In complex with a patient-derived near-germline antibody fragment, the PID motif adopts an elongated random coil, whereas the PID bound to affinity-matured Fab adopts a strand-turn-helix conformation

In complex with a patient-derived near-germline antibody fragment, the PID motif adopts an elongated random coil, whereas the PID bound to affinity-matured Fab adopts a strand-turn-helix conformation. target of these antibodies is the primary immunodominant region (PID) on Eptapirone (F-11440) the gp41 fusion protein. The PID is a highly conserved 15-residue region displayed on the surface of HIV-1 virions. In this study, we analyzed the humoral determinants of HIV-1 gp41 PID binding using biophysical, structural, and computational methods. In complex with a patient-derived near-germline antibody fragment, the PID motif adopts an elongated random coil, whereas the PID bound to affinity-matured Fab adopts a strand-turn-helix conformation. Molecular dynamics simulations showed that the Eptapirone (F-11440) PID is structurally plastic suggesting that the PID can form an ensemble of structural states recognized by various non-neutralizing antibodies, facilitating HIV-1 immunodominance observed in acute and chronic HIV-1 Mouse monoclonal to GLP infections. An improved understanding of how the HIV-1 Eptapirone (F-11440) gp41 PID misdirects the early humoral response should guide the development of an effective HIV-1 vaccine. Subject terms: Immune evasion, Retrovirus, X-ray crystallography The 15-amino-acid primary immunodominant (PID) region on HIV-1 gp41 adopts an ensemble of conformational states. This conformational plasticity is suggested to misdirect the early humoral immune response. Introduction Failure to mount an effective humoral immune response against the HIV-1 envelope glycoprotein (gp160) has been observed in the majority of vaccine trials to date1 and is a hallmark of the natural history of HIV-1 infection. HIV-1 gp160 exists in the viral membrane as a trimeric complex of non-covalently attached gp120-gp41 heterodimers. Owing to the non-covalent and unstable nature of gp160, the gp120 attachment subunit is shed from the native trimers inducing a post-fusion conformation of gp41 on the surface of the mature virus2,3. It has been observed that only 7C14 functional trimeric gp160 spikes exist on the virion surface4,5 and the majority of gp160 have lost gp120 to form fusion-incompetent gp41 stumps6. These post-fusion gp41 stumps produce a hairpin structure with likely both its fusion peptide and transmembrane anchor inserted into the viral membrane, thus exposing the chain reversal region. Likely owing to the abundance of gp41 accessible to the host humoral immune system, anti-gp41 antibodies are detectable at the earliest stages of HIV-1 infection and persist in those afflicted with chronic infection7C10. The vast majority of these antibodies are considered non-neutralizing and do not block HIV-1 entry or fusion. These antibodies can elicit some antibody-dependent cellular cytotoxicity, which was determined to be responsible for the modest protection observed in the RV144 vaccine trial11. However, antibody-dependent cellular cytotoxicity alone is insufficient for robust prophylaxis against a productive infection12C14. Multiple anti-gp41 monoclonal antibodies that specifically target a primary immunodominant region (PID) located within the gp41 ectodomain have been isolated from patient sera. The PID is an amphipathic 15-amino-acid region that separates the two heptad-repeat domains found in the post-fusion conformation of gp41. The PID is flanked by tryptophan residues 596 and 610 and has an internal disulfide bond between C598 and C604. The sequence of the PID is highly conserved across HIV subtypes, and as the moniker suggests, it is particularly immunodominant. In one human study, ~70% of all antibodies generated in an acute HIV-1 infection were toward an HIV-1 gp41 PID-containing peptide10. Of note, the PID is not fully accessible in the gp160 pre-fusion conformation15, suggesting that anti-HIV-1 PID antibodies may predominantly recognize the epitope in the context of virions with gp41 spikes. This hypothesis is supported by multiple studies that have shown non-neutralizing anti-PID antibodies can capture freely circulating HIV-1 virions16,17. Partitioning of viral particles by epitope recognition revealed that HIV-1 virions sort into subpopulations of infectious and non-infectious particles. There are two subsets of infectious virions: those that are almost exclusively bound by neutralizing Env antibodies, and those that are bound by both neutralizing and non-neutralizing antibodies such as those that target the PID. The noninfectious population is readily bound by anti-PID antibodies but is not bound by neutralizing Env antibodies6. How the PID motif misdirects the adaptive immune system.