title: Outer domain of HIV-1 gp120: antigenic optimization, structural malleability, and crystal structure with antibody VRC-PG04.
abstract: The outer domain of the HIV-1 gp120 envelope glycoprotein contains the epitope for broadly neutralizing antibodies directed to the CD4-binding site, many of which are able to neutralize over 90% of circulating HIV-1 isolates. While the outer domain is conformationally more stable than other portions of the HIV-1 envelope, efforts to express the outer domain as an immunogen for eliciting broadly neutralizing antibodies have not been successful, potentially because natural outer domain variants do not bind strongly to antibodies such as VRC01. In this study, we optimized the antigenic properties of the HIV-1 Env outer domain to generate OD4.2.2, from the KER2018 strain of clade A HIV-1, enabling it to bind antibodies such as VRC01 with nanomolar affinity. The crystal structure of OD4.2.2 in complex with VRC-PG04 was solved at 3.0-Å resolution and compared to known crystal structures including (i) the structure of core gp120 bound by VRC-PG04 and (ii) a circularly permutated version of the outer domain in complex with antibody PGT128. Much of the VRC-PG04 epitope was preserved in the OD4.2.2 structure, though with altered N and C termini conformations. Overall, roughly one-third of the outer domain structure appeared to be fixed in conformation, independent of alterations in termini, clade, or ligand, while other portions of the outer domain displayed substantial structural malleability. The crystal structure of OD4.2.2 with VRC-PG04 provides atomic-level details for an HIV-1 domain recognized by broadly neutralizing antibodies and insights relevant to the rational design of an immunogen that could elicit such antibodies by vaccination.
authors.affiliation: Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.
authors.forename: M Gordon
authors.initials: MG
authors.lastname: Joyce
authors.forename: Masaru
authors.initials: M
authors.lastname: Kanekiyo
authors.forename: Ling
authors.initials: L
authors.lastname: Xu
authors.forename: Christian
authors.initials: C
authors.lastname: Biertümpfel
authors.forename: Jeffrey C
authors.initials: JC
authors.lastname: Boyington
authors.forename: Stephanie
authors.initials: S
authors.lastname: Moquin
authors.forename: Wei
authors.initials: W
authors.lastname: Shi
authors.forename: Xueling
authors.initials: X
authors.lastname: Wu
authors.forename: Yongping
authors.initials: Y
authors.lastname: Yang
authors.forename: Zhi-Yong
authors.initials: ZY
authors.lastname: Yang
authors.forename: Baoshan
authors.initials: B
authors.lastname: Zhang
authors.forename: Anqi
authors.initials: A
authors.lastname: Zheng
authors.forename: Tongqing
authors.initials: T
authors.lastname: Zhou
authors.forename: Jiang
authors.initials: J
authors.lastname: Zhu
authors.forename: John R
authors.initials: JR
authors.lastname: Mascola
authors.forename: Peter D
authors.initials: PD
authors.lastname: Kwong
authors.forename: Gary J
authors.initials: GJ
authors.lastname: Nabel
mesh_terms: D000595:Amino Acid Sequence; D057134:Antibodies, Neutralizing / Q000737:chemistry / Q000378:metabolism; D000956:Antigens, Viral / Q000737:chemistry / Q000235:genetics / Q000276:immunology; D018360:Crystallography, X-Ray; D000939:Epitopes / Q000737:chemistry / Q000235:genetics / Q000276:immunology; D015483:HIV Antibodies / Q000737:chemistry* / Q000378:metabolism; D015699:HIV Envelope Protein gp120 / Q000737:chemistry* / Q000235:genetics / Q000276:immunology*; D015497:HIV-1 / Q000737:chemistry* / Q000235:genetics / Q000276:immunology*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D020836:Protein Structure, Quaternary; D016415:Sequence Alignment
chemical_list: D057134:Antibodies, Neutralizing; D000956:Antigens, Viral; D000939:Epitopes; D015483:HIV Antibodies; D015699:HIV Envelope Protein gp120; C514793:gp120 protein, Human immunodeficiency virus 1