Modulating Enzyme–Ligand Binding with External Fields

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

This manuscript presents a well-executed molecular dynamics study exploring how external electric fields (EFs) influence the binding stability of non-cognate ligands in Shikimate Kinase. The results are clearly presented and supported by appropriate analyses, including RMSD, VAMP, and energetic frustration. While the study provides convincing evidence of EF-induced stabilization, it would benefit from additional insight into active site geometry to assess catalytic relevance, and from inclusion of binding free energy estimates to strengthen the ligand binding claims. The figures are informative, though the addition of structural overlays and local frustration visualizations would improve clarity. Overall, the manuscript is well-written and scientifically sound, requiring only minor revisions to enhance its impact.

Comments for author File: Comments.pdf

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

The author has described a molecular dynamic simulation method for quantifying the stability of the enzyme-ligand complex between Shikimate Kinase and its non-cognate ligand ATP and AMP in presence of an electric field. The observation is quite interesting and can be published. However, I have a couple of questions regarding the intricacies of the experiment.

 

1. Is the direction of the electric field important for protein ligand binding? The author can at least show an image of the protein-ligand complex (one frame is enough) and the direction of the electric field. Moreover, a detailed picture of the binding site can also be provided for the convenience of the general readers.
2. SK has a particular mechanism for binding AMP. Upon induction of an external EF, there is a clear reduction of COM-distance between the protein and ligand. Does the author see any new molecular event here?
3. The chemical frustration around R116 is an interesting parameter to discuss while assaying protein ligand binding stability. Does the author see any change in frustration around other associated residues around the ligand? Again, it will be very convenient for the author to show any molecular model. 

Author Response

Please see the attachment.

Author Response File: Author Response.pdf