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Lennartz F, Bengtsson A, Olsen RW, Joergensen L, Brown A, Remy L, Man P, Forest E, Barfod LK, Adams Y, Higgins MK, Jensen ATR. Mapping the Binding Site of a Cross-Reactive Plasmodium falciparum PfEMP1 Monoclonal Antibody Inhibitory of ICAM-1 Binding. THE JOURNAL OF IMMUNOLOGY 2015; 195:3273-83. [PMID: 26320251 PMCID: PMC4574524 DOI: 10.4049/jimmunol.1501404] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 07/23/2015] [Indexed: 12/29/2022]
Abstract
The virulence of Plasmodium falciparum is linked to the ability of infected erythrocytes (IE) to adhere to the vascular endothelium, mediated by P. falciparum erythrocyte membrane protein 1 (PfEMP1). In this article, we report the functional characterization of an mAb that recognizes a panel of PfEMP1s and inhibits ICAM-1 binding. The 24E9 mouse mAb was raised against PFD1235w DBLβ3_D4, a domain from the group A PfEMP1s associated with severe malaria. 24E9 recognizes native PfEMP1 expressed on the IE surface and shows cross-reactivity with and cross-inhibition of the ICAM-1 binding capacity of domain cassette 4 PfEMP1s. 24E9 Fab fragments bind DBLβ3_D4 with nanomolar affinity and inhibit ICAM-1 binding of domain cassette 4–expressing IE. The antigenic regions targeted by 24E9 Fab were identified by hydrogen/deuterium exchange mass spectrometry and revealed three discrete peptides that are solvent protected in the complex. When mapped onto a homology model of DBLβ3_D4, these cluster to a defined, surface-exposed region on the convex surface of DBLβ3_D4. Mutagenesis confirmed that the site most strongly protected is necessary for 24E9 binding, which is consistent with a low-resolution structure of the DBLβ3_D4::24E9 Fab complex derived from small-angle x-ray scattering. The convex surface of DBLβ3_D4 has previously been shown to contain the ICAM-1 binding site of DBLβ domains, suggesting that the mAb acts by occluding the ICAM-1 binding surface. Conserved epitopes, such as those targeted by 24E9, are promising candidates for the inclusion in a vaccine interfering with ICAM-1–specific adhesion of group A PfEMP1 expressed by P. falciparum IE during severe malaria.
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Affiliation(s)
- Frank Lennartz
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Anja Bengtsson
- Department of Immunology and Microbiology, Centre for Medical Parasitology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1014, Denmark; Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen 2100, Denmark
| | - Rebecca W Olsen
- Department of Immunology and Microbiology, Centre for Medical Parasitology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1014, Denmark; Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen 2100, Denmark
| | - Louise Joergensen
- Department of Immunology and Microbiology, Centre for Medical Parasitology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1014, Denmark; Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen 2100, Denmark
| | - Alan Brown
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Louise Remy
- Institut de Biologie Structurale, Grenoble F-38044, France
| | - Petr Man
- Institute of Microbiology, Academy of Sciences of the Czech Republic, 117 20 Prague, Czech Republic; and Faculty of Science, Charles University in Prague, 116 36 Prague, Czech Republic
| | - Eric Forest
- Institut de Biologie Structurale, Grenoble F-38044, France
| | - Lea K Barfod
- Department of Immunology and Microbiology, Centre for Medical Parasitology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1014, Denmark; Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen 2100, Denmark
| | - Yvonne Adams
- Department of Immunology and Microbiology, Centre for Medical Parasitology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1014, Denmark; Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen 2100, Denmark
| | - Matthew K Higgins
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom;
| | - Anja T R Jensen
- Department of Immunology and Microbiology, Centre for Medical Parasitology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1014, Denmark; Department of Infectious Diseases, Copenhagen University Hospital (Rigshospitalet), Copenhagen 2100, Denmark;
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Gomez F, Tomas G, Ko WY, Ranciaro A, Froment A, Ibrahim M, Lema G, Nyambo TB, Omar SA, Wambebe C, Hirbo JB, Rocha J, Tishkoff SA. Patterns of nucleotide and haplotype diversity at ICAM-1 across global human populations with varying levels of malaria exposure. Hum Genet 2013; 132:987-99. [PMID: 23609612 DOI: 10.1007/s00439-013-1284-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 02/27/2013] [Indexed: 10/26/2022]
Abstract
Malaria is one of the strongest selective pressures in recent human evolution. African populations have been and continue to be at risk for malarial infections. However, few studies have re-sequenced malaria susceptibility loci across geographically and genetically diverse groups in Africa. We examined nucleotide diversity at Intercellular adhesion molecule-1 (ICAM-1), a malaria susceptibility candidate locus, in a number of human populations with a specific focus on diverse African ethnic groups. We used tests of neutrality to assess whether natural selection has impacted this locus and tested whether SNP variation at ICAM-1 is correlated with malaria endemicity. We observe differing patterns of nucleotide and haplotype variation in global populations and higher levels of diversity in Africa. Although we do not observe a deviation from neutrality based on the allele frequency distribution, we do observe several alleles at ICAM-1, including the ICAM-1 (Kilifi) allele, that are correlated with malaria endemicity. We show that the ICAM-1 (Kilifi) allele, which is common in Africa and Asia, exists on distinct haplotype backgrounds and is likely to have arisen more recently in Asia. Our results suggest that correlation analyses of allele frequencies and malaria endemicity may be useful for identifying candidate functional variants that play a role in malaria resistance and susceptibility.
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Affiliation(s)
- Felicia Gomez
- Department of Genetics and Biology, School of Medicine and School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Gullingsrud J, Saveria T, Amos E, Duffy PE, Oleinikov AV. Structure-function-immunogenicity studies of PfEMP1 domain DBL2βPF11_0521, a malaria parasite ligand for ICAM-1. PLoS One 2013; 8:e61323. [PMID: 23593462 PMCID: PMC3625211 DOI: 10.1371/journal.pone.0061323] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 03/07/2013] [Indexed: 11/30/2022] Open
Abstract
Plasmodium falciparum virulence has been ascribed to its ability to sequester in deep vascular beds, mediated by the variant surface antigen family PfEMP1 binding endothelial receptors like ICAM-1. We previously observed that naturally-acquired antibodies that block a PfEMP1 domain, DBL2β of PF11_0521 allele, from binding to the human ICAM1 receptor, reduce the risk of malaria hospitalization in children. Here, we find that DBL2βPF11_0521 binds ICAM-1 in the low nM range and relate the structure of this domain with its function and immunogenicity. We demonstrate that the interaction with ICAM-1 is not impaired by point mutations in the N-terminal subdomain or in the flexible Loop 4 of DBL2βPF11_0521, although both substructures were previously implicated in binding ICAM-1. These data will help to refine the existing model of DBLβ::ICAM-1 interactions. Antibodies raised against full-length DBL2βPF11_0521, but not truncated forms lacking the N terminal fragment, block its interaction with ICAM-1. Our data suggest that full length domain is optimal for displaying functional epitopes and has a broad surface of interaction with ICAM-1 that is not disrupted by individual amino acid substitutions at putative key residues. This information might be important for the future design of anti-malarial vaccines based on PfEMP1 antigens.
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Affiliation(s)
- Justin Gullingsrud
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Tracy Saveria
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Emily Amos
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Patrick E. Duffy
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- Department of Global Health, Program of Pathobiology, University of Washington, Seattle, Washington, United States of America
- Laboratory of Malaria Immunology and Vaccinology, NIAID/NIH, Rockville, Maryland, United States of America
| | - Andrew V. Oleinikov
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- * E-mail:
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Brown A, Turner L, Christoffersen S, Andrews KA, Szestak T, Zhao Y, Larsen S, Craig AG, Higgins MK. Molecular architecture of a complex between an adhesion protein from the malaria parasite and intracellular adhesion molecule 1. J Biol Chem 2013; 288:5992-6003. [PMID: 23297413 PMCID: PMC3581401 DOI: 10.1074/jbc.m112.416347] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 12/20/2012] [Indexed: 11/06/2022] Open
Abstract
The adhesion of Plasmodium falciparum-infected erythrocytes to human tissues or endothelium is central to the pathology caused by the parasite during malaria. It contributes to the avoidance of parasite clearance by the spleen and to the specific pathologies of cerebral and placental malaria. The PfEMP1 family of adhesive proteins is responsible for this sequestration by mediating interactions with diverse human ligands. In addition, as the primary targets of acquired, protective immunity, the PfEMP1s are potential vaccine candidates. PfEMP1s contain large extracellular ectodomains made from CIDR (cysteine-rich interdomain regions) and DBL (Duffy-binding-like) domains and show extensive variation in sequence, size, and domain organization. Here we use biophysical methods to characterize the entire ∼300-kDa ectodomain from IT4VAR13, a protein that interacts with the host receptor, intercellular adhesion molecule-1 (ICAM-1). We show through small angle x-ray scattering that IT4VAR13 is rigid, elongated, and monomeric. We also show that it interacts with ICAM-1 through the DBLβ domain alone, forming a 1:1 complex. These studies provide a first low resolution structural view of a PfEMP1 ectodomain in complex with its ligand. They show that it combines a modular domain arrangement consisting of individual ligand binding domains, with a defined higher order architecture that exposes the ICAM-1 binding surface to allow adhesion.
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Affiliation(s)
- Alan Brown
- From the Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | - Louise Turner
- Centre for Molecular Parasitology, University of Copenhagen, Øster Farimagsgade 5, Bygning 221014, Copenhagen, Denmark
| | - Stig Christoffersen
- Centre for Molecular Parasitology, University of Copenhagen, Øster Farimagsgade 5, Bygning 221014, Copenhagen, Denmark
- the Department of Chemistry, University of Copenhagen, Universitetsparken 5 2100 Copenhagen, Denmark
| | - Katrina A. Andrews
- From the Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | - Tadge Szestak
- Molecular and Biochemical Parasitology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, United Kingdom
| | - Yuguang Zhao
- Division of Structural Biology, University of Oxford, Oxford, OX3 7BN, and
| | - Sine Larsen
- the Department of Chemistry, University of Copenhagen, Universitetsparken 5 2100 Copenhagen, Denmark
| | - Alister G. Craig
- Molecular and Biochemical Parasitology, Liverpool School of Tropical Medicine, Liverpool, L3 5QA, United Kingdom
| | - Matthew K. Higgins
- the Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
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Diez D, Hayes N, Joannin N, Normark J, Kanehisa M, Wahlgren M, Wheelock CE, Goto S. varDB: a database of antigenic variant sequences--current status and future prospects. Acta Trop 2010; 114:144-51. [PMID: 19539588 DOI: 10.1016/j.actatropica.2009.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2009] [Revised: 06/03/2009] [Accepted: 06/09/2009] [Indexed: 11/19/2022]
Abstract
Antigenic variation is a common mechanism employed by many pathogenic organisms to avoid recognition of surface proteins by the host immune system. The malaria parasite, Plasmodium falciparum, among many others, exploits this mechanism and manages to survive in an otherwise hostile environment. Although similarities in the mechanisms used among different species to generate antigenic variation are broadly recognized, there is a lack of studies using cross-species data. The varDB project (http://www.vardb.org) was created to study antigenic variation at a range of different levels, both within and among species. The project aims to serve as a resource to increase our understanding of antigenic variation by providing a framework for comparative studies. In this review we describe the varDB project, its construction, and the overall organization of information with the intent of increasing the utility of varDB to the research community. The current version of varDB supports 27 species involved in 19 different diseases affecting humans as well as other species. These data include 42 gene families that are represented by over 67,000 sequences. The varDB project is still in its infancy but is expected to continue to grow with the addition of new organisms and gene families as well as input from the general research community.
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Affiliation(s)
- Diego Diez
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
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Pasini EM, Lutz HU, Mann M, Thomas AW. Red Blood Cell (RBC) membrane proteomics — Part II: Comparative proteomics and RBC patho-physiology. J Proteomics 2010; 73:421-35. [DOI: 10.1016/j.jprot.2009.07.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 07/07/2009] [Accepted: 07/13/2009] [Indexed: 12/23/2022]
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Oleinikov AV, Amos E, Frye IT, Rossnagle E, Mutabingwa TK, Fried M, Duffy PE. High throughput functional assays of the variant antigen PfEMP1 reveal a single domain in the 3D7 Plasmodium falciparum genome that binds ICAM1 with high affinity and is targeted by naturally acquired neutralizing antibodies. PLoS Pathog 2009; 5:e1000386. [PMID: 19381252 PMCID: PMC2663049 DOI: 10.1371/journal.ppat.1000386] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Accepted: 03/18/2009] [Indexed: 12/01/2022] Open
Abstract
Plasmodium falciparum–infected erythrocytes bind endothelial receptors to sequester in vascular beds, and binding to ICAM1 has been implicated in cerebral malaria. Binding to ICAM1 may be mediated by the variant surface antigen family PfEMP1: for example, 6 of 21 DBLβC2 domains from the IT4 strain PfEMP1 repertoire were shown to bind ICAM1, and the PfEMP1 containing these 6 domains are all classified as Group B or C type. In this study, we surveyed binding of ICAM1 to 16 DBLβC2 domains of the 3D7 strain PfEMP1 repertoire, using a high throughput Bioplex assay format. Only one DBL2βC2 domain from the Group A PfEMP1 PF11_0521 showed strong specific binding. Among these 16 domains, DBL2βC2PF11_0521 best preserved the residues previously identified as conserved in ICAM1-binding versus non-binding domains. Our analyses further highlighted the potential role of conserved residues within predominantly non-conserved flexible loops in adhesion, and, therefore, as targets for intervention. Our studies also suggest that the structural/functional DBLβC2 domain involved in ICAM1 binding includes about 80 amino acid residues upstream of the previously suggested DBLβC2 domain. DBL2βC2PF11_0521 binding to ICAM1 was inhibited by immune sera from east Africa but not by control US sera. Neutralizing antibodies were uncommon in children but common in immune adults from east Africa. Inhibition of binding was much more efficient than reversal of binding, indicating a strong interaction between DBL2βC2PF11_0521 and ICAM1. Our high throughput approach will significantly accelerate studies of PfEMP1 binding domains and protective antibody responses. Plasmodium falciparum exports the protein PfEMP1 to the surface of parasitized erythrocytes for roles in immunoevasion and adhesion. The size and structural complexity of this diverse protein family have limited earlier studies of PfEMP1 biology to low throughput and semi-quantitative approaches. We developed a high throughput quantitative assay of PfEMP1 adhesion and used it to analyze structural features of domains that bind the putative cerebral receptor ICAM1, as well as to survey the acquisition of functional antibodies in malaria-exposed children and adults. In studies of the PfEMP1 repertoire of clone 3D7 parasites, a single specific domain bound ICAM1 strongly. PfEMP1 domains that bind ICAM1 strongly have conserved features, including conserved amino acids within otherwise highly variant flexible loops of the protein. While neutralizing antibodies against the PfEMP1–ICAM1 interaction were uncommon in Tanzanian children, such antibodies were common in east African adults, possibly explaining why immune adults rarely carry ICAM1-binding parasites. This high throughput platform will significantly accelerate studies of PfEMP1 binding domains and the corresponding antibody responses involved in protective immunity.
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Abstract
The RosettaDock server (http://rosettadock.graylab.jhu.edu) identifies low-energy conformations of a protein–protein interaction near a given starting configuration by optimizing rigid-body orientation and side-chain conformations. The server requires two protein structures as inputs and a starting location for the search. RosettaDock generates 1000 independent structures, and the server returns pictures, coordinate files and detailed scoring information for the 10 top-scoring models. A plot of the total energy of each of the 1000 models created shows the presence or absence of an energetic binding funnel. RosettaDock has been validated on the docking benchmark set and through the Critical Assessment of PRedicted Interactions blind prediction challenge.
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Affiliation(s)
- Sergey Lyskov
- Department of Chemical and Biomolecular Engineering and Program in Molecular and Computational Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
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9
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Sherman IW. References. ADVANCES IN PARASITOLOGY 2008. [DOI: 10.1016/s0065-308x(08)00430-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Howell DPG, Levin EA, Springer AL, Kraemer SM, Phippard DJ, Schief WR, Smith JD. Mapping a common interaction site used by Plasmodium falciparum Duffy binding-like domains to bind diverse host receptors. Mol Microbiol 2007; 67:78-87. [PMID: 18047571 DOI: 10.1111/j.1365-2958.2007.06019.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Duffy binding-like (DBL) domain is a key adhesive module in Plasmodium falciparum, present in both erythrocyte invasion ligands (EBLs) and the large and diverse P. falciparum erythrocyte membrane protein 1 (PfEMP1) family of cytoadherence receptors. DBL domains bind a variety of different host receptors, including intercellular adhesion molecule 1 (ICAM-1), a receptor interaction that may have a role in infected erythrocyte binding to cerebral blood vessels and cerebral malaria. In this study, we expressed the nearly full complement of DBLbeta-C2 domains from the IT4/25/5 (IT4) parasite isolate and showed that ICAM-1-binding domains (DBLbeta-C2(ICAM-1)) were confined to group B and group C PfEMP1 proteins and were not present in group A, suggesting that ICAM-1 selection pressure differs between PfEMP1 groups. To further dissect the molecular determinants of binding, we modelled a DBLbeta-C2(ICAM-1) domain on a solved DBL structure and created alanine substitution mutants in two DBLbeta-C2(ICAM-1) domains. This analysis indicates that the DBLbeta-C2::ICAM-1 interaction maps to the equivalent glycan binding region of EBLs, and suggests a general model for how DBL domains evolve under dual selection for host receptor binding and immune evasion.
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Affiliation(s)
- Dasein P-G Howell
- Seattle Biomedical Research Institute, 307 Westlake Ave N, Ste 500, Seattle, WA 98109-5219, USA
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