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1. Emerging variants develop total escape from potent monoclonal antibodies induced by BA.4/5 infection

Author

Liu, Chang, Das, Raksha, Dijokaite-Guraliuc, Aiste, Zhou, Daming, Mentzer, Alexander J., Supasa, Piyada, Selvaraj, Muneeswaran, Duyvesteyn, Helen M. E., Ritter, Thomas G., Temperton, Nigel, Klenerman, Paul, Dunachie, Susanna J., Paterson, Neil G., Williams, Mark A., Hall, David R., Fry, Elizabeth E., Mongkolsapaya, Juthathip, Ren, Jingshan, Stuart, David I., and Screaton, Gavin R.

Published
2024
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2. Analysis of the diverse antigenic landscape of the malaria protein RH5 identifies a potent vaccine-induced human public antibody clonotype

Author

Barrett, Jordan R., Pipini, Dimitra, Wright, Nathan D., Cooper, Andrew J.R., Gorini, Giacomo, Quinkert, Doris, Lias, Amelia M., Davies, Hannah, Rigby, Cassandra A., Aleshnick, Maya, Williams, Barnabas G., Bradshaw, William J., Paterson, Neil G., Martinson, Thomas, Kirtley, Payton, Picard, Luc, Wiggins, Christine D., Donnellan, Francesca R., King, Lloyd D.W., Wang, Lawrence T., Popplewell, Jonathan F., Silk, Sarah E., de Ruiter Swain, Jed, Skinner, Katherine, Kotraiah, Vinayaka, Noe, Amy R., MacGill, Randall S., King, C. Richter, Birkett, Ashley J., Soisson, Lorraine A., Minassian, Angela M., Lauffenburger, Douglas A., Miura, Kazutoyo, Long, Carole A., Wilder, Brandon K., Koekemoer, Lizbé, Tan, Joshua, Nielsen, Carolyn M., McHugh, Kirsty, and Draper, Simon J.

Published
2024
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3. Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses

Author

Conlon, Christopher, Deeks, Alexandra, Frater, John, Gardiner, Siobhan, Jämsén, Anni, Jeffery, Katie, Malone, Tom, Phillips, Eloise, Kronsteiner-Dobramysl, Barbara, Abraham, Priyanka, Bibi, Sagida, Lambe, Teresa, Longet, Stephanie, Tipton, Tom, Carrol, Miles, Stafford, Lizzie, Dijokaite-Guraliuc, Aiste, Das, Raksha, Zhou, Daming, Ginn, Helen M., Liu, Chang, Duyvesteyn, Helen M.E., Huo, Jiandong, Nutalai, Rungtiwa, Supasa, Piyada, Selvaraj, Muneeswaran, de Silva, Thushan I., Plowright, Megan, Newman, Thomas A.H., Hornsby, Hailey, Mentzer, Alexander J., Skelly, Donal, Ritter, Thomas G., Temperton, Nigel, Klenerman, Paul, Barnes, Eleanor, Dunachie, Susanna J., Roemer, Cornelius, Peacock, Thomas P., Paterson, Neil G., Williams, Mark A., Hall, David R., Fry, Elizabeth E., Mongkolsapaya, Juthathip, Ren, Jingshan, Stuart, David I., and Screaton, Gavin R.

Published
2023
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4. A delicate balance between antibody evasion and ACE2 affinity for Omicron BA.2.75

Author

Huo, Jiandong, Dijokaite-Guraliuc, Aiste, Liu, Chang, Zhou, Daming, Ginn, Helen M., Das, Raksha, Supasa, Piyada, Selvaraj, Muneeswaran, Nutalai, Rungtiwa, Tuekprakhon, Aekkachai, Duyvesteyn, Helen M.E., Mentzer, Alexander J., Skelly, Donal, Ritter, Thomas G., Amini, Ali, Bibi, Sagida, Adele, Sandra, Johnson, Sile Ann, Paterson, Neil G., Williams, Mark A., Hall, David R., Plowright, Megan, Newman, Thomas A.H., Hornsby, Hailey, de Silva, Thushan I., Temperton, Nigel, Klenerman, Paul, Barnes, Eleanor, Dunachie, Susanna J., Pollard, Andrew J., Lambe, Teresa, Goulder, Philip, Fry, Elizabeth E., Mongkolsapaya, Juthathip, Ren, Jingshan, Stuart, David I., and Screaton, Gavin R.

Published
2023
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10. Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient

Author

Zhou, Daming, Duyvesteyn, Helen M. E., Chen, Cheng-Pin, Huang, Chung-Guei, Chen, Ting-Hua, Shih, Shin-Ru, Lin, Yi-Chun, Cheng, Chien-Yu, Cheng, Shu-Hsing, Huang, Yhu-Chering, Lin, Tzou-Yien, Ma, Che, Huo, Jiandong, Carrique, Loic, Malinauskas, Tomas, Ruza, Reinis R., Shah, Pranav N. M., Tan, Tiong Kit, Rijal, Pramila, Donat, Robert F., Godwin, Kerry, Buttigieg, Karen R., Tree, Julia A., Radecke, Julika, Paterson, Neil G., Supasa, Piyada, Mongkolsapaya, Juthathip, Screaton, Gavin R., Carroll, Miles W., Gilbert-Jaramillo, Javier, Knight, Michael L., James, William, Owens, Raymond J., Naismith, James H., Townsend, Alain R., Fry, Elizabeth E., Zhao, Yuguang, Ren, Jingshan, Stuart, David I., and Huang, Kuan-Ying A.

Published
2020
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11. A slow‐forming isopeptide bond in the structure of the major pilin SpaD from Corynebacterium diphtheriae has implications for pilus assembly

Author

Kang, Hae Joo, Paterson, Neil G, Kim, Chae Un, Middleditch, Martin, Chang, Chungyu, Ton-That, Hung, and Baker, Edward N

Subjects
Biochemistry and Cell Biology, Chemical Sciences, Biological Sciences, Genetics, Corynebacterium diphtheriae, Crystallography, X-Ray, Disulfides, Fimbriae Proteins, Lysine, Models, Molecular, Protein Conformation, Protein Structure, Tertiary, Spectrometry, Mass, Electrospray Ionization, Gram-positive bacterial pili, isopeptide bond, pilus assembly, Physical Sciences, Biophysics, Biological sciences, Chemical sciences, Physical sciences
Abstract

The Gram-positive organism Corynebacterium diphtheriae, the cause of diphtheria in humans, expresses pili on its surface which it uses for adhesion and colonization of its host. These pili are covalent protein polymers composed of three types of pilin subunit that are assembled by specific sortase enzymes. A structural analysis of the major pilin SpaD, which forms the polymeric backbone of one of the three types of pilus expressed by C. diphtheriae, is reported. Mass-spectral and crystallographic analysis shows that SpaD contains three internal Lys-Asn isopeptide bonds. One of these, shown by mass spectrometry to be located in the N-terminal D1 domain of the protein, only forms slowly, implying an energy barrier to bond formation. Two crystal structures, of the full-length three-domain protein at 2.5 Å resolution and of a two-domain (D2-D3) construct at 1.87 Å resolution, show that each of the three Ig-like domains contains a single Lys-Asn isopeptide-bond cross-link, assumed to give mechanical stability as in other such pili. Additional stabilizing features include a disulfide bond in the D3 domain and a calcium-binding loop in D2. The N-terminal D1 domain is more flexible than the others and, by analogy with other major pilins of this type, the slow formation of its isopeptide bond can be attributed to its location adjacent to the lysine used in sortase-mediated polymerization during pilus assembly.

Published
2014

12. Probing a Major DNA Weakness: Resolving the Groove and Sequence Selectivity of the Diimine Complex Λ‐[Ru(phen)2phi]2+.

Author

Prieto Otoya, Tayler D., McQuaid, Kane T., Hennessy, Joseph, Menounou, Georgia, Gibney, Alex, Paterson, Neil G., Cardin, David J., Kellett, Andrew, and Cardin, Christine J.

Subjects
DNA probes, NUCLEIC acids, RUTHENIUM compounds, PROTEIN drugs, CARRIER proteins, OLIGONUCLEOTIDES, ENANTIOMERS
Abstract

The grooves of DNA provide recognition sites for many nucleic acid binding proteins and anticancer drugs such as the covalently binding cisplatin. Here we report a crystal structure showing, for the first time, groove selectivity by an intercalating ruthenium complex. The complex Λ‐[Ru(phen)2phi]2+, where phi=9,10‐phenanthrenediimine, is bound to the DNA decamer duplex d(CCGGTACCGG)2. The structure shows that the metal complex is symmetrically bound in the major groove at the central TA/TA step, and asymmetrically bound in the minor groove at the adjacent GG/CC steps. A third type of binding links the strands, in which each terminal cytosine base stacks with one phen ligand. The overall binding stoichiometry is four Ru complexes per duplex. Complementary biophysical measurements confirm the binding preference for the Λ‐enantiomer and show a high affinity for TA/TA steps and, more generally, TA‐rich sequences. A striking enantiospecific elevation of melting temperatures is found for oligonucleotides which include the TATA box sequence. [ABSTRACT FROM AUTHOR]

Published
2024
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13. Probing a Major DNA Weakness: Resolving the Groove and Sequence Selectivity of the Diimine Complex Λ‐[Ru(phen)2phi]2+.

Author

Prieto Otoya, Tayler D., McQuaid, Kane T., Hennessy, Joseph, Menounou, Georgia, Gibney, Alex, Paterson, Neil G., Cardin, David J., Kellett, Andrew, and Cardin, Christine J.

Subjects
DNA probes, NUCLEIC acids, RUTHENIUM compounds, PROTEIN drugs, CARRIER proteins, OLIGONUCLEOTIDES, ENANTIOMERS
Abstract

The grooves of DNA provide recognition sites for many nucleic acid binding proteins and anticancer drugs such as the covalently binding cisplatin. Here we report a crystal structure showing, for the first time, groove selectivity by an intercalating ruthenium complex. The complex Λ‐[Ru(phen)2phi]2+, where phi=9,10‐phenanthrenediimine, is bound to the DNA decamer duplex d(CCGGTACCGG)2. The structure shows that the metal complex is symmetrically bound in the major groove at the central TA/TA step, and asymmetrically bound in the minor groove at the adjacent GG/CC steps. A third type of binding links the strands, in which each terminal cytosine base stacks with one phen ligand. The overall binding stoichiometry is four Ru complexes per duplex. Complementary biophysical measurements confirm the binding preference for the Λ‐enantiomer and show a high affinity for TA/TA steps and, more generally, TA‐rich sequences. A striking enantiospecific elevation of melting temperatures is found for oligonucleotides which include the TATA box sequence. [ABSTRACT FROM AUTHOR]

Published
2024
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15. Rapid escape of new SARS-CoV-2 Omicron variants from BA.2-directed antibody responses

Author

Dijokaite-Guraliuc, Aiste, primary, Das, Raksha, additional, Zhou, Daming, additional, Ginn, Helen M., additional, Liu, Chang, additional, Duyvesteyn, Helen M.E., additional, Huo, Jiandong, additional, Nutalai, Rungtiwa, additional, Supasa, Piyada, additional, Selvaraj, Muneeswaran, additional, de Silva, Thushan I., additional, Plowright, Megan, additional, Newman, Thomas A.H., additional, Hornsby, Hailey, additional, Mentzer, Alexander J., additional, Skelly, Donal, additional, Ritter, Thomas G., additional, Temperton, Nigel, additional, Klenerman, Paul, additional, Barnes, Eleanor, additional, Dunachie, Susanna J., additional, Roemer, Cornelius, additional, Peacock, Thomas P., additional, Paterson, Neil G., additional, Williams, Mark A., additional, Hall, David R., additional, Fry, Elizabeth E., additional, Mongkolsapaya, Juthathip, additional, Ren, Jingshan, additional, Stuart, David I., additional, Screaton, Gavin R., additional, Conlon, Christopher, additional, Deeks, Alexandra, additional, Frater, John, additional, Gardiner, Siobhan, additional, Jämsén, Anni, additional, Jeffery, Katie, additional, Malone, Tom, additional, Phillips, Eloise, additional, Kronsteiner-Dobramysl, Barbara, additional, Abraham, Priyanka, additional, Bibi, Sagida, additional, Lambe, Teresa, additional, Longet, Stephanie, additional, Tipton, Tom, additional, Carrol, Miles, additional, and Stafford, Lizzie, additional

Published
2023
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16. Room-temperature crystallography reveals altered binding of small-molecule fragments to PTP1B

Author

Skaist Mehlman, Tamar, primary, Biel, Justin T, additional, Azeem, Syeda Maryam, additional, Nelson, Elliot R, additional, Hossain, Sakib, additional, Dunnett, Louise, additional, Paterson, Neil G, additional, Douangamath, Alice, additional, Talon, Romain, additional, Axford, Danny, additional, Orins, Helen, additional, von Delft, Frank, additional, and Keedy, Daniel A, additional

Published
2023
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17. Rapid escape of new SARS-CoV-2 Omicron variants from BA.2 directed antibody responses

Author

Dijokaite-Guraliuc, Aiste, Das, Raksha, Zhou, Daming, Ginn, Helen M., Liu, Chang, Duyvesteyn, Helen M.E., Huo, Jiandong, Nutalai, Rungtiwa, Supasa, Piyada, Selvaraj, Muneeswaran, de Silva, Thushan I., Plowright, Megan, Newman, Thomas A.H., Hornsby, Hailey, Mentzer, Alexander J., Skelly, Donal, Ritter, Thomas G., Temperton, Nigel, Klenerman, Paul, Barnes, Eleanor, Dunachie, Susanna J., Roemer, Cornelius, Peacock, Thomas P., Paterson, Neil G., Williams, Mark A., Hall, David R., Fry, Elizabeth E., Mongkolsapaya, Juthathip, Ren, Jingshan, Stuart, David I., Screaton, Gavin R., Dijokaite-Guraliuc, Aiste, Das, Raksha, Zhou, Daming, Ginn, Helen M., Liu, Chang, Duyvesteyn, Helen M.E., Huo, Jiandong, Nutalai, Rungtiwa, Supasa, Piyada, Selvaraj, Muneeswaran, de Silva, Thushan I., Plowright, Megan, Newman, Thomas A.H., Hornsby, Hailey, Mentzer, Alexander J., Skelly, Donal, Ritter, Thomas G., Temperton, Nigel, Klenerman, Paul, Barnes, Eleanor, Dunachie, Susanna J., Roemer, Cornelius, Peacock, Thomas P., Paterson, Neil G., Williams, Mark A., Hall, David R., Fry, Elizabeth E., Mongkolsapaya, Juthathip, Ren, Jingshan, Stuart, David I., and Screaton, Gavin R.

Abstract

In November 2021 Omicron BA.1, containing a raft of new spike mutations emerged and quickly spread globally. Intense selection pressure to escape the antibody response produced by vaccines or SARS-CoV-2 infection then led to a rapid succession of Omicron sub-lineages with waves of BA.2 then BA.4/5 infection. Recently, many variants have emerged such as BQ.1 and XBB, which carry up to 8 additional RBD amino-acid substitutions compared to BA.2. We describe a panel of 25 potent mAbs generated from vaccinees suffering BA.2 breakthrough infections. Epitope mapping shows potent mAb binding shifting to 3 clusters, 2 corresponding to early-pandemic binding hotspots. The RBD mutations in recent variants map close to these binding sites and knock out or severely knock down neutralization activity of all but 1 potent mAb. This recent mAb escape corresponds with large falls in neutralization titre of vaccine or BA.1, BA.2 or BA.4/5 immune serum.

Published
2023

18. Author response: Room-temperature crystallography reveals altered binding of small-molecule fragments to PTP1B

Author

Skaist Mehlman, Tamar, primary, Biel, Justin T, additional, Azeem, Syeda Maryam, additional, Nelson, Elliot R, additional, Hossain, Sakib, additional, Dunnett, Louise, additional, Paterson, Neil G, additional, Douangamath, Alice, additional, Talon, Romain, additional, Axford, Danny, additional, Orins, Helen, additional, von Delft, Frank, additional, and Keedy, Daniel A, additional

Published
2023
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19. Room-temperature crystallography reveals altered binding of small-molecule fragments to PTP1B

Author

Mehlman, Tamar (Skaist), primary, Biel, Justin T., additional, Azeem, Syeda Maryam, additional, Nelson, Elliot R., additional, Hossain, Sakib, additional, Dunnett, Louise E., additional, Paterson, Neil G., additional, Douangamath, Alice, additional, Talon, Romain, additional, Axford, Danny, additional, Orins, Helen, additional, von Delft, Frank, additional, and Keedy, Daniel A., additional

Published
2022
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20. Structural basis of outer membrane protein insertion by the BAM complex

Author

Gu, Yinghong, Li, Huanyu, Dong, Haohao, Zeng, Yi, Zhang, Zhengyu, Paterson, Neil G., Stansfeld, Phillip J., Wang, Zhongshan, Zhang, Yizheng, Wang, Wenjian, and Dong, Changjiang

Subjects
Crystal structure -- Research, Membrane proteins -- Physiological aspects, Mitochondria -- Physiological aspects, Escherichia coli -- Physiological aspects, Microbiological research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

All Gram-negative bacteria, mitochondria and chloroplasts have outer membrane proteins (OMPs) that perform many fundamental biological processes. The OMPs in Gram-negative bacteria are inserted and folded into the outer membrane by the -barrel assembly machinery (BAM). The mechanism involved is poorly understood, owing to the absence of a structure of the entire BAM complex. Here we report two crystal structures of the Escherichia coli BAM complex in two distinct states: an inward-open state and a lateral-open state. Our structures reveal that the five polypeptide transport-associated domains of BamA form a ring architecture with four associated lipoproteins, BamBBamE, in the periplasm. Our structural, functional studies and molecular dynamics simulations indicate that these subunits rotate with respect to the integral membrane -barrel of BamA to induce movement of the -strands of the barrel and promote insertion of the nascent OMP., Author(s): Yinghong Gu [1]; Huanyu Li [1]; Haohao Dong [1]; Yi Zeng [1]; Zhengyu Zhang [1]; Neil G. Paterson [2]; Phillip J. Stansfeld [3]; Zhongshan Wang [1, 4, 5]; Yizheng [...]

Published
2016
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22. Antibody escape of SARS-CoV-2 Omicron BA.4 and BA.5 from vaccine and BA.1 serum

Author

Tuekprakhon, Aekkachai, primary, Nutalai, Rungtiwa, additional, Dijokaite-Guraliuc, Aiste, additional, Zhou, Daming, additional, Ginn, Helen M., additional, Selvaraj, Muneeswaran, additional, Liu, Chang, additional, Mentzer, Alexander J., additional, Supasa, Piyada, additional, Duyvesteyn, Helen M.E., additional, Das, Raksha, additional, Skelly, Donal, additional, Ritter, Thomas G., additional, Amini, Ali, additional, Bibi, Sagida, additional, Adele, Sandra, additional, Johnson, Sile Ann, additional, Constantinides, Bede, additional, Webster, Hermione, additional, Temperton, Nigel, additional, Klenerman, Paul, additional, Barnes, Eleanor, additional, Dunachie, Susanna J., additional, Crook, Derrick, additional, Pollard, Andrew J., additional, Lambe, Teresa, additional, Goulder, Philip, additional, Paterson, Neil G., additional, Williams, Mark A., additional, Hall, David R., additional, Fry, Elizabeth E., additional, Huo, Jiandong, additional, Mongkolsapaya, Juthathip, additional, Ren, Jingshan, additional, Stuart, David I., additional, Screaton, Gavin R., additional, Conlon, Christopher, additional, Deeks, Alexandra, additional, Frater, John, additional, Frending, Lisa, additional, Gardiner, Siobhan, additional, Jämsén, Anni, additional, Jeffery, Katie, additional, Malone, Tom, additional, Phillips, Eloise, additional, Rothwell, Lucy, additional, and Stafford, Lizzie, additional

Published
2022
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23. Potent cross-reactive antibodies following Omicron breakthrough in vaccinees

Author

Nutalai, Rungtiwa, primary, Zhou, Daming, additional, Tuekprakhon, Aekkachai, additional, Ginn, Helen M., additional, Supasa, Piyada, additional, Liu, Chang, additional, Huo, Jiandong, additional, Mentzer, Alexander J., additional, Duyvesteyn, Helen M.E., additional, Dijokaite-Guraliuc, Aiste, additional, Skelly, Donal, additional, Ritter, Thomas G., additional, Amini, Ali, additional, Bibi, Sagida, additional, Adele, Sandra, additional, Johnson, Sile Ann, additional, Constantinides, Bede, additional, Webster, Hermione, additional, Temperton, Nigel, additional, Klenerman, Paul, additional, Barnes, Eleanor, additional, Dunachie, Susanna J., additional, Crook, Derrick, additional, Pollard, Andrew J., additional, Lambe, Teresa, additional, Goulder, Philip, additional, Paterson, Neil G., additional, Williams, Mark A., additional, Hall, David R., additional, Mongkolsapaya, Juthathip, additional, Fry, Elizabeth E., additional, Dejnirattisai, Wanwisa, additional, Ren, Jingshan, additional, Stuart, David I., additional, and Screaton, Gavin R., additional

Published
2022
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24. Antibody escape of SARS-CoV-2 Omicron BA.4 and BA.5 from vaccine and BA.1 serum

Author

Tuekprakhon, Aekkachai, Huo, Jiandong, Nutalai, Rungtiwa, Dijokaite-Guraliuc, Aiste, Zhou, Daming, Ginn, Helen M., Selvaraj, Muneeswaran, Liu, Chang, Mentzer, Alexander J., Supasa, Piyada, Duyvesteyn, Helen M.E., Das, Raksha, Skelly, Donal, Ritter, Thomas G., Amini, Ali, Bibi, Sagida, Adele, Sandra, Johnson, Sile Ann, Constantinides, Bede, Webster, Hermione, Temperton, Nigel J., Klenerman, Paul, Barnes, Eleanor, Dunachie, Susanna J., Crook, Derrick, Pollard, Andrew J., Lambe, Teresa, Goulder, Philip, Paterson, Neil G., Williams, Mark A., Hall, David R., Fry, Elizabeth E., Mongkolsapaya, Juthathip, Ren, Jingshan, Stuart, David I., Screaton, Gavin R., Conlon, Christopher, Deeks, Alexandra, Frater, John, Frending, Lisa, Gardiner, Siobhan, Jämsén, Anni, Jeffery, Katie, Malone, Tom, Phillips, Eloise, Rothwell, Lucy, Stafford, Lizzie, Tuekprakhon, Aekkachai, Huo, Jiandong, Nutalai, Rungtiwa, Dijokaite-Guraliuc, Aiste, Zhou, Daming, Ginn, Helen M., Selvaraj, Muneeswaran, Liu, Chang, Mentzer, Alexander J., Supasa, Piyada, Duyvesteyn, Helen M.E., Das, Raksha, Skelly, Donal, Ritter, Thomas G., Amini, Ali, Bibi, Sagida, Adele, Sandra, Johnson, Sile Ann, Constantinides, Bede, Webster, Hermione, Temperton, Nigel J., Klenerman, Paul, Barnes, Eleanor, Dunachie, Susanna J., Crook, Derrick, Pollard, Andrew J., Lambe, Teresa, Goulder, Philip, Paterson, Neil G., Williams, Mark A., Hall, David R., Fry, Elizabeth E., Mongkolsapaya, Juthathip, Ren, Jingshan, Stuart, David I., Screaton, Gavin R., Conlon, Christopher, Deeks, Alexandra, Frater, John, Frending, Lisa, Gardiner, Siobhan, Jämsén, Anni, Jeffery, Katie, Malone, Tom, Phillips, Eloise, Rothwell, Lucy, and Stafford, Lizzie

Abstract

The Omicron lineage of SARS-CoV-2, first described in November 2021, spread rapidly to become globally dominant and has split into a number of sub-lineages. BA.1 dominated the initial wave but has been replaced by BA.2 in many countries. Recent sequencing from South Africa’s Gauteng region uncovered two new sub-lineages, BA.4 and BA.5 which are taking over locally, driving a new wave. BA.4 and BA.5 contain identical spike sequences and, although closely related to BA.2, contain further mutations in the receptor binding domain of spike. Here, we study the neutralization of BA.4/5 using a range of vaccine and naturally immune serum and panels of monoclonal antibodies. BA.4/5 shows reduced neutralization by serum from triple AstraZeneca or Pfizer vaccinated individuals compared to BA.1 and BA.2. Furthermore, using serum from BA.1 vaccine breakthrough infections there are likewise, significant reductions in the neutralization of BA.4/5, raising the possibility of repeat Omicron infections.

Published
2022

25. Potent cross-reactive antibodies following Omicron breakthrough in vaccinees

Author

Nutalai, Rungtiwa, Zhou, Daming, Tuekprakhon, Aekkachai, Ginn, Helen M., Supasa, Piyada, Liu, Chang, Huo, Jiandong, Mentzer, Alexander J., Duyvesteyn, Helen M.E., Dijokaite-Guraliuc, Aiste, Skelly, Donal, Ritter, Thomas G., Amini, Ali, Bibi, Sagida, Adele, Sandra, Johnson, Sile Ann, Constantinides, Bede, Webster, Hermione, Temperton, Nigel J., Klenerman, Paul, Barnes, Eleanor, Dunachie, Susanna J., Crook, Derrick, Pollard, Andrew J., Lambe, Teresa, Goulder, Philip, Paterson, Neil G., Williams, Mark A., Hall, David R., Mongkolsapaya, Juthathip, Fry, Elizabeth E., Dejnirattisai, Wanwisa, Ren, Jingshan, Stuart, David I., Screaton, Gavin R., Nutalai, Rungtiwa, Zhou, Daming, Tuekprakhon, Aekkachai, Ginn, Helen M., Supasa, Piyada, Liu, Chang, Huo, Jiandong, Mentzer, Alexander J., Duyvesteyn, Helen M.E., Dijokaite-Guraliuc, Aiste, Skelly, Donal, Ritter, Thomas G., Amini, Ali, Bibi, Sagida, Adele, Sandra, Johnson, Sile Ann, Constantinides, Bede, Webster, Hermione, Temperton, Nigel J., Klenerman, Paul, Barnes, Eleanor, Dunachie, Susanna J., Crook, Derrick, Pollard, Andrew J., Lambe, Teresa, Goulder, Philip, Paterson, Neil G., Williams, Mark A., Hall, David R., Mongkolsapaya, Juthathip, Fry, Elizabeth E., Dejnirattisai, Wanwisa, Ren, Jingshan, Stuart, David I., and Screaton, Gavin R.

Abstract

Highly transmissible Omicron variants of SARS-CoV-2 currently dominate globally. Here, we compare neutralization of Omicron BA.1, BA.1.1 and BA.2. BA.2 RBD has slightly higher ACE2 affinity than BA.1 and slightly reduced neutralization by vaccine serum, possibly associated with its increased transmissibility. Neutralization differences between sub-lineages for mAbs (including therapeutics) mostly arise from variation in residues bordering the ACE2 binding site, however, more distant mutations S371F (BA.2) and R346K (BA.1.1) markedly reduce neutralization by therapeutic antibody Vir-S309. In-depth structure-and-function analyses of 27 potent RBD-binding mAbs isolated from vaccinated volunteers following breakthrough Omicron-BA.1 infection reveals that they are focussed in two main clusters within the RBD, with potent right-shoulder antibodies showing increased prevalence. Selection and somatic maturation have optimized antibody potency in less-mutated epitopes and recovered potency in highly mutated epitopes. All 27 mAbs potently neutralize early pandemic strains and many show broad reactivity with variants of concern.

Published
2022

26. A four-helix bundle stores copper for methane oxidation

Author

Vita, Nicolas, Platsaki, Semeli, Basle, Arnaud, Allen, Stephen J., Paterson, Neil G., Crombie, Andrew T., Murrell, J. Colin, Waldron, Kevin J., and Dennison, Christopher

Subjects
Copper in the body -- Physiological aspects, Methane -- Physiological aspects, Methanotrophs -- Physiological aspects, Microbiological research, Oxidation-reduction reaction -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Methane-oxidizing bacteria (methanotrophs) require large quantities of copper for the membrane-bound (particulate) methane monooxygenase (1,2). Certain methanotrophs are also able to switch to using the iron-containing soluble methane monooxygenase to catalyse methane oxidation, with this switchover regulated by copper (3,4). Methane monooxygenases are nature's primary biological mechanism for suppressing atmospheric levels of methane, a potent greenhouse gas. Furthermore, methanotrophs and methane monooxygenases have enormous potential in bioremediation and for biotransformations producing bulk and fine chemicals, and in bioenergy, particularly considering increased methane availability from renewable sources and hydraulic fracturing of shale rock (5,6). Here we discover and characterize a novel copper storage protein (Csp1) from the methanotroph Methylosinus trichosporium OB3b that is exported from the cytosol, and stores copper for particulate methane monooxygenase. Csp1 is a tetramer of four-helix bundles with each monomer binding up to 13 Cu(I) ions in a previously unseen manner via mainly Cys residues that point into the core of the bundle. Csp1 is the first example of a protein that stores a metal within an established protein-folding motif. This work provides a detailed insight into how methanotrophs accumulate copper for the oxidation of methane. Understanding this process is essential if the wide-ranging biotechnological applications of methanotrophs are to be realized. Cytosolic homologues of Csp1 are present in diverse bacteria, thus challenging the dogma that such organisms do not use copper in this location., Biology exploits copper to catalyse a range of important reactions, but use of this metal has been influenced by its availability and potential toxicity (7-9). In eukaryotes, excess copper is [...]

Published
2015

30. Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses

Author

Dejnirattisai, Wanwisa, Huo, Jiandong, Zhou, Daming, Zahradník, Jiří, Supasa, Piyada, Liu, Chang, Duyvesteyn, Helen M.E., Ginn, Helen M., Mentzer, Alexander J., Tuekprakhon, Aekkachai, Nutalai, Rungtiwa, Wang, Beibei, Dijokaite, Aiste, Khan, Suman, Avinoam, Ori, Bahar, Mohammad, Skelly, Donal, Adele, Sandra, Johnson, Sile Ann, Amini, Ali, Ritter, Thomas, Mason, Chris, Dold, Christina, Pan, Daniel, Assadi, Sara, Bellass, Adam, Omo-Dare, Nikki, Koeckerling, David, Flaxman, Amy, Jenkin, Daniel, Aley, Parvinder K, Voysey, Merryn, Clemens, Sue Ann Costa, Naveca, Felipe Gomes, Nascimento, Valdinete, Nascimento, Fernanda, Fernandes da Costa, Cristiano, Resende, Paola Cristina, Pauvolid-Correa, Alex, Siqueira, Marilda M., Baillie, Vicky, Serafin, Natali, Ditse, Zanele, Da Silva, Kelly, Madhi, Shabir, Nunes, Marta C, Malik, Tariq, Openshaw, Peter JM, Baillie, J Kenneth, Semple, Malcolm G, Townsend, Alain R, Huang, Kuan-Ying A., Tan, Tiong Kit, Carroll, Miles W., Klenerman, Paul, Barnes, Eleanor, Dunachie, Susanna J., Constantinides, Bede, Webster, Hermione, Crook, Derrick, Pollard, Andrew J, Lambe, Teresa, Paterson, Neil G., Williams, Mark A., Hall, David R., Fry, Elizabeth E., Mongkolsapaya, Juthathip, Ren, Jingshan, Schreiber, Gideon, Stuart, David I., and Screaton, Gavin R

Subjects
Article
Abstract

SummaryOn the 24th November 2021 the sequence of a new SARS CoV-2 viral isolate spreading rapidly in Southern Africa was announced, containing far more mutations in Spike (S) than previously reported variants. Neutralization titres of Omicron by sera from vaccinees and convalescent subjects infected with early pandemic as well as Alpha, Beta, Gamma, Delta are substantially reduced or fail to neutralize. Titres against Omicron are boosted by third vaccine doses and are high in cases both vaccinated and infected by Delta. Mutations in Omicron knock out or substantially reduce neutralization by most of a large panel of potent monoclonal antibodies and antibodies under commercial development. Omicron S has structural changes from earlier viruses, combining mutations conferring tight binding to ACE2 to unleash evolution driven by immune escape, leading to a large number of mutations in the ACE2 binding site which rebalance receptor affinity to that of early pandemic viruses.

Published
2021

32. SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses

Author

Dejnirattisai, Wanwisa, primary, Huo, Jiandong, additional, Zhou, Daming, additional, Zahradník, Jiří, additional, Supasa, Piyada, additional, Liu, Chang, additional, Duyvesteyn, Helen M.E., additional, Ginn, Helen M., additional, Mentzer, Alexander J., additional, Tuekprakhon, Aekkachai, additional, Nutalai, Rungtiwa, additional, Wang, Beibei, additional, Dijokaite, Aiste, additional, Khan, Suman, additional, Avinoam, Ori, additional, Bahar, Mohammad, additional, Skelly, Donal, additional, Adele, Sandra, additional, Johnson, Sile Ann, additional, Amini, Ali, additional, Ritter, Thomas G., additional, Mason, Chris, additional, Dold, Christina, additional, Pan, Daniel, additional, Assadi, Sara, additional, Bellass, Adam, additional, Omo-Dare, Nicola, additional, Koeckerling, David, additional, Flaxman, Amy, additional, Jenkin, Daniel, additional, Aley, Parvinder K., additional, Voysey, Merryn, additional, Costa Clemens, Sue Ann, additional, Naveca, Felipe Gomes, additional, Nascimento, Valdinete, additional, Nascimento, Fernanda, additional, Fernandes da Costa, Cristiano, additional, Resende, Paola Cristina, additional, Pauvolid-Correa, Alex, additional, Siqueira, Marilda M., additional, Baillie, Vicky, additional, Serafin, Natali, additional, Kwatra, Gaurav, additional, Da Silva, Kelly, additional, Madhi, Shabir A., additional, Nunes, Marta C., additional, Malik, Tariq, additional, Openshaw, Peter J.M., additional, Baillie, J. Kenneth, additional, Semple, Malcolm G., additional, Townsend, Alain R., additional, Huang, Kuan-Ying A., additional, Tan, Tiong Kit, additional, Carroll, Miles W., additional, Klenerman, Paul, additional, Barnes, Eleanor, additional, Dunachie, Susanna J., additional, Constantinides, Bede, additional, Webster, Hermione, additional, Crook, Derrick, additional, Pollard, Andrew J., additional, Lambe, Teresa, additional, Paterson, Neil G., additional, Williams, Mark A., additional, Hall, David R., additional, Fry, Elizabeth E., additional, Mongkolsapaya, Juthathip, additional, Ren, Jingshan, additional, Schreiber, Gideon, additional, Stuart, David I., additional, Screaton, Gavin R., additional, Conlon, Christopher, additional, Deeks, Alexandra S., additional, Frater, John, additional, Frending, Lisa, additional, Gardiner, Siobhan, additional, Jämsén, Anni, additional, Jeffery, Katie, additional, Malone, Tom, additional, Phillips, Eloise, additional, Rothwell, Lucy, additional, Stafford, Lizzie, additional, Baillie, J Kenneth, additional, Openshaw, Peter JM., additional, Carson, Gail, additional, Alex, Beatrice, additional, Andrikopoulos, Petros, additional, Bach, Benjamin, additional, Barclay, Wendy S., additional, Bogaert, Debby, additional, Chand, Meera, additional, Chechi, Kanta, additional, Cooke, Graham S., additional, da Silva Filipe, Ana, additional, de Silva, Thushan, additional, Docherty, Annemarie B., additional, dos Santos Correia, Gonçalo, additional, Dumas, Marc-Emmanuel, additional, Dunning, Jake, additional, Fletcher, Tom, additional, Green, Christoper A., additional, Greenhalf, William, additional, Griffin, Julian L., additional, Gupta, Rishi K., additional, Harrison, Ewen M., additional, Hiscox, Julian A., additional, Wai Ho, Antonia Ying, additional, Horby, Peter W., additional, Ijaz, Samreen, additional, Khoo, Saye, additional, Law, Andrew, additional, Lewis, Matthew R., additional, Liggi, Sonia, additional, Lim, Wei Shen, additional, Maslen, Lynn, additional, Merson, Laura, additional, Meynert, Alison M., additional, Moore, Shona C., additional, Noursadeghi, Mahdad, additional, Olanipekun, Michael, additional, Osagie, Anthonia, additional, Palmarini, Massimo, additional, Palmieri, Carlo, additional, Paxton, William A., additional, Pollakis, Georgios, additional, Price, Nicholas, additional, Rambaut, Andrew, additional, Robertson, David L., additional, Russell, Clark D., additional, Sancho-Shimizu, Vanessa, additional, Sands, Caroline J., additional, Scott, Janet T., additional, Sigfrid, Louise, additional, Solomon, Tom, additional, Sriskandan, Shiranee, additional, Stuart, David, additional, Summers, Charlotte, additional, Swann, Olivia V., additional, Takats, Zoltan, additional, Takis, Panteleimon, additional, Tedder, Richard S., additional, Thompson, AA Roger, additional, Thomson, Emma C., additional, Thwaites, Ryan S., additional, Turtle, Lance CW., additional, Zambon, Maria, additional, Hardwick, Hayley, additional, Donohue, Chloe, additional, Griffiths, Fiona, additional, Oosthuyzen, Wilna, additional, Donegan, Cara, additional, Spencer, Rebecca G., additional, Norman, Lisa, additional, Pius, Riinu, additional, Drake, Thomas M., additional, Fairfield, Cameron J., additional, Knight, Stephen R., additional, Mclean, Kenneth A., additional, Murphy, Derek, additional, Shaw, Catherine A., additional, Dalton, Jo, additional, Girvan, Michelle, additional, Saviciute, Egle, additional, Roberts, Stephanie, additional, Harrison, Janet, additional, Marsh, Laura, additional, Connor, Marie, additional, Halpin, Sophie, additional, Jackson, Clare, additional, Gamble, Carrol, additional, Plotkin, Daniel, additional, Lee, James, additional, Leeming, Gary, additional, Wham, Murray, additional, Clohisey, Sara, additional, Hendry, Ross, additional, Scott-Brown, James, additional, Shaw, Victoria, additional, McDonald, Sarah E., additional, Keating, Seán, additional, Ahmed, Katie A., additional, Armstrong, Jane A., additional, Ashworth, Milton, additional, Asiimwe, Innocent G., additional, Bakshi, Siddharth, additional, Barlow, Samantha L., additional, Booth, Laura, additional, Brennan, Benjamin, additional, Bullock, Katie, additional, Catterall, Benjamin WA., additional, Clark, Jordan J., additional, Clarke, Emily A., additional, Cole, Sarah, additional, Cooper, Louise, additional, Cox, Helen, additional, Davis, Christopher, additional, Dincarslan, Oslem, additional, Dunn, Chris, additional, Dyer, Philip, additional, Elliott, Angela, additional, Evans, Anthony, additional, Finch, Lorna, additional, Fisher, Lewis WS., additional, Foster, Terry, additional, Garcia-Dorival, Isabel, additional, Gunning, Philip, additional, Hartley, Catherine, additional, Jensen, Rebecca L., additional, Jones, Christopher B., additional, Jones, Trevor R., additional, Khandaker, Shadia, additional, King, Katharine, additional, Kiy, Robyn T., additional, Koukorava, Chrysa, additional, Lake, Annette, additional, Lant, Suzannah, additional, Latawiec, Diane, additional, Lavelle-Langham, Lara, additional, Lefteri, Daniella, additional, Lett, Lauren, additional, Livoti, Lucia A., additional, Mancini, Maria, additional, McDonald, Sarah, additional, McEvoy, Laurence, additional, McLauchlan, John, additional, Metelmann, Soeren, additional, Miah, Nahida S., additional, Middleton, Joanna, additional, Mitchell, Joyce, additional, Murphy, Ellen G., additional, Penrice-Randal, Rebekah, additional, Pilgrim, Jack, additional, Prince, Tessa, additional, Reynolds, Will, additional, Ridley, P. Matthew, additional, Sales, Debby, additional, Shaw, Victoria E., additional, Shears, Rebecca K., additional, Small, Benjamin, additional, Subramaniam, Krishanthi S., additional, Szemiel, Agnieska, additional, Taggart, Aislynn, additional, Tanianis-Hughes, Jolanta, additional, Thomas, Jordan, additional, Trochu, Erwan, additional, van Tonder, Libby, additional, Wilcock, Eve, additional, Zhang, J. Eunice, additional, Flaherty, Lisa, additional, Maziere, Nicole, additional, Cass, Emily, additional, Carracedo, Alejandra Doce, additional, Carlucci, Nicola, additional, Holmes, Anthony, additional, Massey, Hannah, additional, Murphy, Lee, additional, McCafferty, Sarah, additional, Clark, Richard, additional, Fawkes, Angie, additional, Morrice, Kirstie, additional, Maclean, Alan, additional, Wrobel, Nicola, additional, Donnelly, Lorna, additional, Coutts, Audrey, additional, Hafezi, Katarzyna, additional, MacGillivray, Louise, additional, Gilchrist, Tammy, additional, Adeniji, Kayode, additional, Agranoff, Daniel, additional, Agwuh, Ken, additional, Ail, Dhiraj, additional, Aldera, Erin L., additional, Alegria, Ana, additional, Allen, Sam, additional, Angus, Brian, additional, Ashish, Abdul, additional, Atkinson, Dougal, additional, Bari, Shahedal, additional, Barlow, Gavin, additional, Barnass, Stella, additional, Barrett, Nicholas, additional, Bassford, Christopher, additional, Basude, Sneha, additional, Baxter, David, additional, Beadsworth, Michael, additional, Bernatoniene, Jolanta, additional, Berridge, John, additional, Berry, Colin, additional, Best, Nicola, additional, Bothma, Pieter, additional, Chadwick, David, additional, Brittain-Long, Robin, additional, Bulteel, Naomi, additional, Burden, Tom, additional, Burtenshaw, Andrew, additional, Caruth, Vikki, additional, Chambler, Duncan, additional, Chee, Nigel, additional, Child, Jenny, additional, Chukkambotla, Srikanth, additional, Clark, Tom, additional, Collini, Paul, additional, Cosgrove, Catherine, additional, Cupitt, Jason, additional, Cutino-Moguel, Maria-Teresa, additional, Dark, Paul, additional, Dawson, Chris, additional, Dervisevic, Samir, additional, Donnison, Phil, additional, Douthwaite, Sam, additional, Drummond, Andrew, additional, DuRand, Ingrid, additional, Dushianthan, Ahilanadan, additional, Dyer, Tristan, additional, Evans, Cariad, additional, Eziefula, Chi, additional, Fegan, Chrisopher, additional, Finn, Adam, additional, Fullerton, Duncan, additional, Garg, Sanjeev, additional, Garg, Atul, additional, Gkrania-Klotsas, Effrossyni, additional, Godden, Jo, additional, Goldsmith, Arthur, additional, Graham, Clive, additional, Hardy, Elaine, additional, Hartshorn, Stuart, additional, Harvey, Daniel, additional, Havalda, Peter, additional, Hawcutt, Daniel B., additional, Hobrok, Maria, additional, Hodgson, Luke, additional, Hormis, Anil, additional, Jacobs, Michael, additional, Jain, Susan, additional, Jennings, Paul, additional, Kaliappan, Agilan, additional, Kasipandian, Vidya, additional, Kegg, Stephen, additional, Kelsey, Michael, additional, Kendall, Jason, additional, Kerrison, Caroline, additional, Kerslake, Ian, additional, Koch, Oliver, additional, Koduri, Gouri, additional, Koshy, George, additional, Laha, Shondipon, additional, Laird, Steven, additional, Larkin, Susan, additional, Leiner, Tamas, additional, Lillie, Patrick, additional, Limb, James, additional, Linnett, Vanessa, additional, Little, Jeff, additional, Lyttle, Mark, additional, MacMahon, Michael, additional, MacNaughton, Emily, additional, Mankregod, Ravish, additional, Masson, Huw, additional, Matovu, Elijah, additional, McCullough, Katherine, additional, McEwen, Ruth, additional, Meda, Manjula, additional, Mills, Gary, additional, Minton, Jane, additional, Mirfenderesky, Mariyam, additional, Mohandas, Kavya, additional, Mok, Quen, additional, Moon, James, additional, Moore, Elinoor, additional, Morgan, Patrick, additional, Morris, Craig, additional, Mortimore, Katherine, additional, Moses, Samuel, additional, Mpenge, Mbiye, additional, Mulla, Rohinton, additional, Murphy, Michael, additional, Nagel, Megan, additional, Nagarajan, Thapas, additional, Nelson, Mark, additional, Norris, Lillian, additional, O’Shea, Matthew K., additional, Otahal, Igor, additional, Ostermann, Marlies, additional, Pais, Mark, additional, Panchatsharam, Selva, additional, Papakonstantinou, Danai, additional, Paraiso, Hassan, additional, Patel, Brij, additional, Pattison, Natalie, additional, Pepperell, Justin, additional, Peters, Mark, additional, Phull, Mandeep, additional, Pintus, Stefania, additional, Pooni, Jagtur Singh, additional, Planche, Tim, additional, Post, Frank, additional, Price, David, additional, Prout, Rachel, additional, Rae, Nikolas, additional, Reschreiter, Henrik, additional, Reynolds, Tim, additional, Richardson, Neil, additional, Roberts, Mark, additional, Roberts, Devender, additional, Rose, Alistair, additional, Rousseau, Guy, additional, Ruge, Bobby, additional, Ryan, Brendan, additional, Saluja, Taranprit, additional, Schmid, Matthias L., additional, Shah, Aarti, additional, Shanmuga, Prad, additional, Sharma, Anil, additional, Shawcross, Anna, additional, Sizer, Jeremy, additional, Shankar-Hari, Manu, additional, Smith, Richard, additional, Snelson, Catherine, additional, Spittle, Nick, additional, Staines, Nikki, additional, Stambach, Tom, additional, Stewart, Richard, additional, Subudhi, Pradeep, additional, Szakmany, Tamas, additional, Tatham, Kate, additional, Thomas, Jo, additional, Thompson, Chris, additional, Thompson, Robert, additional, Tridente, Ascanio, additional, Tupper-Carey, Darell, additional, Twagira, Mary, additional, Vallotton, Nick, additional, Vancheeswaran, Rama, additional, Vincent-Smith, Lisa, additional, Visuvanathan, Shico, additional, Vuylsteke, Alan, additional, Waddy, Sam, additional, Wake, Rachel, additional, Walden, Andrew, additional, Welters, Ingeborg, additional, Whitehouse, Tony, additional, Whittaker, Paul, additional, Whittington, Ashley, additional, Papineni, Padmasayee, additional, Wijesinghe, Meme, additional, Williams, Martin, additional, Wilson, Lawrence, additional, Winchester, Stephen, additional, Wiselka, Martin, additional, Wolverson, Adam, additional, Wootton, Daniel G., additional, Workman, Andrew, additional, Yates, Bryan, additional, and Young, Peter, additional

Published
2022
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33. The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants

Author

Liu, Chang, primary, Zhou, Daming, additional, Nutalai, Rungtiwa, additional, Duyvesteyn, Helen M.E., additional, Tuekprakhon, Aekkachai, additional, Ginn, Helen M., additional, Dejnirattisai, Wanwisa, additional, Supasa, Piyada, additional, Mentzer, Alexander J., additional, Wang, Beibei, additional, Case, James Brett, additional, Zhao, Yuguang, additional, Skelly, Donal T., additional, Chen, Rita E., additional, Johnson, Sile Ann, additional, Ritter, Thomas G., additional, Mason, Chris, additional, Malik, Tariq, additional, Temperton, Nigel, additional, Paterson, Neil G., additional, Williams, Mark A., additional, Hall, David R., additional, Clare, Daniel K., additional, Howe, Andrew, additional, Goulder, Philip J.R., additional, Fry, Elizabeth E., additional, Diamond, Michael S., additional, Mongkolsapaya, Juthathip, additional, Ren, Jingshan, additional, Stuart, David I., additional, and Screaton, Gavin R., additional

Published
2022
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35. Structural basis for outer membrane lipopolysaccharide insertion

Author

Dong, Haohao, Xiang, Quanju, Gu, Yinghong, Wang, Zhongshan, Paterson, Neil G., Stansfeld, Phillip J., He, Chuan, Zhang, Yizheng, Wang, Wenjian, and Dong, Changjiang

Subjects
Drug resistance in microorganisms -- Physiological aspects -- Research, Lipopolysaccharides -- Physiological aspects -- Structure -- Research, Gram-negative bacteria -- Physiological aspects -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Lipopolysaccharide (LPS) is essential for most Gram-negative bacteria and has crucial roles in protection of the bacteria from harsh environments and toxic compounds, including antibiotics. Seven LPS transport proteins (that is, LptA-LptG) form a trans-envelope protein complex responsible for the transport of LPS from the inner membrane to the outer membrane, the mechanism for which is poorly understood. Here we report the first crystal structure of the unique integral membrane LPS translocon LptD-LptE complex. LptD forms a novel 26- stranded β-barrel, which is to our knowledge the largest β-barrel reported so far. LptE adopts a roll-like structure located inside the barrel of LptD to form an unprecedented two-protein 'barrel and plug' architecture. The structure, molecular dynamics simulations and functional assays suggest that the hydrophilic O-antigen and the core oligosaccharide of the LPS may pass through the barrel and the lipid A of the LPS may be inserted into the outer leaflet of the outer membrane through a lateral opening between strands β1 and β26 of LptD. These findings not only help us to understand important aspects of bacterial outer membrane biogenesis, but also have significant potential for the development of novel drugs against multi-drug resistant pathogenic bacteria., All Gram-negative bacteria have an asymmetric outer membrane, in which the inner leaflet consists of phospholipid and the outer leaflet is comprised of lipopolysaccharide (LPS) (1,2). LPS normally has three [...]

Published
2014
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37. Application of In Situ Diffraction in High-Throughput Structure Determination Platforms

Author

Aller, Pierre, primary, Sanchez-Weatherby, Juan, additional, Foadi, James, additional, Winter, Graeme, additional, Lobley, Carina M. C., additional, Axford, Danny, additional, Ashton, Alun W., additional, Bellini, Domenico, additional, Brandao-Neto, Jose, additional, Culurgioni, Simone, additional, Douangamath, Alice, additional, Duman, Ramona, additional, Evans, Gwyndaf, additional, Fisher, Stuart, additional, Flaig, Ralf, additional, Hall, David R., additional, Lukacik, Petra, additional, Mazzorana, Marco, additional, McAuley, Katherine E., additional, Mykhaylyk, Vitaliy, additional, Owen, Robin L., additional, Paterson, Neil G., additional, Romano, Pierpaolo, additional, Sandy, James, additional, Sorensen, Thomas, additional, von Delft, Frank, additional, Wagner, Armin, additional, Warren, Anna, additional, Williams, Mark, additional, Stuart, David I., additional, and Walsh, Martin A., additional

Published
2014
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38. Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum

Author

Liu, Chang, primary, Ginn, Helen M., additional, Dejnirattisai, Wanwisa, additional, Supasa, Piyada, additional, Wang, Beibei, additional, Tuekprakhon, Aekkachai, additional, Nutalai, Rungtiwa, additional, Zhou, Daming, additional, Mentzer, Alexander J., additional, Zhao, Yuguang, additional, Duyvesteyn, Helen M.E., additional, López-Camacho, César, additional, Slon-Campos, Jose, additional, Walter, Thomas S., additional, Skelly, Donal, additional, Johnson, Sile Ann, additional, Ritter, Thomas G., additional, Mason, Chris, additional, Costa Clemens, Sue Ann, additional, Gomes Naveca, Felipe, additional, Nascimento, Valdinete, additional, Nascimento, Fernanda, additional, Fernandes da Costa, Cristiano, additional, Resende, Paola Cristina, additional, Pauvolid-Correa, Alex, additional, Siqueira, Marilda M., additional, Dold, Christina, additional, Temperton, Nigel, additional, Dong, Tao, additional, Pollard, Andrew J., additional, Knight, Julian C., additional, Crook, Derrick, additional, Lambe, Teresa, additional, Clutterbuck, Elizabeth, additional, Bibi, Sagida, additional, Flaxman, Amy, additional, Bittaye, Mustapha, additional, Belij-Rammerstorfer, Sandra, additional, Gilbert, Sarah C., additional, Malik, Tariq, additional, Carroll, Miles W., additional, Klenerman, Paul, additional, Barnes, Eleanor, additional, Dunachie, Susanna J., additional, Baillie, Vicky, additional, Serafin, Natali, additional, Ditse, Zanele, additional, Da Silva, Kelly, additional, Paterson, Neil G., additional, Williams, Mark A., additional, Hall, David R., additional, Madhi, Shabir, additional, Nunes, Marta C., additional, Goulder, Philip, additional, Fry, Elizabeth E., additional, Mongkolsapaya, Juthathip, additional, Ren, Jingshan, additional, Stuart, David I., additional, and Screaton, Gavin R., additional

Published
2021
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39. High-Throughput Crystallography Reveals Boron-Containing Inhibitors of a Penicillin-Binding Protein with Di- and Tricovalent Binding Modes

Author

Newman, Hector, primary, Krajnc, Alen, additional, Bellini, Dom, additional, Eyermann, Charles J., additional, Boyle, Grant A., additional, Paterson, Neil G., additional, McAuley, Katherine E., additional, Lesniak, Robert, additional, Gangar, Mukesh, additional, von Delft, Frank, additional, Brem, Jürgen, additional, Chibale, Kelly, additional, Schofield, Christopher J., additional, and Dowson, Christopher G., additional

Published
2021
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40. The antibody response to SARS-CoV-2 Beta underscores the antigenic distance to other variants

Author

Liu, Chang, Zhou, Daming, Nutalai, Rungtiwa, Duyvesteyn, Helen M.E., Tuekprakhon, Aekkachai, Ginn, Helen M., Dejnirattisai, Wanwisa, Supasa, Piyada, Mentzer, Alexander J., Wang, Beibei, Case, James Brett, Zhao, Yuguang, Skelly, Donal T., Chen, Rita E., Johnson, Sile Ann, Ritter, Thomas G., Mason, Chris, Malik, Tariq, Temperton, Nigel, Paterson, Neil G., Williams, Mark A., Hall, David R., Clare, Daniel K., Howe, Andrew, Goulder, Philip J.R., Fry, Elizabeth E., Diamond, Michael S., Mongkolsapaya, Juthathip, Ren, Jingshan, Stuart, David I., Screaton, Gavin R., Liu, Chang, Zhou, Daming, Nutalai, Rungtiwa, Duyvesteyn, Helen M.E., Tuekprakhon, Aekkachai, Ginn, Helen M., Dejnirattisai, Wanwisa, Supasa, Piyada, Mentzer, Alexander J., Wang, Beibei, Case, James Brett, Zhao, Yuguang, Skelly, Donal T., Chen, Rita E., Johnson, Sile Ann, Ritter, Thomas G., Mason, Chris, Malik, Tariq, Temperton, Nigel, Paterson, Neil G., Williams, Mark A., Hall, David R., Clare, Daniel K., Howe, Andrew, Goulder, Philip J.R., Fry, Elizabeth E., Diamond, Michael S., Mongkolsapaya, Juthathip, Ren, Jingshan, Stuart, David I., and Screaton, Gavin R.

Abstract

Alpha-B.1.1.7, Beta-B.1.351, Gamma-P.1 and Delta-B.1.617.2 variants of SARS-CoV-2 express multiple mutations in the spike protein (S). These may alter the antigenic structure of S, causing escape from natural or vaccine-induced immunity. Beta is particularly difficult to neutralize using serum induced by early pandemic SARS-CoV-2 strains and is most antigenically separated from Delta. To understand this, we generated 674 mAbs from Beta infected individuals and performed a detailed structure-function analysis of the 27 most potent mAbs: one binding the spike N-terminal domain (NTD), the rest the receptor binding domain (RBD). Two of these RBD-binding mAbs recognise a neutralizing epitope conserved between SARS-CoV-1 and -2, whilst 18 target mutated residues in Beta: K417N, E484K, and N501Y. There is a major response to N501Y including a public IgVH4-39 sequence, with E484K and K417N also targeted. Recognition of these key residues underscores why serum from Beta cases poorly neutralizes early pandemic and Delta viruses.

Published
2021

41. Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum

Author

Liu, Chang, Ginn, Helen M., Dejnirattisai, Wanwisa, Supasa, Piyada, Wang, Beibei, Tuekprakhon, Aekkachai, Nutalai, Rungtiwa, Zhou, Daming, Mentzer, Alexander J., Zhao, Yuguang, Duyvesteyn, Helen M.E., López-Camacho, César, Slon-Campos, Jose, Walter, Thomas S., Skelly, Donal, Johnson, Sile Ann, Ritter, Thomas G., Mason, Chris, Costa Clemens, Sue Ann, Naveca, Felipe Gomes, Nascimento, Valdinete, Nascimento, Fernanda, Fernandes da Costa, Cristiano, Resende, Paola Cristina, Pauvolid-Correa, Alex, Siqueira, Marilda M., Dold, Christina, Temperton, Nigel J., Dong, Tao, Pollard, Andrew J., Knight, Julian C., Crook, Derrick, Lambe, Teresa, Clutterbuck, Elizabeth, Bibi, Sagida, Flaxman, Amy, Bittaye, Mustapha, Belij-Rammerstorfer, Sandra, Gilbert, Sarah C., Malik, Tariq, Carroll, Miles W., Klenerman, Paul, Barnes, Eleanor, Dunachie, Susanna J., Baillie, Vicky, Serafin, Natali, Ditse, Zanele, Da Silva, Kelly, Paterson, Neil G., Williams, Mark A., Hall, David R., Madhi, Shabir, Nunes, Marta C., Goulder, Philip, Fry, Elizabeth E., Mongkolsapaya, Juthathip, Ren, Jingshan, Stuart, David I., Screaton, Gavin R., Liu, Chang, Ginn, Helen M., Dejnirattisai, Wanwisa, Supasa, Piyada, Wang, Beibei, Tuekprakhon, Aekkachai, Nutalai, Rungtiwa, Zhou, Daming, Mentzer, Alexander J., Zhao, Yuguang, Duyvesteyn, Helen M.E., López-Camacho, César, Slon-Campos, Jose, Walter, Thomas S., Skelly, Donal, Johnson, Sile Ann, Ritter, Thomas G., Mason, Chris, Costa Clemens, Sue Ann, Naveca, Felipe Gomes, Nascimento, Valdinete, Nascimento, Fernanda, Fernandes da Costa, Cristiano, Resende, Paola Cristina, Pauvolid-Correa, Alex, Siqueira, Marilda M., Dold, Christina, Temperton, Nigel J., Dong, Tao, Pollard, Andrew J., Knight, Julian C., Crook, Derrick, Lambe, Teresa, Clutterbuck, Elizabeth, Bibi, Sagida, Flaxman, Amy, Bittaye, Mustapha, Belij-Rammerstorfer, Sandra, Gilbert, Sarah C., Malik, Tariq, Carroll, Miles W., Klenerman, Paul, Barnes, Eleanor, Dunachie, Susanna J., Baillie, Vicky, Serafin, Natali, Ditse, Zanele, Da Silva, Kelly, Paterson, Neil G., Williams, Mark A., Hall, David R., Madhi, Shabir, Nunes, Marta C., Goulder, Philip, Fry, Elizabeth E., Mongkolsapaya, Juthathip, Ren, Jingshan, Stuart, David I., and Screaton, Gavin R.

Abstract

SARS-CoV-2 has undergone progressive change with variants conferring advantage rapidly becoming dominant lineages e.g. B.1.617. With apparent increased transmissibility variant B.1.617.2 has contributed to the current wave of infection ravaging the Indian subcontinent and has been designated a variant of concern in the UK. Here we study the ability of monoclonal antibodies, convalescent and vaccine sera to neutralize B.1.617.1 and B.1.617.2 and complement this with structural analyses of Fab/RBD complexes and map the antigenic space of current variants. Neutralization of both viruses is reduced when compared with ancestral Wuhan related strains but there is no evidence of widespread antibody escape as seen with B.1.351. However, B.1.351 and P.1 sera showed markedly more reduction in neutralization of B.1.617.2 suggesting that individuals previously infected by these variants may be more susceptible to reinfection by B.1.617.2. This observation provides important new insight for immunisation policy with future variant vaccines in non-immune populations.

Published
2021

42. Antibody evasion by the P.1 strain of SARS-CoV-2

Author

Dejnirattisai, Wanwisa, primary, Zhou, Daming, additional, Supasa, Piyada, additional, Liu, Chang, additional, Mentzer, Alexander J., additional, Ginn, Helen M., additional, Zhao, Yuguang, additional, Duyvesteyn, Helen M.E., additional, Tuekprakhon, Aekkachai, additional, Nutalai, Rungtiwa, additional, Wang, Beibei, additional, López-Camacho, César, additional, Slon-Campos, Jose, additional, Walter, Thomas S., additional, Skelly, Donal, additional, Costa Clemens, Sue Ann, additional, Naveca, Felipe Gomes, additional, Nascimento, Valdinete, additional, Nascimento, Fernanda, additional, Fernandes da Costa, Cristiano, additional, Resende, Paola Cristina, additional, Pauvolid-Correa, Alex, additional, Siqueira, Marilda M., additional, Dold, Christina, additional, Levin, Robert, additional, Dong, Tao, additional, Pollard, Andrew J., additional, Knight, Julian C., additional, Crook, Derrick, additional, Lambe, Teresa, additional, Clutterbuck, Elizabeth, additional, Bibi, Sagida, additional, Flaxman, Amy, additional, Bittaye, Mustapha, additional, Belij-Rammerstorfer, Sandra, additional, Gilbert, Sarah C., additional, Carroll, Miles W., additional, Klenerman, Paul, additional, Barnes, Eleanor, additional, Dunachie, Susanna J., additional, Paterson, Neil G., additional, Williams, Mark A., additional, Hall, David R., additional, Hulswit, Ruben J.G., additional, Bowden, Thomas A., additional, Fry, Elizabeth E., additional, Mongkolsapaya, Juthathip, additional, Ren, Jingshan, additional, Stuart, David I., additional, and Screaton, Gavin R., additional

Published
2021
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43. De novo design of discrete, stable 310-helix peptide assemblies.

Author

Kumar, Prasun, Paterson, Neil G., Clayden, Jonathan, and Woolfson, Derek N.

Abstract

The α-helix is pre-eminent in structural biology1 and widely exploited in protein folding2, design3 and engineering4. Although other helical peptide conformations do exist near to the α-helical region of conformational space—namely, 310-helices and π-helices5—these occur much less frequently in protein structures. Less favourable internal energies and reduced tendencies to pack into higher-order structures mean that 310-helices rarely exceed six residues in length in natural proteins, and that they tend not to form normal supersecondary, tertiary or quaternary interactions. Here we show that despite their absence in nature, synthetic peptide assemblies can be built from 310-helices. We report the rational design, solution-phase characterization and an X-ray crystal structure for water-soluble bundles of 310-helices with consolidated hydrophobic cores. The design uses six-residue repeats informed by analysing 310-helical conformations in known protein structures, and incorporates α-aminoisobutyric acid residues. Design iterations reveal a tipping point between α-helical and 310-helical folding, and identify features required for stabilizing assemblies of 310-helices. This work provides principles and rules to open opportunities for designing into this hitherto unexplored region of protein-structure space.A study demonstrates the rational de novo design of water-soluble assemblies constructed from long 310-helical peptides, and details their characterization by circular dichroism spectroscopy, analytical ultracentrifugation and X-ray crystallography. [ABSTRACT FROM AUTHOR]

Published
2022
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44. Reduced neutralization of SARS-CoV-2 B.1.1.7 variant by convalescent and vaccine sera

Author

Supasa, Piyada, primary, Zhou, Daming, additional, Dejnirattisai, Wanwisa, additional, Liu, Chang, additional, Mentzer, Alexander J., additional, Ginn, Helen M., additional, Zhao, Yuguang, additional, Duyvesteyn, Helen M.E., additional, Nutalai, Rungtiwa, additional, Tuekprakhon, Aekkachai, additional, Wang, Beibei, additional, Paesen, Guido C., additional, Slon-Campos, Jose, additional, López-Camacho, César, additional, Hallis, Bassam, additional, Coombes, Naomi, additional, Bewley, Kevin R., additional, Charlton, Sue, additional, Walter, Thomas S., additional, Barnes, Eleanor, additional, Dunachie, Susanna J., additional, Skelly, Donal, additional, Lumley, Sheila F., additional, Baker, Natalie, additional, Shaik, Imam, additional, Humphries, Holly E., additional, Godwin, Kerry, additional, Gent, Nick, additional, Sienkiewicz, Alex, additional, Dold, Christina, additional, Levin, Robert, additional, Dong, Tao, additional, Pollard, Andrew J., additional, Knight, Julian C., additional, Klenerman, Paul, additional, Crook, Derrick, additional, Lambe, Teresa, additional, Clutterbuck, Elizabeth, additional, Bibi, Sagida, additional, Flaxman, Amy, additional, Bittaye, Mustapha, additional, Belij-Rammerstorfer, Sandra, additional, Gilbert, Sarah, additional, Hall, David R., additional, Williams, Mark A., additional, Paterson, Neil G., additional, James, William, additional, Carroll, Miles W., additional, Fry, Elizabeth E., additional, Mongkolsapaya, Juthathip, additional, Ren, Jingshan, additional, Stuart, David I., additional, and Screaton, Gavin R., additional

Published
2021
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45. The antigenic anatomy of SARS-CoV-2 receptor binding domain

Author

Dejnirattisai, Wanwisa, primary, Zhou, Daming, additional, Ginn, Helen M., additional, Duyvesteyn, Helen M.E., additional, Supasa, Piyada, additional, Case, James Brett, additional, Zhao, Yuguang, additional, Walter, Thomas S., additional, Mentzer, Alexander J., additional, Liu, Chang, additional, Wang, Beibei, additional, Paesen, Guido C., additional, Slon-Campos, Jose, additional, López-Camacho, César, additional, Kafai, Natasha M., additional, Bailey, Adam L., additional, Chen, Rita E., additional, Ying, Baoling, additional, Thompson, Craig, additional, Bolton, Jai, additional, Fyfe, Alex, additional, Gupta, Sunetra, additional, Tan, Tiong Kit, additional, Gilbert-Jaramillo, Javier, additional, James, William, additional, Knight, Michael, additional, Carroll, Miles W., additional, Skelly, Donal, additional, Dold, Christina, additional, Peng, Yanchun, additional, Levin, Robert, additional, Dong, Tao, additional, Pollard, Andrew J., additional, Knight, Julian C., additional, Klenerman, Paul, additional, Temperton, Nigel, additional, Hall, David R., additional, Williams, Mark A., additional, Paterson, Neil G., additional, Bertram, Felicity K.R., additional, Siebert, C. Alistair, additional, Clare, Daniel K., additional, Howe, Andrew, additional, Radecke, Julika, additional, Song, Yun, additional, Townsend, Alain R., additional, Huang, Kuan-Ying A., additional, Fry, Elizabeth E., additional, Mongkolsapaya, Juthathip, additional, Diamond, Michael S., additional, Ren, Jingshan, additional, Stuart, David I., additional, and Screaton, Gavin R., additional

Published
2021
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46. Antibody evasion by the Brazilian P.1 strain of SARS-CoV-2

Author

Dejnirattisai, Wanwisa, primary, Zhou, Daming, additional, Supasa, Piyada, additional, Liu, Chang, additional, Mentzer, Alexander J., additional, Ginn, Helen M., additional, Zhao, Yuguang, additional, Duyvesteyn, Helen M.E., additional, Tuekprakhon, Aekkachai, additional, Nutalai, Rungtiwa, additional, Wang, Beibei, additional, Paesen, Guido C., additional, López-Camacho, César, additional, Slon-Campos, Jose, additional, Walter, Thomas S., additional, Skelly, Donal, additional, Clemens, Sue Ann Costa, additional, Naveca, Felipe Gomes, additional, Nascimento, Valdinete, additional, Nascimento, Fernanda, additional, da Costa, Cristiano Fernandes, additional, Resende, Paola C., additional, Pauvolid-Correa, Alex, additional, Siqueira, Marilda M., additional, Dold, Christina, additional, Levin, Robert, additional, Dong, Tao, additional, Pollard, Andrew J., additional, Knight, Julian C., additional, Crook, Derrick, additional, Lambe, Teresa, additional, Clutterbuck, Elizabeth, additional, Bibi, Sagida, additional, Flaxman, Amy, additional, Bittaye, Mustapha, additional, Belij-Rammerstorfer, Sandra, additional, Gilbert, Sarah, additional, Carroll, Miles W., additional, Klenerman, Paul, additional, Barnes, Eleanor, additional, Dunachie, Susanna J., additional, Paterson, Neil G., additional, Williams, Mark A., additional, Hall, David R., additional, Hulswit, Ruben J. G., additional, Bowden, Thomas A., additional, Fry, Elizabeth E., additional, Mongkolsapaya, Juthathip, additional, Ren, Jingshan, additional, Stuart, David I., additional, and Screaton, Gavin R., additional

Published
2021
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48. Reduced Neutralization of SARS-CoV-2 B.1.1.7 Variant from Naturally Acquired and Vaccine Induced Antibody Immunity

Author

Supasa, Piyada, primary, Zhou, Daming, additional, Dejnirattisai, Wanwisa, additional, Liu, Chang, additional, Mentzer, Alexander J., additional, Ginn, Helen M., additional, Zhao, Yuguang, additional, Duyvesteyn, Helen ME, additional, Nutalai, Rungtiwa, additional, Tuekprakhon, Aekkachai, additional, Wang, Beibei, additional, Paesen, Guido C., additional, Slon-Campos, Jose, additional, Lopez-Camacho, Cesar, additional, Hallis, Bassam, additional, Coombes, Naomi, additional, Bewley, Kevin, additional, Charlton, Sue, additional, Walter, Thomas S., additional, Barnes, Eleanor, additional, Dunachie, Susanna, additional, Skelly, Donal, additional, Lumley, Sheila, additional, Baker, Natalie, additional, Shaik, Imam, additional, Humphries, Holly, additional, Godwin, Kerry, additional, Gent, Nick, additional, Sienkiewicz, Alex, additional, Dold, Christina, additional, Levin, Robert, additional, Dong, Tao, additional, Pollard, Andrew, additional, Knight, Julian, additional, Klenerman, Paul, additional, Crook, Derrick W., additional, Lambe, Teresa, additional, Clutterbuck, Elizabeth, additional, Bibi, Sagida, additional, Flaxman, Amy, additional, Bittaye, Mustapha, additional, Belij-rammerstorfer, Sandra, additional, Gilbert, Sarah C., additional, Hall, David R., additional, Williams, Mark A., additional, Paterson, Neil G., additional, James, William, additional, Carroll, Miles W., additional, Fry, Elizabeth E., additional, Mongkolspaya, Juthathip, additional, Ren, Jingshan, additional, Stuart, David I., additional, and Screaton, Gavin R., additional

Published
2021
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49. Neutralization of SARS-CoV-2 by Destruction of the Prefusion Spike

Author

Huo, Jiandong, primary, Zhao, Yuguang, additional, Ren, Jingshan, additional, Zhou, Daming, additional, Duyvesteyn, Helen M.E., additional, Ginn, Helen M., additional, Carrique, Loic, additional, Malinauskas, Tomas, additional, Ruza, Reinis R., additional, Shah, Pranav N.M., additional, Tan, Tiong Kit, additional, Rijal, Pramila, additional, Coombes, Naomi, additional, Bewley, Kevin R., additional, Tree, Julia A., additional, Radecke, Julika, additional, Paterson, Neil G., additional, Supasa, Piyada, additional, Mongkolsapaya, Juthathip, additional, Screaton, Gavin R., additional, Carroll, Miles, additional, Townsend, Alain, additional, Fry, Elizabeth E., additional, Owens, Raymond J., additional, and Stuart, David I., additional

Published
2020
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50. Structural basis for the neutralization of SARS-CoV-2 by an antibody from a convalescent patient

Author

Zhou, Daming, primary, Duyvesteyn, Helen ME, additional, Chen, Cheng-Pin, additional, Huang, Chung-Guei, additional, Chen, Ting-Hua, additional, Shih, Shin-Ru, additional, Lin, Yi-Chun, additional, Cheng, Chien-Yu, additional, Cheng, Shu-Hsing, additional, Huang, Yhu-Chering, additional, Lin, Tzou-Yien, additional, Ma, Che, additional, Huo, Jiandong, additional, Carrique, Loic, additional, Malinauskas, Tomas, additional, Ruza, Reinis R, additional, Shah, Pranav NM, additional, Tan, Tiong Kit, additional, Rijal, Pramila, additional, Donat, Robert F., additional, Godwin, Kerry, additional, Buttigieg, Karen, additional, Tree, Julia, additional, Radecke, Julika, additional, Paterson, Neil G, additional, Supasa, Piyasa, additional, Mongkolsapaya, Juthathip, additional, Screaton, Gavin R, additional, Carroll, Miles W., additional, Jaramillo, Javier G., additional, Knight, Michael, additional, James, William, additional, Owens, Raymond J, additional, Naismith, James H., additional, Townsend, Alain, additional, Fry, Elizabeth E, additional, Zhao, Yuguang, additional, Ren, Jingshan, additional, Stuart, David I, additional, and Huang, Kuan-Ying A., additional

Published
2020
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