DEER Spectroscopy Measurements Reveal Multiple Conformations of HIV-1 SOSIP Envelopes that Show Similarities with Envelopes on Native Virions

Stadtmueller, Beth M.; Bridges, Michael D.; Dam, Kim-Marie A; Lerch, Michael T.; Huey-Tubman, Kathryn E.; Hubbell, Wayne L.; Björkman, Pamela J.

doi:10.1016/j.immuni.2018.06.017

Cited by 74 publications

(94 citation statements)

References 44 publications

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“…A correlation between the effects of truncation and disulfide linkage, because of the contact between residues 501 and 663 in SOSIP.664 structures, could influence conformational dynamics of membrane-proximal parts of the ectodomain. DEER spectroscopy measurements indeed show a broader distribution of inter-subunit distances at the base of the SOSIP trimer than at the apex [22], consistent with some loss of constraints from deletion of the MPER, TM and CT segments. The broader distribution indicates an increased dynamic range, but with the centroid of the principal peak still close to the position expected from SOSIP coordinates.…”

Section: Discussionmentioning

confidence: 57%

“…We infer that the antigenic differences at the trimer apex between SOSIP forms of soluble, recombinant gp140s and full-length, processed gp160 are due primarily to the extent to which they visit somewhat more open conformations, rather than to a difference in the most stable, "ground state" conformation. This conclusion acquires importance in view of on-going debate about whether the SOSIP structures indeed represent the conformation of native Env on infectious virions [21,22].…”

Section: Discussionmentioning

confidence: 88%

“…Measurements by DEER spectroscopy of inter-residue distances on two SOSIP.664 gp140s (from clade A BG505 and clade B, B41), reported last year, lead to a different conclusion [22].…”

Section: Discussionmentioning

confidence: 98%

“…Envs that yield stable, homogeneous, trimeric, recombinant ectodomain (gp140) fall into the latter group [7,17,18]. Studies using fluorescence resonance energy transfer (FRET) or DEER spectroscopy have probed the ranges of relevant conformational ensembles [6,21,22].…”

Section: Introductionmentioning

confidence: 99%

“…We expect that potently neutralizing antibodies such as PG16 [26,27] that bind tightly at the trimer apex of virion-borne Env will stabilize the conformation most prevalent on infectious virions. Spectroscopic distance measurements bear out this expectation [22]. To visualize the Env-PG16 complex directly, we have determined by cryo-EM, at 6Å resolution, the structure of a fully processed, full-length, cell-surface expressed Env, isolated directly by binding with affinity tagged PG16 Fab before extracting the complex from the cell membranes.…”

Section: Introductionmentioning

confidence: 99%

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Cryo-EM structure of full-length HIV-1 Env bound with the Fab of antibody PG16

Pan¹,

Peng²,

Chen³

2019

Preprint

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The HIV-1 envelope protein (Env) is the target of neutralizing antibodies and the template for vaccine immunogen design. The dynamic conformational equilibrium of trimeric Env influences its antigenicity and potential immunogenicity. Antibodies that bind at the trimer apex stabilize a "closed" conformation characteristic of the most difficult to neutralize isolates. A goal of vaccine development is therefore to mimic the closed conformation in a designed immunogen. A disulfide-stabilized, trimeric Env ectodomain --the "SOSIP" construct --has many of the relevant properties; it is also particularly suitable for structure determination. Some singlemolecule studies have, however, suggested that the SOSIP trimer is not a good representation of Env on the surface of a virion or an infected cell. We isolated Env (fully cleaved to gp120 and gp41) from the surface of expressing cells using tagged, apex-binding Fab PG16 and determined the structure of the PG16-Env complex by cryo-EM to an overall resolution of 4.6 Å.Placing the only purification tag on the Fab ensured that the isolated Env was continuously stabilized in its closed, native conformation. The Env structure in this complex corresponds closely to the SOSIP structures determined by both x-ray crystallography and cryo-EM.Although the membrane-interacting elements are not resolved in our reconstruction, we can make inferences about the connection between ectodomain and membrane-proximal external region (MPER) by reference to the published cryo-tomography structure of an Env "spike" and the NMR structure of the MPER-transmembrane segment. We discuss these results in view of the conflicting interpretations in the literature.

show abstract

Section: Discussionmentioning

confidence: 57%

Section: Discussionmentioning

confidence: 88%

“…Measurements by DEER spectroscopy of inter-residue distances on two SOSIP.664 gp140s (from clade A BG505 and clade B, B41), reported last year, lead to a different conclusion [22].…”

Section: Discussionmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Cryo-EM structure of full-length HIV-1 Env bound with the Fab of antibody PG16

Pan¹,

Peng²,

Chen³

2019

Preprint

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Structure‐guided envelope trimer design in HIV‐1 vaccine development: a narrative review

Derking

Sanders

2021

J Int AIDS Soc.

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IntroductionThe development of a human immunodeficiency virus 1 (HIV‐1) vaccine remains a formidable challenge. An effective vaccine likely requires the induction of broadly neutralizing antibodies (bNAbs), which likely involves the use of native‐like HIV‐1 envelope (Env) trimers at some or all stages of vaccination. Development of such trimers has been very difficult, but much progress has been made in the past decade, starting with the BG505 SOSIP trimer, elucidation of its atomic structure and implementing subsequent design iterations. This progress facilitated understanding the weaknesses of the Env trimer, fuelled structure‐guided HIV‐1 vaccine design and assisted in the development of new vaccine designs. This review summarizes the relevant literature focusing on studies using structural biology to reveal and define HIV‐1 Env sites of vulnerability; to improve Env trimers, by creating more stable versions; understanding antibody responses in preclinical vaccination studies at the atomic level; understanding the glycan shield; and to improve “on‐target” antibody responses versus “off‐target” responses.MethodsThe authors conducted a narrative review of recently published articles that made a major contribution to HIV‐1 structural biology and vaccine design efforts between the years 2000 and 2021.DiscussionThe field of structural biology is evolving at an unprecedented pace, where cryo‐electron microscopy (cryo‐EM) and X‐ray crystallography provide complementary information. Resolving protein structures is necessary for defining which Env surfaces are accessible for the immune system and can be targeted by neutralizing antibodies. Recently developed techniques, such as electron microscopy‐based polyclonal epitope mapping (EMPEM) are revolutionizing the way we are analysing immune responses and shed light on the immunodominant targets on new vaccine immunogens. Such information accelerates iterative vaccine design; for example, by reducing undesirable off‐target responses, while improving immunogens to drive the more desirable on‐target responses.ConclusionsResolving high‐resolution structures of the HIV‐1 Env trimer was instrumental in understanding and improving recombinant HIV‐1 Env trimers that mimic the structure of viral HIV‐1 Env spikes. Newly emerging techniques in structural biology are aiding vaccine design efforts and improving immunogens. The role of structural biology in HIV‐1 vaccine design has indeed become very prominent and is unlikely to diminish any time soon.

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Illuminating the virus life cycle with single-molecule FRET imaging

Mothes

2019

Advances in Virus Research

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Single-molecule Förster resonance energy transfer (smFRET) imaging has emerged as a powerful tool to probe conformational dynamics of viral proteins, identify novel structural intermediates that are hiding in averaging population-based measurements, permit access to the energetics of transitions and as such to the precise molecular mechanisms of viral replication. One strength of smFRET is the capability of characterizing biological molecules in their fully hydrated/native state, which are not necessarily available to other structural methods. Elegant experimental design for physiologically relevant conditions, such as intact virions, has permitted the detection of previously unknown conformational states of viral glycoproteins, revealed asymmetric intermediates, and allowed access to the real-time imaging of conformational changes during viral fusion. As more laboratories are applying smFRET, our understanding of the molecular mechanisms and the dynamic nature of viral proteins throughout the virus life cycle are predicted to improve and assist the development of novel antiviral therapies and vaccine design.

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DEER Spectroscopy Measurements Reveal Multiple Conformations of HIV-1 SOSIP Envelopes that Show Similarities with Envelopes on Native Virions

Cited by 74 publications

References 44 publications

Cryo-EM structure of full-length HIV-1 Env bound with the Fab of antibody PG16

Cryo-EM structure of full-length HIV-1 Env bound with the Fab of antibody PG16

Structure‐guided envelope trimer design in HIV‐1 vaccine development: a narrative review

Illuminating the virus life cycle with single-molecule FRET imaging

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