Interaction of Uperin Peptides with Model Membranes: Molecular Dynamics Study
Round 1
Reviewer 1 Report
The main question that is addressed by Ermakova and Kurbanov is evaluating the interaction of uperin peptide and its R7A mutant upon interaction with POPG and POPE model membranes using molecular dynamics study. The topic is considered original as it tries to shed light on the type of peptide-membrane interaction. Specific improvements are required regarding the addition of some positive controls. Besides, the abstract can be more informative and the number of references needs to be increased especially in the discussion section for a deeper comparison with similar literature designs.
Author Response
We thank the reviewers for constructive and helpful comments and revised the manuscript accordingly. Below we address each of the points raised by the reviewer. Our answers are in italic.
Reviewer 1.
The main question that is addressed by Ermakova and Kurbanov is evaluating the interaction of uperin peptide and its R7A mutant upon interaction with POPG and POPE model membranes using molecular dynamics study. The topic is considered original as it tries to shed light on the type of peptide-membrane interaction. Specific improvements are required regarding the addition of some positive controls. Besides, the abstract can be more informative and the number of references needs to be increased especially in the discussion section for a deeper comparison with similar literature designs.
Abstract is corrected.
The discussion section is improved, and comparison with known literature data is adact is corrected.ded in the Results and Discussion sections. (p. 10, 13).
Reviewer 2 Report
Please see the attachment.
Comments for author File: 
Comments.pdf
Author Response
We thank the reviewers for constructive and helpful comments and revised the manuscript accordingly. Below we address each of the points raised by the reviewer. Our answers are in italic.
Reviewer 2.
This manuscript by Ermakova et al. investigates the interaction of Uperin peptide (a short peptide with 17 amino acids) with POPE/POPG membrane using molecular dynamics simulations. Authors have utilized all-atom molecular dynamics and umbrella sampling approaches to characterize the process of the peptide binding from water to the lipid bilayer and insertion of peptide into the member bilayer by calculating potential of mean force (PMF). Authors have also characterized the effect of the peptide in the structural properties of the membrane by calculating deuterium order parameters. I think this study is potentially helpful to understand the interaction behavior of Uperin peptide with model membranes. This study will be interesting to the readers of membrane.
However, there are some issues need to be addressed before accepting the manuscript. -Authors have analyzed all-atom MD simulation trajectory data of extended form of the peptide and helical form of the peptide in POPE/POPG membrane environment. They have reported orientation and location of the peptide with respect to membrane but they have not provided detail discussion with the structural conformational dynamics of the peptide (such as helical kink or bending of the peptide) when incorporated into lipid bilayers (Figure 2 and 3). I think it would be helpful to discuss how the structural conformation of the peptide is stabilized in the lipid bilayers at lowest energy conformation of the peptide-membrane system.
Information about the structural conformation of the peptides is added on pages 5 and 6. Values of the angles characterizing the bending of helixes are shown.
Comparison with known literature data is added in the Results section.
- Authors have reported deuterium order parameters of the lipid in the presence and absence of the peptide (Figure 6). However, the information about how they implemented the deuterium in the membrane during the simulation is missing in the method section. How did they account for the deuterium instead of hydrogen for the membrane during the simulation? Authors need to provide additional information in the method section.
“Deuterium order parameters” is a standard term widely used as a measure of the orientation mobility of the lipid hydrocarbon segments along the acyl tails (for example, Chem. Rev. 2019, 119, 6227−6269; Langmuir 2021, 37, 34, 10259–10271). In the Methods section it was written that the angle for SCH calculations “is the angle between the C−H bond vector and the bilayer normal”. However, we agree with the reviewer that sometimes it can mislead the readers and have replaced this term with “order parameters” (p.11).
-The conclusion section is missing in the manuscript. Authors need to provide conclusion or summary section in the manuscript.
Conclusion is added.
-Supporting Information: the unit of the parameters (thickness and area per lipid) in the table and unit of the axis label “angle” in the Figure S1 are missing.
Corrected
- There are several typos and grammatical errors in the manuscript such as: page 10, lclusion is added.ine 362, “…have not observe spontaneous,…” should be “…have not observed spontaneous,…”; page 11, line 421, “Comparison the calculated results” should be “Comparison of the calculated results”; page 12, “ line 412 “…surface or insert into…” should be “ ….surface or inserted into…”. There are several other similar errors in Discussion section and other places.
Manuscript needs extensive revision for typos and grammar errors.
English grammar was carefully checked throughout the text.
Round 2
Reviewer 2 Report
The revised version of the manuscript is now improved.
The authors have addressed the majority of my comments.
So, I would like to recommend the publication of this manuscript.
