Assessing the effects of a two-amino acid flexibility in the hemagglutinin 220-loop receptor-binding domain on the fitness of influenza A(H9N2) viruses

Abstract Under the severe situation of the current global epidemic, researchers have been working hard to find a reliable way to suppress the infection of the virus and prevent the spread of the epidemic. Studies have shown that the recognition and binding of human angiotensin-converting enzyme 2 (ACE2) by the receptor-binding domain (BRD) of spike protein on the surface of SARS-CoV-2 is a crucial step for SARS-CoV-2 to invade human receptor cells, and blocking this process can inhibit the virus from invading human normal cells. Plasma treatment can disrupt the structure of the RBD and effectively block the binding process. However, the mechanism by which plasma blocks the recognition and binding between the two is not clear. In this study, reaction process between reactive oxygen species (ROS) in plasma and the molecular model of RBD was simulated using a reactive molecular dynamics method. The results showed that the destruction of RBD molecule by ROS was triggered by hydrogen abstraction reactions. O and OH abstracted H atoms from RBD, while the H atoms of H2O2 and HO2 were abstracted by RBD. The hydrogen abstraction resulted in the breakage of C-H, N-H, O-H and C=O bonds and the formation of C=C, C=N bonds. The addition reaction of OH increased the number of O-H bonds and caused the formation of C-O, N-O and O-H bonds. The dissociation of N-H bonds led to the destruction of the original structure of peptide bonds and amino acid residues, change the type of amino acid residues, and caused the conversion of N-C and N=C, C=O and C-O. The simulation partially elucidated the microscopic mechanism of the interaction between ROS in plasma and the capsid protein of SARS-CoV-2, providing theoretical support for the control of SARS-CoV-2 infection by plasma, a contribution to overcoming the global epidemic problem.

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Construction and immunogenic studies of a mFc fusion receptor binding domain (RBD) of spike protein as a subunit vaccine against SARS-CoV-2 infection

Chemical Communications ◽

10.1039/d0cc03263h ◽

2020 ◽

Vol 56 (61) ◽

pp. 8683-8686 ◽

Cited By ~ 5

Author(s):

Xiaoxiao Qi ◽

Bixia Ke ◽

Qian Feng ◽

Deying Yang ◽

Qinghai Lian ◽

...

Keyword(s):

Amino Acid ◽

Fusion Protein ◽

Receptor Binding ◽

Neutralizing Antibodies ◽

Subunit Vaccine ◽

Binding Domain ◽

Spike Protein ◽

Receptor Binding Domain ◽

Humoral And Cellular Immunity ◽

A Subunit

Herein, we report that a recombinant fusion protein, containing a 457 amino acid SARS-CoV-2 receptor binding domain and a mouse IgG1 Fc domain, could induce highly potent neutralizing antibodies and stimulate humoral and cellular immunity in mice.

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In vivo evaluation of pathogenicity and transmissibility of influenza A(H1N1)pdm09 hemagglutinin receptor binding domain 222 intrahost variants isolated from a single immunocompromised patient

Virology ◽

10.1016/j.virol.2012.02.018 ◽

2012 ◽

Vol 428 (1) ◽

pp. 21-29 ◽

Cited By ~ 15

Author(s):

Matthew J. Memoli ◽

Tyler Bristol ◽

Kathleen E. Proudfoot ◽

A. Sally Davis ◽

Eleca J. Dunham ◽

...

Keyword(s):

Receptor Binding ◽

Influenza A ◽

Immunocompromised Patient ◽

Binding Domain ◽

Receptor Binding Domain ◽

In Vivo Evaluation ◽

Influenza A H1n1

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Receptor Binding Domain of Escherichia coli F18 Fimbrial Adhesin FedF Can Be both Efficiently Secreted and Surface Displayed in a Functional Form in Lactococcus lactis

Applied and Environmental Microbiology ◽

10.1128/aem.70.4.2061-2071.2004 ◽

2004 ◽

Vol 70 (4) ◽

pp. 2061-2071 ◽

Cited By ~ 40

Author(s):

Agneta Lindholm ◽

Andreas Smeds ◽

Airi Palva

Keyword(s):

Escherichia Coli ◽

Amino Acid ◽

Receptor Binding ◽

Intestinal Epithelial Cells ◽

Surface Display ◽

Cell Surface Display ◽

Binding Domain ◽

Intestinal Epithelial ◽

Receptor Binding Domain ◽

Amino Acid Residues

ABSTRACT Adherence of F18 fimbrial Escherichia coli to porcine intestinal epithelial cells is mediated by the adhesin (FedF) of F18 fimbriae. In a previous study, we demonstrated the specificity of the amino acid residues between 60 and 109 as the receptor binding domain of FedF. In this study, different expression, secretion, and anchoring systems for the receptor binding domain of the FedF adhesin in Lactococcus lactis were evaluated. Two partially overlapping receptor binding domains (42 and 62 amino acid residues) were expressed as fusions with L. lactis subsp. cremoris protein PrtP for evaluation of secretion efficiency. To evaluate the cell surface display of these FedF-PrtP fusions, they were further combined with different lengths of PrtP spacers fused with either the L. lactis AcmA anchor or the PrtP cell wall binding domain. An HtrA-defective L. lactis NZ9000 mutant was constructed to determine its effect on the level of secreted or anchored fusion proteins. Recombinant L. lactis clones secreting the receptor binding domain of F18 fimbriae as a fusion with the H domains of L. lactis protein PrtP were first constructed by using two different signal peptides. FedF-PrtP fusions, directed by the signal sequence of L. brevis SlpA, were throughout found to be secreted at significantly higher quantities than corresponding fusions with the signal peptide of L. lactis Usp45. In the surface display systems tested, the L. lactis AcmA anchor performed significantly better, particularly in the L. lactis NZ9000ΔhtrA strain, compared to the L. lactis PrtP anchor region. Of the cell surface display constructs with the AcmA anchor, only those with the longest PrtP spacer regions resulted in efficient binding of recombinant L. lactis cells to porcine intestinal epithelial cells. These results confirmed that it is possible to efficiently produce the receptor binding domain of the F18 adhesin in a functionally active form in L. lactis.

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An Engineered Receptor-Binding Domain Improves the Immunogenicity of Multivalent SARS-CoV-2 Vaccines

mBio ◽

10.1128/mbio.00930-21 ◽

2021 ◽

Vol 12 (3) ◽

Author(s):

Yan Guo ◽

Wenhui He ◽

Huihui Mou ◽

Lizhou Zhang ◽

Jing Chang ◽

...

Keyword(s):

Amino Acid ◽

Receptor Binding ◽

Binding Domain ◽

Full Length ◽

Vaccine Antigen ◽

Receptor Binding Domain ◽

Protein Vaccine ◽

Wild Type ◽

S Protein ◽

Glycosylation Sites

ABSTRACT The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein mediates viral entry into cells expressing angiotensin-converting enzyme 2 (ACE2). The S protein engages ACE2 through its receptor-binding domain (RBD), an independently folded 197-amino-acid fragment of the 1,273-amino-acid S-protein protomer. The RBD is the primary SARS-CoV-2 neutralizing epitope and a critical target of any SARS-CoV-2 vaccine. Here, we show that this RBD conjugated to each of two carrier proteins elicited more potent neutralizing responses in immunized rodents than did a similarly conjugated proline-stabilized S-protein ectodomain. Nonetheless, the native RBD is expressed inefficiently, limiting its usefulness as a vaccine antigen. However, we show that an RBD engineered with four novel glycosylation sites (gRBD) is expressed markedly more efficiently and generates a more potent neutralizing responses as a DNA vaccine antigen than the wild-type RBD or the full-length S protein, especially when fused to multivalent carriers, such as a Helicobacter pylori ferritin 24-mer. Further, gRBD is more immunogenic than the wild-type RBD when administered as a subunit protein vaccine. Our data suggest that multivalent gRBD antigens can reduce costs and doses, and improve the immunogenicity, of all major classes of SARS-CoV-2 vaccines. IMPORTANCE All available vaccines for coronavirus disease 2019 (COVID-19) express or deliver the full-length SARS-CoV-2 spike (S) protein. We show that this antigen is not optimal, consistent with observations that the vast majority of the neutralizing response to the virus is focused on the S-protein receptor-binding domain (RBD). However, this RBD is not expressed well as an independent domain, especially when expressed as a fusion protein with a multivalent scaffold. We therefore engineered a more highly expressed form of the SARS-CoV-2 RBD by introducing four glycosylation sites into a face of the RBD normally occluded in the full S protein. We show that this engineered protein, gRBD, is more immunogenic than the wild-type RBD or the full-length S protein in both genetic and protein-delivered vaccines.

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An engineered receptor-binding domain improves the immunogenicity of multivalent SARS-CoV-2 vaccines

10.1101/2020.11.18.388934 ◽

2020 ◽

Author(s):

Brian D. Quinlan ◽

Wenhui He ◽

Huihui Mou ◽

Lizhou Zhang ◽

Yan Guo ◽

...

Keyword(s):

Amino Acid ◽

Receptor Binding ◽

Viral Entry ◽

Binding Domain ◽

Vaccine Antigen ◽

Receptor Binding Domain ◽

Protein Vaccine ◽

Wild Type ◽

S Protein ◽

H Pylori

ABSTRACTThe SARS-coronavirus 2 (SARS-CoV-2) spike (S) protein mediates viral entry into cells expressing the angiotensin-converting enzyme 2 (ACE2). The S protein engages ACE2 through its receptor-binding domain (RBD), an independently folded 197-amino acid fragment of the 1273-amino acid S-protein protomer. The RBD is the primary SARS-CoV-2 neutralizing epitope and a critical target of any SARS-CoV-2 vaccine. Here we show that this RBD conjugated to each of two carrier proteins elicited more potent neutralizing responses in immunized rodents than did a similarly conjugated proline-stabilized S-protein ectodomain. Nonetheless, the native RBD expresses inefficiently, limiting its usefulness as a vaccine antigen. However, we show that an RBD engineered with four novel glycosylation sites (gRBD) expresses markedly more efficiently, and generates a more potent neutralizing responses as a DNA vaccine antigen, than the wild-type RBD or the full-length S protein, especially when fused to multivalent carriers such as an H. pylori ferritin 24-mer. Further, gRBD is more immunogenic than the wild-type RBD when administered as a subunit protein vaccine. Our data suggest that multivalent gRBD antigens can reduce costs and doses, and improve the immunogenicity, of all major classes of SARS-CoV-2 vaccines.

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An emerging novel bovine coronavirus with a 4-amino-acid insertion in the receptor-binding domain of the hemagglutinin-esterase gene

Archives of Virology ◽

10.1007/s00705-020-04840-y ◽

2020 ◽

Vol 165 (12) ◽

pp. 3011-3015

Author(s):

Keha-mo Abi ◽

Qi Zhang ◽

Bin Zhang ◽

Long Zhou ◽

Hua Yue ◽

...

Keyword(s):

Amino Acid ◽

Receptor Binding ◽

Binding Domain ◽

Receptor Binding Domain ◽

Bovine Coronavirus ◽

Amino Acid Insertion ◽

Esterase Gene

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Evolutionary characterization of recent human H3N2 influenza A isolates from Japan and China: novel changes in the receptor binding domain

Archives of Virology ◽

10.1007/bf01718836 ◽

1996 ◽

Vol 141 (7) ◽

pp. 1349-1355 ◽

Cited By ~ 25

Author(s):

S. Lindstrom ◽

S. Sugita ◽

A. Endo ◽

M. Ishida ◽

P. Huang ◽

...

Keyword(s):

Receptor Binding ◽

Influenza A ◽

Binding Domain ◽

Receptor Binding Domain ◽

H3n2 Influenza ◽

Japan And China

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Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016

10.1101/2021.02.17.431683 ◽

2021 ◽

Cited By ~ 10

Author(s):

Tyler N. Starr ◽

Allison J. Greaney ◽

Adam S. Dingens ◽

Jesse D. Bloom

Keyword(s):

Monoclonal Antibody ◽

Monoclonal Antibodies ◽

Amino Acid ◽

Receptor Binding ◽

Binding Domain ◽

Single Amino Acid ◽

Receptor Binding Domain ◽

Antigenic Evolution

AbstractMonoclonal antibodies and antibody cocktails are a promising therapeutic and prophylaxis for COVID-19. However, ongoing evolution of SARS-CoV-2 can render monoclonal antibodies ineffective. Here we completely map all mutations to the SARS-CoV-2 spike receptor binding domain (RBD) that escape binding by a leading monoclonal antibody, LY-CoV555, and its cocktail combination with LY-CoV016. Individual mutations that escape binding by each antibody are combined in the circulating B.1.351 and P.1 SARS-CoV-2 lineages (E484K escapes LY-CoV555, K417N/T escape LY-CoV016). Additionally, the L452R mutation in the B.1.429 lineage escapes LY-CoV555. Furthermore, we identify single amino acid changes that escape the combined LY-CoV555+LY-CoV016 cocktail. We suggest that future efforts should diversify the epitopes targeted by antibodies and antibody cocktails to make them more resilient to antigenic evolution of SARS-CoV-2.

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A single de novo substitution in SARS-CoV-2 spike informs enhanced adherence to human ACE2.

10.1101/2021.07.16.452441 ◽

2021 ◽

Author(s):

Elena Erausquin ◽

Jacinto Lopez-Sagaseta

Keyword(s):

Amino Acid ◽

Cell Membrane ◽

Receptor Binding ◽

De Novo ◽

Binding Domain ◽

Host Cells ◽

Structural Basis ◽

Receptor Binding Domain ◽

To Come ◽

Single Substitution

SARS-CoV-2 initiates colonization of host cells by binding to cell membrane ACE2 receptor. This binding is mediated by the viral spike receptor binding domain (RBD). The COVID-19 pandemic has brought devastating consequences at a clinical, social and economical levels. Therefore, anticipation of potential novel SARS-causing species or SARS-CoV-2 variants with enhanced binding to ACE2 is key in the prevention of future threats to come. We have characterized a de novo single substitution, Q498Y, in SARS-CoV-2 RBD that confers stronger adherence to ACE2. While the SARS-CoV-2 beta variant, which includes three simultaneous amino acid replacements, induces a 4-fold stronger affinity, a single Q498Y substitution results in 2.5-fold tighter binding, compared to the Wuhan-Hu-1 SARS-CoV-2 2019 strain. Additionally, we crystallized RBDQ498Y complexed with ACE2 and provide here the structural basis for this enhanced affinity. These studies inform a rationale for prevention of potential SARS-causing viruses to come.

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