Review of Crystal structure of the membrane (M) protein from a SARS-COV-2-related coronavirus

This Zenodo record is a permanently preserved version of a PREreview. You can view the complete PREreview at https://prereview.org/reviews/7086941.

SUMMARY –

The SARS-CoV-2 virus is a causative agent for COVID-19 disease and has become a global pandemic. Protein structures of the SARS-CoV-2 virus such as Spike, and RNA-dependant RNA polymerase have played a key role in developing structure-guided antibodies and drug designing. Xiaodong Wang and colleagues were able to determine the structure of Membrane (M) protein from the bat coronavirus HKU5 by crystallization and also determined the biochemical basis of M protein interaction with other viral proteins. M protein has shown to interact with the nucleocapsid (N) protein and thus play important role in viral assembly.  

STRENGTHS –

1) M protein structure was determined in the "long form", also the authors did a pulldown assay to study the M-N protein interaction. They were also able to determine the region in both M and N protein that is essential for mediating the interaction.

2) The paper also tried to determine the binding site of N in the M protein structure by docking and verification by mutagenesis study.

MAJOR CONCERNS –

1) Recently a study by Zhikuan Zhang et al., showed that the M protein overexpressed in mammalian cells purified in GDN showed higher order oligomers ranging from dimeric to hexameric organization. I think that the detergent or the expression system could have affected the oligomerization behaviour of M protein in two different conditions. It would be interesting to see if the batCOV5-M protein overexpressed in yeast cells and purified in GDN shows similar characteristics.

2) The protein exists in two conformational states as shown by Zhikuan Zhang et al., the structure obtained by crystallization belongs to the "long form". I was curious to know if the docking simulations performed for M-N protein interaction in "short form" will show and difference as there are significant shifts in the CTD structure in both conformations.

MINOR CONCERNS –

1) The protein pull-down assay could have been performed with other viral proteins such as Spike (S) and Envelope (E) to know the basis of interaction with other viral proteins during virus assembly.

2) The dimer interface between the protomer could have been explored in detail and with a section discussing any changes in the dimer interface in the "long" and "short" forms of the protein conformations.