Structure of a pheromone receptor-associated MHC molecule with an open and empty groove

Molecular Characteristics, Functional Definitions, and Regulatory Mechanisms for Cross-Presentation Mediated by the Major Histocompatibility Complex: A Comprehensive Review

The major histocompatibility complexes of vertebrates play a key role in the immune response. Antigen-presenting cells are loaded on MHC I molecules, which mainly present endogenous antigens; when MHC I presents exogenous antigens, this is called cross-presentation. The discovery of cross-presentation provides an important theoretical basis for the study of exogenous antigens. Cross-presentation is a complex process in which MHC I molecules present antigens to the cell surface to activate CD8+ T lymphocytes. The process of cross-representation includes many components, and this article briefly outlines the origins and development of MHC molecules, gene structures, functions, and their classical presentation pathways. The cross-presentation pathways of MHC I molecules, the cell lines that support cross-presentation, and the mechanisms of MHC I molecular transporting are all reviewed. After more than 40 years of research, the specific mechanism of cross-presentation is still unclear. In this paper, we summarize cross-presentation and anticipate the research and development prospects for cross-presentation.

The mode of action of tapasin on major histocompatibility class I (MHC-I) molecules

Tapasin (Tsn) plays a critical role in antigen processing and presentation by major histocompatibility complex class I (MHC-I) molecules. The mechanism of Tsn-mediated peptide loading and exchange hinges on the conformational dynamics governing the interaction of Tsn and MHC-I with recent structural and functional studies pinpointing the critical sites of direct or allosteric regulation. In this review, we highlight these recent findings and relate them to the extensive molecular and cellular data that are available for these evolutionary interdependent proteins. Furthermore, allotypic differences of MHC-I with regard to the editing and chaperoning function of Tsn are reviewed and related to the mechanistic observations. Finally, evolutionary aspects of the mode of action of Tsn will be discussed, a short comparison with the Tsn-related molecule TAPBPR (Tsn-related protein) will be given, and the impact of Tsn on noncanonical MHC-I molecules will be described.

HLA-G and the MHC Cusp Theory

Human leukocyte antigens (HLA) are significant genetic risk factors in a long list of diseases. However, the mechanisms underlying these associations remain elusive in many cases. The best-characterized function of classical major histocompatibility complex (MHC) antigens is to allow safe presentation of antigenic peptides via a self/non-self-discrimination process. Therefore, most hypotheses to date have posited that the observed associations between certain HLA molecules and human diseases involve antigen presentation (AP). However, these hypotheses often represent inconsistencies with current knowledge. To offer answers to the inconsistencies, a decade ago we have invoked the MHC Cusp theory, postulating that in addition to its main role in AP, the MHC codes for allele-specific molecules that act as ligands in a conformationally-conserved cusp-like fold, which upon interaction with cognate receptors can trigger MHC-associated diseases. In the ensuing years, we have provided empirical evidence that substantiates the theory in several HLA-Class II-associated autoimmune diseases. Notably, in a recent study we have demonstrated that HLA-DRB1 alleles known to protect against several autoimmune diseases encode a protective epitope at the cusp region, which activates anti-inflammatory signaling leading to transcriptional and functional modulatory effects. Relevant to the topic of this session, cusp ligands demonstrate several similarities to the functional effects of HLA-G. The overall goal of this opinion article is to delineate the parallels and distinctive features of the MHC Cusp theory with structural and functional aspects of HLA-G molecules.

Structure of MHC class I-like MILL2 reveals heparan-sulfate binding and interdomain flexibility

The MILL family, composed of MILL1 and MILL2, is a group of nonclassical MHC class I molecules that occur in some orders of mammals. It has been reported that mouse MILL2 is involved in wound healing; however, the molecular mechanisms remain unknown. Here, we determine the crystal structure of MILL2 at 2.15 Å resolution, revealing an organization similar to classical MHC class I. However, the α1-α2 domains are not tightly fixed on the α3-β₂m domains, indicating unusual interdomain flexibility. The groove between the two helices in the α1-α2 domains is too narrow to permit ligand binding. Notably, an unusual basic patch on the α3 domain is involved in the binding to heparan sulfate which is essential for MILL2 interactions with fibroblasts. These findings suggest that MILL2 has a unique structural architecture and physiological role, with binding to heparan sulfate proteoglycans on fibroblasts possibly regulating cellular recruitment in biological events.

The MILL (MHC-I-like located near the leukocyte receptor complex) family is a group of related nonclassical MHC-I molecules. Here the authors present the crystal structure of MILL2, which reveals an unusual interdomain flexibility, and show that MILL2 binds heparan sulfate on the surface of fibroblasts through a basic patch.

Proofreading of Peptide-MHC Complexes through Dynamic Multivalent Interactions

The adaptive immune system is able to detect and destroy cells that are malignantly transformed or infected by intracellular pathogens. Specific immune responses against these cells are elicited by antigenic peptides that are presented on major histocompatibility complex class I (MHC I) molecules and recognized by cytotoxic T lymphocytes at the cell surface. Since these MHC I-presented peptides are generated in the cytosol by proteasomal protein degradation, they can be metaphorically described as a window providing immune cells with insights into the state of the cellular proteome. A crucial element of MHC I antigen presentation is the peptide-loading complex (PLC), a multisubunit machinery, which contains as key constituents the transporter associated with antigen processing (TAP) and the MHC I-specific chaperone tapasin (Tsn). While TAP recognizes and shuttles the cytosolic antigenic peptides into the endoplasmic reticulum (ER), Tsn samples peptides in the ER for their ability to form stable complexes with MHC I, a process called peptide proofreading or peptide editing. Through its selection of peptides that improve MHC I stability, Tsn contributes to the hierarchy of immunodominant peptide epitopes. Despite the fact that it concerns a key event in adaptive immunity, insights into the catalytic mechanism of peptide proofreading carried out by Tsn have only lately been gained via biochemical, biophysical, and structural studies. Furthermore, a Tsn homolog called TAP-binding protein-related (TAPBPR) has only recently been demonstrated to function as a second MHC I-specific chaperone and peptide proofreader. Although TAPBPR is PLC-independent and has a distinct allomorph specificity, it is likely to share a common catalytic mechanism with Tsn. This review focuses on the current knowledge of the multivalent protein–protein interactions and the concomitant dynamic molecular processes underlying peptide-proofreading catalysis. We do not only derive a model that highlights the common mechanistic principles shared by the MHC I editors Tsn and TAPBPR, and the MHC II editor HLA-DM, but also illustrate the distinct quality control strategies employed by these chaperones to sample epitopes. Unraveling the mechanistic underpinnings of catalyzed peptide proofreading will be crucial for a thorough understanding of many aspects of immune recognition, from infection control and tumor immunity to autoimmune diseases and transplant rejection.

Expression and alternative splicing of classical and nonclassical MHCI genes in the hippocampus and neuromuscular junction

The major histocompatibility complex class I (MHCI) is a large gene family, with over 20 members in mouse. Some MHCIs are well-known for their critical roles in the immune response. Studies in mice which lack stable cell-surface expression of many MHCI proteins suggest that one or more MHCIs also play unexpected, essential roles in the establishment, function, and modification of neuronal synapses. However, there is little information about which genes mediate MHCI's effects in neurons. In this study, RT-PCR was used to simultaneously assess transcription of many MHCI genes in regions of the central and peripheral nervous system where MHCI has a known or suspected role. In the hippocampus, a part of the CNS where MHCI regulates synapse density, synaptic transmission, and plasticity, we found that more than a dozen MHCI genes are transcribed. Single-cell RT-PCR revealed that individual hippocampal neurons can express more than one MHCI gene, and that the MHCI gene expression profile of CA1 pyramidal neurons differs significantly from that of CA3 pyramidal neurons or granule cells of the dentate gyrus. MHCI gene expression was also assessed at the neuromuscular junction (NMJ), a part of the peripheral nervous system (PNS) where MHCI plays a role in developmental synapse elimination, aging-related synapse loss, and neuronal regeneration. Four MHCI genes are expressed at the NMJ at an age when synapse elimination is occurring in three different muscles. Several MHCI mRNA splice variants were detected in hippocampus, but not at the NMJ. Together, these results establish the first profile of MHCI gene expression at the developing NMJ, and demonstrate that MHCI gene expression is under tight spatial and temporal regulation in the nervous system. They also identify more than a dozen MHCIs that could play important roles in regulating synaptic transmission and plasticity in the central and peripheral nervous systems.

Chaperoning G protein-coupled receptors: from cell biology to therapeutics

G protein-coupled receptors (GPCRs) are membrane proteins that traverse the plasma membrane seven times (hence, are also called 7TM receptors). The polytopic structure of GPCRs makes the folding of GPCRs difficult and complex. Indeed, many wild-type GPCRs are not folded optimally, and defects in folding are the most common cause of genetic diseases due to GPCR mutations. Both general and receptor-specific molecular chaperones aid the folding of GPCRs. Chemical chaperones have been shown to be able to correct the misfolding in mutant GPCRs, proving to be important tools for studying the structure-function relationship of GPCRs. However, their potential therapeutic value is very limited. Pharmacological chaperones (pharmacoperones) are potentially important novel therapeutics for treating genetic diseases caused by mutations in GPCR genes that resulted in misfolded mutant proteins. Pharmacoperones also increase cell surface expression of wild-type GPCRs; therefore, they could be used to treat diseases that do not harbor mutations in GPCRs. Recent studies have shown that indeed pharmacoperones work in both experimental animals and patients. High-throughput assays have been developed to identify new pharmacoperones that could be used as therapeutics for a number of endocrine and other genetic diseases.

The quest for better understanding of HLA-disease association: scenes from a road less travelled by

Dozens of human diseases and health traits are significantly more common among individuals carrying particular human leukocyte antigens (HLA) alleles. The underlying mechanism of this phenomenon, commonly referred to as "HLA-disease association," has been the subject of a decades-long debate. The prevailing hypotheses implicate an auto-aggressive immune response due to aberrant presentation of self-, self-mimicking-, or altered self-antigens by HLA molecules. However, the identity of such putative antigens remains elusive in the vast majority of HLA-associated diseases. Moreover, antigen presentation-based hypotheses are difficult to reconcile with epidemiologic data and functional characteristics of HLA molecules. To provide better answers to these inconsistencies an alternative theory involving allele-based, antigen presentation-independent mechanism is proposed here. Recent research findings in rheumatoid arthritis, an emblematic HLA-associated disease, lend support to the proposed theory.

The adaptable major histocompatibility complex (MHC) fold: structure and function of nonclassical and MHC class I-like molecules

The MHC fold is found in proteins that have a range of functions in the maintenance of an organism's health, from immune regulation to fat metabolism. Well adapted for antigen presentation, as seen for peptides in the classical MHC molecules and for lipids in CD1 molecules, the MHC fold has also been modified to perform Fc-receptor activity (e.g., FcRn) and for roles in host homeostasis (e.g., with HFE and ZAG). The more divergent MHC-like molecules, such as some of those that interact with the NKG2D receptor, represent the minimal MHC fold, doing away with the α3 domain and β2m while maintaining the α1/α2 platform domain for receptor engagement. Viruses have also co-opted the MHC fold for immune-evasive functions. The variations on the theme of a β-sheet topped by two semiparallel α-helices are discussed in this review, highlighting the fantastic adaptability of this fold for good and for bad.

Recognition of the ligand-type specificity of classical and non-classical MHC I proteins

Functional characterization of proteins belonging to the MHC I superfamily involves knowing their cognate ligands, which can be peptides, lipids or none. However, the experimental identification of these ligands is not an easy task and generally requires some a priori knowledge of their chemical nature (ligand-type specificity). Here, we trained k-nearest neighbor and support vector machine classifiers that predict the ligand-type specificity MHC I proteins with great accuracy. Moreover, we applied these classifiers to human and mouse MHC I proteins of uncharacterized ligands, obtaining some results that can be instrumental to unravel the function of these proteins.

A recent class of chemosensory neurons developed in mouse and rat

In most animal species, the vomeronasal organ ensures the individual recognition of conspecifics, a prerequisite for a successful reproduction. The vomeronasal organ expresses several receptors for pheromone detection. Mouse vomeronasal type-2 receptors (V2Rs) are restricted to the basal neurons of this organ and organized in four families. Family-A, B and D (family ABD) V2Rs are expressed monogenically (one receptor per neuron) and coexpress with either Vmn2r1 or Vmn2r2, two members of family-C V2Rs. Thus, basal neurons are characterized by specific combinations of two V2Rs. To investigate this issue, we raised antibodies against all family-C V2Rs and analyzed their expression pattern. We found that six out of seven family-C V2Rs (Vmn2r2-7) largely coexpressed and that none of the anti-Vmn2r2-7 antibodies significantly stained Vmn2r1 positive neurons. Thus, basal neurons are divided into two complementary subsets. The first subset (Vmn2r1-positive) preferentially coexpresses a distinct group of family-ABD V2Rs, whereas the second subset (Vmn2r2-7-positive) coexpresses the remaining group of V2Rs. Phylogenetic reconstruction and the analysis of genetic loci in various species reveal that receptors expressed by this second neuronal subset are recent branches of the V2R tree exclusively present in mouse and rat. Conversely, V2Rs expressed in Vmn2r1 positive neurons, are phylogenetically ancient and found in most vertebrates including rodents. Noticeably, the more recent neuronal subset expresses a type of Major Histocompatibility Complex genes only found in murine species. These results indicate that the expansion of the V2R repertoire in a murine ancestor occurred with the establishment of a new population of vomeronasal neurons in which coexists the polygenic expression of a recent group of family-C V2Rs (Vmn2r2-7) and the monogenic expression of a recent group of family-ABD V2Rs. This evolutionary innovation could provide a molecular rationale for the exquisite ability in individual recognition and mate choice of murine species.

The cell biology of major histocompatibility complex class I assembly: towards a molecular understanding

Major histocompatibility complex class I (MHC I) proteins protect the host from intracellular pathogens and cellular abnormalities through the binding of peptide fragments derived primarily from intracellular proteins. These peptide-MHC complexes are displayed at the cell surface for inspection by cytotoxic T lymphocytes. Here we reveal how MHC I molecules achieve this feat in the face of numerous levels of quality control. Among these is the chaperone tapasin, which governs peptide selection in the endoplasmic reticulum as part of the peptide-loading complex, and we propose key amino acid interactions central to the peptide selection mechanism. We discuss how the aminopeptidase ERAAP fine-tunes the peptide repertoire available to assembling MHC I molecules, before focusing on the journey of MHC I molecules through the secretory pathway, where calreticulin provides additional regulation of MHC I expression. Lastly we discuss how these processes culminate to influence immune responses.

MHC molecules in health and disease: At the cusp of a paradigm shift

Half a century after the major histocompatibility complex (MHC) was discovered, its functional roles in health and disease remain poorly understood. Many hallmarks of the MHC, including its unusual evolution, structurefunction properties of its gene products and allele-specific associations with dozens of diseases and health traits cannot be convincingly explained by the tenets of existing paradigms. It is therefore becoming increasingly apparent that in order to better understand MHC-health/disease association-a phenomenon that impacts the health of millions-heterodox ideas are critically needed. Here we propose a testable, novel theory concerning the functional role of MHC molecules in health and disease. At the focus of this theory is an evolutionarily-conserved, tri-dimensional cusp-like prominence ('kink'), found in the midst of one of the two α helices that form the perimeter of the groove of all MHC molecules. Based on structural, functional and evolutionary considerations, as well as our recent experimental data, it is proposed here that the MHC cusp region is enriched in allele-specific signal transduction ligands that interact with non-MHC cell surface receptors and trigger signaling events. Aberrations in these pathways could lead to disease development, or affect the severity of such diseases.

The TRPC2 channel forms protein-protein interactions with Homer and RTP in the rat vomeronasal organ

BACKGROUND

The signal transduction cascade operational in the vomeronasal organ (VNO) of the olfactory system detects odorants important for prey localization, mating, and social recognition. While the protein machinery transducing these external cues has been individually well characterized, little attention has been paid to the role of protein-protein interactions among these molecules. Development of an in vitro expression system for the transient receptor potential 2 channel (TRPC2), which establishes the first electrical signal in the pheromone transduction pathway, led to the discovery of two protein partners that couple with the channel in the native VNO.

RESULTS

Homer family proteins were expressed in both male and female adult VNO, particularly Homer 1b/c and Homer 3. In addition to this family of scaffolding proteins, the chaperones receptor transporting protein 1 (RTP1) and receptor expression enhancing protein 1 (REEP1) were also expressed. RTP1 was localized broadly across the VNO sensory epithelium, goblet cells, and the soft palate. Both Homer and RTP1 formed protein-protein interactions with TRPC2 in native reciprocal pull-down assays and RTP1 increased surface expression of TRPC2 in in vitro assays. The RTP1-dependent TRPC2 surface expression was paralleled with an increase in ATP-stimulated whole-cell current in an in vitro patch-clamp electrophysiological assay.

CONCLUSIONS

TRPC2 expression and channel activity is regulated by chaperone- and scaffolding-associated proteins, which could modulate the transduction of chemosignals. The developed in vitro expression system, as described here, will be advantageous for detailed investigations into TRPC2 channel activity and cell signalling, for a channel protein that was traditionally difficult to physiologically assess.

The source of self: genetic parasites and the origin of adaptive immunity

Stable colonization of the host by viruses (genetic parasites) can alter the systems of host identity and provide immunity against related viruses. To attain the needed stability, some viruses of prokaryotes (P1 phage) use a strategy called an addiction module. The linked protective and destructive gene functions of an addiction module insures both virus persistence but will also destroy cells that interrupt this module and thereby prevent infection by competitors. Previously, I have generalized this concept to also include persistent and lytic states of virus infection, which can be considered as a virus addiction module. Such states often involve defective viruses. In this report, I examine the origin of the adaptive immune system from the perspective of a virus addiction module. The likely role of both endogenous and exogenous retroviruses, DNA viruses, and their defective elements is considered in the origin of all the basal components of adaptive immunity (T-cell receptor, RAG-mediated gene rearrangement, clonal lymphocyte proliferation, antigen surface presentation, apoptosis, and education of immune cells). It is concluded that colonization by viruses and their defectives provides a more coherent explanation for the origin of adaptive immunity.

The peptide-loading complex--antigen translocation and MHC class I loading

A large and dynamic membrane-associated machinery orchestrates the translocation of antigenic peptides into the endoplasmic reticulum (ER) lumen for subsequent loading onto major histocompatibility complex (MHC) class I molecules. The peptide-loading complex ensures that only high-affinity peptides, which guarantee long-term stability of MHC I complexes, are presented to T-lymphocytes. Adaptive immunity is dependent on surface display of the cellular proteome in the form of protein fragments, thus allowing efficient recognition of infected or malignant transformed cells. In this review, we summarize recent findings of antigen translocation by the transporter associated with antigen processing and loading of MHC class I molecules in the ER, focusing on the mechanisms involved in this process.

Crystal structure of TNFalpha complexed with a poxvirus MHC-related TNF binding protein

The poxvirus 2L protein binds tumor necrosis factor-alpha (TNFalpha) to inhibit host antiviral and immune responses. The 2.8-A 2L-TNFalpha structure reveals three symmetrically arranged 2L molecules per TNFalpha trimer. 2L resembles class I major histocompatibility complex (MHC) molecules but lacks a peptide-binding groove and beta2-microglobulin light chain. Overlap between the 2L and host TNF receptor-binding sites on TNFalpha rationalizes 2L inhibition of TNFalpha-TNF receptor interactions and prevention of TNFalpha-induced immune responses.

Subsystem organization of the mammalian sense of smell

The mammalian olfactory system senses an almost unlimited number of chemical stimuli and initiates a process of neural recognition that influences nearly every aspect of life. This review examines the organizational principles underlying the recognition of olfactory stimuli. The olfactory system is composed of a number of distinct subsystems that can be distinguished by the location of their sensory neurons in the nasal cavity, the receptors they use to detect chemosensory stimuli, the signaling mechanisms they employ to transduce those stimuli, and their axonal projections to specific regions of the olfactory forebrain. An integrative approach that includes gene targeting methods, optical and electrophysiological recording, and behavioral analysis has helped to elucidate the functional significance of this subsystem organization for the sense of smell.

Insights into MHC class I peptide loading from the structure of the tapasin-ERp57 thiol oxidoreductase heterodimer

Tapasin is a glycoprotein critical for loading major histocompatibility complex (MHC) class I molecules with high-affinity peptides. It functions within the multimeric peptide-loading complex (PLC) as a disulfide-linked, stable heterodimer with the thiol oxidoreductase ERp57, and this covalent interaction is required to support optimal PLC activity. Here, we present the 2.6 A resolution structure of the tapasin-ERp57 core of the PLC. The structure revealed that tapasin interacts with both ERp57 catalytic domains, accounting for the stability of the heterodimer, and provided an example of a protein disulfide isomerase family member interacting with substrate. Mutational analysis identified a conserved surface on tapasin that interacted with MHC class I molecules and was critical for peptide loading and editing functions of the tapasin-ERp57 heterodimer. By combining the tapasin-ERp57 structure with those of other defined PLC components, we present a molecular model that illuminates the processes involved in MHC class I peptide loading.

The quality control of MHC class I peptide loading

The assembly of major histocompatibility complex (MHC) class I molecules is one of the more widely studied examples of protein folding in the endoplasmic reticulum (ER). It is also one of the most unusual cases of glycoprotein quality control involving the thiol oxidoreductase ERp57 and the lectin-like chaperones calnexin and calreticulin. The multistep assembly of MHC class I heavy chain with beta(2)-microglobulin and peptide is facilitated by these ER-resident proteins and further tailored by the involvement of a peptide transporter, aminopeptidases, and the chaperone-like molecule tapasin. Here we summarize recent progress in understanding the roles of these general and class I-specific ER proteins in facilitating the optimal assembly of MHC class I molecules with high affinity peptides for antigen presentation.

Expression of nonclassical class I major histocompatibility genes defines a tripartite organization of the mouse vomeronasal system

The epithelium of the mouse vomeronasal organ (VNO) consists of apical and basal layers of neuronal cell bodies. Vomeronasal sensory neurons (VSNs) with cell bodies in the basal layer express the G-protein subunit G alpha(o) and members of the V2R superfamily of vomeronasal receptor genes and project their axons to the posterior accessory bulb (AOB). V2R(+) VSNs also express particular patterns of a family of nine nonclassical class I major histocompatibility Mhc genes, the H2-Mv genes. The function of H2-Mv molecules remains unknown. H2-Mv molecules have been reported to be associated with V2R molecules and have been proposed to participate in pheromone detection. Here, we find that a substantial fraction of V2R(+) VSNs does not express these nine H2-Mv genes. The cell bodies of H2-Mv(+) and H2-Mv(-) VSNs reside in the lower and upper sublayers of the basal layer, respectively. This spatial segregation is maintained at the level of the AOB: H2-Mv(+) and H2-Mv(-) VSNs project their axons to the posterior and anterior subdomains of the posterior AOB, respectively. By generating a C-terminal green fluorescent protein fusion protein with M10.2 in gene-targeted mice, we observe subcellular localization of M10.2 not only in dendrites but also in axons of VSNs. Our results reveal a tripartite organization of the VNO and AOB, question the generality of the requirement of these nine H2-Mv molecules for V2R surface expression, and suggest that H2-Mvs can function in both dendrites and axons.

Pheromone sensing in mice

Beginning with the neuroepithelium of the vomeronasal organ, the accessory olfactory system in rodents runs parallel to the main olfactory system and is specialized in the detection of pheromones. Only a small number of vomeronasal agonists carrying pheromonal information have been identified this far. These structurally diverse classes of chemicals include peptides secreted by exocrine glands and range from small volatile molecules to proteins and fragments thereof present in urine. Most pheromones activate both vomeronasal and main olfactory sensory neurons, making the identification of functionally relevant populations of sensory neurons difficult. Analyses of gene-targeted mice selectively affecting either vomeronasal or main olfactory signaling have attempted to elucidate the functional contribution of the different chemosensory epithelia to pheromone sensing in mice. These mouse models suggest that both the main and the accessory olfactory systems can converge and synergize to express the complex array of stereotyped behaviors and hormonal changes triggered by pheromones.

Mammalian pheromone sensing

The traditional distinction that the mammalian main olfactory system recognizes general odor molecules and the accessory (vomeronasal) system detects pheromones is no longer valid. The emerging picture is that both systems have considerable overlap in terms of the chemosignals they detect and the effects that they mediate. Recent investigations have discovered large families of pheromonal signals together with a rich variety of specific receptor systems and nasal detection pathways. Selective genetic targeting of these subsystems should help to unravel their biological role in pheromone-mediated behavioral responses.

Comparative molecular dynamics analysis of tapasin-dependent and -independent MHC class I alleles

MHC class I molecules load antigenic peptides in the endoplasmic reticulum and present them at the cell surface. Efficiency of peptide loading depends on the class I allele and can involve interaction with tapasin and other proteins of the loading complex. Allele HLA-B*4402 (Asp at position 116) depends on tapasin for efficient peptide loading, whereas HLA-B*4405 (identical to B*4402 except for Tyr116) can efficiently load peptides in the absence of tapasin. Both alleles adopt very similar structures in the presence of the same peptide. Comparative unrestrained molecular dynamics simulations on the alpha(1)/alpha(2) peptide binding domains performed in the presence of bound peptides resulted in structures in close agreement with experiments for both alleles. In the absence of peptides, allele-specific conformational changes occurred in the first segment of the alpha(2)-helix that flanks the peptide C-terminal binding region (F-pocket) and contacts residue 116. This segment is also close to the proposed tapasin contact region. For B*4402, a shift toward an altered F-pocket structure deviating significantly from the bound form was observed. Subsequent free energy simulations on induced F-pocket opening in B*4402 confirmed a conformation that deviated significantly from the bound structure. For B*4405, a free energy minimum close to the bound structure was found. The simulations suggest that B*4405 has a greater tendency to adopt a peptide receptive conformation in the absence of peptide, allowing tapasin-independent peptide loading. A possible role of tapasin could be the stabilization of a peptide-receptive class I conformation for HLA-B*4402 and other tapasin-dependent alleles.

What guides MHC-restricted TCR recognition?

MHC-encoded molecules govern adaptive immune responses by presenting peptides to T cell receptors (TCRs). Based on TCR-MHC crystal structures, we revisit the extent of TCR binding degeneracy, a property with important biological consequences because the diversity of TCR ligands that can be encountered exceeds the number of T cell clones present in a person at any one time. We also discuss whether the approximate diagonal binding of TCR on MHC molecules is due to an intrinsic property of the TCR variable regions, or results from the action of the CD4 and CD8 coreceptors during intrathymic T cell selection. Finally, we discuss how MHC restriction of antigen recognition might have emerged during evolution.

Genetic analysis of brain circuits underlying pheromone signaling

Molecular approaches and genetic manipulations have provided novel insights into the processing of pheromone-mediated information by the olfactory and vomeronasal systems of mammals. We will review and discuss the specific contribution of each of the two chemosensory systems that ensure specific behavioral responses to conspecific animals.

Open conformers: the hidden face of MHC-I molecules

A pool of MHC-I molecules present at the plasma membrane can dissociate from the peptide and/or the light chain, becoming open MHC-I conformers. Whereas peptide-bound MHC-I molecules have an important role in regulating adaptive and innate immune responses, through trans-interactions with T cell and NK cell receptors, the function of the open MHC-I conformers is less clear but seems to be related to their inherent ability to cis-associate, both with themselves and with other receptors. Here, we review data indicating the open MHC-I conformers as regulators of ligand-receptor interactions and discuss the biological implications for immune and non-immune cells. The likelihood that the MHC-I heavy chains have hidden functions that are determined by the amino acid sequence of the alpha1 and alpha2 domains are discussed.

Pheromonal communication in vertebrates

Recent insights have revolutionized our understanding of the importance of chemical signals in influencing vertebrate behaviour. Previously unknown families of pheromonal signals have been identified that are expanding the traditional definition of a pheromone. Although previously regarded as functioning independently, the main olfactory and vomeronasal systems have been found to have considerable overlap in terms of the chemosignals they detect and the effects that they mediate. Studies using gene-targeted mice have revealed an unexpected diversity of chemosensory systems and their underlying cellular and molecular mechanisms. Future developments could show how the functions of the different chemosensory systems are integrated to regulate innate and learned behavioural and physiological responses to pheromones.

Direct peptide-regulatable interactions between MHC class I molecules and tapasin

Tapasin (Tpn) has been implicated in multiple steps of the MHC class I assembly pathway, but the mechanisms of function remain incompletely understood. Using purified proteins, we could demonstrate direct binding of Tpn to peptide-deficient forms of MHC class I molecules at physiological temperatures. Tpn also bound to M10.5, a pheromone receptor-associated MHC molecule that has an open and empty groove and that shares significant sequence identity with class I sequences. Two types of MHC class I-Tpn complexes were detectable in vitro depending on the input proteins; those depleted in beta(2)m, and those containing beta(2)m. Both were competent for subsequent assembly with peptides, but the latter complexes assembled more rapidly. Thus, the assembly rate of Tpn-associated class I was determined by the conditions under which Tpn-MHC class I complexes were induced. Peptide loading of class I inhibited Tpn-class I-binding interactions, and peptide-depletion enhanced binding. In combination with beta(2)m, certain peptides induced efficient dissociation of preformed Tpn-class I complexes. Together, these studies demonstrate direct Tpn-MHC class I interactions and preferential binding of empty MHC class I by Tpn, and that the Tpn-class I interaction is regulated by both beta(2)m and peptide. In cells, Tpn is likely to be a direct mediator of peptide-regulated binding and release of MHC class I from the TAP complex.

MHC homologs in the nervous system — they haven’t lost their groove

Major histocompatibility complex (MHC) molecules have been implicated in a number of non-immune roles in the central nervous system, particularly in synaptic development and plasticity. The discovery of M10 (50% sequence identity to classical MHC molecules) proteins expressed in the vomeronasal organ adds to the list of non-traditional roles of MHC homologs. M10 molecules associate with the V2R class of vomeronasal receptors, a family of G-protein coupled receptors thought to function as pheromone receptors. Recent studies showing that classical MHC-binding peptides activate V2R-expressing neurons offer tempting clues that M10s might participate directly in the recognition of pheromone ligands, but M10 proteins do not bind to these peptides with significant affinity. Instead of presenting MHC-binding peptides, M10s might function as molecular chaperones to V2R receptors or more generally as modulators of neuronal function, as demonstrated elsewhere in the brain for classical MHC molecules.

Co-evolution of a primordial peptide-presentation system and cellular immunity

How did early vertebrates survive when their lymphocytes began to use antigen receptors with random specificities, despite their potential for extensive self-reactivity? Here, I propose that the quality-control mechanisms that tame self-reactivity in the adaptive immune system were derived, at least in part, from an ancient mechanism that guided sexual selection on the basis of evaluating genetic relatedness.

On the mechanism of sensing unfolded protein in the endoplasmic reticulum

Unfolded proteins in the endoplasmic reticulum (ER) activate the ER transmembrane sensor Ire1 to trigger the unfolded protein response (UPR), a homeostatic signaling pathway that adjusts ER protein folding capacity according to need. Ire1 is a bifunctional enzyme, containing cytoplasmic kinase and RNase domains whose roles in signal transduction downstream of Ire1 are understood in some detail. By contrast, the question of how its ER-luminal domain (LD) senses unfolded proteins has remained an enigma. The 3.0-A crystal structure and consequent structure-guided functional analyses of the conserved core region of the LD (cLD) leads us to a proposal for the mechanism of response. cLD exhibits a unique protein fold and is sufficient to control Ire1 activation by unfolded proteins. Dimerization of cLD monomers across a large interface creates a shared central groove formed by alpha-helices that are situated on a beta-sheet floor. This groove is reminiscent of the peptide binding domains of major histocompatibility complexes (MHCs) in its gross architecture. Conserved amino acid side chains in Ire1 that face into the groove are shown to be important for UPR activation in that their mutation reduces the response. Mutational analyses suggest that further interaction between cLD dimers is required to form higher-order oligomers necessary for UPR activation. We propose that cLD directly binds unfolded proteins, which changes the quaternary association of the monomers in the membrane plane. The changes in the ER lumen in turn position Ire1 kinase domains in the cytoplasm optimally for autophosphorylation to initiate the UPR.

MHC peptides and the sensory evaluation of genotype

Social interactions, such as finding and identifying a mate, often rely on the ability to sense molecular cues carrying information about genetic relationship and individuality. We summarize recent evidence for an unexpected mechanistic link between the immune and olfactory systems in enabling this identification process. In addition to their established role in the immune response, peptide ligands of major histocompatibility complex (MHC) molecules constitute a previously unknown family of social recognition signals detected by specific subsets of sensory neurons in the mammalian nose. This sensing of MHC peptides can be viewed as a form of functional genome analysis by the nose. Behavioral studies in mice and fish show that MHC peptides are accepted as olfactory cues that influence mate choice decisions and selective pregnancy failure. These findings provide a molecular mechanism by which an individual can sense the composition and compatibility of vital immune system molecules of a conspecific, with direct consequences for social behavior.