Dear Prof. Dr. Schwarz,

Thank you very much for submitting your manuscript "Electrostatic and bending energies predict staggering and splaying in nonmuscle myosin II minifilaments" for consideration at PLOS Computational Biology. As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board and by two independent reviewers. Based on the reviews and the guest editor's reading, we are likely to accept this manuscript for publication, providing that you modify the manuscript according to the review recommendations as well as to answer three questions by the guest editor listed below. 

Please prepare and submit your revised manuscript within 30 days. If you anticipate any delay, please let us know the expected resubmission date by replying to this email. 

When you are ready to resubmit, please upload the following:

[1] A letter containing a detailed list of your responses to all review comments, and a description of the changes you have made in the manuscript. Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out

[2] Two versions of the revised manuscript: one with either highlights or tracked changes denoting where the text has been changed; the other a clean version (uploaded as the manuscript file).

Important additional instructions are given below your reviewer comments.

Thank you again for your submission to our journal. We hope that our editorial process has been constructive so far, and we welcome your feedback at any time. Please don't hesitate to contact us if you have any questions or comments.

Sincerely,

Dimitrios Vavylonis

Guest Editor

PLOS Computational Biology

Mark Alber

Deputy Editor

PLOS Computational Biology

***********************

A link appears below if there are any accompanying review attachments. If you believe any reviews to be missing, please contact ploscompbiol@plos.org immediately:

[LINK]

The two reviewers of the manuscript as well as myself found your work important and novel. When you resubmit your manuscript, please consider their minor suggestions as well as the following questions I had:

1) Refs 16, 19, 24, 26 are mentioned as earlier studies where electrostatic energy calculations have been performed. Can you discuss any differences or similarities in terms of magnitude and overall trend (between prior and current energy calculations)? Would this comparison justify the level of coarseness used in this work?

2) In line 98 it is stated that “For small ionic strengths, the Poisson-Boltzmann equation can be linearized…” It’s not clear if this means that the linearization approximation is valid considering the stated charge density of the myosin tail. Can you comment on this approximation? Also, is the system far from regimes where counterions may cause attraction between rods of same charge?

3) Would accounting for the entropic fluctuations of the tail modify any of the results?

Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: The authors described an insightful model that combines continuum electrostatics and elasticity to model the assembly of nonmuscle myosin II minifilament. By minimizing the effective energy of the system with different degrees of staggering and computing the relevant mean first passage time (referred to as "contact time"), the authors correctly predicted the favorable staggerings of parallel and anti-parallel dimers. Moreover, they demonstrated that the relatively simple model can also capture the differences between homodimers and heterodimers observed in recent experiments, supporting the general validity of the model.

Overall, the ms is clearly written with solid connection with experimental observations. Further extension of the model to multiple rods will be able to model more diverse behaviors for helping better interpret experimental observations. I support the publication of the work in PLoS Comp Biol.

I have only several minor questions/comments:

1. The model assumes a regular coiled-coil structure and therefore canonical charge distribution associated with such structure. In reality, however, there are skip residues that disrupt the regular coiled-coil pattern and modulate both the helical pitch and solvent-exposed residues (see, for example, recent work of I. Rayment, Cui and co-workers). The authors should discuss the potential impact of the skip residues.

2. Are there predictions that the authors can make for possible experimental tests?

Reviewer #2: This theoretical paper considers the configurations of parallel and antiparallel dimers of non-muscle myosin II molecules using the electrostatic and bending energies. Based on the distribution of charge along myosin rods the parallel dimers with staggers of 14.3, 43.2, and 72 nm present local energy minima. These staggers were previously predicted and observed experimentally. The novelty of this paper is that the authors consider that the length of contact between the two rods is not fully determined by the stagger, but could also change due to bending and splaying of the rods away from each other. Combined electrostatic and bending energy landscape identifies the same favorable staggers, but also suggests that parallel configurations have a strong tendency to splay myosin heads away from the common axis. In contrast, antiparallel configuration with an overlap of 43 nm is very stable and likely serves as nucleus for minifilament nucleation. Using Fokker-Planck equation, the authors compute relative contact times for different configurations and different myosin isoforms suggesting possible order of the assembly of myosin structures in the cell. This approach is novel and elegant, and has important implications for the understanding of the structure and dynamics of myosin II assemblies. I have only one minor comment: given the observations on rich myosin II structure and dynamics that are described in the Introduction, I would appreciate a little more discussion of the relevance of splaying of myosin heads to these variable configurations, e.g. parallel filament stacks.

**********

Have all data underlying the figures and results presented in the manuscript been provided?

Large-scale datasets should be made available via a public repository as described in the PLOS Computational Biology data availability policy, and numerical data that underlies graphs or summary statistics should be provided in spreadsheet form as supporting information.

Reviewer #1: Yes

Reviewer #2: Yes

**********

PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: Yes: Alexander Verkhovsky

Figure Files:

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email us at figures@plos.org.

Data Requirements:

Please note that, as a condition of publication, PLOS' data policy requires that you make available all data used to draw the conclusions outlined in your manuscript. Data must be deposited in an appropriate repository, included within the body of the manuscript, or uploaded as supporting information. This includes all numerical values that were used to generate graphs, histograms etc.. For an example in PLOS Biology see here: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001908#s5.

Reproducibility:

To enhance the reproducibility of your results, PLOS recommends that you deposit laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see http://journals.plos.org/ploscompbiol/s/submission-guidelines#loc-materials-and-methods

Dear Prof. Dr. Schwarz,

We are pleased to inform you that your manuscript 'Electrostatic and bending energies predict staggering and splaying in nonmuscle myosin II minifilaments' has been provisionally accepted for publication in PLOS Computational Biology.

Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests.

Please note that your manuscript will not be scheduled for publication until you have made the required changes, so a swift response is appreciated.

IMPORTANT: The editorial review process is now complete. PLOS will only permit corrections to spelling, formatting or significant scientific errors from this point onwards. Requests for major changes, or any which affect the scientific understanding of your work, will cause delays to the publication date of your manuscript.

Should you, your institution's press office or the journal office choose to press release your paper, you will automatically be opted out of early publication. We ask that you notify us now if you or your institution is planning to press release the article. All press must be co-ordinated with PLOS.

Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Computational Biology. 

Best regards,

Dimitrios Vavylonis

Guest Editor

PLOS Computational Biology

Mark Alber

Deputy Editor

PLOS Computational Biology

***********************************************************

Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Guest Editor: Thanks for the detailed and clear explanations.

Reviewer #1: The authors have done a fine job responding to the questions raised in the last round of review.

**********

Have all data underlying the figures and results presented in the manuscript been provided?

Large-scale datasets should be made available via a public repository as described in the PLOS Computational Biology data availability policy, and numerical data that underlies graphs or summary statistics should be provided in spreadsheet form as supporting information.

Reviewer #1: Yes

**********

PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No