis factor (TNF) receptor superfamily is a structurally and functionally related group of cell surface receptors that play crucial roles in various cellular processes, including apoptosis, cell survival, and immune regulation. This review paper synthesizes key findings from recent studies, highlighting the importance of clustering in TNF receptor superfamily signaling. We discuss the underlying molecular mechanisms of signaling, the functional consequences of receptor clustering, and potential therapeutic implications of targeting surface structures of receptor complexes

Topology of Type II REases revisited; structural classes and the common conserved core

Type II restriction endonucleases (REases) are deoxyribonucleases that cleave DNA sequences with remarkable specificity. Type II REases are highly divergent in sequence as well as in topology, i.e. the connectivity of secondary structure elements. A widely held assumption is that a structural core of five β-strands flanked by two α-helices is common to these enzymes. We introduce a systematic procedure to enumerate secondary structure elements in an unambiguous and reproducible way, and use it to analyze the currently available X-ray structures of Type II REases. Based on this analysis, we propose an alternative definition of the core, which we term the αβα-core. The αβα-core includes the most frequently observed secondary structure elements and is not a sandwich, as it consists of a five-strand β-sheet and two α-helices on the same face of the β-sheet. We use the αβα-core connectivity as a basis for grouping the Type II REases into distinct structural classes. In these new structural classes, the connectivity correlates with the angles between the secondary structure elements and with the cleavage patterns of the REases. We show that there exists a substructure of the αβα-core, namely a common conserved core, ccc, defined here as one α-helix and four β-strands common to all Type II REase of known structure

Signal Amplification in Highly Ordered Networks Is Driven by Geometry

Here, we hypothesize that, in biological systems such as cell surface receptors that relay external signals, clustering leads to substantial improvements in signaling efficiency. Representing cooperative signaling networks as planar graphs and applying Euler’s polyhedron formula, we can show that clustering may result in an up to a 200% boost in signaling amplitude dictated solely by the size and geometry of the network. This is a fundamental relationship that applies to all clustered systems regardless of its components. Nature has figured out a way to maximize the signaling amplitude in receptors that relay weak external signals. In addition, in cell-to-cell interactions, clustering both receptors and ligands may result in maximum efficiency and synchronization. The importance of clustering geometry in signaling efficiency goes beyond biological systems and can inform the design of amplifiers in nonbiological systems

On the TRAIL of Better Therapies: Understanding TNFRSF Structure-Function

Tumor necrosis factor (TNF) superfamily ligands show diverse biological functions, such as the induction of apoptotic cell death or cell survival and proliferation, making them excellent therapeutic targets for cancer and autoimmunity. We review the latest literature on TNF receptor superfamily signaling with a focus on structure-function. Using combinatorics, we argue that receptors that cluster on the cell surface and are activated by membrane-bound ligands need to arrange in a highly ordered manner, as the probability of random ligand and receptor arrangements matching up for receptor activation is very low. A growing body of evidence indicates that antiparallel receptor dimers that sequester the ligand binding site cluster on the cell surface, forming a hexagonal lattice. Upon ligand binding, this arrangement puts the activated receptors at the right distance to accommodate the downstream signaling partners. The data also suggest that the same geometry is utilized regardless of receptor type. The unified model provides important clues about TNF receptor signaling and should aid the design of better therapies for cancer and various immune mediated diseases

Signal Amplification in Highly Ordered Networks Is Driven by Geometry

Here, we hypothesize that, in biological systems such as cell surface receptors that relay external signals, clustering leads to substantial improvements in signaling efficiency. Representing cooperative signaling networks as planar graphs and applying Euler’s polyhedron formula, we can show that clustering may result in an up to a 200% boost in signaling amplitude dictated solely by the size and geometry of the network. This is a fundamental relationship that applies to all clustered systems regardless of its components. Nature has figured out a way to maximize the signaling amplitude in receptors that relay weak external signals. In addition, in cell-to-cell interactions, clustering both receptors and ligands may result in maximum efficiency and synchronization. The importance of clustering geometry in signaling efficiency goes beyond biological systems and can inform the design of amplifiers in nonbiological systems

Strategic internal covalent cross-linking of TNF produces a stable TNF trimer with improved TNFR2 signaling

Background: Soluble TNF superfamily (TNFSF) ligands are less stable and less active than their transmembrane (tm) analogues. This is a problem for the therapeutic use of recombinant TNFSF ligands in diverse diseases including cancer and autoimmunity. Creating TNFSF ligand analogues with improved targeting of their respective receptors is important for research and therapeutic purposes. Findings: Covalent internal cross-linking of TNF monomers by double mutations, S95C/G148C, results in stable trimers with improved TNFR2 function. The resulting mutein induced the selective death of autoreactive CD8 T cells in type-1 diabetic patients and demonstrates targeted proliferation and expansion of human CD4 Tregs. Conclusions: Stable TNF trimers, created by internal covalent cross-linking, show improved signaling. The high structural homology within the TNF superfamily provides an opportunity to extend internal cross-linking to other TNF superfamily proteins to produce active trimers with improved stability and receptor signaling, and with potential applications for cancer, autoimmunity, infections, and transplantation. Electronic supplementary material The online version of this article (doi:10.1186/s40591-015-0044-4) contains supplementary material, which is available to authorized users

Ribbon representation of the six αβα-core connectivity-based structural classes

<p><b>Copyright information:</b></p><p>Taken from "Topology of Type II REases revisited; structural classes and the common conserved core"</p><p></p><p>Nucleic Acids Research 2007;35(7):2227-2237.</p><p>Published online 16 Mar 2007</p><p>PMCID:PMC1874628.</p><p>© 2007 The Author(s)</p> The α-helices H1 and H2, and β-strands S1 to S5, constituting the αβα-core, are shown for superposed structures belonging to each one of the new structural classes: () Structures 1cfr, 1knvA, 1na6B, 1wtdB, 1dc1A, 2fokA, 1fiuA and 1qc9A for class I in stereo view; () 1sdoA, 2bamA and 1dfmA for class II; 1sa3A and 1ynmA for class III; () 1xhvA, 1b94A, 1iawA and 1dmuA for class IV in stereo view; () 3pviA for class V and 2ixs for class VI