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Article ; Online: Can we use structural knowledge to design a protective vaccine against HIV-1?

Bjorkman, Pamela J

2019 Volume 95, Issue 2, Page(s) 95–103

Abstract: Human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) remains one of the most important current threats to global public health. Since its identification in the early 1980s, at least 75 million people have been infected with HIV-1, ... ...

Abstract	Human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS) remains one of the most important current threats to global public health. Since its identification in the early 1980s, at least 75 million people have been infected with HIV-1, the virus that causes AIDS. Although antiretroviral drugs are effective at prolonging life after infection in the developed world, they are associated with significant side effects and are not in widespread use in the developing world. The best way to control the AIDS epidemic would be a vaccine that protects against infection by HIV-1. Most vaccines work by inducing antibodies in serum or mucosa that block infection or prevent invasion of the bloodstream. Here, I describe background related to my laboratory's attempts to develop an immunogen that would elicit protective antibodies against HIV-1.
MeSH term(s)	AIDS Vaccines ; Acquired Immunodeficiency Syndrome/prevention & control ; Alleles ; HIV Infections/prevention & control ; HIV-1 ; Humans
Chemical Substances	AIDS Vaccines
Language	English
Publishing date	2019-11-27
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	2845111-9
ISSN	2059-2310 ; 2059-2302
ISSN (online)	2059-2310
ISSN	2059-2302
DOI	10.1111/tan.13759
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Article ; Online: Publisher Correction: Intermediate conformations of CD4-bound HIV-1 Env heterotrimers.

Dam, Kim-Marie A / Fan, Chengcheng / Yang, Zhi / Bjorkman, Pamela J

Nature

2024 Volume 626, Issue 7998, Page(s) E7

Language	English
Publishing date	2024-01-19
Publishing country	England
Document type	Published Erratum
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-024-07082-z
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Zs.A 26: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article: Structural characterization of HIV-1 Env heterotrimers bound to one or two CD4 receptors reveals intermediate Env conformations.

Dam, Kim-Marie A / Fan, Chengcheng / Yang, Zhi / Bjorkman, Pamela J

bioRxiv : the preprint server for biology

2023

Abstract: HIV-1 envelope (Env) exhibits distinct conformational changes in response to host receptor (CD4) engagement. Env, a trimer of gp120/gp41 heterodimers, has been structurally characterized in a closed, prefusion conformation with closely associated gp120s ... ...

Abstract	HIV-1 envelope (Env) exhibits distinct conformational changes in response to host receptor (CD4) engagement. Env, a trimer of gp120/gp41 heterodimers, has been structurally characterized in a closed, prefusion conformation with closely associated gp120s and coreceptor binding sites on gp120 V3 hidden by V1V2 loops, and in fully-saturated CD4-bound open Env conformations with changes including outwardly rotated gp120s and displaced V1V2 loops. To investigate changes resulting from sub-stoichiometric CD4 binding, we solved 3.4Å and 3.9Å single-particle cryo-EM structures of soluble, native-like Envs bound to one or two CD4 molecules. Env trimer bound to one CD4 adopted the closed, prefusion Env state. When bound to two CD4s, the CD4-bound gp120s exhibited an open Env conformation including a four-stranded gp120 bridging sheet and displaced gp120 V1V2 loops that expose the coreceptor sites on V3. The third gp120 adopted an intermediate, occluded-open state that included gp120 outward rotation but maintained the prefusion, three-stranded gp120 bridging sheet and showed only partial V1V2 displacement and V3 exposure. We conclude that engagement of one CD4 molecule was insufficient to stimulate CD4-induced conformational changes, while binding two CD4 molecules led to Env opening in CD4-bound protomers only. Together, these results illuminate HIV-1 Env intermediate conformations and illustrate the structural plasticity of HIV-1 Env.
Language	English
Publishing date	2023-01-28
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.01.27.525985
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Article ; Online: Intermediate conformations of CD4-bound HIV-1 Env heterotrimers.

Dam, Kim-Marie A / Fan, Chengcheng / Yang, Zhi / Bjorkman, Pamela J

Nature

2023 Volume 623, Issue 7989, Page(s) 1017–1025

Abstract: HIV-1 envelope (Env) exhibits distinct conformational changes in response to host receptor (CD4) engagement. Env, a trimer of gp120 and gp41 heterodimers, has been structurally characterized in a closed, prefusion conformation with closely associated ... ...

Abstract	HIV-1 envelope (Env) exhibits distinct conformational changes in response to host receptor (CD4) engagement. Env, a trimer of gp120 and gp41 heterodimers, has been structurally characterized in a closed, prefusion conformation with closely associated gp120s and coreceptor binding sites on gp120 V3 hidden by V1V2 loops
MeSH term(s)	CD4 Antigens/chemistry ; CD4 Antigens/metabolism ; CD4 Antigens/ultrastructure ; Cryoelectron Microscopy ; HIV Envelope Protein gp120/chemistry ; HIV Envelope Protein gp120/metabolism ; HIV Envelope Protein gp120/ultrastructure ; HIV-1/chemistry ; HIV-1/ultrastructure ; Protein Conformation ; Rotation ; Reproducibility of Results
Chemical Substances	CD4 Antigens ; HIV Envelope Protein gp120
Language	English
Publishing date	2023-11-22
Publishing country	England
Document type	Journal Article
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-023-06639-8
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Article ; Online: Comparing methods for immobilizing HIV-1 SOSIPs in ELISAs that evaluate antibody binding.

Dam, Kim-Marie A / Mutia, Patricia S / Bjorkman, Pamela J

Scientific reports

2022 Volume 12, Issue 1, Page(s) 11172

Abstract: Enzyme-linked immunosorbent assays (ELISAs) are used to evaluate binding of broadly neutralizing antibodies (bNAbs) and polyclonal sera to native-like HIV-1 Env SOSIPs. Methods for immobilizing SOSIPs on plates differ, which can lead to variable or, in ... ...

Abstract	Enzyme-linked immunosorbent assays (ELISAs) are used to evaluate binding of broadly neutralizing antibodies (bNAbs) and polyclonal sera to native-like HIV-1 Env SOSIPs. Methods for immobilizing SOSIPs on plates differ, which can lead to variable or, in some cases, misleading results. Three methods used to immobilize SOSIPs were compared to determine how antigen immobilization methods affect Env conformation and ELISA results. HIV-1 SOSIPs were directly coated on polystyrene plates, captured by a monoclonal antibody against a C-terminal affinity tag, or randomly biotinylated and coated on a streptavidin plate. Binding of bNAbs with known epitopes were compared for each immobilization method. Binding of bNAbs targeting the V1V2, V3, CD4 binding site, and gp120/gp41 interface was comparable for all antigen immobilization methods. However, directly coated HIV-1 SOSIP ELISAs showed detectable binding of 17b, a CD4-induced antibody that binds a V3 epitope that is concealed on closed prefusion Env trimers in the absence of added CD4, whereas antibody-immobilized and randomly biotinylated Env-coated ELISAs did not show detectable binding of 17b in the absence of CD4. We conclude direct coating of HIV-1 SOSIPs on ELISA plates can result in exposure of CD4-induced antibody epitopes, suggesting disruption of Env structure and exposure of epitopes that are hidden in the closed, prefusion trimer.
MeSH term(s)	Antibodies, Neutralizing ; Broadly Neutralizing Antibodies ; Enzyme-Linked Immunosorbent Assay ; Epitopes ; HIV-1
Chemical Substances	Antibodies, Neutralizing ; Broadly Neutralizing Antibodies ; Epitopes
Language	English
Publishing date	2022-07-01
Publishing country	England
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-15506-x
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Not second class: the first class II MHC crystal structure.

Bjorkman, Pamela J

Journal of immunology (Baltimore, Md. : 1950)

2015 Volume 194, Issue 1, Page(s) 3–4

MeSH term(s)	Crystallography, X-Ray ; Histocompatibility Antigens Class I/immunology ; Histocompatibility Antigens Class I/ultrastructure ; Histocompatibility Antigens Class II/immunology ; Histocompatibility Antigens Class II/ultrastructure ; Humans ; Receptors, Antigen, T-Cell/immunology ; T-Lymphocytes, Helper-Inducer/immunology
Chemical Substances	Histocompatibility Antigens Class I ; Histocompatibility Antigens Class II ; Receptors, Antigen, T-Cell
Language	English
Publishing date	2015-01-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	3056-9
ISSN	1550-6606 ; 0022-1767 ; 1048-3233 ; 1047-7381
ISSN (online)	1550-6606
ISSN	0022-1767 ; 1048-3233 ; 1047-7381
DOI	10.4049/jimmunol.1402828
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Article: In vitro

Hoffmann, Magnus A G / Kieffer, Collin / Bjorkman, Pamela J

Molecular therapy. Methods & clinical development

2021 Volume 21, Page(s) 161–170

Abstract: Engineered red blood cells (RBCs) expressing viral receptors could be used therapeutically as viral traps, as RBCs lack nuclei and other organelles required for viral replication. However, expression of viral receptors on RBCs is difficult to achieve ... ...

Abstract	Engineered red blood cells (RBCs) expressing viral receptors could be used therapeutically as viral traps, as RBCs lack nuclei and other organelles required for viral replication. However, expression of viral receptors on RBCs is difficult to achieve since mature erythrocytes lack the cellular machinery to synthesize proteins. Herein, we show that the combination of a powerful erythroid-specific expression system and transgene codon optimization yields high expression levels of the HIV-1 receptors CD4 and CCR5, as well as a CD4-glycophorin A (CD4-GpA) fusion protein in erythroid progenitor cells, which efficiently differentiated into enucleated RBCs. HIV-1 efficiently entered RBCs that co-expressed CD4 and CCR5, but viral entry was not required for neutralization, as CD4 or CD4-GpA expression in the absence of CCR5 was sufficient to potently neutralize HIV-1 and prevent infection of CD4
Language	English
Publishing date	2021-03-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	2872938-9
ISSN	2329-0501 ; 2329-0501
ISSN (online)	2329-0501
ISSN	2329-0501
DOI	10.1016/j.omtm.2021.03.003
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Article ; Online: Antibody Recognition of CD4-Induced Open HIV-1 Env Trimers.

Yang, Zhi / Dam, Kim-Marie A / Gershoni, Jonathan M / Zolla-Pazner, Susan / Bjorkman, Pamela J

Journal of virology

2022 Volume 96, Issue 24, Page(s) e0108222

Abstract: Human immunodeficiency virus type 1 (HIV-1) envelope (Env), a heterotrimer of gp120-gp41 subunits, mediates fusion of the viral and host cell membranes after interactions with the host receptor CD4 and a coreceptor. CD4 binding induces rearrangements in ... ...

Abstract	Human immunodeficiency virus type 1 (HIV-1) envelope (Env), a heterotrimer of gp120-gp41 subunits, mediates fusion of the viral and host cell membranes after interactions with the host receptor CD4 and a coreceptor. CD4 binding induces rearrangements in Env trimer, resulting in a CD4-induced (CD4i) open Env conformation. Structural studies of antibodies isolated from infected donors have defined antibody-Env interactions, with one class of antibodies specifically recognizing the CD4i open Env conformation. In this study, we characterized a group of monoclonal antibodies isolated from HIV-1 infected donors (V2i MAbs) that displayed characteristics of CD4i antibodies. Binding experiments demonstrated that the V2i MAbs preferentially recognize CD4-bound open Env trimers. Structural characterizations of V2i MAb-Env-CD4 trimer complexes using single-particle cryo-electron microscopy showed recognition by V2i MAbs using different angles of approach to the gp120 V1V2 domain and the β2/β3 strands on a CD4i open conformation Env with no direct interactions of the MAbs with CD4. We also characterized CG10, a CD4i antibody that was raised in mice immunized with a gp120-CD4 complex, bound to an Env trimer plus CD4. CG10 exhibited characteristics similar to those of the V2i antibodies, i.e., recognition of the open Env conformation, but showed direct contacts to both CD4 and gp120. Structural comparisons of these and previously characterized CD4i antibody interactions with Env provide a suggested mechanism for how these antibodies are elicited during HIV-1 infection.
MeSH term(s)	Animals ; Humans ; Mice ; Antibodies, Monoclonal/metabolism ; Antibodies, Neutralizing/metabolism ; CD4 Antigens/metabolism ; Cryoelectron Microscopy ; HIV Antibodies/metabolism ; HIV Envelope Protein gp120/metabolism ; HIV Infections/immunology ; HIV Infections/virology ; HIV-1 ; Simian Immunodeficiency Virus ; env Gene Products, Human Immunodeficiency Virus ; Protein Binding ; Protein Conformation
Chemical Substances	Antibodies, Monoclonal ; Antibodies, Neutralizing ; CD4 Antigens ; HIV Antibodies ; HIV Envelope Protein gp120 ; env Gene Products, Human Immunodeficiency Virus
Language	English
Publishing date	2022-11-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/jvi.01082-22
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Article ; Online: Timeline of changes in spike conformational dynamics in emergent SARS-CoV-2 variants reveal progressive stabilization of trimer stalk with altered NTD dynamics.

Braet, Sean M / Buckley, Theresa S C / Venkatakrishnan, Varun / Dam, Kim-Marie A / Bjorkman, Pamela J / Anand, Ganesh S

eLife

2023 Volume 12

Abstract: SARS-CoV-2 emergent variants are characterized by increased viral fitness and each shows multiple mutations predominantly localized to the spike (S) protein. Here, amide hydrogen/deuterium exchange mass spectrometry has been applied to track changes in S ...

Abstract	SARS-CoV-2 emergent variants are characterized by increased viral fitness and each shows multiple mutations predominantly localized to the spike (S) protein. Here, amide hydrogen/deuterium exchange mass spectrometry has been applied to track changes in S dynamics from multiple SARS-CoV-2 variants. Our results highlight large differences across variants at two loci with impacts on S dynamics and stability. A significant enhancement in stabilization first occurred with the emergence of D614G S followed by smaller, progressive stabilization in subsequent variants. Stabilization preceded altered dynamics in the N-terminal domain, wherein Omicron BA.1 S showed the largest magnitude increases relative to other preceding variants. Changes in stabilization and dynamics resulting from S mutations detail the evolutionary trajectory of S in emerging variants. These carry major implications for SARS-CoV-2 viral fitness and offer new insights into variant-specific therapeutic development.
MeSH term(s)	Humans ; COVID-19 ; SARS-CoV-2/genetics ; Amides ; Biological Evolution
Chemical Substances	Amides
Language	English
Publishing date	2023-03-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.82584
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Article: Designed mosaic nanoparticles enhance cross-reactive immune responses in mice.

Wang, Eric / Cohen, Alexander A / Caldera, Luis F / Keeffe, Jennifer R / Rorick, Annie V / Aida, Yusuf M / Gnanapragasam, Priyanthi N P / Bjorkman, Pamela J / Chakraborty, Arup K

bioRxiv : the preprint server for biology

2024

Abstract: 1Using computational methods, we designed 60-mer nanoparticles displaying SARS-like betacoronavirus (sarbecovirus) receptor-binding domains (RBDs) by ( ...

Abstract	1Using computational methods, we designed 60-mer nanoparticles displaying SARS-like betacoronavirus (sarbecovirus) receptor-binding domains (RBDs) by (
Language	English
Publishing date	2024-02-28
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.02.28.582544
Database	MEDical Literature Analysis and Retrieval System OnLINE

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