Adsorption of Heparin-Binding Fragments of Fibronectin onto Hydrophobic Surfaces

Round 1

Reviewer 1 Report

The work entitled “Adsorption of Heparin Binding Fragments of Fibronectin onto Hydrophobic Surfaces” reports on the adsorption of heparin binding fibronectin domains onto hydrophobic surfaces using molecular dynamics simulations. The work is very well put together and very well organize. The subject is also very pertinent within its field. The question that is raised and answer by this research is something that we have been dealing for long and there is not yet a definitive proof about the mutual influence proteins and surfaces exert on each other. This research is a step forward in that direction. I would only recommend the authors to reduce the introductory part of the abstract and they should also make it clearer in the introduction the novelty of this line on inquiry. Otherwise, the manuscript is ready for publication after this minor revisions.  

Author Response

I recommend the authors to reduce the introductory part of the abstract

The introduction to the abstract has been condensed.

 

They should also make it clearer in the introduction the novelty of this line on inquiry.

A statement outlining the novelty of this work has been added to the introduction (lines 72-75).

Reviewer 2 Report

Comments in attached document

Comments for author File: Comments.pdf

Very good level of English, nevertheless I would suggest a second reading of the manuscript and editing some long and complicated sequences in the text. Sometimes is to easy to loose the track,

Author Response

The paper is a little bit difficult to read – numerous sentences are usually long and complicated, although usually grammatically correct. I would suggest for the Authors to read the manuscript and shorten / simplify the sentences if possible

Overly long sentences have been simplified where possible.

 

typo line 87 - type-II -> type-III

This has been corrected

 

The Authors compare the list of adsorbing residues with previous MD results, I would be grateful if I could also see a similar comparison regarding the adsorption stability of other FN-III domains on hydrophobic surfaces

Comparison of the stability of different fibronectin fragments from previous simulations has been added to the conclusions (lines 314-327 and Table 3).

Reviewer 3 Report

Comments for author File: Comments.pdf

Review for “Adsorption of Heparin Binding Fragments of Fibronectin onto Hydrophobic Surfaces” by Viswanath Vitteladevaram et al.

 

In this manuscript, the authors developed a molecular dynamics model and performed molecular dynamics simulations to study the adsorption of heparin binding fibronectin domains onto hydrophobic surfaces. The results in this study suggest that the interplay between protein structure and surface chemistry is vital for understanding the protein adsorption process. Overall, this manuscript is well-written and easy to understand. The discoveries in this work will be of interests to readers of Biophysica. However, the minor comments below should be addressed before this manuscript is ready for publication.

 

1.     There are some typos and grammatical mistakes in this manuscript. Please check through to correct them.

2.     Have the simulations been repeated to ensure the repeatability of findings in this manuscript?

3.     Some of the acronyms are not defined before use, e.g., vdW.

4.     X-direction is mentioned in the methods section but not labeled in the figures, which might cause confusion.

5.     What are the dimensions and boundary conditions of the simulation box?

Author Response

There are some typos and grammatical mistakes in this manuscript. Please check through to correct them.

Typos and grammatical mistakes have been corrected.

 

Have the simulations been repeated to ensure the repeatability of findings in this manuscript?

For each domain four different simulations were performed. This is now stated explicitly in the manuscript (lines 89-91)

Some of the acronyms are not defined before use, e.g., vdW.

The definition of acronyms has been added to the manuscript

 

X-direction is mentioned in the methods section but not labeled in the figures, which might cause confusion.

A figure illustrating the simulation set up, including definition of the x direction has been added to the manuscript (Figure 1).

 

What are the dimensions and boundary conditions of the simulation box?

The dimensions and boundary conditions are now stated in the manuscript (line 87 and lines 107-109)