Computational Protein Design Using Flexible Backbone Remodeling and Resurfacing: Case Studies in Structure-Based Antigen Design

Correia, Bruno E.; Ban, Yih En Andrew; Friend, Della; Ellingson, Katharine; Xu, Hengyu; Boni, Erica; Bradley-Hewitt, Tyler; Bruhn-Johannsen, Jessica F.; Stamatatos, Leonidas; Strong, Roland K.; Schief, William R.

doi:10.1016/j.jmb.2010.09.061

Cited by 61 publications

(67 citation statements)

References 41 publications

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“…glycosylation sites either to occlude immunodominant but variable regions or to enhance the exposure of conserved neutralization epitopes, respectively (10,17,32,50,64,66); repositioning of conserved epitopes within more variable, but also more immunogenic, regions of the HIV Env (48, 51); design of non-HIV Env scaffold proteins that express epitopes of broadly neutralizing antibodies (11,18,19,39,62,63); molecular evolution-based approaches (24); generation of ancestral or consensus Env sequences (23,31,45,46,52); and others. Thus far, all of these approaches have had a very limited success in the elicitation of broad and potent neutralizing antibody responses against tier 2 HIV-1 viruses.…”

Section: Discussionmentioning

confidence: 99%

Engineering, Expression, Purification, and Characterization of Stable Clade A/B Recombinant Soluble Heterotrimeric gp140 Proteins

Sellhorn

Kraft

Caldwell

et al. 2012

J Virol

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The envelope glycoprotein (Env) of human immunodeficiency virus type 1 (HIV-1) is composed of two noncovalently associated subunits: an extracellular subunit (gp120) and a transmembrane subunit (gp41). The functional unit of Env on the surface of infectious virions is a trimer of gp120/gp41 heterodimers. Env is the target of anti-HIV neutralizing antibodies. A considerable effort has been invested in the engineering of recombinant soluble forms of the virion-associated Env trimer as vaccine candidates to elicit anti-HIV neutralizing antibody responses. These soluble constructs contain three gp120 subunits and the extracellular segments of the corresponding gp41 subunits. The individual gp120/gp41 protomers on these soluble trimers are identical in amino acid sequence (homotrimers). Here, we engineered novel soluble trimeric gp140 proteins that are formed by the association of gp140 protomers that differ in amino acid sequence and glycosylation patterns (heterotrimers). Specifically, we engineered soluble heterotrimeric proteins composed of clade A and clade B Env protomers. The clade A gp140 protomers were derived from viruses isolated during acute infection (Q168a2, Q259d2.17, and Q461e2), whereas the clade B gp140 protomers were derived from a virus isolated during chronic infection (SF162). The amino acid sequence divergence between the clade A and the clade B Envs is approximately 24%. Neutralization epitopes in the CD4 binding sites and coreceptor binding sites, as well as the membrane-proximal external region (MPER), were differentially expressed on the heterotrimeric and homotrimeric proteins. The heterotrimeric gp140s elicited broader anti-tier 1 isolate neutralizing antibody responses than did the homotrimeric gp140s.

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Section: Discussionmentioning

confidence: 99%

Engineering, Expression, Purification, and Characterization of Stable Clade A/B Recombinant Soluble Heterotrimeric gp140 Proteins

Sellhorn

Kraft

Caldwell

et al. 2012

J Virol

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“…Thus, by directing the immune response to the HA2 domain of the protein, higher cross-reactive titers are achieved. Computational redesigning and trimming of immunodominant epitopes have been successfully used to focus immune responses to conserved epitopes and identify broadly neutralizing Abs in other highly variable viral proteins like HIV envelope (6,36). Competition experiments with broadly neutralizing antibody CR6261.…”

Section: Figmentioning

confidence: 99%

Design of Escherichia coli-Expressed Stalk Domain Immunogens of H1N1 Hemagglutinin That Protect Mice from Lethal Challenge

Bommakanti

Citron

et al. 2012

J Virol

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The hemagglutinin protein (HA) on the surface of influenza virus is essential for viral entry into the host cells. The HA1 subunit of HA is also the primary target for neutralizing antibodies. The HA2 subunit is less exposed on the virion surface and more conserved than HA1. We have previously designed an HA2-based immunogen derived from the sequence of the H3N2 A/HK/68 virus. In the present study, we report the design of an HA2-based immunogen from the H1N1 subtype (PR/8/34). This immunogen (H1HA0HA6) and its circular permutant (H1HA6) were well folded and provided complete protection against homologous viral challenge. Antisera of immunized mice showed cross-reactivity with HA proteins of different strains and subtypes. Although no neutralization was observable in a conventional neutralization assay, sera of immunized guinea pigs competed with a broadly neutralizing antibody, CR6261, for binding to recombinant Viet/04 HA protein, suggesting that CR6261-like antibodies were elicited by the immunogens. Stem domain immunogens from a seasonal H1N1 strain (A/NC/20/99) and a recent pandemic strain (A/Cal/07/09) provided cross-protection against A/PR/8/34 viral challenge. HA2-containing stem domain immunogens therefore have the potential to provide subtype-specific protection. Influenza virus, the causative agent of flu, is responsible for yearly epidemics and frequent pandemics around the world. The virus changes its genetic makeup constantly to escape the immune pressure from the host, causing fresh epidemics. The envelope of the virus has two major glycoproteins: hemagglutinin (HA) and neuraminidase (NA). HA is a trimer of HA1 and HA2 dimers that are produced by cleavage of the precursor HA0. The globular head domain of the protein is composed exclusively of HA1 and is involved in binding of the virus to host cell sialic acid receptors leading to endosomal uptake of the virus into the cell. HA2, along with regions of HA1, forms the membrane-proximal stalk that is in a metastable conformation, poised to change its conformation upon exposure to the low pH of the endosomes. This conformational change brings about fusion of viral and host endosomal membranes and release of the viral contents into the cytoplasm (25).Antibodies (Abs) generated against the HA glycoprotein are responsible for conferring protection against viral infection (12). The antibodies generated against the HA protein during natural infection are primarily directed against the exposed head domain (35). Mutations or recombination events involving the HA and NA genes lead to genetic drift and shift, giving rise to new viruses that are not susceptible to previously acquired immunity by the host. In order to be effective, vaccines have to match the currently circulating viral strains, necessitating the production of new vaccines every season. Therefore, the search for a universal vaccine that provides broader protection and alleviates the need for frequent vaccination is ongoing.A sequence analysis of the HA sequences from various strains and subtypes r...

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“…Side-chain and backbone remodeling were recently proposed as protein design strategies to stabilize and optimize protein antigens for presentation of contiguous conformational epitopes (35)(36)(37).…”

Section: Discussionmentioning

confidence: 99%

Molecular Engineering of Ghfp, the Gonococcal Orthologue of Neisseria meningitidis Factor H Binding Protein

Rippa¹,

Santini²,

Surdo³

et al. 2015

Clin. Vaccine Immunol.

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bKnowledge of the sequences and structures of proteins produced by microbial pathogens is continuously increasing. Besides offering the possibility of unraveling the mechanisms of pathogenesis at the molecular level, structural information provides new tools for vaccine development, such as the opportunity to improve viral and bacterial vaccine candidates by rational design. Structure-based rational design of antigens can optimize the epitope repertoire in terms of accessibility, stability, and variability. In the present study, we used epitope mapping information on the well-characterized antigen of Neisseria meningitidis factor H binding protein (fHbp) to engineer its gonococcal homologue, Ghfp. Meningococcal fHbp is typically classified in three distinct antigenic variants. We introduced epitopes of fHbp variant 1 onto the surface of Ghfp, which is naturally able to protect against meningococcal strains expressing fHbp of variants 2 and 3. Heterologous epitopes were successfully transplanted, as engineered Ghfp induced functional antibodies against all three fHbp variants. These results confirm that structural vaccinology represents a successful strategy for modulating immune responses, and it is a powerful tool for investigating the extension and localization of immunodominant epitopes.

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Computational Protein Design Using Flexible Backbone Remodeling and Resurfacing: Case Studies in Structure-Based Antigen Design

Cited by 61 publications

References 41 publications

Engineering, Expression, Purification, and Characterization of Stable Clade A/B Recombinant Soluble Heterotrimeric gp140 Proteins

Engineering, Expression, Purification, and Characterization of Stable Clade A/B Recombinant Soluble Heterotrimeric gp140 Proteins

Design of Escherichia coli-Expressed Stalk Domain Immunogens of H1N1 Hemagglutinin That Protect Mice from Lethal Challenge

Molecular Engineering of Ghfp, the Gonococcal Orthologue of Neisseria meningitidis Factor H Binding Protein

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