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Article ; Online: Development of high affinity broadly reactive aptamers for spike protein of multiple SARS-CoV-2 variants.

Le, Thao T / Benton, Donald J / Wrobel, Antoni G / Gamblin, Steven J

RSC advances

2023 Volume 13, Issue 22, Page(s) 15322–15326

Abstract: We have developed broadly reactive aptamers against multiple variants by alternating the target between spike proteins from different SARS-CoV-2 variants during the selection process. In this process we have developed aptamers which can recognise all ... ...

Abstract	We have developed broadly reactive aptamers against multiple variants by alternating the target between spike proteins from different SARS-CoV-2 variants during the selection process. In this process we have developed aptamers which can recognise all variants, from the original wild-type 'Wuhan' strain to Omicron, with high affinity (
Language	English
Publishing date	2023-05-19
Publishing country	England
Document type	Journal Article
ISSN	2046-2069
ISSN (online)	2046-2069
DOI	10.1039/d3ra01382k
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Article ; Online: A key to unlocking chromatin revealed by complex structures.

Gamblin, Steven J / Wilson, Jon R

Nature

2019 Volume 573, Issue 7774, Page(s) 355–356

MeSH term(s)	Chromatin ; Epigenesis, Genetic ; Histones ; Methyltransferases ; Nucleosomes
Chemical Substances	Chromatin ; Histones ; Nucleosomes ; Methyltransferases (EC 2.1.1.-)
Language	English
Publishing date	2019-09-12
Publishing country	England
Document type	News ; Comment
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/d41586-019-02593-6
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Article ; Online: Structural transitions in influenza haemagglutinin at membrane fusion pH.

Benton, Donald J / Gamblin, Steven J / Rosenthal, Peter B / Skehel, John J

Nature

2020 Volume 583, Issue 7814, Page(s) 150–153

Abstract: Infection by enveloped viruses involves fusion of their lipid envelopes with cellular membranes to release the viral genome into cells. For HIV, Ebola, influenza and numerous other viruses, envelope glycoproteins bind the infecting virion to cell-surface ...

Abstract	Infection by enveloped viruses involves fusion of their lipid envelopes with cellular membranes to release the viral genome into cells. For HIV, Ebola, influenza and numerous other viruses, envelope glycoproteins bind the infecting virion to cell-surface receptors and mediate membrane fusion. In the case of influenza, the receptor-binding glycoprotein is the haemagglutinin (HA), and following receptor-mediated uptake of the bound virus by endocytosis
MeSH term(s)	Cryoelectron Microscopy ; Endosomes/metabolism ; Hemagglutinin Glycoproteins, Influenza Virus/chemistry ; Hemagglutinin Glycoproteins, Influenza Virus/metabolism ; Hemagglutinin Glycoproteins, Influenza Virus/ultrastructure ; Hydrogen-Ion Concentration ; Influenza A Virus, H3N2 Subtype/chemistry ; Influenza A Virus, H3N2 Subtype/metabolism ; Influenza A Virus, H3N2 Subtype/ultrastructure ; Membrane Fusion ; Models, Molecular ; Protein Conformation ; Time Factors
Chemical Substances	Hemagglutinin Glycoproteins, Influenza Virus
Language	English
Publishing date	2020-05-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-020-2333-6
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Article ; Online: Hemagglutinin Structure and Activities.

Gamblin, Steven J / Vachieri, Sébastien G / Xiong, Xiaoli / Zhang, Jie / Martin, Stephen R / Skehel, John J

Cold Spring Harbor perspectives in medicine

2021 Volume 11, Issue 10

Abstract: Hemagglutinins (HAs) are the receptor-binding and membrane fusion glycoproteins of influenza viruses. They recognize sialic acid-containing, cell-surface glycoconjugates as receptors but have limited affinity for them, and, as a consequence, virus ... ...

Abstract	Hemagglutinins (HAs) are the receptor-binding and membrane fusion glycoproteins of influenza viruses. They recognize sialic acid-containing, cell-surface glycoconjugates as receptors but have limited affinity for them, and, as a consequence, virus attachment to cells requires their interaction with several virus HAs. Receptor-bound virus is transferred into endosomes where membrane fusion by HAs is activated at pH between 5 and 6.5, depending on the strain of virus. Fusion activity requires extensive rearrangements in HA conformation that include extrusion of a buried "fusion peptide" to connect with the endosomal membrane, form a bridge to the virus membrane, and eventually bring both membranes close together. In this review, we give an overview of the structures of the 16 genetically and antigenically distinct subtypes of influenza A HA in relation to these two functions in virus replication and in relation to recognition of HA by antibodies that neutralize infection.
MeSH term(s)	Hemagglutinins/immunology ; Hemagglutinins/physiology ; Humans ; Hydrogen-Ion Concentration ; Membrane Fusion/immunology ; Orthomyxoviridae/immunology
Chemical Substances	Hemagglutinins
Language	English
Publishing date	2021-10-01
Publishing country	United States
Document type	Journal Article ; Review
ISSN	2157-1422
ISSN (online)	2157-1422
DOI	10.1101/cshperspect.a038638
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Article ; Online: Reversible structural changes in the influenza hemagglutinin precursor at membrane fusion pH.

Garcia-Moro, Eva / Zhang, Jie / Calder, Lesley J / Brown, Nick R / Gamblin, Steven J / Skehel, John J / Rosenthal, Peter B

Proceedings of the National Academy of Sciences of the United States of America

2022 Volume 119, Issue 33, Page(s) e2208011119

Abstract: The subunits of the influenza hemagglutinin (HA) trimer are synthesized as single-chain precursors (HA0s) that are proteolytically cleaved into the disulfide-linked polypeptides HA1 and HA2. Cleavage is required for activation of membrane fusion at low ... ...

Abstract	The subunits of the influenza hemagglutinin (HA) trimer are synthesized as single-chain precursors (HA0s) that are proteolytically cleaved into the disulfide-linked polypeptides HA1 and HA2. Cleavage is required for activation of membrane fusion at low pH, which occurs at the beginning of infection following transfer of cell-surface-bound viruses into endosomes. Activation results in extensive changes in the conformation of cleaved HA. To establish the overall contribution of cleavage to the mechanism of HA-mediated membrane fusion, we used cryogenic electron microscopy (cryo-EM) to directly image HA0 at neutral and low pH. We found extensive pH-induced structural changes, some of which were similar to those described for intermediates in the refolding of cleaved HA at low pH. They involve a partial extension of the long central coiled coil formed by melting of the preexisting secondary structure, threading it between the membrane-distal domains, and subsequent refolding as extended helices. The fusion peptide, covalently linked at its N terminus, adopts an amphipathic helical conformation over part of its length and is repositioned and packed against a complementary surface groove of conserved residues. Furthermore, and in contrast to cleaved HA, the changes in HA0 structure at low pH are reversible on reincubation at neutral pH. We discuss the implications of covalently restricted HA0 refolding for the cleaved HA conformational changes that mediate membrane fusion and for the action of antiviral drug candidates and cross-reactive anti-HA antibodies that can block influenza infectivity.
MeSH term(s)	Hemagglutinin Glycoproteins, Influenza Virus/chemistry ; Humans ; Hydrogen-Ion Concentration ; Membrane Fusion ; Orthomyxoviridae/physiology ; Protein Conformation ; Virus Internalization
Chemical Substances	Hemagglutinin Glycoproteins, Influenza Virus
Language	English
Publishing date	2022-08-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2208011119
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Article ; Online: Evolution of the SARS-CoV-2 spike protein in the human host.

Wrobel, Antoni G / Benton, Donald J / Roustan, Chloë / Borg, Annabel / Hussain, Saira / Martin, Stephen R / Rosenthal, Peter B / Skehel, John J / Gamblin, Steven J

Nature communications

2022 Volume 13, Issue 1, Page(s) 1178

Abstract: Recently emerged variants of SARS-CoV-2 contain in their surface spike glycoproteins multiple substitutions associated with increased transmission and resistance to neutralising antibodies. We have examined the structure and receptor binding properties ... ...

Abstract	Recently emerged variants of SARS-CoV-2 contain in their surface spike glycoproteins multiple substitutions associated with increased transmission and resistance to neutralising antibodies. We have examined the structure and receptor binding properties of spike proteins from the B.1.1.7 (Alpha) and B.1.351 (Beta) variants to better understand the evolution of the virus in humans. Spikes of both variants have the same mutation, N501Y, in the receptor-binding domains. This substitution confers tighter ACE2 binding, dependent on the common earlier substitution, D614G. Each variant spike has acquired other key changes in structure that likely impact virus pathogenesis. The spike from the Alpha variant is more stable against disruption upon binding ACE2 receptor than all other spikes studied. This feature is linked to the acquisition of a more basic substitution at the S1-S2 furin site (also observed for the variants of concern Delta, Kappa, and Omicron) which allows for near-complete cleavage. In the Beta variant spike, the presence of a new substitution, K417N (also observed in the Omicron variant), in combination with the D614G, stabilises a more open spike trimer, a conformation required for receptor binding. Our observations suggest ways these viruses have evolved to achieve greater transmissibility in humans.
MeSH term(s)	Angiotensin-Converting Enzyme 2/chemistry ; Angiotensin-Converting Enzyme 2/metabolism ; Angiotensin-Converting Enzyme 2/ultrastructure ; Binding Sites/genetics ; COVID-19/metabolism ; COVID-19/transmission ; COVID-19/virology ; Cryoelectron Microscopy ; Cytopathogenic Effect, Viral/genetics ; Evolution, Molecular ; Host-Pathogen Interactions ; Humans ; Kinetics ; Models, Molecular ; Mutation, Missense ; Protein Binding ; Protein Domains ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; SARS-CoV-2/physiology ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism
Chemical Substances	Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23)
Language	English
Publishing date	2022-03-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-28768-w
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Article ; Online: Receptor binding and priming of the spike protein of SARS-CoV-2 for membrane fusion.

Benton, Donald J / Wrobel, Antoni G / Xu, Pengqi / Roustan, Chloë / Martin, Stephen R / Rosenthal, Peter B / Skehel, John J / Gamblin, Steven J

Nature

2020 Volume 588, Issue 7837, Page(s) 327–330

Abstract: Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is initiated by virus binding to the ACE2 cell-surface ... ...

Abstract	Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is initiated by virus binding to the ACE2 cell-surface receptors
MeSH term(s)	Angiotensin-Converting Enzyme 2/chemistry ; Angiotensin-Converting Enzyme 2/metabolism ; Angiotensin-Converting Enzyme 2/ultrastructure ; Cryoelectron Microscopy ; Furin/metabolism ; Humans ; Membrane Fusion/physiology ; Models, Molecular ; Protein Binding ; Protein Folding ; Protein Subunits/chemistry ; Protein Subunits/metabolism ; Proteolysis ; Receptors, Coronavirus/chemistry ; Receptors, Coronavirus/metabolism ; Receptors, Coronavirus/ultrastructure ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/metabolism ; Spike Glycoprotein, Coronavirus/ultrastructure
Chemical Substances	Protein Subunits ; Receptors, Coronavirus ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; Furin (EC 3.4.21.75)
Keywords	covid19
Language	English
Publishing date	2020-09-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-020-2772-0
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Article ; Online: SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects.

Wrobel, Antoni G / Benton, Donald J / Xu, Pengqi / Roustan, Chloë / Martin, Stephen R / Rosenthal, Peter B / Skehel, John J / Gamblin, Steven J

Nature structural & molecular biology

2020 Volume 27, Issue 8, Page(s) 763–767

Abstract: SARS-CoV-2 is thought to have emerged from bats, possibly via a secondary host. Here, we investigate the relationship of spike (S) glycoprotein from SARS-CoV-2 with the S protein of a closely related bat virus, RaTG13. We determined cryo-EM structures ... ...

Abstract	SARS-CoV-2 is thought to have emerged from bats, possibly via a secondary host. Here, we investigate the relationship of spike (S) glycoprotein from SARS-CoV-2 with the S protein of a closely related bat virus, RaTG13. We determined cryo-EM structures for RaTG13 S and for both furin-cleaved and uncleaved SARS-CoV-2 S; we compared these with recently reported structures for uncleaved SARS-CoV-2 S. We also biochemically characterized their relative stabilities and affinities for the SARS-CoV-2 receptor ACE2. Although the overall structures of human and bat virus S proteins are similar, there are key differences in their properties, including a more stable precleavage form of human S and about 1,000-fold tighter binding of SARS-CoV-2 to human receptor. These observations suggest that cleavage at the furin-cleavage site decreases the overall stability of SARS-CoV-2 S and facilitates the adoption of the open conformation that is required for S to bind to the ACE2 receptor.
MeSH term(s)	Angiotensin-Converting Enzyme 2 ; Animals ; Betacoronavirus/genetics ; Betacoronavirus/metabolism ; Betacoronavirus/ultrastructure ; Binding Sites ; COVID-19 ; Chiroptera/virology ; Coronavirus Infections/virology ; Cryoelectron Microscopy ; Evolution, Molecular ; Furin/chemistry ; Gene Expression ; HEK293 Cells ; Host-Pathogen Interactions/genetics ; Humans ; Models, Molecular ; Pandemics ; Peptidyl-Dipeptidase A/chemistry ; Peptidyl-Dipeptidase A/genetics ; Peptidyl-Dipeptidase A/metabolism ; Pneumonia, Viral/virology ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Protein Isoforms/chemistry ; Protein Isoforms/genetics ; Protein Isoforms/metabolism ; Protein Stability ; Proteolysis ; Receptors, Virus/chemistry ; Receptors, Virus/genetics ; Receptors, Virus/metabolism ; Recombinant Proteins/chemistry ; Recombinant Proteins/genetics ; Recombinant Proteins/metabolism ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/genetics ; Spike Glycoprotein, Coronavirus/metabolism ; Structural Homology, Protein
Chemical Substances	Protein Isoforms ; Receptors, Virus ; Recombinant Proteins ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2 ; Peptidyl-Dipeptidase A (EC 3.4.15.1) ; ACE2 protein, human (EC 3.4.17.23) ; Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; Furin (EC 3.4.21.75)
Keywords	covid19
Language	English
Publishing date	2020-07-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2126708-X
ISSN	1545-9985 ; 1545-9993
ISSN (online)	1545-9985
ISSN	1545-9993
DOI	10.1038/s41594-020-0468-7
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Article ; Online: Author Correction: SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects.

Wrobel, Antoni G / Benton, Donald J / Xu, Pengqi / Roustan, Chloë / Martin, Stephen R / Rosenthal, Peter B / Skehel, John J / Gamblin, Steven J

Nature structural & molecular biology

2020 Volume 27, Issue 10, Page(s) 1001

Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

Abstract	An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Keywords	covid19
Language	English
Publishing date	2020-08-14
Publishing country	United States
Document type	Published Erratum
ZDB-ID	2126708-X
ISSN	1545-9985 ; 1545-9993
ISSN (online)	1545-9985
ISSN	1545-9993
DOI	10.1038/s41594-020-0509-2
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Article ; Online: Comment on "Structural basis of histone H3K27 trimethylation by an active polycomb repressive complex 2".

Zhang, Ying / Justin, Neil / Wilson, Jon R / Gamblin, Steven J

Science (New York, N.Y.)

2016 Volume 354, Issue 6319, Page(s) 1543

Abstract: Jiao and Liu (Research Articles, 16 October 2015, aac4383) reported the crystal structure of the protein complex polycomb repressive complex 2 from Chaetomium thermophilum This landmark structure has brought invaluable insights into the activation ... ...

Abstract	Jiao and Liu (Research Articles, 16 October 2015, aac4383) reported the crystal structure of the protein complex polycomb repressive complex 2 from Chaetomium thermophilum This landmark structure has brought invaluable insights into the activation mechanism of this essential methyltransferase. However, the analysis of the x-ray data discussed below suggests that the description of oncogenic H3K27M peptide binding to the active site is incorrect.
MeSH term(s)	Chaetomium/metabolism ; Histones/metabolism ; Methylation ; Polycomb Repressive Complex 1/metabolism ; Polycomb Repressive Complex 2/chemistry
Chemical Substances	Histones ; Polycomb Repressive Complex 2 (EC 2.1.1.43) ; Polycomb Repressive Complex 1 (EC 2.3.2.27)
Language	English
Publishing date	2016-12-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Comment
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.aaf6236
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