Structure of SARS-CoV-2 M protein in lipid nanodiscs

Decision letter after peer review:

Thank you for submitting your article "Structure of SARS-CoV-2 M protein in lipid nanodiscs" for consideration by eLife. Your article has been reviewed by 2 peer reviewers, and the evaluation has been overseen by a Reviewing Editor and Sara Sawyer as the Senior Editor. The reviewers have opted to remain anonymous.

The reviewers have discussed their reviews with one another, and the Reviewing Editor has drafted this to help you prepare a revised submission.

Essential revisions:

The Reviewers are in agreement that the paper reports an important structure. Both reviewers highlight some questions that they would like the authors to address in a revision:

1) Please elaborate on the time scale of the MD simulation and how it is informative on protein function.

2) Please update the discussion on available functional data, in light of the new structure.

Reviewer #1 (Recommendations for the authors):

I have no strong comments or criticisms. The work is very well done, the writing is clear, and the figures are well designed and very clear. The work is overall relatively simple, with the structure being the main result and the supporting molecular dynamics contributing somewhat.

One point I would hope that the authors could clarify concerns the molecular dynamics simulations: These were apparently carried out to determine whether the M protein is flexible, as had been suggested by some prior (indirect) data. But, is 1.6 microseconds enough time to confidently say that the M protein is conformationally stable? I'm not familiar with the literature concerning MD to study conformational changes, but my naive sense is that one needs to do a very long simulation to see large-scale conformational changes. However, I'm not sure what "very long" means in this context. Some clarification, and perhaps a bit more explanation in the text, would be helpful.

I am hopeful that the authors are using their ability to purify this protein for further interesting experiments, which need not be included in this work but would nonetheless be very interesting for future studies. For example, direct interaction assays with the cytosolic domain of the S protein or the C-terminal domain of the N protein. Biochemical and even structural characterization of these interactions, should they prove to be specific enough, would be extremely exciting.

Reviewer #2 (Recommendations for the authors):

Dolan and colleagues report cryo-EM structure of the SARS-CoV-2 M protein. It is an impressive achievement in that the authors obtained ~3.5 Å resolution structure of a small 50 kDa membrane protein. The structural data and analyses were clearly presented in this manuscript. Molecular dynamics simulations supported the rather rigid structural scaffold of the M protein. One concern is that the study did not include any functional data of M, thus providing no mechanistic insight into its role in viral assembly. Otherwise, the manuscript is well written and suitable for publication.