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1.
J Biol Chem ; 296: 100173, 2021.
Article in English | MEDLINE | ID: mdl-33303633

ABSTRACT

M17 leucyl aminopeptidases are metal-dependent exopeptidases that rely on oligomerization to diversify their functional roles. The M17 aminopeptidases from Plasmodium falciparum (PfA-M17) and Plasmodium vivax (Pv-M17) function as catalytically active hexamers to generate free amino acids from human hemoglobin and are drug targets for the design of novel antimalarial agents. However, the molecular basis for oligomeric assembly is not fully understood. In this study, we found that the active site metal ions essential for catalytic activity have a secondary structural role mediating the formation of active hexamers. We found that PfA-M17 and Pv-M17 exist in a metal-dependent dynamic equilibrium between active hexameric species and smaller inactive species that can be controlled by manipulating the identity and concentration of metals available. Mutation of residues involved in metal ion binding impaired catalytic activity and the formation of active hexamers. Structural resolution of Pv-M17 by cryoelectron microscopy and X-ray crystallography together with solution studies revealed that PfA-M17 and Pv-M17 bind metal ions and substrates in a conserved fashion, although Pv-M17 forms the active hexamer more readily and processes substrates faster than PfA-M17. On the basis of these studies, we propose a dynamic equilibrium between monomer ↔ dimer ↔ tetramer ↔ hexamer, which becomes directional toward the large oligomeric states with the addition of metal ions. This sophisticated metal-dependent dynamic equilibrium may apply to other M17 aminopeptidases and underpin the moonlighting capabilities of this enzyme family.


Subject(s)
Aminopeptidases/chemistry , Manganese/chemistry , Plasmodium falciparum/enzymology , Plasmodium vivax/enzymology , Protein Multimerization , Protozoan Proteins/chemistry , Aminopeptidases/genetics , Aminopeptidases/metabolism , Catalytic Domain , Cations, Divalent , Cloning, Molecular , Cobalt/chemistry , Cobalt/metabolism , Cryoelectron Microscopy , Crystallography, X-Ray , Dipeptides/chemistry , Dipeptides/metabolism , Escherichia coli/genetics , Escherichia coli/metabolism , Gene Expression , Kinetics , Magnesium/chemistry , Magnesium/metabolism , Manganese/metabolism , Models, Molecular , Mutation , Plasmodium falciparum/genetics , Plasmodium vivax/genetics , Protein Binding , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Protein Interaction Domains and Motifs , Protozoan Proteins/genetics , Protozoan Proteins/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Substrate Specificity , Zinc/chemistry , Zinc/metabolism
2.
Int J Mol Sci ; 22(16)2021 Aug 23.
Article in English | MEDLINE | ID: mdl-34445801

ABSTRACT

The cytoplasmic retinoic acid-inducible gene-I (RIG-I)-like receptors (RLRs) initiate interferon (IFN) production and antiviral gene expression in response to RNA virus infection. Consequently, RLR signalling is tightly regulated by both host and viral factors. Tripartite motif protein 25 (TRIM25) is an E3 ligase that ubiquitinates multiple substrates within the RLR signalling cascade, playing both ubiquitination-dependent and -independent roles in RIG-I-mediated IFN induction. However, additional regulatory roles are emerging. Here, we show a novel interaction between TRIM25 and another protein in the RLR pathway that is essential for type I IFN induction, DEAD-box helicase 3X (DDX3X). In vitro assays and knockdown studies reveal that TRIM25 ubiquitinates DDX3X at lysine 55 (K55) and that TRIM25 and DDX3X cooperatively enhance IFNB1 induction following RIG-I activation, but the latter is independent of TRIM25's catalytic activity. Furthermore, we found that the influenza A virus non-structural protein 1 (NS1) disrupts the TRIM25:DDX3X interaction, abrogating both TRIM25-mediated ubiquitination of DDX3X and cooperative activation of the IFNB1 promoter. Thus, our results reveal a new interplay between two RLR-host proteins that cooperatively enhance IFN-ß production. We also uncover a new and further mechanism by which influenza A virus NS1 suppresses host antiviral defence.


Subject(s)
Antiviral Agents/immunology , DEAD Box Protein 58/immunology , DEAD-box RNA Helicases/immunology , Immunity/immunology , Receptors, Immunologic/immunology , Transcription Factors/immunology , Tripartite Motif Proteins/immunology , Ubiquitin-Protein Ligases/immunology , Cell Line , Gene Expression Regulation/immunology , HEK293 Cells , Humans , Influenza A virus/immunology , Interferons/immunology , Promoter Regions, Genetic/immunology , Protein Binding/immunology , Signal Transduction/immunology , Ubiquitination/immunology
3.
J Immunol ; 200(12): 4134-4145, 2018 06 15.
Article in English | MEDLINE | ID: mdl-29728507

ABSTRACT

A structural characterization of the interaction between αß TCRs and cognate peptide-MHC (pMHC) is central to understanding adaptive T cell-mediated immunity. X-ray crystallography, although the source of much structural data, traditionally provides only a static snapshot of the protein. Given the emerging evidence for the important role of conformational dynamics in protein function, we interrogated 309 crystallographic structures of pMHC complexes using ensemble refinement, a technique that can extract dynamic information from the x-ray data. Focusing on a subset of human pMHC class I systems, we found that in many cases, ensemble methods were able to uncover previously hidden evidence of significant conformational plasticity, thereby revealing additional information that can build upon and significantly enhance functional interpretations that are based on a single static structure. Notable examples include the interpretation of differences in the disease association of HLA subtypes, the relationship between peptide prominence and TCR recognition, the role of conformational flexibility in vaccine design, and the discrimination between induced fit and conformational selection models of TCR binding. We show that the currently widespread practice of analyzing pMHC interactions via the study of a single crystallographic structure does not make use of pertinent and easily accessible information from x-ray data concerning alternative protein conformations. This new analysis therefore not only highlights the capacity for ensemble methods to significantly enrich the interpretation of decades of structural data but also provides previously missing information concerning the dynamics of existing characterized TCR-pMHC interactions.


Subject(s)
Major Histocompatibility Complex/immunology , Peptides/immunology , Receptors, Antigen, T-Cell/immunology , Crystallography, X-Ray/methods , Humans , Protein Binding/immunology , Protein Conformation , T-Lymphocytes/immunology
4.
J Proteome Res ; 17(4): 1485-1499, 2018 04 06.
Article in English | MEDLINE | ID: mdl-29508616

ABSTRACT

Macrophages, which accumulate in tissues during inflammation, may be polarized toward pro-inflammatory (M1) or tissue reparative (M2) phenotypes. The balance between these phenotypes can have a substantial influence on the outcome of inflammatory diseases such as atherosclerosis. Improved biomarkers of M1 and M2 macrophages would be beneficial for research, diagnosis, and monitoring the effects of trial therapeutics in such diseases. To identify novel biomarkers, we have characterized the global proteomes of THP-1 macrophages polarized to M1 and M2 states in comparison with unpolarized (M0) macrophages. M1 polarization resulted in increased expression of numerous pro-inflammatory proteins including the products of 31 genes under the transcriptional control of interferon regulatory factor 1 (IRF-1). In contrast, M2 polarization identified proteins regulated by components of the transcription factor AP-1. Among the most highly upregulated proteins under M1 conditions were the three interferon-induced proteins with tetratricopeptide repeats (IFITs: IFIT1, IFIT2, and IFIT3), which function in antiviral defense. Moreover, IFIT1, IFIT2, and IFIT3 mRNA were strongly upregulated in M1 polarized human primary macrophages and IFIT1 was also expressed in a subset of macrophages in aortic sinus and brachiocephalic artery sections from atherosclerotic ApoE-/- mice. On the basis of these results, we propose that IFITs may serve as useful markers of atherosclerosis and potentially other inflammatory diseases.


Subject(s)
Interferon Regulatory Factor-1/genetics , Macrophages/immunology , Proteins/analysis , Proteomics/methods , Tetratricopeptide Repeat , Animals , Atherosclerosis/diagnosis , Atherosclerosis/pathology , Biomarkers/analysis , Humans , Inflammation/diagnosis , Inflammation/pathology , Macrophages/chemistry , Mice , Mice, Knockout , Proteins/genetics , THP-1 Cells , Up-Regulation/genetics
5.
Trends Immunol ; 35(12): 604-612, 2014 12.
Article in English | MEDLINE | ID: mdl-25466310

ABSTRACT

Dynamics plays an important but underappreciated role in the interaction between the T cell receptor (TCR) and peptide-bound major histocompatibility complex (pMHC). Crystallographic studies have provided key molecular insights into this interaction; however, due to inherent features of the structural approach, the image of TCR-pMHC interactions that has emerged is a static one. In this review, we discuss how molecular dynamics (MD) simulations can complement and extend current experimental methods aimed at examining TCR-pMHC dynamics. We review the insights obtained from studies that leverage MD approaches, and propose that an integrative strategy that harnesses both MD simulations and structural and biophysical methods will provide new inroads into understanding the transitory and dynamic molecular events that dictate TCR signaling and T cell activation.

6.
PLoS Pathog ; 9(11): e1003757, 2013.
Article in English | MEDLINE | ID: mdl-24278017

ABSTRACT

Malaria transmission-blocking (T-B) interventions are essential for malaria elimination. Small molecules that inhibit the Plasmodium ookinete-to-oocyst transition in the midgut of Anopheles mosquitoes, thereby blocking sporogony, represent one approach to achieving this goal. Chondroitin sulfate glycosaminoglycans (CS-GAGs) on the Anopheles gambiae midgut surface are putative ligands for Plasmodium falciparum ookinetes. We hypothesized that our synthetic polysulfonated polymer, VS1, acting as a decoy molecular mimetic of midgut CS-GAGs confers malaria T-B activity. In our study, VS1 repeatedly reduced midgut oocyst development by as much as 99% (P<0.0001) in mosquitoes fed with P. falciparum and Plasmodium berghei. Through direct-binding assays, we observed that VS1 bound to two critical ookinete micronemal proteins, each containing at least one von Willebrand factor A (vWA) domain: (i) circumsporozoite protein and thrombospondin-related anonymous protein-related protein (CTRP) and (ii) vWA domain-related protein (WARP). By immunofluorescence microscopy, we observed that VS1 stains permeabilized P. falciparum and P. berghei ookinetes but does not stain P. berghei CTRP knockouts or transgenic parasites lacking the vWA domains of CTRP while retaining the thrombospondin repeat region. We produced structural homology models of the first vWA domain of CTRP and identified, as expected, putative GAG-binding sites on CTRP that align closely with those predicted for the human vWA A1 domain and the Toxoplasma gondii MIC2 adhesin. Importantly, the models also identified patches of electropositive residues that may extend CTRP's GAG-binding motif and thus potentiate VS1 binding. Our molecule binds to a critical, conserved ookinete protein, CTRP, and exhibits potent malaria T-B activity. This study lays the framework for a high-throughput screen of existing libraries of safe compounds to identify those with potent T-B activity. We envision that such compounds when used as partner drugs with current antimalarial regimens and with RTS,S vaccine delivery could prevent the transmission of drug-resistant and vaccine-breakthrough strains.


Subject(s)
Anopheles/parasitology , Biomimetic Materials , Glycosaminoglycans/metabolism , Intestines/parasitology , Oocysts/metabolism , Plasmodium berghei/metabolism , Plasmodium falciparum/metabolism , Animals , Biomimetic Materials/chemistry , Biomimetic Materials/pharmacology , Humans
7.
Infect Immun ; 82(2): 818-29, 2014 Feb.
Article in English | MEDLINE | ID: mdl-24478095

ABSTRACT

Malaria transmission-blocking vaccines (TBVs) represent a promising approach for the elimination and eradication of this disease. AnAPN1 is a lead TBV candidate that targets a surface antigen on the midgut of the obligate vector of the Plasmodium parasite, the Anopheles mosquito. In this study, we demonstrated that antibodies targeting AnAPN1 block transmission of Plasmodium falciparum and Plasmodium vivax across distantly related anopheline species in countries to which malaria is endemic. Using a biochemical and immunological approach, we determined that the mechanism of action for this phenomenon stems from antibody recognition of a single protective epitope on AnAPN1, which we found to be immunogenic in murine and nonhuman primate models and highly conserved among anophelines. These data indicate that AnAPN1 meets the established target product profile for TBVs and suggest a potential key role for an AnAPN1-based panmalaria TBV in the effort to eradicate malaria.


Subject(s)
Anopheles/parasitology , Disease Transmission, Infectious/prevention & control , Insect Proteins/immunology , Malaria Vaccines/immunology , Malaria, Falciparum/prevention & control , Malaria, Vivax/prevention & control , Animals , Female , Insect Proteins/administration & dosage , Malaria Vaccines/administration & dosage , Malaria, Falciparum/transmission , Malaria, Vivax/transmission , Male , Mice , Mice, Inbred BALB C
8.
ACS Nano ; 18(2): 1404-1419, 2024 Jan 16.
Article in English | MEDLINE | ID: mdl-38127731

ABSTRACT

This paper presents a comprehensive experimental and theoretical investigation into the antiviral properties of nanostructured surfaces and explains the underlying virucidal mechanism. We used reactive ion etching to fabricate silicon (Si) surfaces featuring an array of sharp nanospikes with an approximate tip diameter of 2 nm and a height of 290 nm. The nanospike surfaces exhibited a 1.5 log reduction in infectivity of human parainfluenza virus type 3 (hPIV-3) after 6 h, a substantially enhanced efficiency, compared to that of smooth Si. Theoretical modeling of the virus-nanospike interactions determined the virucidal action of the nanostructured substrata to be associated with the ability of the sharp nanofeatures to effectively penetrate the viral envelope, resulting in the loss of viral infectivity. Our research highlights the significance of the potential application of nanostructured surfaces in combating the spread of viruses and bacteria. Notably, our study provides valuable insights into the design and optimization of antiviral surfaces with a particular emphasis on the crucial role played by sharp nanofeatures in maximizing their effectiveness.


Subject(s)
Nanostructures , Paramyxoviridae Infections , Humans , Silicon , Parainfluenza Virus 3, Human , Antiviral Agents
9.
Immunol Cell Biol ; 91(4): 321-30, 2013 Apr.
Article in English | MEDLINE | ID: mdl-23399697

ABSTRACT

The innate immune response to virus must be balanced to eliminate infection yet limit damaging inflammation. A critical arm of the antiviral response is launched by the retinoic acid-inducible-gene I (RIG-I) protein. RIG-I is activated by viral RNA then associates with the mitochondrial antiviral signaling (MAVS) protein to subsequently induce potent inflammatory cytokines. Here, we demonstrate the mitochondrial E3 ubiquitin protein ligase 1 (MUL1) is a crucial moderator of RIG-I signaling. MUL1 is localized to the mitochondria where it interacts with MAVS and catalyzes RIG-I post-translational modifications that inhibit RIG-I-dependent cell signaling. Accordingly, depletion of MUL1 potentiated RIG-I mediated nuclear factor-kappa B (NF-κB) and interferon (IFN) ß reporter activity. Moreover, depletion of MUL1 boosted the antiviral response and increased proinflammatory cytokines following challenge with the RNA mimetic poly I:C and Sendai virus. We therefore submit that MUL1 is a novel regulator of the RIG-I-like receptor-dependent antiviral response, that otherwise functions to limit inflammation.


Subject(s)
Antiviral Agents/metabolism , Mitochondria/metabolism , Signal Transduction/immunology , Ubiquitin-Protein Ligases/metabolism , Adaptor Proteins, Signal Transducing/metabolism , Chemokine CCL5/metabolism , Cytokines/metabolism , DEAD Box Protein 58 , DEAD-box RNA Helicases/metabolism , HEK293 Cells , Humans , Inflammation/pathology , Polyubiquitin/metabolism , Protein Binding , Protein Processing, Post-Translational , Protein Transport , Receptors, Immunologic , SUMO-1 Protein/metabolism , Ubiquitination
10.
PLoS Comput Biol ; 8(3): e1002404, 2012.
Article in English | MEDLINE | ID: mdl-22412359

ABSTRACT

The crystal structures of unliganded and liganded pMHC molecules provide a structural basis for TCR recognition yet they represent 'snapshots' and offer limited insight into dynamics that may be important for interaction and T cell activation. MHC molecules HLA-B*3501 and HLA-B*3508 both bind a 13 mer viral peptide (LPEP) yet only HLA-B*3508-LPEP induces a CTL response characterised by the dominant TCR clonetype SB27. HLA-B*3508-LPEP forms a tight and long-lived complex with SB27, but the relatively weak interaction between HLA-B*3501-LPEP and SB27 fails to trigger an immune response. HLA-B*3501 and HLA-B*3508 differ by only one amino acid (L/R156) located on α2-helix, but this does not alter the MHC or peptide structure nor does this polymorphic residue interact with the peptide or SB27. In the absence of a structural rationalisation for the differences in TCR engagement we performed a molecular dynamics study of both pMHC complexes and HLA-B*3508-LPEP in complex with SB27. This reveals that the high flexibility of the peptide in HLA-B*3501 compared to HLA-B*3508, which was not apparent in the crystal structure alone, may have an under-appreciated role in SB27 recognition. The TCR pivots atop peptide residues 6-9 and makes transient MHC contacts that extend those observed in the crystal structure. Thus MD offers an insight into 'scanning' mechanism of SB27 that extends the role of the germline encoded CDR2α and CDR2ß loops. Our data are consistent with the vast body of experimental observations for the pMHC-LPEP-SB27 interaction and provide additional insights not accessible using crystallography.


Subject(s)
Histocompatibility Antigens/chemistry , Histocompatibility Antigens/immunology , Major Histocompatibility Complex/immunology , Models, Chemical , Models, Molecular , Receptors, Antigen, T-Cell/chemistry , Receptors, Antigen, T-Cell/immunology , Binding Sites , Computer Simulation , Epitope Mapping , Multiprotein Complexes/chemistry , Multiprotein Complexes/ultrastructure , Protein Binding , Protein Conformation
11.
Nature ; 448(7149): 44-9, 2007 Jul 05.
Article in English | MEDLINE | ID: mdl-17581592

ABSTRACT

The CD1 family is a large cluster of non-polymorphic, major histocompatibility complex (MHC) class-I-like molecules that bind distinct lipid-based antigens that are recognized by T cells. The most studied group of T cells that interact with lipid antigens are natural killer T (NKT) cells, which characteristically express a semi-invariant T-cell receptor (NKT TCR) that specifically recognizes the CD1 family member, CD1d. NKT-cell-mediated recognition of the CD1d-antigen complex has been implicated in microbial immunity, tumour immunity, autoimmunity and allergy. Here we describe the structure of a human NKT TCR in complex with CD1d bound to the potent NKT-cell agonist alpha-galactosylceramide, the archetypal CD1d-restricted glycolipid. In contrast to T-cell receptor-peptide-antigen-MHC complexes, the NKT TCR docked parallel to, and at the extreme end of the CD1d-binding cleft, which enables a lock-and-key type interaction with the lipid antigen. The structure provides a basis for the interaction between the highly conserved NKT TCR alpha-chain and the CD1d-antigen complex that is typified in innate immunity, and also indicates how variability of the NKT TCR beta-chain can impact on recognition of other CD1d-antigen complexes. These findings provide direct insight into how a T-cell receptor recognizes a lipid-antigen-presenting molecule of the immune system.


Subject(s)
Antigens, CD1/immunology , Killer Cells, Natural/immunology , Receptors, Antigen, T-Cell, alpha-beta/immunology , T-Lymphocytes/immunology , Animals , Antigen Presentation , Antigens, CD1/chemistry , Antigens, CD1d , Carbohydrate Conformation , Crystallography, X-Ray , Galactosylceramides/chemistry , Galactosylceramides/immunology , Humans , Mice , Protein Conformation , Receptors, Antigen, T-Cell, alpha-beta/chemistry , Species Specificity , T-Lymphocyte Subsets/immunology
12.
Trends Microbiol ; 31(4): 393-404, 2023 04.
Article in English | MEDLINE | ID: mdl-36463019

ABSTRACT

Antiretroviral therapy (ART) reduces human immunodeficiency virus type 1 (HIV-1) infection, but selection of treatment-refractory variants remains a major challenge. HIV-1 encodes 16 canonical proteins, a small number of which are the singular targets of nearly all antiretrovirals developed to date. Cellular factors are increasingly being explored, which may present more therapeutic targets, more effectively target certain aspects of the viral replication cycle, and/or limit viral escape. Unlike most other positive-sense RNA viruses that encode at least one helicase, retroviruses are limited to the host repertoire. Accordingly, HIV-1 subverts DEAD-box helicase 3X (DDX3X) and numerous other cellular helicases of the Asp-Glu-x-Asp/His (DExD/H)-box family to service multiple aspects of its replication cycle. Here we review DDX3X and other DExD/H-box helicases in HIV-1 replication and their inhibition.


Subject(s)
DEAD-box RNA Helicases , HIV Infections , HIV-1 , Humans , HIV Infections/drug therapy , HIV-1/metabolism , Virus Replication/genetics
13.
J Exp Med ; 203(3): 661-73, 2006 Mar 20.
Article in English | MEDLINE | ID: mdl-16505140

ABSTRACT

Little is known regarding the basis for selection of the semi-invariant alphabeta T cell receptor (TCR) expressed by natural killer T (NKT) cells or how this mediates recognition of CD1d-glycolipid complexes. We have determined the structures of two human NKT TCRs that differ in their CDR3beta composition and length. Both TCRs contain a conserved, positively charged pocket at the ligand interface that is lined by residues from the invariant TCR alpha- and semi-invariant beta-chains. The cavity is centrally located and ideally suited to interact with the exposed glycosyl head group of glycolipid antigens. Sequences common to mouse and human invariant NKT TCRs reveal a contiguous conserved "hot spot" that provides a basis for the reactivity of NKT cells across species. Structural and functional data suggest that the CDR3beta loop provides a plasticity mechanism that accommodates recognition of a variety of glycolipid antigens presented by CD1d. We propose a model of NKT TCR-CD1d-glycolipid interaction in which the invariant CDR3alpha loop is predicted to play a major role in determining the inherent bias toward CD1d. The findings define a structural basis for the selection of the semi-invariant alphabeta TCR and the unique antigen specificity of NKT cells.


Subject(s)
Antigen Presentation/immunology , Antigens, CD1/immunology , Glycolipids/immunology , Killer Cells, Natural/immunology , Receptors, Antigen, T-Cell, alpha-beta/immunology , T-Lymphocytes/immunology , Animals , Antigen Presentation/genetics , Antigens, CD1/genetics , Genes, T-Cell Receptor alpha/genetics , Genes, T-Cell Receptor alpha/immunology , Genes, T-Cell Receptor beta/genetics , Genes, T-Cell Receptor beta/immunology , Humans , Mice , Protein Binding/genetics , Protein Binding/immunology , Protein Structure, Quaternary , Protein Structure, Tertiary/physiology , Species Specificity , Structural Homology, Protein , Structure-Activity Relationship
14.
Front Immunol ; 13: 987453, 2022.
Article in English | MEDLINE | ID: mdl-36110852

ABSTRACT

The innate immune response to viruses is critical for the correct establishment of protective adaptive immunity. Amongst the many pathways involved, the NLRP3 [nucleotide-binding oligomerisation domain (NOD)-like receptor protein 3 (NLRP3)] inflammasome has received considerable attention, particularly in the context of immunity and pathogenesis during infection with influenza A (IAV) and SARS-CoV-2, the causative agent of COVID-19. Activation of the NLRP3 inflammasome results in the secretion of the proinflammatory cytokines IL-1ß and IL-18, commonly coupled with pyroptotic cell death. While this mechanism is protective and key to host defense, aberrant NLRP3 inflammasome activation causes a hyperinflammatory response and excessive release of cytokines, both locally and systemically. Here, we discuss key molecules in the NLRP3 pathway that have also been shown to have significant roles in innate and adaptive immunity to viruses, including DEAD box helicase X-linked (DDX3X), vimentin and macrophage migration inhibitory factor (MIF). We also discuss the clinical opportunities to suppress NLRP3-mediated inflammation and reduce disease severity.


Subject(s)
COVID-19 , Macrophage Migration-Inhibitory Factors , Carrier Proteins/metabolism , DEAD-box RNA Helicases/metabolism , Humans , Inflammasomes/metabolism , Interleukin-18/metabolism , Macrophage Migration-Inhibitory Factors/metabolism , NLR Family, Pyrin Domain-Containing 3 Protein/metabolism , Nucleotides/metabolism , SARS-CoV-2 , Vimentin/metabolism
15.
J Exp Med ; 202(9): 1249-60, 2005 Nov 07.
Article in English | MEDLINE | ID: mdl-16275762

ABSTRACT

Thousands of potentially antigenic peptides are encoded by an infecting pathogen; however, only a small proportion induce measurable CD8(+) T cell responses. To investigate the factors that control peptide immunogenicity, we have examined the cytotoxic T lymphocyte (CTL) response to a previously undefined epitope ((77)APQPAPENAY(86)) from the BZLF1 protein of Epstein-Barr virus (EBV). This peptide binds well to two human histocompatibility leukocyte antigen (HLA) allotypes, HLA-B*3501 and HLA-B*3508, which differ by a single amino acid at position 156 ((156)Leucine vs. (156)Arginine, respectively). Surprisingly, only individuals expressing HLA-B*3508 show evidence of a CTL response to the (77)APQPAPENAY(86) epitope even though EBV-infected cells expressing HLA-B*3501 process and present similar amounts of peptide for CTL recognition, suggesting that factors other than peptide presentation levels are influencing immunogenicity. Functional and structural analysis revealed marked conformational differences in the peptide, when bound to each HLA-B35 allotype, that are dictated by the polymorphic HLA residue 156 and that directly affected T cell receptor recognition. These data indicate that the immunogenicity of an antigenic peptide is influenced not only by how well the peptide binds to major histocompatibility complex (MHC) molecules but also by its bound conformation. It also illustrates a novel mechanism through which MHC polymorphism can further diversify the immune response to infecting pathogens.


Subject(s)
DNA-Binding Proteins/immunology , Epitopes, T-Lymphocyte/immunology , Epitopes, T-Lymphocyte/metabolism , HLA-B Antigens/metabolism , Herpesvirus 4, Human/immunology , T-Lymphocytes, Cytotoxic/immunology , Trans-Activators/immunology , Viral Proteins/immunology , Alleles , Clone Cells , DNA-Binding Proteins/chemistry , DNA-Binding Proteins/metabolism , Epitopes, T-Lymphocyte/chemistry , Epstein-Barr Virus Infections/immunology , Epstein-Barr Virus Infections/metabolism , HLA-B35 Antigen , HLA-B38 Antigen , Herpesvirus 4, Human/metabolism , Humans , Peptides/chemistry , Peptides/immunology , Peptides/metabolism , Protein Conformation , Protein Structure, Tertiary , T-Lymphocytes, Cytotoxic/metabolism , T-Lymphocytes, Cytotoxic/virology , Trans-Activators/chemistry , Trans-Activators/metabolism , Viral Proteins/chemistry , Viral Proteins/metabolism
16.
Cells ; 9(12)2020 12 10.
Article in English | MEDLINE | ID: mdl-33321790

ABSTRACT

The transport of host proteins into and out of the nucleus is key to host function. However, nuclear transport is restricted by nuclear pores that perforate the nuclear envelope. Protein intrinsic disorder is an inherent feature of this selective transport barrier and is also a feature of the nuclear transport receptors that facilitate the active nuclear transport of cargo, and the nuclear transport signals on the cargo itself. Furthermore, intrinsic disorder is an inherent feature of viral proteins and viral strategies to disrupt host nucleocytoplasmic transport to benefit their replication. In this review, we highlight the role that intrinsic disorder plays in the nuclear transport of host and viral proteins. We also describe viral subversion mechanisms of the host nuclear transport machinery in which intrinsic disorder is a feature. Finally, we discuss nuclear import and export as therapeutic targets for viral infectious disease.


Subject(s)
Cell Nucleus/metabolism , Viral Proteins/metabolism , Active Transport, Cell Nucleus , Animals , Humans , Protein Stability , Viral Proteins/chemistry , Virus Replication
17.
Antiviral Res ; 177: 104760, 2020 05.
Article in English | MEDLINE | ID: mdl-32135219

ABSTRACT

Infection by RNA viruses such as human immunodeficiency virus (HIV)-1, influenza, and dengue virus (DENV) represent a major burden for human health worldwide. Although RNA viruses replicate in the infected host cell cytoplasm, the nucleus is central to key stages of the infectious cycle of HIV-1 and influenza, and an important target of DENV nonstructural protein 5 (NS5) in limiting the host antiviral response. We previously identified the small molecule ivermectin as an inhibitor of HIV-1 integrase nuclear entry, subsequently showing ivermectin could inhibit DENV NS5 nuclear import, as well as limit infection by viruses such as HIV-1 and DENV. We show here that ivermectin's broad spectrum antiviral activity relates to its ability to target the host importin (IMP) α/ß1 nuclear transport proteins responsible for nuclear entry of cargoes such as integrase and NS5. We establish for the first time that ivermectin can dissociate the preformed IMPα/ß1 heterodimer, as well as prevent its formation, through binding to the IMPα armadillo (ARM) repeat domain to impact IMPα thermal stability and α-helicity. We show that ivermectin inhibits NS5-IMPα interaction in a cell context using quantitative bimolecular fluorescence complementation. Finally, we show for the first time that ivermectin can limit infection by the DENV-related West Nile virus at low (µM) concentrations. Since it is FDA approved for parasitic indications, ivermectin merits closer consideration as a broad spectrum antiviral of interest.


Subject(s)
Active Transport, Cell Nucleus/drug effects , Ivermectin/pharmacology , alpha Karyopherins/antagonists & inhibitors , beta Karyopherins/antagonists & inhibitors , Animals , Cell Line , Chlorocebus aethiops , Cricetinae , Flavivirus Infections/drug therapy , Kidney/cytology , Protein Binding , Vero Cells , alpha Karyopherins/metabolism , beta Karyopherins/metabolism
18.
Cells ; 9(1)2020 01 09.
Article in English | MEDLINE | ID: mdl-31936642

ABSTRACT

Viral disease is one of the greatest burdens for human health worldwide, with an urgent need for efficacious antiviral strategies. While antiviral drugs are available, in many cases, they are prone to the development of drug resistance. A way to overcome drug resistance associated with common antiviral therapies is to develop antivirals targeting host cellular co-factors critical to viral replication, such as DEAD-box helicase 3 X-linked (DDX3X), which plays key roles in RNA metabolism and the antiviral response. Here, we use biochemical/biophysical approaches and infectious assays to show for the first time that the small molecule RK-33 has broad-spectrum antiviral action by inhibiting the enzymatic activities of DDX3X. Importantly, we show that RK-33 is efficacious at low micromolar concentrations in limiting infection by human parainfluenza virus type 3 (hPIV-3), respiratory syncytial virus (RSV), dengue virus (DENV), Zika virus (ZIKV) or West Nile virus (WNV)-for all of which, no Food and Drug Administration (FDA)-approved therapeutic is widely available. These findings establish for the first time that RK-33 is a broad-spectrum antiviral agent that blocks DDX3X's catalytic activities in vitro and limits viral replication in cells.


Subject(s)
Antiviral Agents/pharmacology , Azepines/pharmacology , DEAD-box RNA Helicases/antagonists & inhibitors , Imidazoles/pharmacology , Animals , Catalytic Domain , Cell Death/drug effects , Cell Line , Cell Survival/drug effects , DEAD-box RNA Helicases/metabolism , Virus Replication/drug effects
19.
Sci Rep ; 9(1): 10523, 2019 07 19.
Article in English | MEDLINE | ID: mdl-31324847

ABSTRACT

Abacavir is an antiretroviral drug used to reduce human immunodeficiency virus (HIV) replication and decrease the risk of developing acquired immune deficiency syndrome (AIDS). However, its therapeutic value is diminished by the fact that it is associated with drug hypersensitivity reactions in up to 8% of treated patients. This hypersensitivity is strongly associated with patients carrying human leukocyte antigen (HLA)-B*57:01, but not patients carrying closely related alleles. Abacavir's specificity to HLA-B*57:01 is attributed to its binding site within the peptide-binding cleft and subsequent influence of the repertoire of peptides that can bind HLA-B*57:01. To further our understanding of abacavir-induced hypersensitivity we used molecular dynamics (MD) to analyze the dynamics of three different peptides bound to HLA-B*57:01 in the presence and absence of abacavir or abacavir analogues. We found that abacavir and associated peptides bind to HLA-B*57:01 in a highly diverse range of conformations that are not apparent from static crystallographic snapshots, but observed no difference in either the conformations, nor degree of flexibility when compared to abacavir-unbound systems. Our results support hypersensitivity models in which abacavir-binding alters the conformational ensemble of neopeptides, so as to favour exposed peptide surfaces that are no longer recognized as self by circulating CD8+ T cells, and are conducive to TCR binding. Our findings highlight the need to also consider the role of dynamics in understanding drug-induced hypersensitivities at the molecular and mechanistic level. This additional insight can help inform the chemical modification of abacavir to prevent hypersensitivity reactions in HLA-B*57:01+ HIV patients whilst retaining potent antiretroviral activity.


Subject(s)
Anti-HIV Agents/adverse effects , Dideoxynucleosides/adverse effects , Drug Hypersensitivity/etiology , HLA-B Antigens/metabolism , Amino Acid Sequence , Anti-HIV Agents/metabolism , Anti-HIV Agents/pharmacology , Binding Sites , Crystallography, X-Ray , Dideoxynucleosides/metabolism , Dideoxynucleosides/pharmacology , Drug Hypersensitivity/genetics , Genetic Predisposition to Disease , HLA-B Antigens/drug effects , Humans , Models, Molecular , Molecular Dynamics Simulation , Oligopeptides/metabolism , Protein Binding , Protein Conformation/drug effects
20.
Cells ; 8(10)2019 09 30.
Article in English | MEDLINE | ID: mdl-31575075

ABSTRACT

DEAD-box helicase 3, X-linked (DDX3X) regulates the retinoic acid-inducible gene I (RIG-I)-like receptor (RLR)-mediated antiviral response, but can also be a host factor contributing to the replication of viruses of significance to human health, such as human immunodeficiency virus type 1 (HIV-1). These roles are mediated in part through its ability to actively shuttle between the nucleus and the cytoplasm to modulate gene expression, although the trafficking mechanisms, and impact thereof on immune signaling and viral infection, are incompletely defined. We confirm that DDX3X nuclear export is mediated by the nuclear transporter exportin-1/CRM1, dependent on an N-terminal, leucine-rich nuclear export signal (NES) and the monomeric guanine nucleotide binding protein Ran in activated GTP-bound form. Transcriptome profiling and ELISA show that exportin-1-dependent export of DDX3X to the cytoplasm strongly impacts IFN-ß production and the upregulation of immune genes in response to infection. That this is key to DDX3X's antiviral role was indicated by enhanced infection by human parainfluenza virus-3 (hPIV-3)/elevated virus production when the DDX3X NES was inactivated. Our results highlight a link between nucleocytoplasmic distribution of DDX3X and its role in antiviral immunity, with strong relevance to hPIV-3, as well as other viruses such as HIV-1.


Subject(s)
Cell Nucleus/metabolism , DEAD-box RNA Helicases/metabolism , Karyopherins/physiology , Parainfluenza Virus 3, Human/immunology , Receptors, Cytoplasmic and Nuclear/physiology , Respirovirus Infections/immunology , A549 Cells , Active Transport, Cell Nucleus , Animals , Chlorocebus aethiops , Cytoplasm/metabolism , HEK293 Cells , HeLa Cells , Humans , Karyopherins/genetics , Receptors, Cytoplasmic and Nuclear/genetics , Vero Cells , Exportin 1 Protein
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