Biology subjects

Mangala Prasad, V.

Publications and source records attributed to Mangala Prasad, V..

6 recordsLinked to original sources

bioRxiv2026

HIV-1 envelope glycan loss links receptor adaptation and innate immune escape in SHIVs

Simian-human immunodeficiency viruses (SHIVs) are widely used to model HIV-1 infection in macaques, yet most SHIVs encoding circulating HIV-1 envelope glycoproteins (Env) replicate poorly because of inefficient use of macaque CD4 and sensitivity to host antiviral responses. During adaptation to macaques, Env is therefore subject to multiple selective pressures to improve receptor utilization while maintaining function in the face of host immune restriction. Type I interferon (IFN) is a major component of the host antiviral response during acute infection, and IFN resistance increases during SHIV adaptation to macaques through serial passage. However, the viral determinants of this resistance have remained unclear. Here, we show that serial passage of a lineage of SHIVs in macaques selected Env variants with markedly increased resistance to IFN- and enhanced replication in macaque CD4+ T lymphocytes. IFN- resistance mapped principally to loss of two highly conserved N-linked glycans at N197 and N276 near the CD4-binding site. Glycan loss altered the conformational landscape of virus-associated Env, enhanced macaque CD4-dependent entry and membrane fusion without increasing human CD4-dependent entry, and reduced incorporation of the IFN-inducible restriction factors IFITM3 and IFITM3A into progeny virions. Depletion of IFITM3/3A rendered the parental SHIV highly resistant to IFN- and abolished differential IFN- sensitivity among parental, adapted, and glycan-loss viruses. These findings reveal that loss of receptor-proximal Env glycans can simultaneously improve utilization of a heterologous CD4 receptor and promote escape from IFN-mediated restriction, linking receptor adaptation and innate immune evasion during lentiviral adaptation to a new host.

microbiology↗

bioRxiv2026

Structural determinants of broadly neutralizing human antibodies binding to morphological dengue virus variants.

Dengue virus (DENV) is a global health threat, with four antigenically distinct serotypes impeding vaccine and therapeutic development. We describe here, structural features of patient-derived, heavy chain-driven E-dimer-recognizing (HEDR) antibodies that achieve potent, pan-serotype activity by binding a conserved quaternary epitope on DENVs envelope (E) glycoprotein dimer. Single-particle cryo-EM structures of three HEDR broadly neutralizing antibodies (bnAbs) complexed to DENV delineate epitope engagement via E-glycoproteins fusion loop region and conserved glycans. We also identify capsule-shaped DENV, with helical cryo-EM reconstructions of Fab-bound tubular DENV from different strains revealing that the E-glycoprotein arrangement is determined by virus strain, not bnAb identity. Our findings elucidate key binding features of HEDR bnAbs and signify the need for intervention strategies capable of neutralizing diverse DENV morphologies.

biophysics↗

bioRxiv2022

Visualization of conformational changes and membrane remodeling leading to genome delivery by viral class-II fusion machinery

Chikungunya virus (CHIKV) is a human pathogen that delivers its genome to the host cell cytoplasm through endocytic low pH-activated membrane fusion mediated by class-II fusion proteins. Though structures of prefusion, icosahedral CHIKV are available, structural characterization of virion interaction with membranes has been limited. Here, we have used cryo-electron tomography to visualize CHIKVs complete membrane fusion pathway, identifying key intermediary glycoprotein conformations coupled to membrane remodeling events. Using sub-tomogram averaging, we elucidate features of the low pH-exposed virion, nucleocapsid and full-length E1-glycoproteins post-fusion structure. Contrary to class-I fusion systems, CHIKV achieves membrane apposition by protrusion of extended E1-glycoprotein homotrimers into the target membrane. The fusion process also features a large hemifusion diaphragm that transitions to a wide pore for intact nucleocapsid delivery. Our analyses provide comprehensive ultrastructural insights into the class-II virus fusion system function and direct mechanistic characterization of the fundamental process of protein-mediated membrane fusion.

biophysics↗

bioRxiv2021

Cryo-ET of HIV reveals Env positioning on Gag lattice and structural variation among Env trimers

HIV-1 Env mediates viral entry into host cells and is the sole target for neutralizing antibodies. However, Env structure and organization in its native virion context has eluded detailed characterization. Here we used cryo-electron tomography to analyze Env in mature and immature HIV-1 particles. Immature particles showed distinct Env positioning relative to the underlying Gag lattice, providing insights into long-standing questions about Env incorporation. A 9.1[A] sub-tomogram averaged reconstruction of virion-bound Env in conjunction with structural mass spectrometry revealed unexpected features, including a variable central core of the gp41 subunit, heterogeneous glycosylation between protomers plus a flexible stalk that allows Env tilting and variable exposure of neutralizing epitopes. Together, our results provide an integrative understanding of HIV assembly and structural variation in Env antigen presentation.

biophysics↗

bioRxiv2021

Functional development of a V3-specific broadly neutralizing antibody isolated from a case of HIV superinfection

Stimulating broadly neutralizing antibodies (bnAbs) directly from germline remains a barrier for HIV vaccines. HIV superinfection elicits bnAbs more frequently than single infection, providing clues of how to elicit such responses. We used longitudinal antibody sequencing and structural studies to characterize bnAb development from a superinfection case. Mature bnAb QA013.2 bound both initial transmitted and superinfecting virus, but its inferred naive bound only the superinfecting strain and was not neutralizing. QA013.2 requires residues spanning FWRH1-CDRH1 to attain breadth, which is uncommon for V3-specific bnAbs. A 4.15 [A] cryo-EM structure of QA013.2 bound to heterologous native-like trimer showed recognition of V3 signatures (N301, N332, and GDIR). Antigenic profiling revealed that viral escape was achieved not only by changes in the structurally-defined epitope, but also by mutations in V1. These results highlight shared and distinct properties of QA013.2 relative to other V3-specific bnAbs in the setting of sequential, diverse antigenic variants.

microbiology↗

bioRxiv2018

Rapid development of an infant-derived HIV-1 broadly neutralizing antibody lineage

HIV-infected infants develop broadly neutralizing plasma responses with more rapid kinetics than adults, suggesting the ontogeny of infant responses could better inform a path to achievable vaccine targets. We developed computational methods to reconstruct the developmental lineage of BF520.1, the first example of a HIV-specific broadly neutralizing antibody (bnAb) from an infant. The BF520.1 inferred naive precursor binds HIV Env and a bnAb evolved within six months of infection and required only 3% mutation. Mutagenesis and structural analyses revealed that for this infant bnAb, substitutions in the kappa chain were critical for activity, particularly in CDRL1. Overall, the developmental pathway of this infant antibody includes features distinct from adult antibodies, including several that may be amenable to better vaccine responses.

immunology↗