Christopher O. Barnes

All Publications

• Vaccine design via antigen reorientation. Nature chemical biology Xu, D., Carter, J. J., Li, C., Utz, A., Weidenbacher, P. A., Tang, S., Sanyal, M., Pulendran, B., Barnes, C. O., Kim, P. S. 2024

  Abstract

  A major challenge in creating universal influenza vaccines is to focus immune responses away from the immunodominant, variable head region of hemagglutinin (HA-head) and toward the evolutionarily conserved stem region (HA-stem). Here we introduce an approach to control antigen orientation via site-specific insertion of aspartate residues that facilitates antigen binding to alum. We demonstrate the generalizability of this approach with antigens from Ebola, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza viruses and observe enhanced neutralizing antibody responses in all cases. We then reorient an H2 HA in an 'upside-down' configuration to increase the exposure and immunogenicity of HA-stem. The reoriented H2 HA (reoH2HA) on alum induced stem-directed antibodies that cross-react with both group 1 and group 2 influenza A subtypes. Electron microscopy polyclonal epitope mapping (EMPEM) revealed that reoH2HA (group 1) elicits cross-reactive antibodies targeting group 2 HA-stems. Our results highlight antigen reorientation as a generalizable approach for designing epitope-focused vaccines.

  View details for DOI 10.1038/s41589-023-01529-6

  View details for PubMedID 38225471

  View details for PubMedCentralID 9345323

• Structural basis of transcription: RNA Polymerase II substrate binding and metal coordination at 3.0 A using a free-electron laser. bioRxiv : the preprint server for biology Lin, G., Barnes, C. O., Weiss, S., Dutagaci, B., Qiu, C., Feig, M., Song, J., Lyubimov, A., Cohen, A. E., Kaplan, C. D., Calero, G. 2023

  Abstract

  Catalysis and translocation of multi-subunit DNA-directed RNA polymerases underlie all cellular mRNA synthesis. RNA polymerase II (Pol II) synthesizes eukaryotic pre-mRNAs from a DNA template strand buried in its active site. Structural details of catalysis at near atomic resolution and precise arrangement of key active site components have been elusive. Here we present the free electron laser (FEL) structure of a matched ATP-bound Pol II, revealing the full active site interaction network at the highest resolution to date, including the trigger loop (TL) in the closed conformation, bonafide occupancy of both site A and B Mg2+, and a putative third (site C) Mg2+ analogous to that described for some DNA polymerases but not observed previously for cellular RNA polymerases. Molecular dynamics (MD) simulations of the structure indicate that the third Mg2+ is coordinated and stabilized at its observed position. TL residues provide half of the substrate binding pocket while multiple TL/bridge helix (BH) interactions induce conformational changes that could propel translocation upon substrate hydrolysis. Consistent with TL/BH communication, a FEL structure and MD simulations of the hyperactive Rpb1 T834P bridge helix mutant reveals rearrangement of some active site interactions supporting potential plasticity in active site function and long-distance effects on both the width of the central channel and TL conformation, likely underlying its increased elongation rate at the expense of fidelity.

  View details for DOI 10.1101/2023.09.22.559052

  View details for PubMedID 37790421

• Juneteenth in STEMM and the barriers to equitable science. Cell Mays, A., Byars-Winston, A., Hinton, A., Marshall, A. G., Kirabo, A., August, A., Marlin, B. J., Riggs, B., Tolbert, B., Wanjalla, C., Womack, C., Evans, C. S., Barnes, C., Starbird, C., Williams, C., Reynolds, C., Taabazuing, C., Cameron, C. E., Murray, D. D., Applewhite, D., Morton, D. J., Lee, D., Williams, D. W., Lynch, D., Brady, D., Lynch, E., Rutaganira, F. U., Silva, G. M., Shuler, H., Saboor, I. A., Davis, J., Dzirasa, K., Hammonds-Odie, L., Reyes, L., Sweetwyne, M. T., McReynolds, M. R., Johnson, M. D., Smith, N. A., Pittman, N., Ajijola, O. A., Smith, Q., Robinson, R. A., Lewis, S. C., Murray, S. A., Black, S., Neal, S. E., Andrisse, S., Townsend, S., Damo, S. M., Griffith, T. N., Lambert, W. M., Clemons, W. M. 2023; 186 (12): 2510-2517

  Abstract

  We are 52 Black scientists. Here, we establish the context of Juneteenth in STEMM and discuss the barriers Black scientists face, the struggles they endure, and the lack of recognition they receive. We review racism's history in science and provide institutional-level solutions to reduce the burdens on Black scientists.

  View details for DOI 10.1016/j.cell.2023.05.016

  View details for PubMedID 37295396

• Pan-sarbecovirus prophylaxis with human anti-ACE2 monoclonal antibodies. Nature microbiology Zhang, F., Jenkins, J., de Carvalho, R. V., Nakandakari-Higa, S., Chen, T., Abernathy, M. E., Baharani, V. A., Nyakatura, E. K., Andrew, D., Lebedeva, I. V., Lorenz, I. C., Hoffmann, H. H., Rice, C. M., Victora, G. D., Barnes, C. O., Hatziioannou, T., Bieniasz, P. D. 2023

  Abstract

  Human monoclonal antibodies (mAbs) that target the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein have been isolated from convalescent individuals and developed into therapeutics for SARS-CoV-2 infection. However, therapeutic mAbs for SARS-CoV-2 have been rendered obsolete by the emergence of mAb-resistant virus variants. Here we report the generation of a set of six human mAbs that bind the human angiotensin-converting enzyme-2 (hACE2) receptor, rather than the SARS-CoV-2 spike protein. We show that these antibodies block infection by all hACE2 binding sarbecoviruses tested, including SARS-CoV-2 ancestral, Delta and Omicron variants at concentrations of ~7-100 ng ml-1. These antibodies target an hACE2 epitope that binds to the SARS-CoV-2 spike, but they do not inhibit hACE2 enzymatic activity nor do they induce cell-surface depletion of hACE2. They have favourable pharmacology, protect hACE2 knock-in mice against SARS-CoV-2 infection and should present a high genetic barrier to the acquisition of resistance. These antibodies should be useful prophylactic and treatment agents against any current or future SARS-CoV-2 variants and might be useful to treat infection with any hACE2-binding sarbecoviruses that emerge in the future.

  View details for DOI 10.1038/s41564-023-01389-9

  View details for PubMedID 37188812

  View details for PubMedCentralID 8152891

• Human neutralizing antibodies to cold linear epitopes and subdomain 1 of the SARS-CoV-2 spike glycoprotein. Science immunology Bianchini, F., Crivelli, V., Abernathy, M. E., Guerra, C., Palus, M., Muri, J., Marcotte, H., Piralla, A., Pedotti, M., De Gasparo, R., Simonelli, L., Matkovic, M., Toscano, C., Biggiogero, M., Calvaruso, V., Svoboda, P., Cervantes Rincon, T., Fava, T., Podesvova, L., Shanbhag, A. A., Celoria, A., Sgrignani, J., Stefanik, M., Honig, V., Pranclova, V., Michalcikova, T., Prochazka, J., Guerrini, G., Mehn, D., Ciabattini, A., Abolhassani, H., Jarrossay, D., Uguccioni, M., Medaglini, D., Pan-Hammarstrom, Q., Calzolai, L., Fernandez, D., Baldanti, F., Franzetti-Pellanda, A., Garzoni, C., Sedlacek, R., Ruzek, D., Varani, L., Cavalli, A., Barnes, C. O., Robbiani, D. F. 2023: eade0958

  Abstract

  Emergence of SARS-CoV-2 variants diminishes the efficacy of vaccines and antiviral monoclonal antibodies. Continued development of immunotherapies and vaccine immunogens resilient to viral evolution is therefore necessary. Using coldspot-guided antibody discovery, a screening approach that focuses on portions of the virus spike glycoprotein that are both functionally relevant and averse to change, we identified human neutralizing antibodies to highly conserved viral epitopes. Antibody fp.006 binds the fusion peptide and cross-reacts against coronaviruses of the four genera, including the nine human coronaviruses, through recognition of a conserved motif that includes the S2 site of proteolytic cleavage. Antibody hr2.016 targets the stem helix and neutralizes SARS-CoV-2 variants. Antibody sd1.040 binds to subdomain 1, synergizes with antibody rbd.042 for neutralization and, like fp.006 and hr2.016, protects mice expressing human ACE2 against infection when present as bispecific antibody. Thus, coldspot-guided antibody discovery reveals donor-derived neutralizing antibodies that are cross-reactive with Orthocoronavirinae, including SARS-CoV-2 variants.

  View details for DOI 10.1126/sciimmunol.ade0958

  View details for PubMedID 36701425

• Human neutralizing antibodies to cold linear epitopes and to subdomain 1 of SARS-CoV-2. bioRxiv : the preprint server for biology Bianchini, F., Crivelli, V., Abernathy, M. E., Guerra, C., Palus, M., Muri, J., Marcotte, H., Piralla, A., Pedotti, M., De Gasparo, R., Simonelli, L., Matkovic, M., Toscano, C., Biggiogero, M., Calvaruso, V., Svoboda, P., Rincón, T. C., Fava, T., Podešvová, L., Shanbhag, A. A., Celoria, A., Sgrignani, J., Stefanik, M., Hönig, V., Pranclova, V., Michalcikova, T., Prochazka, J., Guerrini, G., Mehn, D., Ciabattini, A., Abolhassani, H., Jarrossay, D., Uguccioni, M., Medaglini, D., Pan-Hammarström, Q., Calzolai, L., Fernandez, D., Baldanti, F., Franzetti-Pellanda, A., Garzoni, C., Sedlacek, R., Ruzek, D., Varani, L., Cavalli, A., Barnes, C. O., Robbiani, D. F. 2022

  Abstract

  Emergence of SARS-CoV-2 variants diminishes the efficacy of vaccines and antiviral monoclonal antibodies. Continued development of immunotherapies and vaccine immunogens resilient to viral evolution is therefore necessary. Using coldspot-guided antibody discovery, a screening approach that focuses on portions of the virus spike that are both functionally relevant and averse to change, we identified human neutralizing antibodies to highly conserved viral epitopes. Antibody fp.006 binds the fusion peptide and cross-reacts against coronaviruses of the four genera , including the nine human coronaviruses, through recognition of a conserved motif that includes the S2' site of proteolytic cleavage. Antibody hr2.016 targets the stem helix and neutralizes SARS-CoV-2 variants. Antibody sd1.040 binds to subdomain 1, synergizes with antibody rbd.042 for neutralization and, like fp.006 and hr2.016, protects mice when present as bispecific antibody. Thus, coldspot-guided antibody discovery reveals donor-derived neutralizing antibodies that are cross-reactive with Orthocoronavirinae , including SARS-CoV-2 variants.Broadly cross-reactive antibodies that protect from SARS-CoV-2 variants are revealed by virus coldspot-driven discovery.

  View details for DOI 10.1101/2022.11.24.515932

  View details for PubMedID 36482967

  View details for PubMedCentralID PMC9727766

• HIV-1 CD4-binding site germline antibody-Env structures inform vaccine design. Nature communications Dam, K. A., Barnes, C. O., Gristick, H. B., Schoofs, T., Gnanapragasam, P. N., Nussenzweig, M. C., Bjorkman, P. J. 2022; 13 (1): 6123

  Abstract

  BG24, a VRC01-class broadly neutralizing antibody (bNAb) against HIV-1 Env with relatively few somatic hypermutations (SHMs), represents a promising target for vaccine strategies to elicit CD4-binding site (CD4bs) bNAbs. To understand how SHMs correlate with BG24 neutralization of HIV-1, we report 4.1 A and 3.4 A single-particle cryo-EM structures of two inferred germline (iGL) BG24 precursors complexed with engineered Env-based immunogens lacking CD4bs N-glycans. Structures reveal critical Env contacts by BG24iGL and identify antibody light chain structural features that impede Env recognition. In addition, biochemical data and cryo-EM structures of BG24iGL variants bound to Envs with CD4bs glycans present provide insights into N-glycan accommodation, including structural modes of light chain adaptations in the presence of the N276gp120 glycan. Together, these findings reveal Env regions critical for germline antibody recognition and potential sites to alter in immunogen design.

  View details for DOI 10.1038/s41467-022-33860-2

  View details for PubMedID 36253376

• A naturally arising broad and potent CD4-binding site antibody with low somatic mutation SCIENCE ADVANCES Barnes, C. O., Schoofs, T., Gnanapragasam, P. P., Golijanin, J., Huey-Tubman, K. E., Gruell, H., Schommers, P., Suh-Toma, N., Lee, Y., Lorenzi, J., Piechocka-Trocha, A., Scheid, J. F., Jr, A., Walker, B. D., Seaman, M. S., Klein, F., Nussenzweig, M. C., Bjorkman, P. J. 2022; 8 (32): eabp8155

  Abstract

  The induction of broadly neutralizing antibodies (bNAbs) is a potential strategy for a vaccine against HIV-1. However, most bNAbs exhibit features such as unusually high somatic hypermutation, including insertions and deletions, which make their induction challenging. VRC01-class bNAbs not only exhibit extraordinary breadth and potency but also rank among the most highly somatically mutated bNAbs. Here, we describe a VRC01-class antibody isolated from a viremic controller, BG24, that is much less mutated than most relatives of its class while achieving comparable breadth and potency. A 3.8-Å x-ray crystal structure of a BG24-BG505 Env trimer complex revealed conserved contacts at the gp120 interface characteristic of the VRC01-class Abs, despite lacking common CDR3 sequence motifs. The existence of moderately mutated CD4-binding site (CD4bs) bNAbs such as BG24 provides a simpler blueprint for CD4bs antibody induction by a vaccine, raising the prospect that such an induction might be feasible with a germline-targeting approach.

  View details for DOI 10.1126/sciadv.abp8155

  View details for Web of Science ID 000841491100026

  View details for PubMedID 35960796

  View details for PubMedCentralID PMC9374330

• Antibody-mediated neutralization of SARS-CoV-2. Immunity Gruell, H., Vanshylla, K., Weber, T., Barnes, C. O., Kreer, C., Klein, F. 2022

  Abstract

  Neutralizing antibodies can block infection, clear pathogens, and are essential to provide long-term immunity. Since the onset of the pandemic, SARS-CoV-2 neutralizing antibodies have been comprehensively investigated and critical information on their development, function, and potential use to prevent and treat COVID-19 have been revealed. With the emergence of SARS-CoV-2 immune escape variants, humoral immunity is being challenged, and a detailed understanding of neutralizing antibodies is essential to guide vaccine design strategies as well as antibody-mediated therapies. In this review, we summarize some of the key findings on SARS-CoV-2 neutralizing antibodies, with a focus on their clinical application.

  View details for DOI 10.1016/j.immuni.2022.05.005

  View details for PubMedID 35623355

• Analysis of memory B cells identifies conserved neutralizing epitopes on the N-terminal domain of variant SARS-Cov-2 spike proteins. Immunity Wang, Z., Muecksch, F., Cho, A., Gaebler, C., Hoffmann, H., Ramos, V., Zong, S., Cipolla, M., Johnson, B., Schmidt, F., DaSilva, J., Bednarski, E., Ben Tanfous, T., Raspe, R., Yao, K., Lee, Y. E., Chen, T., Turroja, M., Milard, K. G., Dizon, J., Kaczynska, A., Gazumyan, A., Oliveira, T. Y., Rice, C. M., Caskey, M., Bieniasz, P. D., Hatziioannou, T., Barnes, C. O., Nussenzweig, M. C. 2022

  Abstract

  SARS-CoV-2 infection or vaccination produces neutralizing antibody responses that contribute to better clinical outcomes. The receptor-binding domain (RBD) and the N-terminal domain (NTD) of the spike trimer (S)constitute the two major neutralizing targets for antibodies. Here, we use NTD-specific probes to capture anti-NTD memory B cells in a longitudinal cohort of infected individuals, some of whom were vaccinated. We found 6 complementation groups of neutralizing antibodies. 58% targeted epitopes outside the NTD supersite, 58% neutralized either Gamma or Omicron, and 14% were broad neutralizers that also neutralized Omicron. Structural characterization revealed that broadly active antibodies targeted three epitopes outside the NTD supersite including a class that recognized both the NTD and SD2 domain. Rapid recruitment of memory B cells producing these antibodies into the plasma cell compartment upon re-infection likely contributes to the relatively benign course of subsequent infections with SARS-CoV-2 variants, including Omicron.

  View details for DOI 10.1016/j.immuni.2022.04.003

  View details for PubMedID 35447092

• Structural insights into antibody-mediated neutralization of SARS-CoV-2 Barnes, C., Scheid, J. F., Eraslan, B., Hudak, A., Muecksch, F., Weisblum, Y., Bjorkman, P. J., Xavier, R. J. OXFORD UNIV PRESS INC. 2021: 1696-1697

  View details for Web of Science ID 000754737200053

• Sequential immunization of macaques elicits heterologous neutralizing antibodies targeting the V3-glycan patch of HIV-1 Env SCIENCE TRANSLATIONAL MEDICINE Escolano, A., Gristick, H. B., Gautam, R., DeLaitsch, A. T., Abernathy, M. E., Yang, Z., Wang, H., Hoffmann, M. G., Nishimura, Y., Wang, Z., Koranda, N., Kakutani, L. M., Gao, H., Gnanapragasam, P. P., Raina, H., Gazumyan, A., Cipolla, M., Oliveira, T. Y., Ramos, V., Irvine, D. J., Silva, M., Jr, A., Keeffe, J. R., Barnes, C. O., Seaman, M. S., Nussenzweig, M. C., Martin, M. A., Bjorkman, P. J. 2021; 13 (621): eabk1533

  Abstract

  [Figure: see text].

  View details for DOI 10.1126/scitranslmed.abk1533

  View details for Web of Science ID 000722202500007

  View details for PubMedID 34818054

• Broad cross-reactivity across sarbecoviruses exhibited by a subset of COVID-19 donor-derived neutralizing antibodies CELL REPORTS Jette, C. A., Cohen, A. A., Gnanapragasam, P. P., Muecksch, F., Lee, Y. E., Huey-Tubman, K. E., Schmidt, F., Hatziioannou, T., Bieniasz, P. D., Nussenzweig, M. C., West, A. P., Keeffe, J. R., Bjorkman, P. J., Barnes, C. O. 2021; 36 (13)

  Abstract

  Many anti-SARS-CoV-2 neutralizing antibodies target the ACE2-binding site on viral spike receptor-binding domains (RBDs). The most potent antibodies recognize exposed variable epitopes, often rendering them ineffective against other sarbecoviruses and SARS-CoV-2 variants. Class 4 anti-RBD antibodies against a less-exposed, but more-conserved, cryptic epitope could recognize newly-emergent zoonotic sarbecoviruses and variants, but usually show only weak neutralization potencies. We characterized two class 4 anti-RBD antibodies derived from COVID-19 donors that exhibited broad recognition and potent neutralization of zoonotic coronavirus and SARS-CoV-2 variants. C118-RBD and C022-RBD structures revealed CDRH3 mainchain H-bond interactions that extended an RBD β-sheet, thus reducing sensitivity to RBD sidechain changes, and epitopes that extended from the cryptic epitope to occlude ACE2 binding. A C118-spike trimer structure revealed rotated RBDs to allow cryptic epitope access and the potential for intra-spike crosslinking to increase avidity. These studies facilitate vaccine design and illustrate potential advantages of class 4 RBD-binding antibody therapeutics.

  View details for DOI 10.1016/j.celrep.2021.109760

  View details for Web of Science ID 000704199700012

  View details for PubMedID 33948592

  View details for PubMedCentralID PMC8095199

• Naturally enhanced neutralizing breadth against SARS-CoV-2 one year after infection. Nature Wang, Z., Muecksch, F., Schaefer-Babajew, D., Finkin, S., Viant, C., Gaebler, C., Hoffmann, H. H., Barnes, C. O., Cipolla, M., Ramos, V., Oliveira, T. Y., Cho, A., Schmidt, F., da Silva, J., Bednarski, E., Aguado, L., Yee, J., Daga, M., Turroja, M., Millard, K. G., Jankovic, M., Gazumyan, A., Zhao, Z., Rice, C. M., Bieniasz, P. D., Caskey, M., Hatziioannou, T., Nussenzweig, M. C. 2021

  Abstract

  Over one year after its inception, the coronavirus disease-2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) remains difficult to control despite the availability of several excellent vaccines. Progress in controlling the pandemic is slowed by the emergence of variants that appear to be more transmissible and more resistant to antibodies1,2. Here we report on a cohort of 63 COVID-19-convalescent individuals assessed at 1.3, 6.2 and 12 months after infection, 41% of whom also received mRNA vaccines3,4. In the absence of vaccination antibody reactivity to the receptor binding domain (RBD) of SARS-CoV-2, neutralizing activity and the number of RBD-specific memory B cells remain relatively stable from 6 to 12 months. Vaccination increases all components of the humoral response, and as expected, results in serum neutralizing activities against variants of concern that are comparable to or greater than neutralizing activity against the original Wuhan Hu-1 achieved by vaccination of naive individuals2,5-8. The mechanism underlying these broad-based responses involves ongoing antibody somatic mutation, memory B cell clonal turnover, and development of monoclonal antibodies that are exceptionally resistant to SARS-CoV-2 RBD mutations, including those found in variants of concern4,9. In addition, B cell clones expressing broad and potent antibodies are selectively retained in the repertoire over time and expand dramatically after vaccination. The data suggest that immunity in convalescent individuals will be very long lasting and that convalescent individuals who receive available mRNA vaccines will produce antibodies and memory B cells that should be protective against circulating SARS-CoV-2 variants.

  View details for DOI 10.1038/s41586-021-03696-9

  View details for PubMedID 34126625

• B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV. Cell Scheid, J. F., Barnes, C. O., Eraslan, B., Hudak, A., Keeffe, J. R., Cosimi, L. A., Brown, E. M., Muecksch, F., Weisblum, Y., Zhang, S., Delorey, T., Woolley, A. E., Ghantous, F., Park, S. M., Phillips, D., Tusi, B., Huey-Tubman, K. E., Cohen, A. A., Gnanapragasam, P. N., Rzasa, K., Hatziioanno, T., Durney, M. A., Gu, X., Tada, T., Landau, N. R., West, A. P., Rozenblatt-Rosen, O., Seaman, M. S., Baden, L. R., Graham, D. B., Deguine, J., Bieniasz, P. D., Regev, A., Hung, D., Bjorkman, P. J., Xavier, R. J. 2021; 184 (12): 3205-3221.e24

  Abstract

  Monoclonal antibodies (mAbs) are a focus in vaccine and therapeutic design to counteract severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants. Here, we combined B cell sorting with single-cell VDJ and RNA sequencing (RNA-seq) and mAb structures to characterize B cell responses against SARS-CoV-2. We show that the SARS-CoV-2-specific B cell repertoire consists of transcriptionally distinct B cell populations with cells producing potently neutralizing antibodies (nAbs) localized in two clusters that resemble memory and activated B cells. Cryo-electron microscopy structures of selected nAbs from these two clusters complexed with SARS-CoV-2 spike trimers show recognition of various receptor-binding domain (RBD) epitopes. One of these mAbs, BG10-19, locks the spike trimer in a closed conformation to potently neutralize SARS-CoV-2, the recently arising mutants B.1.1.7 and B.1.351, and SARS-CoV and cross-reacts with heterologous RBDs. Together, our results characterize transcriptional differences among SARS-CoV-2-specific B cells and uncover cross-neutralizing Ab targets that will inform immunogen and therapeutic design against coronaviruses.

  View details for DOI 10.1016/j.cell.2021.04.032

  View details for PubMedID 34015271

  View details for PubMedCentralID PMC8064835

• mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants. Nature Wang, Z., Schmidt, F., Weisblum, Y., Muecksch, F., Barnes, C. O., Finkin, S., Schaefer-Babajew, D., Cipolla, M., Gaebler, C., Lieberman, J. A., Oliveira, T. Y., Yang, Z., Abernathy, M. E., Huey-Tubman, K. E., Hurley, A., Turroja, M., West, K. A., Gordon, K., Millard, K. G., Ramos, V., Da Silva, J., Xu, J., Colbert, R. A., Patel, R., Dizon, J., Unson-O'Brien, C., Shimeliovich, I., Gazumyan, A., Caskey, M., Bjorkman, P. J., Casellas, R., Hatziioannou, T., Bieniasz, P. D., Nussenzweig, M. C. 2021; 592 (7855): 616-622

  Abstract

  Here we report on the antibody and memory B cell responses of a cohort of 20 volunteers who received the Moderna (mRNA-1273) or Pfizer-BioNTech (BNT162b2) vaccine against SARS-CoV-21-4. Eight weeks after the second injection of vaccine, volunteers showed high levels of IgM and IgG anti-SARS-CoV-2 spike protein (S) and receptor-binding-domain (RBD) binding titre. Moreover, the plasma neutralizing activity and relative numbers of RBD-specific memory B cells of vaccinated volunteers were equivalent to those of individuals who had recovered from natural infection5,6. However, activity against SARS-CoV-2 variants that encode E484K-, N501Y- or K417N/E484K/N501-mutant S was reduced by a small-but significant-margin. The monoclonal antibodies elicited by the vaccines potently neutralize SARS-CoV-2, and target a number of different RBD epitopes in common with monoclonal antibodies isolated from infected donors5-8. However, neutralization by 14 of the 17 most-potent monoclonal antibodies that we tested was reduced or abolished by the K417N, E484K or N501Y mutation. Notably, these mutations were selected when we cultured recombinant vesicular stomatitis virus expressing SARS-CoV-2 S in the presence of the monoclonal antibodies elicited by the vaccines. Together, these results suggest that the monoclonal antibodies in clinical use should be tested against newly arising variants, and that mRNA vaccines may need to be updated periodically to avoid a potential loss of clinical efficacy.

  View details for DOI 10.1038/s41586-021-03324-6

  View details for PubMedID 33567448

• Mosaic nanoparticles elicit cross-reactive immune responses to zoonotic coronaviruses in mice. Science (New York, N.Y.) Cohen, A. A., Gnanapragasam, P. N., Lee, Y. E., Hoffman, P. R., Ou, S., Kakutani, L. M., Keeffe, J. R., Wu, H. J., Howarth, M., West, A. P., Barnes, C. O., Nussenzweig, M. C., Bjorkman, P. J. 2021; 371 (6530): 735-741

  Abstract

  Protection against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and SARS-related emergent zoonotic coronaviruses is urgently needed. We made homotypic nanoparticles displaying the receptor binding domain (RBD) of SARS-CoV-2 or co-displaying SARS-CoV-2 RBD along with RBDs from animal betacoronaviruses that represent threats to humans (mosaic nanoparticles with four to eight distinct RBDs). Mice immunized with RBD nanoparticles, but not soluble antigen, elicited cross-reactive binding and neutralization responses. Mosaic RBD nanoparticles elicited antibodies with superior cross-reactive recognition of heterologous RBDs relative to sera from immunizations with homotypic SARS-CoV-2-RBD nanoparticles or COVID-19 convalescent human plasmas. Moreover, after priming, sera from mosaic RBD-immunized mice neutralized heterologous pseudotyped coronaviruses as well as or better than sera from homotypic SARS-CoV-2-RBD nanoparticle immunizations, demonstrating no loss of immunogenicity against particular RBDs resulting from co-display. A single immunization with mosaic RBD nanoparticles provides a potential strategy to simultaneously protect against SARS-CoV-2 and emerging zoonotic coronaviruses.

  View details for DOI 10.1126/science.abf6840

  View details for PubMedID 33436524

  View details for PubMedCentralID PMC7928838

• De novo design of potent and resilient hACE2 decoys to neutralize SARS-CoV-2. Science (New York, N.Y.) Linsky, T. W., Vergara, R., Codina, N., Nelson, J. W., Walker, M. J., Su, W., Barnes, C. O., Hsiang, T. Y., Esser-Nobis, K., Yu, K., Reneer, Z. B., Hou, Y. J., Priya, T., Mitsumoto, M., Pong, A., Lau, U. Y., Mason, M. L., Chen, J., Chen, A., Berrocal, T., Peng, H., Clairmont, N. S., Castellanos, J., Lin, Y. R., Josephson-Day, A., Baric, R. S., Fuller, D. H., Walkey, C. D., Ross, T. M., Swanson, R., Bjorkman, P. J., Gale, M., Blancas-Mejia, L. M., Yen, H. L., Silva, D. A. 2020; 370 (6521): 1208-1214

  Abstract

  We developed a de novo protein design strategy to swiftly engineer decoys for neutralizing pathogens that exploit extracellular host proteins to infect the cell. Our pipeline allowed the design, validation, and optimization of de novo human angiotensin-converting enzyme 2 (hACE2) decoys to neutralize severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The best monovalent decoy, CTC-445.2, bound with low nanomolar affinity and high specificity to the receptor-binding domain (RBD) of the spike protein. Cryo-electron microscopy (cryo-EM) showed that the design is accurate and can simultaneously bind to all three RBDs of a single spike protein. Because the decoy replicates the spike protein target interface in hACE2, it is intrinsically resilient to viral mutational escape. A bivalent decoy, CTC-445.2d, showed ~10-fold improvement in binding. CTC-445.2d potently neutralized SARS-CoV-2 infection of cells in vitro, and a single intranasal prophylactic dose of decoy protected Syrian hamsters from a subsequent lethal SARS-CoV-2 challenge.

  View details for DOI 10.1126/science.abe0075

  View details for PubMedID 33154107

  View details for PubMedCentralID PMC7920261

• SARS-CoV-2 neutralizing antibody structures inform therapeutic strategies. Nature Barnes, C. O., Jette, C. A., Abernathy, M. E., Dam, K. A., Esswein, S. R., Gristick, H. B., Malyutin, A. G., Sharaf, N. G., Huey-Tubman, K. E., Lee, Y. E., Robbiani, D. F., Nussenzweig, M. C., West, A. P., Bjorkman, P. J. 2020; 588 (7839): 682-687

  Abstract

  The coronavirus disease 2019 (COVID-19) pandemic presents an urgent health crisis. Human neutralizing antibodies that target the host ACE2 receptor-binding domain (RBD) of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike protein1-5 show promise therapeutically and are being evaluated clinically6-8. Here, to identify the structural correlates of SARS-CoV-2 neutralization, we solved eight new structures of distinct COVID-19 human neutralizing antibodies5 in complex with the SARS-CoV-2 spike trimer or RBD. Structural comparisons allowed us to classify the antibodies into categories: (1) neutralizing antibodies encoded by the VH3-53 gene segment with short CDRH3 loops that block ACE2 and bind only to 'up' RBDs; (2) ACE2-blocking neutralizing antibodies that bind both up and 'down' RBDs and can contact adjacent RBDs; (3) neutralizing antibodies that bind outside the ACE2 site and recognize both up and down RBDs; and (4) previously described antibodies that do not block ACE2 and bind only to up RBDs9. Class 2 contained four neutralizing antibodies with epitopes that bridged RBDs, including a VH3-53 antibody that used a long CDRH3 with a hydrophobic tip to bridge between adjacent down RBDs, thereby locking the spike into a closed conformation. Epitope and paratope mapping revealed few interactions with host-derived N-glycans and minor contributions of antibody somatic hypermutations to epitope contacts. Affinity measurements and mapping of naturally occurring and in vitro-selected spike mutants in 3D provided insight into the potential for SARS-CoV-2 to escape from antibodies elicited during infection or delivered therapeutically. These classifications and structural analyses provide rules for assigning current and future human RBD-targeting antibodies into classes, evaluating avidity effects and suggesting combinations for clinical use, and provide insight into immune responses against SARS-CoV-2.

  View details for DOI 10.1038/s41586-020-2852-1

  View details for PubMedID 33045718

  View details for PubMedCentralID PMC8092461

• A broadly neutralizing macaque monoclonal antibody against the HIV-1 V3-Glycan patch. eLife Wang, Z., Barnes, C. O., Gautam, R., Cetrulo Lorenzi, J. C., Mayer, C. T., Oliveira, T. Y., Ramos, V., Cipolla, M., Gordon, K. M., Gristick, H. B., West, A. P., Nishimura, Y., Raina, H., Seaman, M. S., Gazumyan, A., Martin, M., Bjorkman, P. J., Nussenzweig, M. C., Escolano, A. 2020; 9

  Abstract

  A small fraction of HIV-1- infected humans develop broadly neutralizing antibodies (bNAbs) against HIV-1 that protect macaques from simian immunodeficiency HIV chimeric virus (SHIV). Similarly, a small number of macaques infected with SHIVs develop broadly neutralizing serologic activity, but less is known about the nature of simian antibodies. Here, we report on a monoclonal antibody, Ab1485, isolated from a macaque infected with SHIVAD8 that developed broadly neutralizing serologic activity targeting the V3-glycan region of HIV-1 Env. Ab1485 neutralizes 38.1% of HIV-1 isolates in a 42-pseudovirus panel with a geometric mean IC50 of 0.055 µg/mLl and SHIVAD8 with an IC50 of 0.028 µg/mLl. Ab1485 binds the V3-glycan epitope in a glycan-dependent manner. A 3.5 Å cryo-electron microscopy structure of Ab1485 in complex with a native-like SOSIP Env trimer showed conserved contacts with the N332gp120 glycan and gp120 GDIR peptide motif, but in a distinct Env-binding orientation relative to human V3/N332gp120 glycan-targeting bNAbs. Intravenous infusion of Ab1485 protected macaques from a high dose challenge with SHIVAD8. We conclude that macaques can develop bNAbs against the V3-glycan patch that resemble human V3-glycan bNAbs.

  View details for DOI 10.7554/eLife.61991

  View details for PubMedID 33084569

  View details for PubMedCentralID PMC7577740

• Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies. Cell Barnes, C. O., West, A. P., Huey-Tubman, K. E., Hoffmann, M. A., Sharaf, N. G., Hoffman, P. R., Koranda, N., Gristick, H. B., Gaebler, C., Muecksch, F., Lorenzi, J. C., Finkin, S., Hägglöf, T., Hurley, A., Millard, K. G., Weisblum, Y., Schmidt, F., Hatziioannou, T., Bieniasz, P. D., Caskey, M., Robbiani, D. F., Nussenzweig, M. C., Bjorkman, P. J. 2020; 182 (4): 828-842.e16

  Abstract

  Neutralizing antibody responses to coronaviruses mainly target the receptor-binding domain (RBD) of the trimeric spike. Here, we characterized polyclonal immunoglobulin Gs (IgGs) and Fabs from COVID-19 convalescent individuals for recognition of coronavirus spikes. Plasma IgGs differed in their focus on RBD epitopes, recognition of alpha- and beta-coronaviruses, and contributions of avidity to increased binding/neutralization of IgGs over Fabs. Using electron microscopy, we examined specificities of polyclonal plasma Fabs, revealing recognition of both S1A and RBD epitopes on SARS-CoV-2 spike. Moreover, a 3.4 Å cryo-electron microscopy (cryo-EM) structure of a neutralizing monoclonal Fab-spike complex revealed an epitope that blocks ACE2 receptor binding. Modeling based on these structures suggested different potentials for inter-spike crosslinking by IgGs on viruses, and characterized IgGs would not be affected by identified SARS-CoV-2 spike mutations. Overall, our studies structurally define a recurrent anti-SARS-CoV-2 antibody class derived from VH3-53/VH3-66 and similarity to a SARS-CoV VH3-30 antibody, providing criteria for evaluating vaccine-elicited antibodies.

  View details for DOI 10.1016/j.cell.2020.06.025

  View details for PubMedID 32645326

  View details for PubMedCentralID PMC7311918

• Convergent antibody responses to SARS-CoV-2 in convalescent individuals. Nature Robbiani, D. F., Gaebler, C., Muecksch, F., Lorenzi, J. C., Wang, Z., Cho, A., Agudelo, M., Barnes, C. O., Gazumyan, A., Finkin, S., Hägglöf, T., Oliveira, T. Y., Viant, C., Hurley, A., Hoffmann, H. H., Millard, K. G., Kost, R. G., Cipolla, M., Gordon, K., Bianchini, F., Chen, S. T., Ramos, V., Patel, R., Dizon, J., Shimeliovich, I., Mendoza, P., Hartweger, H., Nogueira, L., Pack, M., Horowitz, J., Schmidt, F., Weisblum, Y., Michailidis, E., Ashbrook, A. W., Waltari, E., Pak, J. E., Huey-Tubman, K. E., Koranda, N., Hoffman, P. R., West, A. P., Rice, C. M., Hatziioannou, T., Bjorkman, P. J., Bieniasz, P. D., Caskey, M., Nussenzweig, M. C. 2020; 584 (7821): 437-442

  Abstract

  During the coronavirus disease-2019 (COVID-19) pandemic, severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) has led to the infection of millions of people and has claimed hundreds of thousands of lives. The entry of the virus into cells depends on the receptor-binding domain (RBD) of the spike (S) protein of SARS-CoV-2. Although there is currently no vaccine, it is likely that antibodies will be essential for protection. However, little is known about the human antibody response to SARS-CoV-21-5. Here we report on 149 COVID-19-convalescent individuals. Plasma samples collected an average of 39 days after the onset of symptoms had variable half-maximal pseudovirus neutralizing titres; titres were less than 50 in 33% of samples, below 1,000 in 79% of samples and only 1% of samples had titres above 5,000. Antibody sequencing revealed the expansion of clones of RBD-specific memory B cells that expressed closely related antibodies in different individuals. Despite low plasma titres, antibodies to three distinct epitopes on the RBD neutralized the virus with half-maximal inhibitory concentrations (IC50 values) as low as 2 ng ml-1. In conclusion, most convalescent plasma samples obtained from individuals who recover from COVID-19 do not contain high levels of neutralizing activity. Nevertheless, rare but recurring RBD-specific antibodies with potent antiviral activity were found in all individuals tested, suggesting that a vaccine designed to elicit such antibodies could be broadly effective.

  View details for DOI 10.1038/s41586-020-2456-9

  View details for PubMedID 32555388

  View details for PubMedCentralID PMC7442695

• Broad and Potent Neutralizing Antibodies Recognize the Silent Face of the HIV Envelope. Immunity Schoofs, T., Barnes, C. O., Suh-Toma, N., Golijanin, J., Schommers, P., Gruell, H., West, A. P., Bach, F., Lee, Y. E., Nogueira, L., Georgiev, I. S., Bailer, R. T., Czartoski, J., Mascola, J. R., Seaman, M. S., McElrath, M. J., Doria-Rose, N. A., Klein, F., Nussenzweig, M. C., Bjorkman, P. J. 2019; 50 (6): 1513-1529.e9

  Abstract

  Broadly neutralizing antibodies (bNAbs) against HIV-1 envelope (Env) inform vaccine design and are potential therapeutic agents. We identified SF12 and related bNAbs with up to 62% neutralization breadth from an HIV-infected donor. SF12 recognized a glycan-dominated epitope on Env's silent face and was potent against clade AE viruses, which are poorly covered by V3-glycan bNAbs. A 3.3Å cryo-EM structure of a SF12-Env trimer complex showed additional contacts to Env protein residues by SF12 compared with VRC-PG05, the only other known donor-derived silentface antibody, explaining SF12's increased neutralization breadth, potency, and resistance to Env mutation routes. Asymmetric binding of SF12 was associated with distinct N-glycan conformations across Env protomers, demonstrating intra-Env glycan heterogeneity. Administrating SF12 to HIV-1-infected humanized mice suppressed viremia and selected for viruses lacking the N448gp120 glycan. Effective bNAbs can therefore be raised against HIV-1 Env's silent face, suggesting their potential for HIV-1 prevention, therapy, and vaccine development.

  View details for DOI 10.1016/j.immuni.2019.04.014

  View details for PubMedID 31126879

  View details for PubMedCentralID PMC6591006

• Immunization expands B cells specific to HIV-1 V3 glycan in mice and macaques. Nature Escolano, A., Gristick, H. B., Abernathy, M. E., Merkenschlager, J., Gautam, R., Oliveira, T. Y., Pai, J., West, A. P., Barnes, C. O., Cohen, A. A., Wang, H., Golijanin, J., Yost, D., Keeffe, J. R., Wang, Z., Zhao, P., Yao, K. H., Bauer, J., Nogueira, L., Gao, H., Voll, A. V., Montefiori, D. C., Seaman, M. S., Gazumyan, A., Silva, M., McGuire, A. T., Stamatatos, L., Irvine, D. J., Wells, L., Martin, M. A., Bjorkman, P. J., Nussenzweig, M. C. 2019; 570 (7762): 468-473

  Abstract

  Broadly neutralizing monoclonal antibodies protect against infection with HIV-1 in animal models, suggesting that a vaccine that elicits these antibodies would be protective in humans. However, it has not yet been possible to induce adequate serological responses by vaccination. Here, to activate B cells that express precursors of broadly neutralizing antibodies within polyclonal repertoires, we developed an immunogen, RC1, that facilitates the recognition of the variable loop 3 (V3)-glycan patch on the envelope protein of HIV-1. RC1 conceals non-conserved immunodominant regions by the addition of glycans and/or multimerization on virus-like particles. Immunization of mice, rabbits and rhesus macaques with RC1 elicited serological responses that targeted the V3-glycan patch. Antibody cloning and cryo-electron microscopy structures of antibody-envelope complexes confirmed that immunization with RC1 expands clones of B cells that carry the anti-V3-glycan patch antibodies, which resemble precursors of human broadly neutralizing antibodies. Thus, RC1 may be a suitable priming immunogen for sequential vaccination strategies in the context of polyclonal repertoires.

  View details for DOI 10.1038/s41586-019-1250-z

  View details for PubMedID 31142836

  View details for PubMedCentralID PMC6657810

• The crystal structure of dGTPase reveals the molecular basis of dGTP selectivity PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Barnes, C. O., Wu, Y., Song, J., Lin, G., Baxter, E. L., Brewster, A. S., Nagarajan, V., Holmes, A., Soltis, S., Sauter, N. K., Ahn, J., Cohen, A. E., Calero, G. 2019; 116 (19): 9333-9339

  Abstract

  Deoxynucleotide triphosphohydrolases (dNTPases) play a critical role in cellular survival and DNA replication through the proper maintenance of cellular dNTP pools. While the vast majority of these enzymes display broad activity toward canonical dNTPs, such as the dNTPase SAMHD1 that blocks reverse transcription of retroviruses in macrophages by maintaining dNTP pools at low levels, Escherichia coli (Ec)-dGTPase is the only known enzyme that specifically hydrolyzes dGTP. However, the mechanism behind dGTP selectivity is unclear. Here we present the free-, ligand (dGTP)- and inhibitor (GTP)-bound structures of hexameric Ec-dGTPase, including an X-ray free-electron laser structure of the free Ec-dGTPase enzyme to 3.2 Å. To obtain this structure, we developed a method that applied UV-fluorescence microscopy, video analysis, and highly automated goniometer-based instrumentation to map and rapidly position individual crystals randomly located on fixed target holders, resulting in the highest indexing rates observed for a serial femtosecond crystallography experiment. Our structures show a highly dynamic active site where conformational changes are coupled to substrate (dGTP), but not inhibitor binding, since GTP locks dGTPase in its apo- form. Moreover, despite no sequence homology, Ec-dGTPase and SAMHD1 share similar active-site and HD motif architectures; however, Ec-dGTPase residues at the end of the substrate-binding pocket mimic Watson-Crick interactions providing guanine base specificity, while a 7-Å cleft separates SAMHD1 residues from dNTP bases, abolishing nucleotide-type discrimination. Furthermore, the structures shed light on the mechanism by which long distance binding (25 Å) of single-stranded DNA in an allosteric site primes the active site by conformationally "opening" a tyrosine gate allowing enhanced substrate binding.

  View details for DOI 10.1073/pnas.1814999116

  View details for Web of Science ID 000467226400032

  View details for PubMedID 31019074

  View details for PubMedCentralID PMC6511015

• Partially Open HIV-1 Envelope Structures Exhibit Conformational Changes Relevant for Coreceptor Binding and Fusion. Cell host & microbe Wang, H., Barnes, C. O., Yang, Z., Nussenzweig, M. C., Bjorkman, P. J. 2018; 24 (4): 579-592.e4

  Abstract

  HIV-1 Env, a trimer of gp120-gp41 heterodimers, mediates membrane fusion after binding host receptor CD4. Receptor binding displaces V1V2 loops from Env's apex, allowing coreceptor binding and opening Env to enable gp41-mediated fusion. We present 3.54 Å and 4.06 Å cryoelectron microscopy structures of partially open soluble native-like Env trimers (SOSIPs) bound to CD4. One structure, a complex with a coreceptor-mimicking antibody that binds both CD4 and gp120, stabilizes the displaced V1V2 and reveals its structure. Comparing partially and fully open Envs with closed Envs shows that gp41 rearrangements are independent of the CD4-induced rearrangements that result in V1V2 displacement and formation of a 4-stranded bridging sheet. These findings suggest ordered conformational changes before coreceptor binding: (1) gp120 opening inducing side-chain rearrangements and a compact gp41 central helix conformation, and (2) 4-stranded bridging-sheet formation and V1V2 displacement. These analyses illuminate potential receptor-induced Env changes and inform design of therapeutics disrupting viral entry.

  View details for DOI 10.1016/j.chom.2018.09.003

  View details for PubMedID 30308160

  View details for PubMedCentralID PMC6185872

• Structural characterization of a highly-potent V3-glycan broadly neutralizing antibody bound to natively-glycosylated HIV-1 envelope NATURE COMMUNICATIONS Barnes, C. O., Gristick, H. B., Freund, N. T., Escolano, A., Lyubimov, A. Y., Hartweger, H., West, A. P., Cohen, A. E., Nussenzweig, M. C., Bjorkman, P. J. 2018; 9: 1251

  Abstract

  Broadly neutralizing antibodies (bNAbs) isolated from HIV-1-infected individuals inform HIV-1 vaccine design efforts. Developing bNAbs with increased efficacy requires understanding how antibodies interact with the native oligomannose and complex-type N-glycan shield that hides most protein epitopes on HIV-1 envelope (Env). Here we present crystal structures, including a 3.8-Å X-ray free electron laser dataset, of natively glycosylated Env trimers complexed with BG18, the most potent V3/N332gp120 glycan-targeting bNAb reported to date. Our structures show conserved contacts mediated by common D gene-encoded residues with the N332gp120 glycan and the gp120 GDIR peptide motif, but a distinct Env-binding orientation relative to PGT121/10-1074 bNAbs. BG18's binding orientation provides additional contacts with N392gp120 and N386gp120 glycans near the V3-loop base and engages protein components of the V1-loop. The BG18-natively-glycosylated Env structures facilitate understanding of bNAb-glycan interactions critical for using V3/N332gp120 bNAbs therapeutically and targeting their epitope for immunogen design.

  View details for DOI 10.1038/s41467-018-03632-y

  View details for Web of Science ID 000428520600006

  View details for PubMedID 29593217

  View details for PubMedCentralID PMC5871869

• The DDB1-DCAF1-Vpr-UNG2 crystal structure reveals how HIV-1 Vpr steers human UNG2 toward destruction NATURE STRUCTURAL & MOLECULAR BIOLOGY Wu, Y., Zhou, X., Barnes, C. O., DeLucia, M., Cohen, A. E., Gronenborn, A. M., Ahn, J., Calero, G. 2016; 23 (10): 933-940

  Abstract

  The HIV-1 accessory protein Vpr is required for efficient viral infection of macrophages and promotion of viral replication in T cells. Vpr's biological activities are closely linked to the interaction with human DCAF1, a cellular substrate receptor of the Cullin4-RING E3 ubiquitin ligase (CRL4) of the host ubiquitin-proteasome-mediated protein degradation pathway. The molecular details of how Vpr usurps the protein degradation pathway have not been delineated. Here we present the crystal structure of the DDB1-DCAF1-HIV-1-Vpr-uracil-DNA glycosylase (UNG2) complex. The structure reveals how Vpr engages with DCAF1, creating a binding interface for UNG2 recruitment in a manner distinct from the recruitment of SAMHD1 by Vpx proteins. Vpr and Vpx use similar N-terminal and helical regions to bind the substrate receptor, whereas different regions target the specific cellular substrates. Furthermore, Vpr uses molecular mimicry of DNA by a variable loop for specific recruitment of the UNG2 substrate.

  View details for DOI 10.1038/nsmb.3284

  View details for Web of Science ID 000384964500011

  View details for PubMedID 27571178

  View details for PubMedCentralID PMC5385928

• Assessment of microcrystal quality by transmission electron microscopy for efficient serial femtosecond crystallography ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS Barnes, C. O., Kovaleva, E. G., Fu, X., Stevenson, H. P., Brewster, A. S., Deponte, D. P., Baxter, E. L., Cohen, A. E., Calero, G. 2016; 602: 61-68

  Abstract

  Serial femtosecond crystallography (SFX) employing high-intensity X-ray free-electron laser (XFEL) sources has enabled structural studies on microcrystalline protein samples at non-cryogenic temperatures. However, the identification and optimization of conditions that produce well diffracting microcrystals remains an experimental challenge. Here, we report parallel SFX and transmission electron microscopy (TEM) experiments using fragmented microcrystals of wild type (WT) homoprotocatechuate 2,3-dioxygenase (HPCD) and an active site variant (H200Q). Despite identical crystallization conditions and morphology, as well as similar crystal size and density, the indexing efficiency of the diffraction data collected using the H200Q variant sample was over 7-fold higher compared to the diffraction results obtained using the WT sample. TEM analysis revealed an abundance of protein aggregates, crystal conglomerates and a smaller population of highly ordered lattices in the WT sample as compared to the H200Q variant sample. While not reported herein, the 1.75 Å resolution structure of the H200Q variant was determined from ∼16 min of beam time, demonstrating the utility of TEM analysis in evaluating sample monodispersity and lattice quality, parameters critical to the efficiency of SFX experiments.

  View details for DOI 10.1016/j.abb.2016.02.011

  View details for Web of Science ID 000378364900007

  View details for PubMedID 26944553

• Transmission electron microscopy for the evaluation and optimization of crystal growth ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY Stevenson, H. P., Lin, G., Barnes, C. O., Sutkeviciute, I., Krzysiak, T., Weiss, S. C., Reynolds, S., Wu, Y., Nagarajan, V., Makhov, A. M., Lawrence, R., Lamm, E., Clark, L., Gardella, T. J., Hogue, B. G., Ogata, C. M., Ahn, J., Gronenborn, A. M., Conway, J. F., Vilardaga, J., Cohen, A. E., Calero, G. 2016; 72: 603-615

  Abstract

  The crystallization of protein samples remains the most significant challenge in structure determination by X-ray crystallography. Here, the effectiveness of transmission electron microscopy (TEM) analysis to aid in the crystallization of biological macromolecules is demonstrated. It was found that the presence of well ordered lattices with higher order Bragg spots, revealed by Fourier analysis of TEM images, is a good predictor of diffraction-quality crystals. Moreover, the use of TEM allowed (i) comparison of lattice quality among crystals from different conditions in crystallization screens; (ii) the detection of crystal pathologies that could contribute to poor X-ray diffraction, including crystal lattice defects, anisotropic diffraction and crystal contamination by heavy protein aggregates and nanocrystal nuclei; (iii) the qualitative estimation of crystal solvent content to explore the effect of lattice dehydration on diffraction and (iv) the selection of high-quality crystal fragments for microseeding experiments to generate reproducibly larger sized crystals. Applications to X-ray free-electron laser (XFEL) and micro-electron diffraction (microED) experiments are also discussed.

  View details for DOI 10.1107/S2059798316001546

  View details for Web of Science ID 000375851700002

  View details for PubMedID 27139624

• High-density grids for efficient data collection from multiple crystals. Acta crystallographica. Section D, Structural biology Baxter, E. L., Aguila, L., Alonso-Mori, R., Barnes, C. O., Bonagura, C. A., Brehmer, W., Brunger, A. T., Calero, G., Caradoc-Davies, T. T., Chatterjee, R., DeGrado, W. F., Fraser, J. S., Ibrahim, M., Kern, J., Kobilka, B. K., Kruse, A. C., Larsson, K. M., Lemke, H. T., Lyubimov, A. Y., Manglik, A., McPhillips, S. E., Norgren, E., Pang, S. S., Soltis, S. M., Song, J., Thomaston, J., Tsai, Y., Weis, W. I., Woldeyes, R. A., Yachandra, V., Yano, J., Zouni, A., Cohen, A. E. 2016; 72: 2-11

  Abstract

  Higher throughput methods to mount and collect data from multiple small and radiation-sensitive crystals are important to support challenging structural investigations using microfocus synchrotron beamlines. Furthermore, efficient sample-delivery methods are essential to carry out productive femtosecond crystallography experiments at X-ray free-electron laser (XFEL) sources such as the Linac Coherent Light Source (LCLS). To address these needs, a high-density sample grid useful as a scaffold for both crystal growth and diffraction data collection has been developed and utilized for efficient goniometer-based sample delivery at synchrotron and XFEL sources. A single grid contains 75 mounting ports and fits inside an SSRL cassette or uni-puck storage container. The use of grids with an SSRL cassette expands the cassette capacity up to 7200 samples. Grids may also be covered with a polymer film or sleeve for efficient room-temperature data collection from multiple samples. New automated routines have been incorporated into the Blu-Ice/DCSS experimental control system to support grids, including semi-automated grid alignment, fully automated positioning of grid ports, rastering and automated data collection. Specialized tools have been developed to support crystallization experiments on grids, including a universal adaptor, which allows grids to be filled by commercial liquid-handling robots, as well as incubation chambers, which support vapor-diffusion and lipidic cubic phase crystallization experiments. Experiments in which crystals were loaded into grids or grown on grids using liquid-handling robots and incubation chambers are described. Crystals were screened at LCLS-XPP and SSRL BL12-2 at room temperature and cryogenic temperatures.

  View details for DOI 10.1107/S2059798315020847

  View details for PubMedID 26894529

  View details for PubMedCentralID PMC4756618

• Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble MOLECULAR CELL Barnes, C. O., Calero, M., Malik, I., Graham, B. W., Spahr, H., Lin, G., Cohen, A. E., Brown, I. S., Zhang, Q., Pullara, F., Trakselis, M. A., Kaplan, C. D., Calero, G. 2015; 59 (2): 258–69

  Abstract

  Notwithstanding numerous published structures of RNA Polymerase II (Pol II), structural details of Pol II engaging a complete nucleic acid scaffold have been lacking. Here, we report the structures of TFIIF-stabilized transcribing Pol II complexes, revealing the upstream duplex and full transcription bubble. The upstream duplex lies over a wedge-shaped loop from Rpb2 that engages its minor groove, providing part of the structural framework for DNA tracking during elongation. At the upstream transcription bubble fork, rudder and fork loop 1 residues spatially coordinate strand annealing and the nascent RNA transcript. At the downstream fork, a network of Pol II interactions with the non-template strand forms a rigid domain with the trigger loop (TL), allowing visualization of its open state. Overall, our observations suggest that "open/closed" conformational transitions of the TL may be linked to interactions with the non-template strand, possibly in a synchronized ratcheting manner conducive to polymerase translocation.

  View details for PubMedID 26186291

• Goniometer-based femtosecond crystallography with X-ray free electron lasers PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Cohen, A. E., Soltis, S. M., Gonzalez, A., Aguila, L., Alonso-Mori, R., Barnes, C. O., Baxter, E. L., Brehmer, W., Brewster, A. S., Brunger, A. T., Calero, G., Chang, J. F., Chollet, M., Ehrensberger, P., Eriksson, T. L., Feng, Y., Hattne, J., Hedman, B., Hollenbeck, M., Holton, J. M., Keable, S., Kobilka, B. K., Kovaleva, E. G., Kruse, A. C., Lemke, H. T., Lin, G., Lyubimov, A. Y., Manglik, A., Mathews, I. I., McPhillips, S. E., Nelson, S., Peters, J. W., Sauter, N. K., Smith, C. A., Song, J., Stevenson, H. P., Tsai, Y., Uervirojnangkoorn, M., Vinetsky, V., Wakatsuki, S., Weis, W. I., Zadvornyy, O. A., Zeldin, O. B., Zhu, D., Hodgson, K. O. 2014; 111 (48): 17122-17127

  Abstract

  The emerging method of femtosecond crystallography (FX) may extend the diffraction resolution accessible from small radiation-sensitive crystals and provides a means to determine catalytically accurate structures of acutely radiation-sensitive metalloenzymes. Automated goniometer-based instrumentation developed for use at the Linac Coherent Light Source enabled efficient and flexible FX experiments to be performed on a variety of sample types. In the case of rod-shaped Cpl hydrogenase crystals, only five crystals and about 30 min of beam time were used to obtain the 125 still diffraction patterns used to produce a 1.6-Å resolution electron density map. For smaller crystals, high-density grids were used to increase sample throughput; 930 myoglobin crystals mounted at random orientation inside 32 grids were exposed, demonstrating the utility of this approach. Screening results from cryocooled crystals of β2-adrenoreceptor and an RNA polymerase II complex indicate the potential to extend the diffraction resolution obtainable from very radiation-sensitive samples beyond that possible with undulator-based synchrotron sources.

  View details for DOI 10.1073/pnas.1418733111

  View details for Web of Science ID 000345920800042

  View details for PubMedID 25362050

  View details for PubMedCentralID PMC4260607

• Use of transmission electron microscopy to identify nanocrystals of challenging protein targets PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Stevenson, H. P., Makhov, A. M., Calero, M., Edwards, A. L., Zeldin, O. B., Mathews, I. I., Lin, G., Barnes, C. O., Santamaria, H., Ross, T. M., Soltis, S. M., Khosla, C., Nagarajan, V., Conway, J. F., Cohen, A. E., Calero, G. 2014; 111 (23): 8470-8475

  Abstract

  The current practice for identifying crystal hits for X-ray crystallography relies on optical microscopy techniques that are limited to detecting crystals no smaller than 5 μm. Because of these limitations, nanometer-sized protein crystals cannot be distinguished from common amorphous precipitates, and therefore go unnoticed during screening. These crystals would be ideal candidates for further optimization or for femtosecond X-ray protein nanocrystallography. The latter technique offers the possibility to solve high-resolution structures using submicron crystals. Transmission electron microscopy (TEM) was used to visualize nanocrystals (NCs) found in crystallization drops that would classically not be considered as "hits." We found that protein NCs were readily detected in all samples tested, including multiprotein complexes and membrane proteins. NC quality was evaluated by TEM visualization of lattices, and diffraction quality was validated by experiments in an X-ray free electron laser.

  View details for DOI 10.1073/pnas.1400240111

  View details for Web of Science ID 000336976000051

  View details for PubMedID 24872454

  View details for PubMedCentralID PMC4060711