Landscape-Based Mutational Sensitivity Cartography and Network Community Analysis of the SARS-CoV-2 Spike Protein Structures: Quantifying Functional Effects of the Circulating D614G Variant
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SciScore for 10.1101/2021.05.18.444742: (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
Software and Algorithms Sentences Resources All-atom MD simulations were performed for an N, P, T ensemble in explicit solvent using NAMD 2.13 package74 with CHARMM36 force field. NAMDsuggested: (NAMD, RRID:SCR_014894)91,92 The network parameters were computed using the python package NetworkX87 and Cytoscape package for network analysis.93,94 A community-based analysis and modularity assessment of allosteric interaction networks is based on the notion that groups of residues that form local interacting communities are expected to be highly correlated and can switch their conformational states cooperatively. pythonsuggested: …SciScore for 10.1101/2021.05.18.444742: (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
Software and Algorithms Sentences Resources All-atom MD simulations were performed for an N, P, T ensemble in explicit solvent using NAMD 2.13 package74 with CHARMM36 force field. NAMDsuggested: (NAMD, RRID:SCR_014894)91,92 The network parameters were computed using the python package NetworkX87 and Cytoscape package for network analysis.93,94 A community-based analysis and modularity assessment of allosteric interaction networks is based on the notion that groups of residues that form local interacting communities are expected to be highly correlated and can switch their conformational states cooperatively. pythonsuggested: (IPython, RRID:SCR_001658)Cytoscapesuggested: (Cytoscape, RRID:SCR_003032)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: We detected the following sentences addressing limitations in the study:In this analysis, positive folding free energy contributions indicate stability weaknesses sites and highly negative folding free energy contributions characterized sites of local stability in the S protein. For the locked closed form of the D614 S trimer, the stability hotspots are distributed across multiple regions including the NTD residues, the RBD core and the S2 domain regions (Figure 7A). It is worth noting that the most prominent stability centers were found in the RBD core and the region near the hinge hotspot cluster (residues 591-600) that featured stability peaks for hinge sites S591, F592 and G593 (Figure 7A). In both closed and open forms of the D614 S trimer, the receptor binding motif (RBM) of the RBD region (residues 470-491) showed only marginal stability as the energetic plasticity of this region is required for functional interactions with ACE2. In the open form of the D614 S trimer, the stability of the RBD core and S2 regions was partially reduced while maintaining the overall stabilizing signature in these positions (Figure 7B). By highlighting positions of circulating mutations K417, E484, N501 and D614 we noticed that D614 corresponds to a moderately stable position while other sites are marginally destabilizing (Figure 7A,B). Hence, mutations in these sites can be easily tolerated without impairing protein stability of the S trimer (Figure S1A) The overall stability pattern in the G614 S trimer remained preserved, highlighting similar regions of hig...
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Results from JetFighter: Please consider improving the rainbow (“jet”) colormap(s) used on pages 65, 15, 19, 23, 58, 59, 60 and 61. At least one figure is not accessible to readers with colorblindness and/or is not true to the data, i.e. not perceptually uniform.
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Results from scite Reference Check: We found no unreliable references.
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