Viral immune evasion molecules attack the ER peptide-loading complex and exploit ER-associated degradation pathways Lonnie Lybarger1, Xiaoli Wang2, Michael Harris2 and Ted H Hansen2 The CD8+ cytotoxic-T-cell response is a potent mechanism that controls intracellular pathogens, including many viruses. To facilitate transmission, viruses often counter this response by inhibiting the cell surface display of virus-derived peptides on MHC class I molecules. More specifically, recent studies have demonstrated that viruses have evolved remarkable mechanisms to inhibit MHC class I expression by interfering with the function of the MHC class I assembly machinery (the peptide-loading complex) in the endoplasmic reticulum and/or by exploiting endoplasmic-reticulum-associated degradation pathways. These viral molecules are proving invaluable as research tools to illuminate the novel features of physiological pathways that are central to normal cell biology. Furthermore, the detailed characterization of such pathways has yielded significant new insights into host–pathogen interplay. Addresses 1 University of Arizona Health Sciences Center, Department of Cell Biology and Anatomy, 1501 North Campbell Avenue, Tucson, AZ 85724, USA 2 Washington University Medical School, Department of Pathology and Immunology, Campus Box 8118, 4566 Scott Avenue, St. Louis, MO 63110, USA Corresponding author: Hansen, Ted H (
[email protected])
This is certainly the case for the MHC class I antigen presentation pathway. Virus-encoded molecules have been described that can affect this pathway at essentially every step: from peptide generation by the proteasome and early assembly events in the endoplasmic reticulum (ER) to trafficking through the secretory pathway and cell surface turnover (reviewed recently in [1,2]). The fact that viruses have evolved such diverse mechanisms to target this pathway highlights the importance of MHC class I molecules in host defense against viruses. Here, we review a subset of these immune evasion molecules (referred to here as viral proteins interfering with antigen presentation; VIPRs; [3]) that interrupt early MHC class I assembly, some by interfering with the class I peptideloading complex (PLC) and others that exploit ER-associated degradation (ERAD) pathways. Emerging details of the molecular interactions between VIPRs and host ER proteins are also summarized. In addition, we discuss the implications of these findings on elucidating key molecular interactions in the ER together with recent evidence of host adaptation to these viral immune evasion molecules.
MHC class I assembly Current Opinion in Immunology 2005, 17:71–78 This review comes from a themed issue on Antigen processing and recognition Edited by Clifford V Harding and Jacques Neefjes Available online 8th December 2004 0952-7915/$ – see front matter # 2005 Elsevier Ltd. All rights reserved. DOI 10.1016/j.coi.2004.11.009 Abbreviations b2m beta-2 microglobulin ER endoplasmic reticulum ERAD ER-associated degradation HC heavy chain HCMV human cytomegalovirus HSV herpes simplex virus HV68 g-herpesvirus 68 PLC peptide-loading complex TAP transporter associated with antigen processing VCP valosin-containing protein VIPR viral protein interfering with antigen presentation
Introduction Research into the molecular interactions between viruses and their hosts has revealed that viruses manipulate a multitude of cellular pathways to facilitate dissemination. www.sciencedirect.com
MHC class I molecules bind to peptides derived from endogenously synthesized proteins and present them at the cell surface for sampling by CD8+ T cells. In this way, CD8+ T cells can survey the contents of virtually all cells in the body and detect the presence of foreign proteins, which could be indicative of viral infection. Most peptides that bind to MHC class I molecules are derived from defective ribosomal products (DRiPs) of normal cellular proteins, which are degraded by proteasomes and then further trimmed by cytosolic and ER peptidases [4,5]. In some professional antigen-presenting cells, such as dendritic cells, MHC class I peptides can be derived from exogenously acquired sources through a process termed cross-presentation. This appears to be important for the initiation of CD8+ T-cell responses [6,7]. The conventional loading of peptides onto MHC class I heavy chains occurs in the ER and requires the concerted action of several accessory molecules, collectively known as the PLC (Figure 1a) [8]. The transporter associated with antigen processing (TAP) molecules, TAP1 and TAP2, form a peptide pump that is required for most antigenic peptides to gain entry into the ER. When class I heavy chains bind to beta-2 microglobulin (b2m), tapasin forms a bridge between class I–b2m heterodimers and TAP. In addition to TAP and tapasin there are two other prominent members of the PLC: calreticulin and ERp57. Current Opinion in Immunology 2005, 17:71–78
72 Antigen processing and recognition
Figure 1
(a)
(b)
PLC
ERp57
ERp57
ERp57 Tapasin CRT
(c) TAP ATP hydrolysis blocker
TAP pump blocker
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ERp57
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The peptide-loading complex and viral proteins that exploit it. (a) PLC. Before peptide binding, the class I HC–b2m heterodimer is in physical association with the PLC. Tapasin forms a bridge between class I HC and TAP whereby the extracellular domain of tapasin appears to bind to the a2 and a3 domains of the class I HC and the transmembrane and cytosolic domains of tapasin bind TAP. The ER chaperone calreticulin (CRT) binds primarily the N-linked glycan conserved among all mouse and human class I HCs, whereas ERp57 forms a stable complex with the stalk region of CRT and a transient complex with tapasin. Shapes representing the PLC components were adapted with permission from Dick et al. [11]. (b) TAP pump blocker. The HSV protein ICP47 binds to the cytosolic side of TAP and blocks transport of peptides into the ER. (c) TAP ATP hydrolysis blocker. The HCMV protein US6 binds to the luminal side of TAP and prevents peptide transport by blocking ATP hydrolysis. (d) Tapasin competitive inhibitor. The adenovirus (AdV) protein E19 appears to bind to both class I HC molecules and TAP and thus was proposed to be a tapasin competitive inhibitor. In this model, class I peptide loading is impaired by a lack of class I HC–b2m engagement with the PLC. (e) Tapasin function blocker. The HCMV protein US3 appears to bind to the class I HC, TAP and tapasin. This causes impaired binding of US3 to class I molecules. Thus it was proposed that US3 functions as a tapasin function blocker [36]. It should be noted, however, that US3 also partially impairs the TAP–tapasin interaction and thus US3 might also function a competitive inhibitor of tapasin. (f) Loading complex stowaway. The HV68 protein mK3 appears to bind primarily to TAP, but tapasin also stabilizes mK3 expression [49,50,51]. The carboxyl terminus of mK3 is critical for the interaction of mK3 with TAP–tapasin and is reported to confer substrate specificity. More specifically, the interaction of mK3 with TAP–tapasin was proposed to impose the required proximity and orientation on mK3 so it can specifically interact with the class I HC [50]. Rapid class I degradation by mK3 is dependent upon its RING-CH domain (shown as a terminal rectangle) and a class I HC with a cytoplasmic tail.
These molecules are chaperones to many other oligomeric glycoproteins in addition to MHC class I, whereas tapasin is thought to be a class-I-dedicated chaperone. There is considerable controversy regarding the specific roles of individual components of the PLC in class I assembly. However, calreticulin is known to monitor the glycosylation status of class I MHC molecules, specifically recognizing immature N-linked glycans on nascent heavy chains (especially at residue Asn86) [9,10], whereas ERp57 is a thiol oxido-reductase that is involved in intrachain disulfide bond isomerization within the class I heavy chain. This effect might be indirect, resulting from transient intermolecular disulfide bonding between ERp57 and tapasin, which affects tapasin function [11]. The net effect of these interactions between class I MHC molecules and the PLC is the production of class I complexes that contain pepCurrent Opinion in Immunology 2005, 17:71–78
tides of relatively high affinity, which then transit to the cell surface by way of the secretory pathway. Indeed, class I molecules contain suboptimal peptides in cells that lack either tapasin or calreticulin [12,13]. Cooperative binding between PLC members and the lack of a structural perspective of the PLC have made it difficult to define the function of each PLC component. Models have been proposed in which tapasin, calreticulin or ERp57 is the crucial PLC component that monitors and/ or facilitates the optimization of peptide binding to class I molecules [11,13,14]. The importance of the PLC in the efficient assembly of class I molecules was not lost on viruses, which have evolved elaborate mechanisms to interfere with the PLC. Indeed, the sheer number of VIPRs that inhibit class I antigen presentation, as well as the mechanistic diversity www.sciencedirect.com
Viral immune evasion molecules Lybarger et al. 73
of these molecules, provides strong evidence that they are important for viral dissemination. Curiously, establishing the in vivo role of VIPRs has been difficult, despite the documented importance of CD8+ T cells in viral control in many instances. There are several factors that confound this issue; these have been discussed in detail in the past [3,15]. However, examples are emerging of VIPRs that affect CD8+ T-cell responses [16,17,18]. Although much work remains to be done on this front, our understanding of the molecular details of VIPR function has expanded rapidly. In the following three sections we describe different strategies by which viruses affect the PLC.
E19 in order to broaden the spectrum of class I molecules that are susceptible to E19.
Peptide restrictors
Ahn and co-workers [36] recently shed light on this problem, demonstrating that US3 can bind to tapasin and inhibit its ability to facilitate high-affinity peptide acquisition by class I molecules. A correlation was noted between the tapasin-dependency of an MHC class I allele for surface expression and its susceptibility to US3. Class I thermostability assays further showed that US3 inhibits high-affinity peptide binding by tapasin-dependent molecules or alleles. Interestingly, US3 expression decreased the maturation kinetics and the quality of peptides acquired by one tapasin-dependent molecule (HLA-B*2705 His114Asp mutant), despite the inability of US3 to detectably associate with this molecule. This is consistent with US3 inhibiting the function of tapasin, leading to a delay in class I maturation. The extent to which these two modes of US3 action (direct ER retention by physical association and tapasin inhibition) are operative for a given class I molecule remain to be resolved. This issue is further complicated by the fact that wild-type HLA-B*2705, although tapasin-independent in terms of surface expression [37], undergoes peptide optimization in the presence of tapasin [14]. Therefore, the finding that US3 inhibits tapasin function, yet wild-type HLA-B*2705 is resistant to US3 [36], might indicate that the US3 blockade of tapasin is only partial. However, this might be enough for HCMV infection as this virus has multiple mechanisms in place to target class I MHC molecules.
An efficient way to inhibit class I expression is to cut off the source of peptides. There are two well-characterized examples of VIPRs that inhibit TAP function, thereby decreasing the import of peptides into the ER. These include the ICP47 protein of herpes simplex virus (HSV) [19,20] and the US6 protein of human cytomegalovirus (HCMV) [21–23]. The molecular details of the function of these proteins and their interactions with the TAP molecules have been reviewed recently [24,25]. Briefly, ICP47 is a small protein (10 kDa) that binds to the cytosolic face of the TAP heterodimer, preventing the binding of peptide substrates to TAP (Figure 1b) [26,27]. US6 is an ER integral membrane glycoprotein that blocks peptide transport into the ER by interacting with TAP in the ER lumen (Figure 1c). This interaction prevents the binding of ATP to the cytosolic side of TAP1 [28,29]. Thus, these two unrelated molecules use distinct mechanisms to achieve the same goal — peptide starvation of nascent class I molecules in the PLC.
Chaperone blockers Tapasin has chaperone-like properties and is the lynchpin of the PLC — in its absence, TAP, calreticulin and ERp57 fail to associate with class I MHC molecules. The critical role of tapasin in class I biogenesis has been targeted by multiple viruses. Adenovirus encodes the E3 protein of 19 kDa (E19), which is the first reported example of a viral inhibitor of MHC class I molecules. E19 was originally shown to bind nascent class I molecules and retain them in the ER [30,31]. More recently, it was reported that E19 also regulates class I molecules by a second mechanism. Specifically, E19 was observed to bind independently to class I heavy chains and to TAP, preventing class I molecules from entering the PLC (Figure 1d) [32]. Thus, although E19 doesn’t bind directly to tapasin, it is proposed to be a tapasin inhibitor [32]. The failure of tapasin-dependent class I molecules to enter the PLC (for details see below) typically results in poor peptide loading. In addition, TAP–tapasin complexes containing E19 might exclude class I heavy chains from the PLC that are not, themselves, directly bound by www.sciencedirect.com
A second molecule was recently shown to interfere with the function of tapasin — the US3 protein of HCMV. US3 is an ER-resident 23 kDa glycoprotein that, similar to E19, was first described as a molecule that caused the ER retention of class I molecules [33,34]. US3 transiently associates with class I molecules [33–35] and has a much shorter half-life than class I molecules in the same cells. These combined findings suggested that simple ER retention of class I by US3 alone might be insufficient to explain all of the effects of US3 on class I molecules.
US3 associates with both free and b2m-associated class I heavy chains [33,34,36], and binds directly and independently to tapasin and TAP (Figure 1e) [36]. US3 was also shown to affect MHC class II antigen presentation by binding to HLA DR molecules and preventing their association with the invariant chain [38]. The finding that US3 can form homo-oligomers in vitro and in vivo adds to the complexity [39]. This is a remarkable set of interactions considering that US3 is such a small protein. In any case, it is noteworthy that US3 prevents peptide optimization and appears to bind directly to tapasin (but presumably not calreticulin or ERp57). This is consistent with tapasin having a primary role as a peptide editor, analogous to the relationship of HLA DM molecules with Current Opinion in Immunology 2005, 17:71–78
74 Antigen processing and recognition
MHC class II molecules. Structural resolution of US3 with its primary PLC binding partner could thus provide important insights into the paramount question in this field — what is the class I peptide editor?
A PLC stowaway — mK3 A distinct mode for evasion of class I antigen presentation has emerged recently that invokes cellular ubiquitinmediated pathways. A family (called here K3 homologs) of structurally related molecules has been identified in several different g-herpesviruses and poxviruses [40–43] as well as mammalian homologs [44,45]. They are all characterized by conserved integral membrane topology and the presence of an amino-terminal RING-finger domain, of the RING-CH subset (the RING-CH domain is a ring finger motif with a cysteine residue in the fourth zinc-coordinating position and a histidine residue in the fifth). In the context of K3 homologs, the RING-CH domain has ubiquitin ligase (E3) activity. As a general rule, the transmembrane domains and cytosolic carboxyterminal tails (which vary in length) mediate interaction of the viral molecules with substrate molecules. The bestcharacterized examples of K3 family members are the kK3 and kK5 molecules of Kaposi’s-sarcoma-associated herpesvirus, the mK3 molecule of g-herpesvirus 68 (HV68) and the M153R molecule of myxoma virus [46]. With the exception of mK3, other K3 homologs ubiquitinate class I heavy chains, probably in a post-ER compartment, which leads to the rapid endocytosis of class I molecules from the cell surface followed by degradation in lysosomes. In addition, some of these K3 homologs can target the degradation of other immune modulatory molecules such as B7.2, ICAM-1 and CD4. By contrast, mK3 functions at a much earlier stage of the class I expression pathway, and has a unique requirement for the PLC. The initial characterization of mK3 showed that its expression in transfectants reduced surface class I expression by causing the rapid degradation of nascent class I heavy chains in the ER, with a half-life of 15 minutes [40]. The same group subsequently reported that mK3 associates with class I molecules, leading to ubiquitination of class I heavy chains, the ultimate degradation of which is proteasome dependent [47]. Ubiquitination required an intact RING-CH domain, but mK3 association with class I MHC molecules did not. As the kinetics of class I turnover by mK3 and class I association with the PLC were similar, it was of interest to determine if mK3 associated with the PLC. Co-immunoprecipitation experiments readily demonstrated an interaction between mK3 and TAP complexes containing class I molecules [48]. This raised the possibility that the PLC was involved in mK3-mediated turnover of class I. To assess this possibility, mK3 function was analyzed in cells devoid of different PLC members [49]. mK3 was incapable of regulating class I stability and expression Current Opinion in Immunology 2005, 17:71–78
in cells lacking TAP-1 or tapasin, but did function in the absence of calreticulin. It was also found that mK3 associated readily with TAP–tapasin, even in the absence of class I heavy chains. Further, class I mutants that could not associate with TAP–tapasin were resistant to rapid degradation mediated by mK3. It should be noted that rapid degradation by mK3 appears to be specific for class I heavy chains within the PLC. These combined observations support a model of mK3 targeting of class I, in which mK3 associates with TAP–tapasin and then awaits the entry of nascent class I into the PLC. The interaction with TAP–tapasin properly orients the mK3 RING-CH domain so that it specifically catalyzes ubiquitin addition to the class I heavy chain. This model is supported by a second study showing that it is the entry of class I into the PLC, and not class-I-specific recognition sequences on class I, that is the primary determinant of susceptibility to rapid mK3-mediated turnover [50]. Recent reports indicate that mK3 directly binds to TAP-1 or TAP-1–TAP-2 (Figure 1f) [50,51]. Tapasin might not be a direct binding partner for mK3, but it is nonetheless required for mK3 function as it recruits class I into the PLC. Boname et al. [51] also revealed that, in some cell types (especially lymphoid cells), mK3 expression not only affects class I heavy chains, but also leads to a decrease in steady-state levels of TAP-1–TAP-2 and tapasin. Turnover of TAP–tapasin required the mK3 RING-CH domain, but was modest when compared to the turnover of class I in the same cells. It is unclear whether the TAP and tapasin turnover induced by mK3 is direct or if it reflects collateral damage to PLC members as a result of class I degradation induced by mK3. Nonetheless, it might be relevant to HV68 infection, as it could permit mK3 to indirectly affect class I molecules that do not bind to the PLC by decreasing peptide availability in cells where this occurs [51]. It has been assumed, on the basis of analogy to homologous viral proteins [43,52,53], that mK3 ubiquitinates the cytosolic tail of class I within the PLC to trigger the downstream events in class I degradation; however, this has not been proven. In fact, class I molecules devoid of tail lysines are still ubiquitinated [47] and are rapidly degraded in the presence of mK3 (X Wang et al., unpublished; see update). These results imply that mK3 somehow gains access to the ectodomain of class I molecules and ubiquitinates lysine residues within them. This is similar to the mechanism proposed for the ER turnover of class I molecules initiated by the HCMV proteins US2 and US11 (see below). Overall, mK3 is an astonishing example of a VIPR that co-opts the PLC to affect class I presentation.
Viral proteins exploit ERAD pathways The best characterized examples of VIPRs that cause rapid degradation of ER-resident class I molecules are the www.sciencedirect.com
Viral immune evasion molecules Lybarger et al. 75
Figure 2
HCMV US2/US11
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The putative dislocation pathway used by US2, US11 and perhaps mK3. Recognition: (a) when in the ER, HCMV US2 and US11 recognize the lumenal domains of nascent class I molecules [58]. (b) Alternatively, mK3 binds TAP–tapasin and detects class I molecules associated with the PLC [49,50,51]. (c) Dislocation and ubiquitination. The association between the viral proteins and the class I HC triggers the association of the class I HC with a dislocation channel (probably Derlin-1 in the case of US11 [61,62]) through their transmembrane domains. Subsequently, an ATPase complex (p97 and its cofactors, Ufd1-Npl4) and ubiquitination components are recruited by the dislocation channel complex [56,57]. This interaction then induces the partial dislocation of the class I HC, which allows the polyubiquitination of the lumenal class I HC domain [61,62]. (d) Release: following polyubiquitination, release of the class I HC is driven by the hydrolysis of the ATP. (e) Degradation: when released into the cytosol, the class I HC is deglycosylated and degraded by the 26S proteasome [55].
HCMV proteins US2 and US11. Similar to mK3, US2 and US11 induce rapid proteasome-dependent degradation of nascent class I molecules [54–57], yet, distinct from mK3, these molecules are located in the ER lumen and are not ubiquitin ligases. Instead, they bind directly to class I molecules [58] and cause them to be purged from the ER through a process termed ‘dislocation’ (Figure 2). It is now known that dislocation is a central component of ERAD, an important mechanism used by cells to degrade improperly assembled or misfolded ER proteins (reviewed in [59,60]). US2 and US11 have proven to be valuable tools for advancing our understanding of the dislocation pathway. In this system, the substrate requirements for dislocation and the fate of dislocated molecules have been investigated. Recently, two groups reported the preliminary characterization of a novel mammalian protein, Derlin-1, which is involved in dislocation [61,62]. Derlin-1 is a homolog of the yeast Der1, a protein initially identified through genetics as required for ERAD [63]. In one study, Derlin-1 was identified by virtue of its interaction with US11 [61], and both groups showed that US11 and Derlin-1 interact in cells [61,62]. Derlin-1 is localized to the ER and is predicted to span the membrane four times. Importantly, a dominant-negative form of Derlin-1 inhibited US11www.sciencedirect.com
mediated dislocation of class I molecules [61], proving the function of Derlin-1 in dislocation. Curiously, it did not affect US2-mediated dislocation, suggesting that other downstream effector molecules can also initiate the dislocation pathway. In a report by Ye et al. [62], a second ER membrane protein was identified (valosincontaining protein [VCP; also called p97]-interacting membrane protein) that could be precipitated with US11 and Derlin-1. The working model for the function of these proteins in ERAD is that Derlin-1 (and perhaps VCP-interacting membrane protein) recruits dislocation substrates to a ‘dislocation pore’. When a dislocation substrate emerges on the cytosolic face of the ER it is ubiquitinated and then recognized by a cytosolic ATPase, p97 (VCP), and associated cofactors that provide the mechanical force to extrude the substrate [59,60]. US11 bridges Derlin-1 with MHC class I, probably delivering class I molecules to the dislocation pore. This evolving story underscores the ingenious ways in which viral proteins co-opt cellular pathways, and demonstrates the value of characterizing these viral molecules and the cellular processes that they manipulate, which extends far beyond the host–pathogen environment. Comparisons between US2 or US11 and mK3, for example, will define the host molecules that each viral protein exploits, and might thereby identify different initiators of ERAD. Current Opinion in Immunology 2005, 17:71–78
76 Antigen processing and recognition
The host fights back — adaptation to immune evasion molecules The existence of VIPRs provides proof of the evolutionary pressure applied by the host immune system. To what extent is the converse true? For pathogens that have a long natural history with their hosts (e.g. herpesviruses and poxviruses) a balance has typically been achieved whereby the pathogen causes minimal disease, but manipulates the host immune system enough to avoid elimination. To help keep the scales balanced, the host might have evolved mechanisms to relieve some of the suppressive effects of its parasites. Although difficult to prove, it is intriguing to consider the possibility of specific host adaptations to class I antigen presentation that counteract VIPRs. As many viral proteins target class I molecules within the PLC, it has been proposed that class I molecules and alleles that are less reliant upon the PLC for expression arose in response to selective pressure exerted by microbial pathogens that subvert class I presentation [37,64]. Support for this notion has surfaced recently from distinct systems. In the mK3 system, as mentioned above, a mutation in the MHC class I heavy chain that prevents PLC association also renders the molecule resistant to rapid degradation initiated by mK3 [49]. A similar observation was made for the US3 protein of HCMV, the dependence of class I molecules and alleles on tapasin correlated with susceptibility to US3 [36]. In addition, the tapasin-independent molecule HLA B*4405 was resistant to the effects of HSV ICP47 when compared to tapasin-dependent molecules [65]. Collectively, these findings demonstrate a suspicious correlation between PLC dependence and sensitivity to some VIPRs. It is interesting to note that cross-presentation of exogenous peptides on class I molecules has also been proposed as an evolutionary response to VIPRs [3,66]. Because cells that cross-present viral peptides on class I molecules are not infected, they might escape inhibition by VIPRs. Of course, the virus is free to counter the host countermeasures. The fact that many of the viral proteins discussed above (including E19, US3 and mK3) block class I expression by multiple mechanisms might be evidence of this phenomenon. Interfering with or degrading TAP and tapasin, for example, could permit viral molecules to expand the range of class I molecules they inhibit beyond those that they can directly attack [32,36,51]. On the one hand, tapasin-independent class I molecules can avoid complete inhibition by viral proteins. On the other hand, even molecules that are classified as tapasinindependent for surface expression still show some measure of peptide optimization in the presence of tapasin [14]. Thus, tapasin inhibition by viruses could affect most class I molecules, although the degree to which this occurs varies considerably between different class I Current Opinion in Immunology 2005, 17:71–78
molecules. The degree of inhibition of class I presentation during viral infection is likely to be a dynamic function influenced by several host factors (including MHC haplotype and PLC expression levels) and viral factors (viral gene expression levels and expression of multiple evasion molecules).
Conclusion Continued study of the fascinating molecular interplay between the host and viral pathogens will undoubtedly yield fresh insights into the co-evolution of the mammalian immune system and VIPRs. It is certain that viruses will continue to teach us about the cell biology of the immune system, including precise definitions of the molecular interactions that regulate class I assembly and degradation.
Update The manuscript previously referred to as (Wang et al., unpublished) is now in press [67]. This paper provides evidence that mK3 uses a dislocation pathway similar to that previously proposed for HCMV proteins US2 and US11.
Acknowledgements With apologies to our antigen-presentation colleagues and authors of papers prior to 2003, we have confined our annotations to recent studies of viral immune evasion.
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78 Antigen processing and recognition
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