Structure and immunogenicity of a stabilized HIV-1 envelope trimer based on a group-M consensus sequence

Sliepen, Kwinten; Han, Byung Woo; Bontjer, Ilja; Mooij, Petra; Garcés, Fernando; Behrens, Anna‐Janina; Rantalainen, Kimmo; Kumar, Sonu; Sarkar, Achyut; Brouwer, Philip J.M.; Hua, Yuanzi; Tolazzi, Monica; Schermer, Edith E.; Torres, Jonathan L.; Ozorowski, Gabriel; Woude, Patricia van der; Peña, Alba Torrents de la; Breemen, Mariëlle J. van; Camacho-Sánchez, Juan Miguel; Burger, Judith A.; Medina-Ramírez, Max; Gonzàlez, Núria; Alcamí, José; LaBranche, Celia C.; Scarlatti, Gabriella; Gils, Marit J. van; Crispin, Max; Montefiori, David C.; Ward, Andrew B.; Koopman, Gerrit; Moore, John P.; Shattock, Robin J.; Bogers, Willy; Wilson, Ian A.; Sanders, Rogier W.

doi:10.1038/s41467-019-10262-5

Cited by 132 publications

(197 citation statements)

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“…A multitude of broadly neutralizing antibodies (bNAbs) have now been characterized, targeting various sites on HIV-1 Env (Haynes and Mascola, 2017;Sok and Burton, 2018). Structures of these bNAbs in complex with Env have paved the way for structure-based vaccine design by facilitating the identification of stabilizing mutations that allow large scale expression and purification of the unliganded ectodomain (Dey et al, 2018;Guenaga et al, 2017;Joyce et al, 2017;Klein et al, 2013;Kulp et al, 2017;Kwon et al, 2015;Ringe et al, 2017;Rutten et al, 2018;Schoofs et al, 2019;Sliepen et al, 2019;Torrents de la Pena and Sanders, 2018;Ward and Wilson, 2017;Yuan et al, 2019). The epitopes of MPER-targeting bNAbs were however truncated along with TMD and CTD from almost all of these Envs to increase solubility and stability and, therefore, remains perhaps the least understood epitope.…”

Section: Introductionmentioning

confidence: 99%

HIV-1 Envelope and MPER antibody structures in lipid assemblies

Rantalainen

Berndsen

Antanasijevic

et al. 2019

Preprint

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SummaryStructural and functional studies of HIV Env as a transmembrane protein have long been complicated by challenges associated with inherent flexibility of the molecule and the membrane-embedded hydrophobic regions. Thus, most structural studies have utilized soluble forms where the regions C-terminal to the ectodomain are deleted. Here, we present approaches for incorporating full-length, wild-type HIV-1 Env, as well as C-terminally truncated and stabilized versions, into lipid assemblies, providing a modular platform for Env structural studies by single particle electron microscopy. We reconstituted a full-length Env clone into a nanodisc with MSP1D1 scaffold, complexed it with an MPER targeting antibody 10E8, and structurally defined the full quaternary epitope of 10E8 consisting of lipid, MPER and ectodomain contacts. By aligning this and other Env-MPER antibody complex reconstructions with the lipid bilayer, we observe evidence of Env tilting as part of the neutralization mechanism for MPER-targeting antibodies. We also adapted the platform toward vaccine design purposes by introducing stabilizing mutations that allow purification of unliganded Env with peptidisc scaffold.

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Section: Introductionmentioning

confidence: 99%

HIV-1 Envelope and MPER antibody structures in lipid assemblies

Rantalainen

Berndsen

Antanasijevic

et al. 2019

Preprint

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“…Indeed, many studies have succeeded in stabilizing the closed conformation of the HIV-1 Env both in the soluble Env format, as well on the cell surface, with varying levels of success in eliciting autologous and heterologous neutralization. 10–21…”

Section: Discussionmentioning

confidence: 99%

“…Centroids for the vectors in the analysis included a K46-K490 Cα centroid, W571 and W596 c-αs, c-αs of gp120 excluding variable loops the V1/V1 region residues, and the N- and C-termni, and a V1/V2+V3 c-α centroid Vectors between these reference positions were generated and included a projection of the W596 to K46-K490 centroid vector on to the W596 to W571 vector. Angles, distances, and dihedrals between these vectors were then compiled for a set of available crystal and cryo-EM structures with PDB IDs 4TVP 71 , 4ZMJ 25 , 5ACO 72 , 5CEZ 37 , 5CJX 73 , 5D9Q 74 , 5FYJ 75 , 5FYK 75 , 5FYL 75 , 5T3X 76 , 5T3Z 76 , 5U7M 33 , 5U7O 33 , 5UTF 13 , 5V7J 77 , 5V8L 78 , 5V8M 78 , 6CDE 38 , 6CDI 38 , 6CH7 79 , 6CH8 79 , 6CUE 80 , 6CUF 81 , and 6DE7 12 , 5THR 26 , 5VN3 27 , 5VN8 73 , 6CM3 31 , 6EDU 31 , 5FUU 82 , 6DCQ 46 , 6MAR 83 , 5U1F 55 , 5C7K 84 , 5I8H 85 , 5UM8 86 , 5UTY 13 , 5VIY 87 , 5VJ6 87 , 5WDU 14 , 6B0N 88 , 6CCB 89 , 6CE0 11 , 6CH9 79 , 6CHB 79 , 6CK9 90 , 6DCQ 46 , 6DID 91 , 6E5P 92 , 6IEQ 93 , 6MCO 94 , 6MDT 94 , 6MN7 95 , 6MPG 96 , 6MPH 96 , 6MTJ 97 , 6MTN 97 , 6MU6 97 , 6MU7 97 , 6MU8 97 , 6MUF 97 , 6MUG 97 , 6N1V 96 , 6N1W 96 , 6NC2 98 , 6NC3 98 , 6NF2 96 , 6NIJ 47 , 6NM6 99 , 6NNF 99 , 6NNJ 99 , 6OHY 100 , 6OKP 101 , 6OLP 47 , 6ORN 39 , 6ORO 39 , 6OR...…”

Section: Methodsmentioning

confidence: 99%

“…10 Indeed, design efforts to improve the Env SOSIP by further stabilizing the closed Env conformation have resulted in multiple prefusion stabilized trimer designs capable of inducing improved autologous, difficult-to-neutralize tier 2 virus antibody responses. 10–21 However, to date, no trimer design has successfully induced robust heterologous antibody responses.…”

Section: Introductionmentioning

confidence: 99%

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Disruption of the HIV-1 Envelope allosteric network blocks CD4-induced rearrangements

Henderson

Zhou

et al. 2019

Preprint

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30The trimeric HIV-1 Envelope protein (Env) mediates viral-host cell fusion via a network of 31 conformational transitions, with allosteric elements in each protomer orchestrating host 32 receptor-induced exposure of the co-receptor binding site and fusion elements. To 33 understand the molecular details of this allostery, we introduced Env mutations aimed to 34 prevent CD4-induced rearrangements in the HIV-1 BG505 Env trimer. Binding analysis 35 performed on the soluble ectodomain BG505 SOSIP Env trimers, cell-surface expressed 36 BG505 full-length trimers and single-molecule Förster Resonance Energy Transfer 37 (smFRET) performed on the full-length virion-bound Env confirmed that these mutations 38 prevented CD4-induced transitions of the HIV-1 Env. Structural analysis by single-39 particle cryo-electron microscopy performed on the BG505 SOSIP mutant Env proteins 40 revealed rearrangements in the gp120 topological layer contacts with gp41. Specifically, 41 a conserved tryptophan at position 571 (W571) was displaced from its typical pocket at 42 the interface of gp120 topological layers 1 and 2 by lysine 567, disrupting key gp120-43 gp41 contacts and rendering the Env insensitive to CD4 binding. Vector based analysis 44 of closed Env SOSIP structures revealed the newly designed trimers exhibited a 45 quaternary structure distinct from that typical of SOSIPs and residing near a cluster of 46 Env trimers bound to vaccine-induced fusion peptide-directed antibodies (vFP Mabs). 47These results reveal the critical function of W571 as a conformational switch in Env 48 allostery and receptor-mediated viral entry and provide insights on Env conformation that 49 are relevant for vaccine design.50 51 52 53 54Host cell entry of HIV-1 is accomplished by the envelope glycoprotein (Env) spike. HIV-1 55Env is a trimer of heterodimers comprised of gp120 and gp41 protomers, and exists in a 56 metastable conformation capable of transitioning from a prefusion closed configuration to a 57 fusion-competent open state upon triggering by CD4. 1,2 The C-terminal gp41 domain contains a 58 single transmembrane helix and the membrane fusion elements of the trimer. 3-5 The gp12059 segment binds the primary receptor CD4, triggering conformational changes leading to the 60 binding of co-receptor CCR5/CXCR4 that causes global rearrangements in the trimer structure 61 leading to viral and cell membrane fusion and gp120 shedding. 6-8 While many studies have 62 sought to understand the nature of the communication between the CD4 binding site, the 63 coreceptor binding site and the fusogenic elements of the HIV-1 Env, a complete understanding 64 of the allosteric mechanism and metastability in HIV-1 Env remains lacking. 65The design of a soluble, stabilized ectodomain Env (SOSIP), containing an engineered 66 gp120 to gp41 disulfide (SOS) and an HR1 helix breaking I to P mutation, has revealed 67 structural details regarding broadly neutralizing antibody (bnAb) epitopes and as an immunogen 68 has induced autologous neutralizing antibodies. 2,9 The...

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“…bnAbs target the envelope glycoprotein (env) of HIV-1 within defined epitopes, though inferred germlines (iGLs) of several bnAbs do not bind to most of the difficult-to-neutralize HIV-1 isolate. Identification and/or engineering of env variants capable of engaging and shepherding bnAb development pathway are a key focus of lineage-based vaccine approach (8–12).…”

Section: Introductionmentioning

confidence: 99%