HIV-1 fusion with host cells is initiated upon engagement of the viral envelope (Env) protein by its receptors and co-receptors. Receptor-induced conformational changes in the Env ectodomain expose the fusion machinery and position the HIV-1 fusion peptide for release and transit to the host membrane. However, no allosteric rearrangements in the envelope receptor/co-receptor binding domain that could induce fusion peptide release have been identified, and the trigger for the structural cascade that brings the viral and host membranes together remains unknown. Here, we identified two sequential conformational gates that control fusion peptide release, thereby facilitating its transition to the host membrane. We show that destabilizing a clasp holding the fusion peptide proximal motif enhances fusion peptide release, and that a coupled downstream gate controls the release of the receptor-binding gp120 subunit. Single-particle cryo-EM structures, biased and unbiased atomistic simulations, and functional experiments reveal that this process is controlled by shifts in the angular orientation of the gp120 subunits, induced by the geometries required for receptor and co-receptor binding. These results show how HIV-1 senses contact with the host cell to initiate fusion, thereby permitting viral entry.

The HIV-1 Envelope (Env) in its pre-receptor “closed” conformation is targeted by broadly neutralizing antibodies (bnAbs), while its receptor-bound “open” conformation, exposes immunodominant epitopes targeted by non-neutralizing antibodies. A human immunoglobin G (IgG) monoclonal antibody (mAb), 19b, binds an Env third variable (V3) loop epitope that is only exposed in the open Env conformation. Despite widespread use of 19b to detect the open Env conformation in immunoassays, its epitope has not yet been structurally defined. Here we determine crystal structures of ligand-free and V3 peptide-bound 19b Fab to visualize details of this interaction. 19b utilizes both its heavy and light chains to interact with the V3 loop. The 5-residue heavy chain complementarity-determining region (CDR H3) facilitates a hydrophobic pocket for V3 residues to associate with. 19b adopts a cradle binding mode with its CDRH1, CDRL2 and CDRL3 mediating interactions with V3 regions that flank the conserved GPGR/Q motif, without making substantial contacts with the GPGR arch region. Our high-resolution structures by elucidating the epitope, binding mode and the structural basis for the broad reactivity of 19b, fill a gap in our knowledge of a reagent that is widely used in immunoassays.

Antibodies initiate antigen recognition through short-lived encounter states. These states are structurally distinct from the bound state and allow an antibody to reach the epitope from diverse approach angles. We previously showed that encounter states enable broadly neutralizing HIV-1 antibodies to access protected epitopes, but how these states evolve during affinity maturation is unknown. Here, we defined encounter-state ensembles for two intermediates in a glycan-dependent antibody clonal lineage using extensive molecular dynamics simulations and Markov state modeling. Somatic mutations in the more mature member did not stabilize the bound state. Instead, they created early glycan-mediated interactions that reoriented the antibody during approach and markedly increased the association rate. This reorientation redistributed productive encounter states across a larger antigen surface. This expanded the antigen surface area over which collisions led to productive binding. The modified encounter state landscape positioned germline residues for conserved contacts and provided a kinetic route that naturally bypasses steric barriers at the epitope. Together, these results show that affinity maturation can proceed by reshaping encounter pathways rather than altering the final complex, revealing a generalizable mechanism by which somatic-germline synergy enhances antigen recognition.

Induction of HIV broadly neutralizing antibodies (bnAbs) is a major vaccine goal. We evaluated in a Phase I trial the immunogenicity of a transmitted/founder (TF) envelope trimer designed to prime the heavy chain third complementarity determining region (CDRH3)-dominant class of CD4-binding site (CD4bs) HIV bnAb precursors. B cells producing neutralizing antibodies were isolated from all participants. CD4bs-directed, CDRH3-dominant candidate bnAb precursors were identified in 73% of vaccinees, including one lineage with heterologous neutralization of global HIV isolates. Structural studies elucidated the epitopes of CD4bs CDRH3-dominant, non-CD4bs V1/V3-directed, and gp120/gp41 interface-targeting neutralizing antibodies. Thus, a TF Env trimer can prime a diverse, polyclonal neutralizing B cell repertoire in humans, providing multiple B cell lineages for advancement by sequential boosting toward HIV bnAb breadth.

Understanding broadly neutralizing antibody (bnAb) lineage development in rhesus macaques (RMs) infected with simian-human immunodeficiency virus (SHIV) may inform HIV-1 vaccine designs. We analyzed HIV-1 envelope (Env)-antibody coevolution in 18 RMs infected with SHIV.BG505 (subtype A) and found conserved patterns of antibody recognition and Env escape, including in three animals that developed V3-glycan-reactive bnAbs. From one RM with V3-glycan-targeted plasma Abs that neutralized heterologous HIV-1 strains, we isolated 203 members of a single clonal antibody lineage designated DH1030. DH1030 antibodies demonstrated genetic, functional, and structural similarities with the human V3-glycan bnAb lineage DH270, which was isolated from an individual with subtype C HIV-1 CH848 infection. Human-DH270 and macaque-DH1030 bnAbs shared early improbable mutations in the heavy chain complementarity determining region 2 that were critical for bnAb development. These convergent patterns of antibody evolution, accumulation of key improbable mutations, and mode of epitope recognition were shared across primate species and distinct HIV-1 subtypes, findings that may be leveraged in HIV-1 vaccine designs. Furthermore, our data highlight the value of SHIV-infected macaques as an outbred model system to explore conserved molecular pathways of bnAb development after infection and vaccination.

HIV-1 envelope glycoprotein (Env), a gp120-gp41 trimer, undergoes coordinated conformational changes that drive membrane fusion and allow immune evasion by transiently concealing neutralization-sensitive epitopes. Most broadly neutralizing antibodies (bNAbs) target gp120, whereas a distinct subset recognizes conserved gp41 regions, such as the fusion peptide and the membrane-proximal external region; however, their impact on Env dynamics and associated neutralization mechanisms remains unclear. Using bioorthogonal tagging for single-molecule FRET, we monitored real-time bNAb-induced conformational sampling of Env on intact virions. Most gp41-directed bNAbs allosterically stabilized the prefusion-closed (PC) state, whereas the bivalent 10E8.4/iMab favored both PC and CD4-bound open (predominant) states. Antibodies redistributed the conformational populations of Env with modest kinetic effects, preserving the sequential transition pathway. These findings reveal two modes of neutralization for gp41-directed antibodies, fixing the prefusion-closed conformation and opening it up - in both cases, with neutralization occurring via long-range allosteric control of Env dynamics.

ABSTRACT Due to the complex biology of HIV-1 broadly neutralizing antibodies (bnAbs), HIV-1 vaccines must target unmutated germline precursor antibodies with B cell receptors that have the appropriate specificity and genetic features to develop neutralization breadth. Previous work has shown that immunization or infection in macaques primes unmutated precursor antibodies that target the broadly neutralizing epitope composed of the second variable region and proximal glycans (termed V2-apex site) of HIV-1 envelope (Env). Macaque V2-apex bnAb precursors elicited thus far have homogeneous usage of the second reading frame of a diversity (D) gene found only in macaques, calling into question whether HIV-1 Env immunogens can elicit only this canonical, macaque-specific V2-apex antibody response, limiting human vaccination success. Here, we show that vaccination of rhesus macaques with Env conjugated to a ferritin nanoparticle (OPT4-scNP) rapidly elicited V2-apex bnAbs with distinct D gene segment usage and motifs that are not restricted only to macaques. After two priming immunizations, V2-apex antibodies with non-canonical HCDR3s exhibited greater neutralization potency and breadth than V2-apex antibodies with previously observed HCDR3 motifs. Following sequential boosting immunizations, a V2-apex bnAb lineage with a novel HCDR3-encoded EDGED motif increased its neutralization breadth, including neutralization of viral isolates bearing the N130 glycan, which shields the V2-apex from recognition. High-resolution structures of two members of this V2-apex bnAb lineage, called DH2050, defined a novel binding mode in which it used its EDGED motif to contact the C-strand peptide and the N160 glycan within the V2-apex site. Altogether, we define a novel bnAb binding mode to the V2 Apex and demonstrate that HIV-1 Env sequential vaccination elicits V2-apex bnAbs with immunogenetic signatures that are potentially translatable to the human immune system.

Henipaviruses, in the Paramyxoviridae family, includes the highly virulent Nipah virus that causes reoccurring outbreaks of deadly disease. Recent discoveries of Henipavirus-like species, including the zoonotic Langya virus, have revealed much higher antigenic diversity than currently characterized and prompted the reorganization of these viruses into the Henipavirus and Parahenipavirus genera. Here, to explore the limits of structural and antigenic variation in both genera, collectively referred to as HNVs, we construct an expanded, diverse panel of HNV fusion and attachment glycoproteins from non-redundant HNV strains that better reflect global HNV diversity. We express and purify the fusion protein ectodomains and the attachment protein head domains and study their biochemical and biophysical properties. We perform immunization experiments in mice, eliciting antibodies reactive to multiple HNV fusion proteins. Cryo-electron microscopy structures elucidate molecular determinants of differential pre-fusion state stability and higher order contacts. A crystal structure of the Gamak virus attachment head domain reveals an additional domain appended to the conserved 6-bladed, β-propeller fold. Taken together, these studies expand the known structural and antigenic limits of the HNVs, reveal cross-reactive epitopes within both genera and provide foundational data for the development of broadly reactive countermeasures.

Zoonotic Sarbecoviruses present a documented threat to global health. Here, we report the recovery of an African clade-3 recombinant Sarbecovirus, PRD0038, and derivatives encoding reporter genes. Cryo-EM structural analyses of rPRD0038 revealed spike glycoprotein sites that facilitate the receptor-binding domain (RBD)-up conformation, enhancing replication in R. affinis but not human ACE2 expressing cells. Host range analysis of rPRD0038 identified civets, rabbits, camels, and cows as potential intermediate hosts, while confirming the lack of human ACE2 usage and replication in primary human airway epithelial cells. Despite significant divergence from SARS-CoV-2, PRD0038 remains susceptible to FDA-approved nucleoside and mPro-targeted antivirals as well as some monoclonal antibodies that target select conserved spike epitopes. Pre-existing SARS-CoV-2 immune memory conferred reduced cross-neutralizing activity against PRD0038. Finally, we present an R. affinis ACE2-expressing mouse model for assessing PRD0038 in vivo replication and pathogenesis, and testing countermeasures. Together, these data illustrate functional and immunological constraints that regulate the emergence potential of clade-3 bat Sarbecoviruses while identifying protective therapeutics.

The role of tumor-infiltrating B cells (TIL-Bs) in shaping anti-tumor responses in the context of immune checkpoint blockade remains incompletely understood. Here, we interrogate the humoral response in resected lung tumors from patients with non-small cell lung cancer (NSCLC) treated with neoadjuvant PD-1 blockade. We find that tumors orchestrate tertiary lymphoid structures with CD138+ plasma cells, from which we clone recombinant monoclonal antibodies (mAbs) using B cell receptors (BCRs) exhibiting somatic hypermutation and class switching. Several mAbs bind cell-surface citrullinated proteins, characteristic of cancer cells. Chimeric antigen receptor (CAR) T redirected with the soluble chain fragment variable (scFv) of our lead candidate antibody (PC-1) specifically target tumor cells and tumor-promoting myeloid cells in vivo without off-target activity. Moreover, ablation of the citrullination enzyme PADI2 in tumor-bearing mice eliminates reactivity to PC-1 and cytotoxic killing by the CAR. Our results implicate a therapeutic potential for tumor-infiltrating plasma cells that may be harnessed for cancer treatment.

Cryo-EM has revolutionized structural biology, especially for flexible and heterogeneous samples, although access to high end microscopes that enable these studies remains a bottleneck. While 300 keV microscopes have been the go-to for high-resolution structural determination, they are expensive and restricted to institutional and national facilities needing specialized expertise, with access falling far short of the demand. Here, we present the user-managed operation of a cheaper 100 keV electron microscope within a structural biology laboratory enabling close integration with protein production, biochemical and biophysical studies. We provide details and considerations for the installation of the microscope, its day-to-day maintenance, and operations. Using virus surface glycoproteins as case studies, we illustrate the workflow from grid screening, data collection, and data processing, and provide examples of data quality. This user-administered setup provides a training platform for researchers at all levels, with beginners in cryo-EM achieving proficiency to independently operate the microscope within a month of regular use and training. We have demonstrated routine high-quality low-resolution reconstructions using a Ceta CMOS camera and high-resolution reconstructions enabling building of atomic models using a Falcon C direct detector. While there are several examples of facilities that manage cryo-EM and individual laboratories leveraging cryo-EM, we provide here the first demonstration of a modern group independently doing both successfully, something that has been talked about frequently but rarely seen.

The hydrophobic fusion peptide (FP), a critical component of the HIV-1 entry machinery, is located at the N terminus of the envelope (Env) gp41 subunit. The receptor-binding gp120 subunit of Env forms a heterodimer with gp41. The gp120/gp41 heterodimer assembles into a homotrimer, in which FP is accessible for antibody binding. Env conformational changes or "opening" that follow receptor binding result in FP relocating to a newly formed interprotomer pocket at the gp41-gp120 interface where it is sterically inaccessible to antibodies. The mechanistic steps connecting the entry-related transition of antibody accessible-to-inaccessible FP configurations remain unresolved. Here, using SOSIP-stabilized Env ectodomains, we visualize that the FP remains accessible for antibody binding despite substantial receptor-induced Env opening. We delineate stepwise Env opening from its closed state to a functional CD4-bound symmetrically open Env in which we show that FP was accessible for antibody binding. We define downstream re-organizations that lead to the formation of a gp120/gp41 cavity into which the FP buries to become inaccessible for antibody binding. These findings improve our understanding of HIV-1 entry and delineate the entry-related conformational trajectory of a key site of HIV vulnerability to neutralizing antibody.

Broadly neutralizing antibodies (bnAbs) that target the HIV gp41 membrane-proximal external region (MPER) have some of the highest neutralization breadth. An MPER peptide-liposome vaccine has been found to expand MPER bnAb precursors in monkeys. The HVTN133 phase 1 clinical trial (NCT03934541) studied the MPER peptide-liposome immunogen in 24 HIV-1 seronegative individuals. Participants were randomized in a dose-escalation design to either 500 mcg or 2000 mcg of the MPER-peptide liposome or placebo. Four intramuscular injections were planned at months 0, 2, 6, and 12. The trial was stopped prematurely due to an anaphylaxis reaction in one participant attributed to vaccine-associated polyethylene glycol. The immunogen induced MPER-specific serum antibodies and CD4+ T-cell responses in 95% and 85% of vaccinees, respectively, and 35% of vaccine recipients had circulating IgG+ memory B cells with an MPER-bnAb binding phenotype. Affinity purification of plasma MPER-specific IgG demonstrated tier 2 HIV-1 neutralizing activity in two of five participants after 3 immunizations and tier 2 HIV-1 neutralizing B cell clonal lineages were isolated from MPER-reactive B cells. These results demonstrate that the HIV gp41 MPER region is a promising target for induction of heterologous neutralizing antibodies by a candidate HIV vaccine. Trial Registration:http://www.clinicaltrials.gov/ Identifier: NCT03934541.

Due to the lack of an effective vaccine or a cure, HIV-1 continues to be a major global health threat with the World Health Organization (WHO) reporting 39.0 million people living with HIV-1 and 1.3 new infections in 2022. The HIV-1 Envelope (Env) protein mediates viral entry through interactions with host cell receptors. The pre-receptor Env conformation is targeted by broadly neutralizing antibodies and is the focus of vaccine design, while its altered conformation post receptor binding exposes immunodominant epitopes that are targeted by non-neutralizing antibodies. 19b is a non-neutralizing human immunoglobin G (IgG) monoclonal antibody (mAb) isolated from an asymptomatic person infected with HIV-1 that binds the third variable region (V3) of Env. We expressed and purified 19b IgG. We characterized 19b binding using Surface Plasmon Resonance (SPR). We determined crystal structures of the unliganded 19b Fab and in complex with its V3 peptide epitope from three different HIV-1 strains. Env V3 peptide interacts with both the heavy and light chains of 19b Fab via the complementarity-determining regions (CDRs) L2 and H1. We see a novel V3-Fab binding motif when compared to previously published Env V3 - Fab structures wherein the bulk of 19b recognition occurs at the circlet and band regions of V3. These structures lack the GPGR V3 crown – Fab interaction which agrees with the cradle binding V3 epitopes seen in other non-neutralizing antibodies. 19b is a commonly used reagent in vaccine studies and is widely used to detect the exposure of non-neutralizing Env epitopes. Our high-resolution structures elucidate the epitope and binding mode of 19b, thereby filling a long-standing gap in knowledge that will aid vaccine design against HIV-1.

SARS-CoV-2 continues to evolve, with new variants emerging that evade pre-existing immunity and limit the efficacy of existing vaccines. One approach toward developing superior, variant-proof vaccines is to engineer immunogens that preferentially elicit antibodies with broad cross-reactivity against SARS-CoV-2 and its variants by targeting conserved epitopes on spike. The inner and outer faces of the receptor binding domain (RBD) are two such conserved regions targeted by antibodies that recognize diverse human and animal coronaviruses. To promote the elicitation of such antibodies by vaccination, we engineered "resurfaced" RBD immunogens that contained mutations at exposed RBD residues outside the target epitopes. In the context of pre-existing immunity, these vaccine candidates aim to disfavor the elicitation of strain-specific antibodies against the immunodominant receptor binding motif (RBM) while boosting the induction of inner and outer face antibodies. The engineered resurfaced RBD immunogens were stable, lacked binding to monoclonal antibodies with limited breadth, and maintained strong interactions with target broadly neutralizing antibodies. When used as vaccines, they limited humoral responses against the RBM as intended. Multimerization on nanoparticles further increased the immunogenicity of the resurfaced RBD immunogens, thus supporting resurfacing as a promising immunogen design approach to rationally shift natural immune responses to develop more protective vaccines.IMPORTANCESARS-CoV-2 is the third coronavirus to cause significant human disease over the last two decades. Despite their success in preventing serious disease, current SARS-CoV-2 vaccines must be updated regularly to match the circulating strains for continued protection. Therefore, it would be advantageous to develop vaccines that protect more broadly against SARS-CoV-2, its variants, and other pre-emergent coronaviruses. This may be achieved by preferentially eliciting antibodies against conserved regions of the spike protein that decorates the virus. Toward this goal, we engineered vaccine candidates to target the conserved inner and outer domains of the Receptor Binding Domain of SARS-CoV-2, by altering the surface of the wild-type protein such that strain-specific antibodies that bind outside these regions are no longer recognized. When used in animals with pre-existing SARS-CoV-2 immunity, these molecules reduce the elicitation of variant-specific antibodies, thus providing a blueprint to alter the natural immunodominance hierarchies of SARS-CoV-2 proteins.

A critical roadblock to HIV vaccine development is the inability to induce B cell lineages of broadly neutralizing antibodies (bnAbs) in humans. In people living with HIV-1, bnAbs take years to develop. The HVTN 133 clinical trial studied a peptide/liposome immunogen targeting B cell lineages of HIV-1 envelope (Env) membrane-proximal external region (MPER) bnAbs (NCT03934541). Here, we report MPER peptide-liposome induction of polyclonal HIV-1 B cell lineages of mature bnAbs and their precursors, the most potent of which neutralized 15% of global tier 2 HIV-1 strains and 35% of clade B strains with lineage initiation after the second immunization. Neutralization was enhanced by vaccine selection of improbable mutations that increased antibody binding to gp41 and lipids. This study demonstrates proof of concept for rapid vaccine induction of human B cell lineages with heterologous neutralizing activity and selection of antibody improbable mutations and outlines a path for successful HIV-1 vaccine development.

Henipaviruses, a genus within the Paramyxoviridae family, include the highly virulent Nipah and Hendra viruses that cause reoccurring outbreaks of deadly disease. Recent discoveries of several new Paramyxoviridae species, including the zoonotic Langya virus, have revealed much higher antigenic diversity than currently characterized and prompted the reorganization of these viruses into the Henipavirus and Parahenipavirus genera. Here, to explore the limits of structural and antigenic variation in both genera, collectively referred to here as HNVs, we constructed an expanded, antigenically diverse panel of HNV fusion and attachment glycoproteins from 56 unique HNV strains that better reflects global HNV diversity. We expressed and purified the fusion protein ectodomains and the attachment protein head domains and characterized their biochemical, biophysical and structural properties. We performed immunization experiments in mice leading to the elicitation of antibodies reactive to multiple HNV fusion proteins. Cryo-electron microscopy structures of diverse fusion proteins elucidated molecular determinants of differential pre-fusion state metastability and higher order contacts. A crystal structure of the Gamak virus attachment head domain revealed an additional domain added to the conserved 6-bladed, β-propeller fold. Taken together, these studies expand the known structural and antigenic limits of the HNVs, reveal new cross-reactive epitopes within both genera and provide foundational data for the development of broadly reactive countermeasures.