Free-Energy Landscape Analysis of Protein-Ligand Binding: The Case of Human Glutathione Transferase A1

Round 1

Reviewer 1 Report

The authors conducted a computational study on the ligand-binding to human glutathione transferase A1 using millisecond molecular dynamics simulations with their unique analysis of free energy landscape. They addressed an important issue in life science. The paper is very well written and technically sound. This reviewer recommend this paper for publication in Applied Sciences if the following questions and comments are considered in the revised manuscript.

[1] As the authors described, GSTs are functional as dimers. However, they mentioned little about the monomer-monomer interaction. Any cooperativity observed for the GSH binding to apo hGSTA1? Why are they functional as dimers?

[2] They observed association/dissociation of GSH from the apo hGSTA1 during their millisecond molecular dynamics simulations. How often? It would be helpful for readers if the time points of association/dissociation are indicated during the simulations. Are association/dissociation of GSH from one monomer synchronized with those of the other monomer in the GSH bound dimer?

[3] Their method effectively illustrates what happens in the protein part of GST as a result of the ligand-protein interactions. Can we neglect the role of waters or ions during the ligand-binding process? 

[4] Maybe they could characterize the GSH binding to GST as population shift or induced-fit type?

[5] I am afraid that APO traj1, 2; and GSH traj 1 are not converged (Fig. S2). Are they OK? 

[6] Probably, the authors could describe something about the release of GS-DNB?

[7] Although the authors describe "the network of important residues", I found no Figure entry for this. It would be very helpful for readers if there is a "network graph of key residues" provided in the paper. 

minor comment:

[1] LINE 5: whith -> with?

Author Response

see attached

Author Response File: Author Response.pdf

Reviewer 2 Report

1. In what way this study can on a real time basis help in future research.

2. Did the authors validate these variations noticed after simulation affecting the binding of GSH with other ligands.  

3. Abstract is focusing mainly on introduction and methodology rather than results and conlcusion. Abstract has to reframed highlighting the results 

4. The content provided in methodology and results were elaborate and extensive. 

5. Conclusion was also lengthy and repeated the methodology again. This has to be concised.

6. Typographical and grammatical errors are noticed. Please do a thorough check on the manuscript 

Author Response

see attached

Author Response File: Author Response.pdf