Structural Biology in Immunology

Structure/Function of Novel Molecules of Immunologic Importance

Chaim Putterman, David Cowburn, Steven Almo

• Publisher: Academic Press
• Year: 2018
• Print ISBN: 9780128033692
• eBook ISBN: 9780128033708
• Topic: Medicine
• Subtopic: Immunology

Structural Biology in Immunology, Structure/Function of Novel Molecules of Immunologic Importance delivers important information on the structure and functional relationships in novel molecules of immunologic interest. Due to an increasingly sophisticated understanding of the immune system, the approach to the treatment of many immune-mediated diseases, including multiple sclerosis, systemic lupus erythematosus, rheumatoid arthritis, and inflammatory bowel disease has been dramatically altered. Furthermore, there is an increasing awareness of the critical role of the immune system in cancer biology. The improved central structure function relationships presented in this book will further enhance our ability to understand what defects in normal individuals can lead to disease.- Describes novel/recently discovered immunomodulatory proteins, including antibodies and co-stimulatory or co-inhibitory molecules- Emphasizes new biologic and small molecule drug design through the exploration of structure-function relationship- Features a collaborative editorial effort, involving clinical immunologists and structural biologists- Provides useful and practical insights on developing the necessary links between basic science and clinical therapy in immunology- Gives interested parties a bridge to learn about computer modeling and structure based design principles

Chapter 1

Organization of Immunological Synapses and Kinapses

Marco Fritzsche*^,†; Michael L. Dustin*^{,‡ *} Kennedy Institute of Rheumatology, Oxford, United Kingdom,
^† Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom,
^‡ New York University School of Medicine, New York, NY, United States

Abstract

Immunological synapses and kinapses describe two modes through which cells of the immune system exchange information based on specific recognition. This chapter focuses on T-cell immunological synapses, particularly, the structural aspects building from molecules that undergo stepwise assembly into the complex supramolecular activation clusters that captivated biology 20 years ago. Modern imaging methods have provided insights into the linkage between physical processes such as liquid-phase separation in adhesion, membrane, and signaling layers of the interface. These processes then link to the F-actin cortex and dramatic changes in membrane topology emerging from exocytic, endocytic, and extracellular vesicle budding mechanisms to shape and maintain this intricate communication interface.

Keywords

Synapse; Kinapse; Signaling; Activation; Phase separation; Actin; Cortex; Extracellular vesicles; Exosomes; Ectosomes; Exocytosis

Abbreviations

Ag antigen

Arp actin-related protein

CD(#) cluster of differentiation (1,2,3…)

CRTAM class-I MHC-restricted T-cell-associated molecule

CSK C-terminal Src kinase

CTLA-4 cytotoxic T lymphocyte antigen-4

DC dendritic cell

ICAM(#) intercellular adhesion molecule-(1,2,3…)

ICOS(L) inducible T-cell costimulator (ligand)

ITAM immunotyrosine activation motif

LAT linker of activated T cells

LFA-(#) lymphocyte function associated-(1,2,3)

(p)MHC (peptide) major histocompatibility complex

PD-1 programmed cell death-1

SH(#) Src homology domain (1,2,3)

SIM structured illumination microscopy

SLAM signaling lymphocyte activation molecule

SLB supported lipid bilayer

(c,p,d)SMAC (central, peripheral, distal) supramolecular activation cluster

STED stimulated excitation depletion

TCR T-cell antigen receptor

(e)TIRF(M) (extended) total internal reflection fluorescence (microscopy)

VASP vasodilator-stimulated phosphoprotein

WASp Wiscott Aldrich syndrome protein

ZAP-70 TCR zeta-associated protein of 70 kili-Daltons

Acknowledgments

We thank our groups for stimulating data and discussions. MLD was supported by Wellcome Trust and Kennedy Trust for Rheumatology Research (PRF 100262Z/12/Z).

1.1 Introduction

Immunological synapses are stable adhesive junctions formed by immune cells for priming of immune responses and effector function.¹ The archetype is based on radially symmetric junctions formed by helper or cytotoxic T cells, with B cells as antigen-presenting cells in which concentric zones referred to as supramolecular activation clusters (SMACs) can be resolved by wide-field microscopy in vitro and in vivo.^2,3 The most important function of the immunological synapses is directed secretion of regulatory signals in the form of proteins and vesicles between immune cells, and also killing of pathogens in the context of innate immune recognition (,^4–7 p. 5140). Immunological synapses are formed by T cells, innate lymphoid cells, B cells, mast cells, neutrophils, macrophages (phagocytic synapse), and likely others.^5,7–10 The key common denominator is that specificity is driven by receptors that couple to nonreceptor tyrosine kinases, often through immunotyrosine activation motifs in the cytoplasmic domain.¹¹ The T-cell antigen receptor (TCR) is the relevant receptor for T cells,¹² which will be the major focus of this chapter.

The formation of the archetypal T-cell immunological synapse can also be reconstituted with supported lipid bilayers (SLBs) containing major histocompatibility complex (MHC) proteins with bound agonist peptides (p^AgMHC) and the adhesion molecule intercellular adhesion molecule-1 (ICAM-1, CD54) in which SMACs form in a time-dependent manner.¹⁰ The two major SMACs are the central SMAC (cSMAC), which is enriched in T-cell receptors (TCRs), p^AgMHC, and some costimulatory receptors such as CD28, and the peripheral SMAC (pSMAC) that is enriched in the integrin lymphocyte function associated 1 (LFA-1, CD11a) and ICAM-1² (Fig. 1.1A). Subsequently, Freiberg et al. defined the distal SMAC (dSMAC) as a ring outside the pSMAC enriched in CD45 and dynamic filamentous actin (F-actin).^13,14 Some aspects of immunological synapse formation can also be reconstituted with glass substrates coated with anti-CD3 antibodies to trigger TCR signals and other surface treatments, such as poly-l-lysine or serum attachment factors (fibronectin, vitronectin, etc.) that provide an adhesion component.^15,16 In the absence of this adhesion component, anti-CD3 elicits actin-rich protrusions that push the cell away from the anti-CD3-coated surface.^17,18 We will incorporate data from cell-cell systems and model substrates to generate a current picture and trajectory for future questions.

Fig. 1.1 Supramolecular activation clusters in synapse and kinapse. (A) Schematic view of the Kupferian SMACs as originally defined in immunological synapse and remapped to kinapse. Note that the cSMAC, pSMAC, and dSMAC (defined in text) are related to structures in kinapse by symmetry breaking. Based on Sims et al.¹³ the activity of PKC-θ favors kinapse whereas the activity of WASp favors synapse. (B) eTIRF-SIM image of F-actin network in Jurkat T cell. The regions of the rosette-like network that correspond to the SMACs are indicated. See text for further discussion of the limitations of these assignments.

Stability of the immunological synapse depends on its symmetry. Breaking of the symmetry of the immunological synapse leads to a migratory junction defined as a kinapse, which appears to be an important mode of T-cell interaction with, for example, dendritic cells (DCs) and germinal center B cells in vivo^{10,13,19–23} (Fig. 1.1B). Kinapse formation may lead to “multifocal synapses” observed in T-DC interactions in vitro and in vivo.^24,25 The immunological synapse and kinapse share signaling elements, referred to as microclusters, which are formed by both the TCR and LFA-1.^26–29 While the formation of microclusters likely has some aspects driven by the biophysics of receptor- ligand-driven self-assembly in the interface, most aspects of immunological synapse and kinapse formation and maturation are dependent upon intact F-actin cytoskeleton and later stages of synapse maturation are regulated by microtubules.^30–32 The chapter will build a structural model for the immunological synapse beginning with some major classes of receptors and then moving to the underlying cytoskeletal networks and important issues of membrane topology.

1.2 Receptors and Ligands of the Immunological Synapse and Kinapse

1.2.1 T-cell Receptor and p^AgMHC

There are two known TCR heterodimers—αβ and γδ—that are expressed on distinct subsets of T cells.¹² The classical adaptive T-cell subsets use the αβ TCR, whereas subsets of tissue-resident T cells use the γδ TCR.³³ Most γδ T cells and a small subset of αβ T cells are innate like, meaning that they use stereotypical rearrangements to generate largely invariant receptors for conserved ligands that are often presented on nonclassical MHC-like proteins. For example, the so-called natural killer T cells use invariant αβ TCR to recognize glycolipids bound to CD1d, which has a structure similar to MHC class I, but possesses a binding groove adapted for the recognition of glycolipids.³⁴ Mucosal-associated invariant T cells recognize microbial metabolites presented on MHC-related protein.³⁵ This chapter focuses on the majority of αβ T cells that use MHC class I or class II proteins as ligands in combinations with short peptides. Each of these αβ T cells expresses one TCR that binds weakly to self-peptide (p^self)-MHC based on thymic selection and has the potential to bind a variety of p^AgMHC.³⁶ Since each TCR is generated through multiple recombination events involving germline V, (D), and J segments with random addition of base pairs during joining, there is huge diversity of these weakly self-reactive TCR in the “naïve” repertoire that are selected for expansion and conversion into memory T cells over the life of an individual. The interaction of TCR with p^self–MHC is challenging to measure physically using the available methods, but in solution have dissociation constants on the order of 100 μM to > 1 mM,^37,38 yet these interactions are essential for thymic selection during development and appear to influence mature T cells continuously.³⁹ The interactions of TCR with p^AgMHC typically have Kd in the range of 100 nM–10 μM.³⁸ All individuals seem to harbor some higher affinity p^self-MHC-specific T cells that often take on suppressive roles as regulatory T cells (Treg),⁴⁰ but can also be rec...

Table of contents

• Cover image
• Title page
• Table of Contents
• Copyright
• Dedication
• Contributors
• Acknowledgments
• Chapter 1: Organization of Immunological Synapses and Kinapses
• Chapter 2: Principles of Protein Recognition by Small T-Cell Adhesion Proteins and Costimulatory Receptors
• Chapter 3: Synthetic Antibody Engineering: Concepts and Applications
• Chapter 4: Natural Killer Cell Receptors
• Chapter 5: Structure-Function in Antibodies to Double-Stranded DNA
• Chapter 6: The Role of the Constant Region in Antibody-Antigen Interactions: Redefining the Modular Model of Immunoglobulin Structure
• Index