Computational Refinement and Validation Protocol for Proteins with Large Variable Regions Applied to Model HIV Env Spike in CD4 and 17b Bound State

Rasheed, Muhibur; Bettadapura, Radhakrishna; Bajaj, Chandrajit L.

doi:10.1016/j.str.2015.03.026

Cited by 32 publications

(37 citation statements)

References 50 publications

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“…Conformational state 1 (CS1) is a metastable, native ‘high-energy’ state that corresponds to the native Env trimer4041424344. Conformational state 2 (CS2) is the pre-fusion CD4-bound state that exposes the co-receptor binding site4445. Conformational state 3 (CS3) is the “pre-hairpin” intermediate that is thought to occur upon co-receptor binding to the CD4-bound state414246.…”

Section: Discussionmentioning

confidence: 99%

Molecular basis for epitope recognition by non-neutralizing anti-gp41 antibody F240

Gohain

Tolbert

Orlandi

et al. 2016

Sci Rep

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Antibody-dependent cell-mediated cytotoxicity (ADCC) by non-neutralizing antibodies (nnAbs) specific to the HIV envelope (Env) glycoproteins present at the surface of virus sensitized or infected cells plays a role in the effective adaptive immune response to HIV. Here, we explore the molecular basis for the epitope at the disulfide loop region (DLR) of the principal immunodominant domain of gp41, recognized by the well-known nnAb F240. Our structural studies reveal details of the F240-gp41 interface and describe a structure of DLR that is distinct from known conformations of this region studied in the context of either CD4-unliganded Env trimer or the gp41 peptide in the unbound state. These data coupled with binding and functional analyses indicate that F240 recognizes non-trimeric Env forms which are significantly overexpressed on intact virions but poorly represented at surfaces of cells infected with infectious molecular clones and endogenously-infected CD4 T cells from HIV-1-infected individuals. Furthermore, although we detect ADCC activities of F240 against cells spinoculated with intact virions, our data suggest that these activities result from F240 recognition of gp41 stumps or misfolded Env variants present on virions rather than its ability to recognize functional gp41 transition structures emerging on trimeric Env post CD4 receptor engagement.

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Section: Discussionmentioning

confidence: 99%

Molecular basis for epitope recognition by non-neutralizing anti-gp41 antibody F240

Gohain

Tolbert

Orlandi

et al. 2016

Sci Rep

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“…Model of (a) gp120 and (b) trimeric structure of Env. The model is from Protein Data Bank ID: 3J70 (Rasheed et al, 2015) and visualized by UCSF Chimera software. The mutations associated with MK38#814 and MK38#818 were fitted into the model.…”

Section: In Vivo Inoculation Experiments Involving Mk38#818mentioning

confidence: 99%

Generation of a neutralization-resistant CCR5 tropic simian/human immunodeficiency virus (SHIV-MK38) molecular clone, a derivative of SHIV-89.6

Ishida

Yoneda

Otsuki

et al. 2016

Journal of General Virology

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“…The details of V1V2 rearrangements in the open structure of HIV-1 Env trimer have not been addressed: The V1V2 loops were not localized in the Env trimer used in a cryo-EM single particle structure of an open KNH1144 SOSIP bound to the coreceptormimicking antibody 17b (7) or in lower-resolution cryoelectron tomography structures of CD4-bound open Env trimers on virions (4,7). However, computational modeling suggested displacement of V1V2 toward CD4 in CD4-bound Env structures (20,21), consistent with earlier studies demonstrating involvement of V1V2 in the induction of the epitopes of coreceptor mimic/CD4-induced antibodies such as 17b (22).…”

mentioning

confidence: 99%

Cryo-EM structure of a CD4-bound open HIV-1 envelope trimer reveals structural rearrangements of the gp120 V1V2 loop

Wang

Cohen

Galimidi

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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The HIV-1 envelope (Env) glycoprotein, a trimer of gp120-gp41 heterodimers, relies on conformational flexibility to function in fusing the viral and host membranes. Fusion is achieved after gp120 binds to CD4, the HIV-1 receptor, and a coreceptor, capturing an open conformational state in which the fusion machinery on gp41 gains access to the target cell membrane. In the well-characterized closed Env conformation, the gp120 V1V2 loops interact at the apex of the Env trimer. Less is known about the structure of the open CD4-bound state, in which the V1V2 loops must rearrange and separate to allow access to the coreceptor binding site. We identified two anti-HIV-1 antibodies, the coreceptor mimicking antibody 17b and the gp120-gp41 interface-spanning antibody 8ANC195, that can be added as Fabs to a soluble native-like Env trimer to stabilize it in a CD4-bound conformation. Here, we present an 8.9-Å cryo-electron microscopy structure of a BG505 Env-sCD4-17b-8ANC195 complex, which reveals large structural rearrangements in gp120, but small changes in gp41, compared with closed Env structures. The gp120 protomers are rotated and separated in the CD4-bound structure, and the three V1V2 loops are displaced by ∼40 Å from their positions at the trimer apex in closed Env to the sides of the trimer in positions adjacent to, and interacting with, the three bound CD4s. These results are relevant to understanding CD4-induced conformational changes leading to coreceptor binding and fusion, and HIV-1 Env conformational dynamics, and describe a target structure relevant to drug design and vaccine efforts.T he HIV-1 envelope (Env) glycoprotein, a trimer of gp120-gp41 heterodimers, mediates recognition of host receptors and fusion of the viral and target cell membranes (1). Structural flexibility of HIV-1 Env is required for its function in membrane fusion; thus, Env exists in multiple conformational states on the surface of virions (2). Fusion involves several steps: The gp120 portion of Env trimer first binds to the host receptor CD4 to capture a conformational state of Env that exposes the binding site for an HIV-1 coreceptor (CCR5 or CXCR4), which, in turn, leads to gp41-mediated fusion of the viral and host cell membranes. CD4-induced conformational changes within the Env trimer are incompletely understood. The binding of soluble CD4 (sCD4) produces little to no changes in the structures of gp120 cores (gp120 monomers with truncations in the N and C termini and variable V1V2 and V3 loops) (3), but results in rotation of the gp120 protomers within virion-bound Env trimers to create an open conformation distinct from the closed conformation of unliganded virion-bound trimers (4). Single-particle electron microscopy (EM) structures of recombinant native-like soluble Env gp140 trimers (SOSIPs) confirmed that they can adopt the same closed and open architectures as virion-bound Env trimers (5-7), thus the SOSIP substitutions (introduction of a disulfide bond linking gp120 to gp41 and an Ile→Pro mutation in gp41; ref. The closed co...

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Computational Refinement and Validation Protocol for Proteins with Large Variable Regions Applied to Model HIV Env Spike in CD4 and 17b Bound State

Cited by 32 publications

References 50 publications

Molecular basis for epitope recognition by non-neutralizing anti-gp41 antibody F240

Molecular basis for epitope recognition by non-neutralizing anti-gp41 antibody F240

Generation of a neutralization-resistant CCR5 tropic simian/human immunodeficiency virus (SHIV-MK38) molecular clone, a derivative of SHIV-89.6

Cryo-EM structure of a CD4-bound open HIV-1 envelope trimer reveals structural rearrangements of the gp120 V1V2 loop

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