Yuhang-CADD
commented
2 years ago My personal perspective toward the last paper (Promising Antimicrobial peptide):
A good paper though it is (demonstrating the whole process of molecular modelling and bioinformatic analysis), there is no actual in vivo/vitro data for the predicted result; it's purely based on molecular modelling using the Swiss programme for homology modelling and Hdock for docking predictions.
But, really nice work Zige! Keep feeding us with frontier papers!
ZigBu
KatoLeonard
@mattodd @KatoLeonard @Yuhang-CADD Conformation for MurD The previous study trapped the intermediate conformation of MurD that is not open despite the absence of ligands, nor closed in the presence of ligands. Thus it is suggested that the closure conformation of MurD might not be triggered by the substrate recognition or binding. Instead, the domain rotation and movement might be an inherent feature that has less association with the binding of ligand or substrate. (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0152075)
Figure 1. Superposition of Intermediate Free MurD (blue PDB code: 5a5e) and Intermediate Bound MurD (green PDB code: 5a5f) .
Conformation for MurE Among the Mur ligases, the open and close conformation of MurE has the less difference. (Figure A) The articles suggest that the structural of T. maritima MurF with ADP reveals the location of C-terminal domain which is in between the closed and open structures. This intermediate conformation after binding the nucleotide indicates that the trigger of the C terminal domain movement still needs to be researched.
The article also suggests that the residues from the central and C-terminal domain connecting loop were conserved comparing with the surrounding residues. They are important for the movement of the C-terminal domain which makes the loop a functionally important region and might become a potential target for developing inhibitor. (Figure B) (https://febs.onlinelibrary.wiley.com/doi/10.1002/1873-3468.14007)
Promising Antimicrobial peptide I haven't started reading the paper yet. Maybe I'll be able to summarise it and draw a conclusion next week. (https://link.springer.com/article/10.1007/s10989-021-10165-4])