Targeted in situ cross-linking mass spectrometry and integrative modeling reveal the architectures of three proteins from SARS-CoV-2
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Abstract
We present a generic methodology that extracts structural data from living, intact cells for any protein of interest. Application of this methodology to different viral proteins resulted in significant cross-link sets that revealed the connectivity within their structures. Importantly, we show that these cross-link sets are detailed enough to enable the integrative modeling of the full-length protein sequence. Consequently, we report the global structural organization of Nsp2 and the dimer of the nucleocapsid protein. We foresee that similar applications will be highly useful to study other recalcitrant proteins on which the mainstream structural approaches currently fail.
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SciScore for 10.1101/2021.02.04.429751: (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
Experimental Models: Cell Lines Sentences Resources Cell culture and transfection: Human embryonic kidney cells 293 (HEK293, ATCC) were cultured (DMEM High glucose 10% FBS) at 37°C, 5% CO2, and high humidity. HEK293suggested: NoneSoftware and Algorithms Sentences Resources Label-free quantification (LFQ) was performed with MaxQuant 1.551 using the default parameters. MaxQuantsuggested: (MaxQuant, RRID:SCR_014485)Identification of cross-links: The RAW data files from the mass spectrometer were converted to MGF format by Proteome Discoverer (Thermo). Proteome Discoverersuggested: (Proteome Discoverer, RRID:SCR_014477)PatchDock employs an … SciScore for 10.1101/2021.02.04.429751: (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
Experimental Models: Cell Lines Sentences Resources Cell culture and transfection: Human embryonic kidney cells 293 (HEK293, ATCC) were cultured (DMEM High glucose 10% FBS) at 37°C, 5% CO2, and high humidity. HEK293suggested: NoneSoftware and Algorithms Sentences Resources Label-free quantification (LFQ) was performed with MaxQuant 1.551 using the default parameters. MaxQuantsuggested: (MaxQuant, RRID:SCR_014485)Identification of cross-links: The RAW data files from the mass spectrometer were converted to MGF format by Proteome Discoverer (Thermo). Proteome Discoverersuggested: (Proteome Discoverer, RRID:SCR_014477)PatchDock employs an efficient rigid docking algorithm that maximizes geometric shape complementarity. PatchDocksuggested: (PatchDock, RRID:SCR_017589)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
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 10. 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.
- No funding statement was detected.
- No protocol registration statement was detected.
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