Sequence of the SARS-CoV-2 Spike Transmembrane Domain Encodes Conformational Dynamics
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SARS-CoV-2 spike TMD dynamics may enhance viral fusion by stabilizing a crucial intermediate during conformational transitions. by Lall S, Balaram P, Mathew MK and Gosavi S in J Phys Chem B #MedSky 📖 read the article: https://pubs.acs.org/doi/10.1021/acs.jpcb.4c05270
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Thanks to the mentorship of Profs P. Balaram, M.K. Mathew and Shachi Gosavi (still not here) This marks publication of some of my PhD thesis work. More to follow! Preprint: www.biorxiv.org/content/10.1...
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In 2020, during COVID lockdown we distracted ourselves by dunking the SARS-CoV-2 spike protein in membranes (atomistic and martini) The outcome just got published🧵👇 Sequence of the SARS-CoV-2 Spike Transmembrane Domain Encodes Conformational Dynamics pubs.acs.org/doi/10.1021/...
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SARS-CoV-2 spike protein transmembrane domain (TMD) is dynamic and may actively aid viral fusion, not just anchor the spike. Simulations showed TMD tilts, bobs, and alters membrane thickness, suggesting conformational transitions key to infection. pubs.acs.org/doi/10.1021/...
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SciScore for 10.1101/2021.06.07.447334: (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 The sequence Pro1213-Cys1236 was modelled with ideal α-helical backbone torsion angles and the rest of the amino acids were designed as random coil, using PyMOL (v2.3.3; Schrodinger). PyMOLsuggested: (PyMOL, RRID:SCR_000305)All the simulations were performed using GROMACS 4.6.7 (www.gromacs.org) on our high performance computing cluster. GROMACSsuggested: (GROMACS, RRID:SCR_014565)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Caveats: There is a dearth of experimental data on …
SciScore for 10.1101/2021.06.07.447334: (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 The sequence Pro1213-Cys1236 was modelled with ideal α-helical backbone torsion angles and the rest of the amino acids were designed as random coil, using PyMOL (v2.3.3; Schrodinger). PyMOLsuggested: (PyMOL, RRID:SCR_000305)All the simulations were performed using GROMACS 4.6.7 (www.gromacs.org) on our high performance computing cluster. GROMACSsuggested: (GROMACS, RRID:SCR_014565)Results from OddPub: Thank you for sharing your data.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:Caveats: There is a dearth of experimental data on the composition of the coronavirus envelope. For our simulations, we used only phosphatidylcholine (POPC) lipid which has a single unsaturation in one of the lipid tails. POPC has been shown to be the most abundant lipid comprising up to 70% of phospholipids in a model coronavirus (59) and also has been used as a model lipid for long. Although common for enveloped viruses like influenza and HIV (76, 77), our POPC and cholesterol ratio is an averaged approximation for the various environments that the transmembrane domain of the SARS-CoV-2 would likely experience. Further, the curvature of the viral envelope could have a bearing on transmembrane conformations but is not studied here. Given the sequence of the TRACS, a tantalizing possibility is the Pro1213 residue sandwiched between the two Trp residues, exists in a cis conformation which was not considered here. Finally, the other domains of the spike protein, not included in the simulations here may influence the equilibrium ensemble of conformations of the transmembrane domain.
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: We did not find any issues relating to colormaps.
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.
Results from scite Reference Check: We found no unreliable references.
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