Antibodies are crucial components of our immune system, effectively inhibiting pathogens by binding to their surface antigens and aiding in their elimination. Antibodies neutralize pathogens such as viruses either directly by blocking entry or via their Fc functions. In case of large viral diversity, the generation of broadly neutralizing antibodies (bNAbs) is required to efficiently protect from infection from a wide range of circulating viruses. These bNAbs have been explored in HIV-1 vaccine development, but so far, no vaccine has successfully elicited a bNAb response in animals or humans. Researchers are actively searching for Env-derived immunogens that can trigger bNAb activity. Understanding the structure of bNAbs bound to the Env trimer is essential, as it might reveal the immunogen that induces bNAb production in HIV-1-infected individuals. In this study, we use structural approaches to characterize three novel bNAbs : LN02-ML85, SHCS-3L6, and SHCS-0380.
We employed molecular biology techniques and various purification strategies to produce complexes of soluble Envelope glycoprotein with these antibodies. Single-particle cryo-EM was employed to reconstruct the structures of these complexes, followed by computational analysis to identify the antibody epitopes and describe key interactions between the Env and the antibodies. The cryo-EM structures of Env complexes with LN02-ML85, SHCS-3L6, and SHCS-0380 were resolved at resolutions of 3.1, 2.9, and 3.3 Å, respectively. LN02-ML85 and SHCS-0380 target the gp120-gp41 interface, while SHCS-3L6 targets the glycan patch proximal to V3-loop. LN02-ML85 binds through hydrophobic interactions, potentially neutralizing the virus by destabilizing interprotomer ​interactions of the trimer, leading to its disassembly in vitro. SHCS-3L6 binds the trimer by penetrating with its heavy chain into four glycans linked to positions N301, N332, N295, and N262, possibly neutralizing the virus by allosterically competing with the CD4 receptor. These structures provide atomic resolution details on the binding of the novel bNAbs LN02 -ML85, SHCS-3L6, and SHCS-0380, enhancing our understanding of antibodies neutralizing HIV-1.
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