Biology subjects

Harkins, S. S.

Publications and source records attributed to Harkins, S. S..

5 recordsLinked to original sources

bioRxiv2026

Antigenic landscape of rabies and related lyssaviruses revealed by cryo-EM

Rabies continues to kill over 60,000 people per year despite life-saving vaccines and post-exposure treatments, and costs billions of dollars in prevention and treatment. Preventing rabies deaths and reducing the global economic burden of the virus will require both developing a monoclonal antibody cocktail to replace human serum in treatment and improving rabies vaccines to elicit long-lasting protection. Here, we solve nine cryo-EM structures of neutralizing monoclonal antibodies in complex with the rabies virus surface glycoprotein (RABV-G). The nine structures span three known antigenic sites plus two new antigenic sites, not previously mapped. We further find that these two new sites are the targets of antibodies with the desired broad neutralization of rabies as well as other emerging lyssaviruses. Across the mAb panel, fusion inhibition and binding affinity correlate best with neutralization. Together, these results provide a roadmap for structure-guided vaccine and therapeutic antibody design for rabies and related lyssaviruses.

microbiology↗

bioRxiv2025

Uncovering the features of Measles-targeting human antibodies elicited by the MMR vaccine

Measles virus (MeV), a highly transmissible paramyxovirus, causes disease that can lead to severe complications and death, particularly in babies and young children. Deployment of the durable, highly effective, live-attenuated measles vaccine has saved an estimated 94 million lives in the past 50 years,1 yet the immunological explanation for this vaccines unique success and its landscape of antibody recognition remains unclear. Here we report the first panel of human monoclonal antibodies (mAbs) specific for the MeV hemagglutinin (H) and fusion (F) surface proteins, derived from the memory B cells of an MMR vaccinee. From over 100 cloned human mAbs, we mapped four major epitope clusters on H and another five major clusters on F, and structurally characterized 17 representative mAbs including one or more examples of each of the nine epitope clusters on the two surface antigens. We find that antibodies against both H and F can lead to potent virus neutralization and reduction of viral loads in vivo, including one mAb against F that reduces viral loads to below the limit of detection for all animals. High-resolution cryo-EM reveals contact sites of the most protective antibodies against both surface antigens. Discovery, characterization, and in vitro and in vivo success of these fully human mAbs now provide new avenues for prophylactic or therapeutic intervention against this re-emerging virus. HighlightsO_LIA large panel of Measles-specific monoclonal antibodies was isolated from a human MMR vaccinee, years after vaccination. C_LIO_LIStructural and biochemical mapping paints a landscape of antibody recognition with nine major competition groups, including four major sites on Hemagglutinin (H) and five on the fusion protein (F). C_LIO_LIAntibodies against both H and F confer in vitro neutralization and in vivo protection, including, in one case, undetectable viral load after antibody treatment. C_LIO_LIThe most protective H-specific mAbs, 4D08 and 1C08, target the receptor-binding site and the F-proximal outside of the H dimer, and likely function by interfering with receptor binding and H-F interactions, respectively. C_LIO_LIThe most protective F-specific mAbs, 3A12 and 4F09, target the sides and apex of the prefusion F trimer, and likely function by locking F into its pre-fusion state C_LI

immunology↗

bioRxiv2025

Human endogenous retrovirus K (HERV-K) envelope structures in pre- and post-fusion by Cryo-EM

The HERV-K envelope glycoprotein (Env) is aberrantly expressed in diseases including cancers and autoimmune disorders and is targeted by antibodies. The lack of structural information has hindered functional and immune recognition studies. We solved structures of the HERV-K Env in both pre- and post-fusion states with novel monoclonal antibodies using cryo-EM. The pre-fusion Env assembles as a trimer with a distinct fold and architecture compared to other retroviruses, while the post-fusion conformation features a unique "tether" helix within the TM subunit. A panel of monoclonal antibodies, elicited to facilitate structure determination, have been characterized for conformational and subunit specificity, serving as valuable research tools. These findings establish a structural framework for mechanistic studies of HERV-K Env in diseases and evaluation as a potential therapeutic target.

biochemistry↗

bioRxiv2023

Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation

The 800 million human infections with SARS-CoV-2 and the likely emergence of new variants and additional coronaviruses necessitate a better understanding of the essential spike glycoprotein and the development of immunogens that foster broader and more durable immunity. The S2 fusion subunit is more conserved in sequence, is essential to function, and would be a desirable immunogen to boost broadly reactive antibodies. It is, however, unstable in structure and in its wild-type form, cannot be expressed alone without irreversible collapse into a six-helix bundle. In addition to the irreversible conformational changes of fusion, biophysical measurements indicate that spike also undergoes a reversible breathing action. However, spike in an open, "breathing" conformation has not yet been visualized at high resolution. Here we describe an S2-only antigen, engineered to remain in its relevant, pre-fusion viral surface conformation in the absence of S1. We also describe a panel of natural human antibodies specific for S2 from vaccinated and convalescent individuals. One of these mAbs, from a convalescent individual, afforded a high-resolution cryo-EM structure of the prefusion S2. The structure reveals a complex captured in an "open" conformation with greater stabilizing intermolecular interactions at the base and a repositioned fusion peptide. Together, this work provides an antigen for advancement of next-generation "booster" immunogens and illuminates the likely breathing adjustments of the coronavirus spike.

microbiology↗

bioRxiv2021

Molecular assembly of measles and Nipah virus: specific lipid binding drives conformational change and matrix polymerization

Measles virus, Nipah virus, and multiple other paramyxoviruses cause disease outbreaks in humans and animals worldwide. The paramyxovirus matrix (M) protein mediates virion assembly and budding from host cell membranes. M is thus a key target for antivirals, but few high-resolution structures of paramyxovirus M are available, and we lack the clear understanding of how viral M proteins interact with membrane lipids to mediate viral assembly and egress needed to guide antiviral design. Here, we reveal that M proteins associate with phosphatidylserine and phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) at the plasma membrane. Using X-ray crystallography, electron microscopy, and molecular dynamics we demonstrate that PI(4,5)P2 binding induces conformational and electrostatic changes in the M protein surface that trigger membrane deformation, matrix layer polymerization, and virion assembly.

microbiology↗