Potent SARS-CoV-2 neutralizing antibodies directed against spike N-terminal domain target a single supersite
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SciScore for 10.1101/2021.01.10.426120: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources These surfaces were generated using the His-capture kit (Cytiva, MA) according to the instructions of the manufacturer, resulting in approximately 10,000 RU of anti-his antibody over each surface. anti-hissuggested: NoneThe binding affinities of full IgG antibodies to SARS-CoV-2 spike protein were determined using surface plasmon resonance (SPR) and a BIAcore T200 instrument (GE Healthcare) at 25°C. SARS-CoV-2 spike proteinsuggested: NoneDMEM supplemented with anti-VSV-G antibody (I1, mouse hybridoma supernatant from CRL-2700; ATCC) was added to the infected cells and they were cultured overnight as … SciScore for 10.1101/2021.01.10.426120: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Antibodies Sentences Resources These surfaces were generated using the His-capture kit (Cytiva, MA) according to the instructions of the manufacturer, resulting in approximately 10,000 RU of anti-his antibody over each surface. anti-hissuggested: NoneThe binding affinities of full IgG antibodies to SARS-CoV-2 spike protein were determined using surface plasmon resonance (SPR) and a BIAcore T200 instrument (GE Healthcare) at 25°C. SARS-CoV-2 spike proteinsuggested: NoneDMEM supplemented with anti-VSV-G antibody (I1, mouse hybridoma supernatant from CRL-2700; ATCC) was added to the infected cells and they were cultured overnight as described above. anti-VSV-Gsuggested: NoneI1suggested: NoneC α distance calculation: The Cα distances per residue between superimposed ligand-free and antibody-bound NTD were calculated by Python 3.8. antibody-bound NTDsuggested: NoneExperimental Models: Cell Lines Sentences Resources They were expressed in Human Embryonic Kidney (HEK) 293 Freestyle cells (Invitrogen) in suspension culture using serum-free media (Invitrogen) and transfected into HEK293 cells using polyethyleneimine (Polysciences). HEKsuggested: NoneThe NTD construct was transiently transfected into HEK293 GnTI-Freestyle cells suspension culture in serum-free media using polyethyleneimine. HEK293suggested: CLS Cat# 300192/p777_HEK293, RRID:CVCL_0045)HEK293T cells were grown to 80% confluency before transfection with pCMV3-SARS-CoV-2-spike (kindly provided by Dr. Peihui Wang, Shandong University, China) using FuGENE 6 (Promega). HEK293Tsuggested: NoneIn brief, Vero E6 cells were seeded in a 96-well plate at a concentration of 2 × 104 cells per well. Vero E6suggested: NoneSoftware and Algorithms Sentences Resources The data was processed and fit to 1:1 single cycle model using the Scrubber 2.0 (BioLogic Software) Scrubbersuggested: (Scrubber2, RRID:SCR_015745)The resulting data were fit to a 1:1 binding model using Biacore Evaluation Software and were plotted using Graphpad. Graphpadsuggested: (GraphPad, RRID:SCR_000306)The IC50 values were calculated using non-linear regression in GraphPad Prism. GraphPad Prismsuggested: (GraphPad Prism, RRID:SCR_002798)To identify somatic hypermutations, each antibody sequence was aligned to the assigned germline gene using MUSCLE v3.8.31 (Edgar, 2004) MUSCLEsuggested: (MUSCLE, RRID:SCR_011812)Symmetry expansion and focused classification in RELION 3.1 (Scheres, 2012) was used for S2P spike complex with 2-51. RELIONsuggested: (RELION, RRID:SCR_016274)Geometry validation and structure quality assessment were performed using EMRinger (Barad et al., 2015) and Molprobity (Davis et al., 2004). Molprobitysuggested: (MolProbity, RRID:SCR_014226)Map-fitting cross correlation (Fit-in-Map tool) and figures preparation were carried out using PyMOL and UCSF Chimera (Pettersen et al., 2004) and Chimera X (Pettersen et al., 2021). PyMOLsuggested: (PyMOL, RRID:SCR_000305)Diffraction data were processed with XDS (Kabsch, 2010) and scaled using AIMLESS (Evans and Murshudov, 2013) from the CCP4 software suite (Winn et al., 2011) CCP4suggested: (CCP4, RRID:SCR_007255)Structure refinement was performed with a 3.65 Å high-resolution cutoff using Phenix refine (Adams et al., 2010) and PDB-redo (Joosten et al., 2014) alternated with manual model building using Coot. Cootsuggested: (Coot, RRID:SCR_014222)C α distance calculation: The Cα distances per residue between superimposed ligand-free and antibody-bound NTD were calculated by Python 3.8. Pythonsuggested: (IPython, RRID:SCR_001658)Sequence entropy of betacoronavirus spike: Human coronavirus reference amino acid sequences of OC43 (UniProt ID: P36334), HKU1 (UniProt ID: Q5MQD0), SARS (UniProt ID: P59594), and MERS (UniProt ID: W5ZZF5), as well as the initial SARS-CoV-2 (GenBank: QHO60594.1) sequence reported in Washington state were aligned using MAFFT software with default parameters (Katoh et al., 2002). MAFFTsuggested: (MAFFT, RRID:SCR_011811)Cryo-EM data were processed and analyzed using cryoSPARC and Relion. cryoSPARCsuggested: (cryoSPARC, RRID:SCR_016501)Cryo-EM and crystallographic structural statistics were analyzed using Phenix, Molprobity, EMringer and Chimera. Phenixsuggested: (Phenix, RRID:SCR_014224)Results from OddPub: Thank you for sharing your code and data.
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on page 45. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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