Biology subjects

Raghavan, S. S. R.

Publications and source records attributed to Raghavan, S. S. R..

4 recordsLinked to original sources

bioRxiv2025

Structural basis for synergistic antibody protection against the essential malaria invasion complex protein RIPR

Plasmodium falciparum RH5-interacting protein (RIPR) is central to the essential PTRAMP-CSS-RIPR-CyRPA-RH5 (PCRCR)-complex; a leading target of blood-stage malaria vaccines. However, mechanisms whereby anti-RIPR antibodies inhibit parasite invasion are poorly understood. Here, we characterise 83 human IgG mAbs from RIPR-vaccinated Kymouse platform mice. Single mAbs have minimal neutralising activity, however, high-level synergistic inhibition is observed with pools of mAbs targeting the RIPR-Tail region. Structural characterisation and molecular dynamics simulations of RIPR-Tail show that mAbs targeting EGF-like domains 6-8 (RIPREGF (6-8)), but not EGF-like domains 9-10 or the C-terminal domain (RIPREGF (9-10)-CTD), synergise to constrain the RIPR-Tail conformation. The same antibodies dissociate PTRAMP-CSS from RIPR, thereby enabling anti-RIPREGF (9-10)-CTD mAbs or anti-CSS sdAbs to bind and potentiate anti-RIPREGF (6-8) IgG. Addition of these mAbs to IgG from humans immunised with the R78C (RIPREGF (7-8)-CyRPA) candidate vaccine enhances malaria growth inhibition. These data provide a framework to guide next-generation blood-stage malaria vaccine design.

immunology↗

bioRxiv2025

Predicting the conformational flexibility of antibody and T-cell receptor CDRs

AbstractMany proteins are highly flexible and their ability to adapt their shape can be fundamental to their functional properties. We can now computationally predict a single, static protein structure with high accuracy. However, we are not yet able to reliably predict structural flexibility. A major factor limiting such predictions is the scarcity of suitable training data. Here, we focus on predicting the structural flexibility of the functionally important antibody and T-cell receptor CDR3 loops. We extracted a dataset of CDR3 like loop motifs from the PDB to create ALL-conformations, a dataset containing 1.2 million structures and more than 100,000 unique sequences. Using this dataset, we develop ITsFlexible a method classifying CDR3 flexibility, which outperforms all alternative approaches on our crystal structure datasets and successfully generalises to MD simulations. We also used ITsFlexible to predict the flexibility of three completely novel CDRH3 loops and experimentally determined their conformations using cryo-EM.

bioinformatics↗

bioRxiv2024

Functional and epitope specific monoclonal antibody discovery directly from immune sera using cryoEM

Antibodies are crucial therapeutics, comprising a significant portion of approved drugs due to their safety and clinical efficacy. Traditional antibody discovery methods are labor-intensive, limiting scalability and high-throughput analysis. Here, we improved upon our streamlined approach combining structural analysis and bioinformatics to infer heavy and light chain sequences from electron potential maps of serum-derived polyclonal antibodies (pAbs) bound to antigens. Using ModelAngelo, an automated structure-building tool, we accelerated pAb sequence determination and identified sequence matches in B cell repertoires via ModelAngelo derived Hidden Markov Models (HMMs) associated with pAb structures. Benchmarking against results from a non-human primate HIV vaccine trial, our pipeline reduced analysis time from weeks to under a day with higher precision. Validation with murine immune sera from influenza vaccination revealed multiple protective antibodies. This workflow enhances antibody discovery, enabling faster, more accurate mapping of polyclonal responses with broad applications in vaccine development and therapeutic antibody discovery.

immunology↗

bioRxiv2024

Broadly inhibitory antibodies against severe malaria virulence proteins

Plasmodium falciparum pathology is driven by the accumulation of parasite-infected erythrocytes in microvessels. This process is mediated by the parasites polymorphic erythrocyte membrane protein 1 (PfEMP1) adhesion proteins. A subset of PfEMP1 variants that bind human endothelial protein C receptor (EPCR) through their CIDR1 domains is responsible for severe malaria pathogenesis. A longstanding question is whether individual antibodies can recognize the large repertoire of circulating PfEMP1 variants. Here, we describe two broadly reactive and binding-inhibitory human monoclonal antibodies against CIDR1. The antibodies isolated from two different individuals exhibited a similar and consistent EPCR-binding inhibition of 34 CIDR1 domains, representing five of the six subclasses of CIDR1. Both antibodies inhibited EPCR binding of both recombinant full-length and native PfEMP1 proteins as well as parasite sequestration in bioengineered 3D brain microvessels under physiologically relevant flow conditions. Structural analyses of the two antibodies in complex with two different CIDR1 antigen variants reveal similar binding mechanisms that depend on interactions with three highly conserved amino acid residues of the EPCR-binding site in CIDR1. These broadly reactive antibodies likely represent a common mechanism of acquired immunity to severe malaria and offer novel insights for the design of a vaccine or treatment targeting severe malaria.

immunology↗