Dataset Information

Structural basis of malaria RIFIN binding by LILRB1-containing antibodies.

ABSTRACT: Some Plasmodium falciparum repetitive interspersed families of polypeptides (RIFINs)-variant surface antigens that are expressed on infected erythrocytes¹-bind to the inhibitory receptor LAIR1, and insertion of DNA that encodes LAIR1 into immunoglobulin genes generates RIFIN-specific antibodies^2,3. Here we address the general relevance of this finding by searching for antibodies that incorporate LILRB1, another inhibitory receptor that binds to β2 microglobulin and RIFINs through their apical domains^4,5. By screening plasma from a cohort of donors from Mali, we identified individuals with LILRB1-containing antibodies. B cell clones isolated from three donors showed large DNA insertions in the switch region that encodes non-apical LILRB1 extracellular domain 3 and 4 (D3D4) or D3 alone in the variable-constant (VH-CH1) elbow. Through mass spectrometry and binding assays, we identified a large set of RIFINs that bind to LILRB1 D3. Crystal and cryo-electron microscopy structures of a RIFIN in complex with either LILRB1 D3D4 or a D3D4-containing antibody Fab revealed a mode of RIFIN-LILRB1 D3 interaction that is similar to that of RIFIN-LAIR1. The Fab showed an unconventional triangular architecture with the inserted LILRB1 domains opening up the VH-CH1 elbow without affecting VH-VL or CH1-CL pairing. Collectively, these findings show that RIFINs bind to LILRB1 through D3 and illustrate, with a naturally selected example, the general principle of creating novel antibodies by inserting receptor domains into the VH-CH1 elbow.

SUBMITTER: Chen Y

PROVIDER: S-EPMC8068667 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Structural basis of malaria RIFIN binding by LILRB1-containing antibodies.

Chen Yiwei Y Xu Kai K Piccoli Luca L Foglierini Mathilde M Tan Joshua J Jin Wenjie W Gorman Jason J Tsybovsky Yaroslav Y Zhang Baoshan B Traore Boubacar B Silacci-Fregni Chiara C Daubenberger Claudia C Crompton Peter D PD Geiger Roger R Sallusto Federica F Kwong Peter D PD Lanzavecchia Antonio A

Nature 20210331 7855

Some Plasmodium falciparum repetitive interspersed families of polypeptides (RIFINs)-variant surface antigens that are expressed on infected erythrocytes<sup>1</sup>-bind to the inhibitory receptor LAIR1, and insertion of DNA that encodes LAIR1 into immunoglobulin genes generates RIFIN-specific antibodies<sup>2,3</sup>. Here we address the general relevance of this finding by searching for antibodies that incorporate LILRB1, another inhibitory receptor that binds to β2 microglobulin and RIFINs t ...[more]

PMID: 33790470

Similar Datasets

Project description:The psychiatric risk-associated transcription factor 4 (TCF4) is linked to schizophrenia. Rare TCF4 coding variants are found in individuals with Pitt-Hopkins syndrome-an intellectual disability and autism spectrum disorder. TCF4 contains a C-terminal basic-helix-loop-helix (bHLH) DNA binding domain which recognizes the enhancer-box (E-box) element 5'-CANNTG-3' (where N = any nucleotide). A subset of the TCF4-occupancy sites have the expanded consensus binding specificity 5'-C(A/G)-CANNTG-3', with an added outer Cp(A/G) dinucleotide; for example in the promoter for CNIH3, a gene involved in opioid dependence. In mammalian genomes, particularly brain, the CpG and CpA dinucleotides can be methylated at the 5-position of cytosine (5mC), and then may undergo successive oxidations to the 5-hydroxymethyl (5hmC), 5-formyl (5fC), and 5-carboxyl (5caC) forms. We find that, in the context of 5'-0CG-1CA-2CG-3TG-3'(where the numbers indicate successive dinucleotides), modification of the central E-box 2CG has very little effect on TCF4 binding, E-box 1CA modification has a negative influence on binding, while modification of the flanking 0CG, particularly carboxylation, has a strong positive impact on TCF4 binding to DNA. Crystallization of TCF4 in complex with unmodified or 5caC-modified oligonucleotides revealed that the basic region of bHLH domain adopts multiple conformations, including an extended loop going through the DNA minor groove, or the N-terminal portion of a long helix binding in the DNA major groove. The different protein conformations enable arginine 576 (R576) to interact, respectively, with a thymine in the minor groove, a phosphate group of DNA backbone, or 5caC in the major groove. The Pitt-Hopkins syndrome mutations affect five arginine residues in the basic region, two of them (R569 and R576) involved in 5caC recognition. Our analyses indicate, and suggest a structural basis for, the preferential recognition of 5caC by a transcription factor centrally important in brain development.

Project description:A series of human autoantibodies against thyroglobulin (Tg) which exhibit different specificities for iodothyronines were studied. The ability of a thyroxine (T4)-containing peptide (T4P) isolated from human thyroglobulin (Tg) to displace [125I]T3 from human T3-specific autoantisera was 11-50 times greater than that of T4 alone. These antisera therefore strongly recognize amino acids adjacent to T4 in the Tg structure. This was confirmed when a Tg preparation (Tg[0.05]) containing an average of only 0.05 of a T4 residue/molecule and much less T3 had good cross-reactivities with these antisera. Cross-reactivities of other Tg preparations with different T4 contents increased only slowly with increase of T4 content up to a mean of 6.6 residues/molecule and were not proportional to T3 content. In contrast, cross-reactivities with a human T4-specific autoantiserum were strongly dependent on T4 content. Tg[0.05] was 500 times less reactive than T4P and 615 times less than T4. Cross-reactivities rose rapidly as the T4 content of Tg preparations increased from a mean of 0.05 to approx. 1-2 residues/molecule. Thyroxine is therefore a dominant feature of the antigenic site for this antiserum. There was little further increase in cross-reactivities for those Tg preparations containing up to an average of 6.6 residues T4 per molecule, confirming previous conclusions that all T4-containing sites are not immunologically identical and that autoantibodies exhibit a preference for particular sites on Tg. Similar conclusions were reached for a non-specific iodothyronine-binding antiserum. These results indicate that iodothyronine specificity in human autoantisera is not necessarily determined by the iodothyronine present in the immunogenic area, but by the precise site selected by the immune response. T4- or non-specific antibodies have thyroxine as a dominant feature of the antigenic site. T3- specific antibodies have the thyroxine residue as a peripheral feature of the binding site, and it is not necessary to postulate that T3 was part of the immunogen or is required in the epitope. These antisera may have value in mapping the hormonogenic regions in Tg from human and other species.

Project description:Clostridioides difficile is a Gram-positive opportunistic human pathogen that causes 15,000 deaths annually in the United States, prompting a need for vaccine development. In addition to the important toxins TcdA and TcdB, binary toxin (CDT) plays a significant role in the pathogenesis of certain C. difficile ribotypes by catalyzing the ADP-ribosylation of actin in host cells. However, the mechanisms of CDT neutralization by antibodies have not been studied, limiting our understanding of key epitopes for CDT antigen design. Therefore, we isolated neutralizing monoclonal antibodies against CDT and characterized their mechanisms of neutralization structurally and biochemically. Here, 2.5-Å and 2.6-Å resolution X-ray crystal structures of the antibodies BINTOXB/22 and BINTOXB/9, respectively, in complex with CDTb-the CDT subunit that forms a heptameric pore for the delivery of toxic CDTa enzyme into the host cytosol-showed that both antibodies sterically clash with adjacent protomers in the assembled heptamer. Assessment of trypsin-induced oligomerization of the purified CDTb protoxin in vitro showed that BINTOXB/22 and BINTOXB/9 prevented the assembly of di-heptamers upon prodomain cleavage. This work suggests that the CDT oligomerization process can be effectively targeted by antibodies, which will aid in the development of C. difficile vaccines and therapeutics. IMPORTANCE Clostridioides difficile strains associated with worse clinical outcomes have been found to secrete a toxin called CDT (or binary toxin). As blocking the function of this toxin could help mitigate C. difficile infections, we sought to determine the molecular basis for the inhibition of CDT by monoclonal antibodies. We isolated monoclonal antibodies targeting the B-component of CDT (CDTb) and selected two with neutralizing activity for detailed structural and biochemical characterization. High-resolution crystal structures of each antibody bound to CDTb showed that their presence would preclude the assembly of a CDTb oligomer required for activity. Oligomerization of CDTb in vitro was shown to be blocked in the presence of the neutralizing antibodies, but not a control antibody.

Dataset Information

Structural basis of malaria RIFIN binding by LILRB1-containing antibodies.

Publications

Structural basis of malaria RIFIN binding by LILRB1-containing antibodies.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets