PONE-D-21-38609idpr: A package for profiling and analyzing Intrinsically Disordered Proteins in RPLOS ONE

Dear Dr. Yanowitz,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

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ACADEMIC EDITOR:Please try to improve your manuscript according to the reviewers' criticism. It would be good to add some more examples of successful predictions carriied out by your software package. 

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Kind regards,

Eugene A. Permyakov, Ph.D., Dr.Sci.

Academic Editor

PLOS ONE

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- https://rdrr.io/bioc/idpr/f/inst/doc/idpr-vignette.Rmd

In your revision ensure you cite all your sources (including your own works), and quote or rephrase any duplicated text outside the methods section. Further consideration is dependent on these concerns being addressed.

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Reviewers' comments:

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Comments to the Author

1. Does the manuscript report a protocol which is of utility to the research community and adds value to the published literature?

Reviewer #1: Yes

Reviewer #2: Yes

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2. Has the protocol been described in sufficient detail?

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Reviewer #1: Yes

Reviewer #2: Yes

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3. Does the protocol describe a validated method?

The manuscript must demonstrate that the protocol achieves its intended purpose: either by containing appropriate validation data, or referencing at least one original research article in which the protocol was used to generate data.

Reviewer #1: No

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: N/A

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Reviewer #1: Yes

Reviewer #2: Yes

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6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: The manuscript PONE-D-21-38609 presents “idpr”, a software package aimed at the analysis of sequence properties of Intrinsically Disordered Proteins (IDPs) and unfolded protein regions, written by using the programming language R (one of the most common for statistical computing, data mining, and graphical representation). Following the general practice/tradition of reports of software packages, the manuscript illustrates the main features of “idpr” in a succinct way, includes test cases for two well-known IDPs (alpha-synuclein and p53), and refers to the program at the internet address https://bioconductor.org/packages/idpr/ for further info; a workflow including instructions for the installation is also provided as Supporting Information.

This work is interesting and provides a useful tool, because IDPs are currently widely investigated - as explained in the text, they are increasingly recognized as ubiquitously present in all organisms, and heavily involved in many pathologies. The language used is concise and direct, and the presentation is clear enough. Overall, it can be improved as described hereafter.

Major points:

- The two test cases presented both involve IDPs that possess large ordered regions. Alpha-synuclein in its functional conformation has 66% of its sequence in helical conformation, and such secondary structure is even folded in a sort of tertiary hairpin structure. Similarly, p53 has a high structural plasticity, but 63% of the sequence adopts a (labile) secondary and tertiary structure. A test case for an entirely unfolded IDP is lacking, and must be added to fully validate the software/protocol presented.

Any full-unstructured IDP can be chosen to this aim. For instance, NUPR1 (UniProt ID: O60356), a small protein of 82 residues with 0% secondary/tertiary structure (in spite of the wrong prediction of AlphaFold shown on the UniProt page). This protein remains disordered even in molecular complexes, thus is considered a model for a “perfect” IDP. Peaks in the hydropathy plot of NUPR1 nicely identify hot spots for the binding to molecular partners that include other (folded/unfolded) proteins, peptides, DNA, inorganic polymers, and various drugs, thus it constitutes an interesting and very easy test case. Other proteins, on top of my head, may include p21, prothymosin alpha, and perhaps even some unstructured proteins of SARS-CoV-1/2.

Minor points:

- Abstract: please consider mentioning https://bioconductor.org/packages/idpr/ already there or, alternatively, as soon as possible.

- Line 27: “these proteins have been implicated in several human diseases such as Parkinson’s Disease, Alzheimer’s Disease, and various cancers (5-7)”. Given the enormous progress of the research in this field, it is disappointing to see that the only papers cited are 10-15 years old. Please consider substituting or complementing them with updated references.

- Line 46: “the R package idpr stands for a few things: “Intrinsically Disordered Proteins in R” and “IDp PRofiles””. This seems to contradict the Abstract, where a single meaning of the acronym is given. Please correct either the Abstract or, more easily, the text, e.g. “stands for “Intrinsically Disordered Proteins in R”, although other acronyms such as “IDp PRofiles” are possible”.

- Line 64: “fasta files”. Please call it either FASTA (the correct name for the format) or .fasta (its file extension).

- Line 67: “tidverse packages”. Typo, it is “tidyverse”.

- Line 77: “If a UniPot ID is not included, the IUPred plot is skipped”. What happens if one wants to investigate a sequence that has not a UniProt ID, e.g. a new mutant of a known sequence? If this is already possible, it should be explained in the text; otherwise, it should be addressed in a future release of “idpr”.

- Line 81: “Method described in (16). Mean Scaled Hydropathy calculated with The Kyte and Doolittle measurement of hydropathy”. It should be “Methods are described...”, and “the Kyte and Doolittle” (lowercase “the”).

- Line 98: “extreme net charge and deficiency in hydropathy are characteristics of intrinsic disorder (16)”. It should be specified “intrinsic disorder in proteins” (or polypeptides).

- Line 109: “ The resulting figure is similar to ProtScale from ExPASy (38)”. It should be a bit expanded, e.g. “similar to the one that can be obtained by using the ProtScale tool from ExPASy”.

- Line 116: “Order promoting residues, meaning those enriched in structured proteins, tend to be aliphatic, hydrophobic, aromatic, or can form tertiary structures”. It should be “those more frequent in structured proteins” (structured proteins are enriched of these residues, not the other way around). Also, it should be “prone to form secondary/tertiary structures” (any residue “can form” such structures, with a few exception such as Prolines in secondary structures; the difference is again in the frequency).

- Line 117: “Disorder neutral residues”. It should be “Disorder-neutral residues”, the hyphen is crucial. Please also delete the space in “disorder- neutral residues”, three lines below.

- Line 139: “Residues with an IUPred2 long score”. The term “long” is unclear.

- Line 162: “This function can also visualize continuous values”. I cannot understand why it is important to specify this, or imagine an example of an use of such continuous values.

- Line 181: “aSyn is an IDP, experimentally determined using various methods”. Please use “investigated”, “validated”, “identified”, etc., instead of “determined”.

- Line 189: “Although the protein is deficient in Arg, the local charges of the protein are mostly neutral, apart from...”. I do not see the point of using “Although”.

- Line 201: “identifying biochemical features related to IDPs within a protein of interest”. Either it was meant “IDRs” instead of “IDPs”, or it is not clear.

- Discussion. This looks more like a Conclusion to me; maybe it can be slightly enlarged.

- Acknowledgments: It would be nice to state explicitly the names of Dr. M. Buszczak and Dr. M. Brieno-Enriquez.

Reviewer #2: The manuscript describes a relative simple but useful tool for profiling and analysis of intrinsically disordered proteins. The tool is available in R and provides quick analysis and visualization of several relative basic sequence properties of IDPs. These tools should be useful for someone who needs to do quick analysis of these sequence based properties. However, I have some reservation on how useful this tool will be. These properties are quite basic and the targeted users are probably non-experts; yet it require some proficiency in R and scripting to use. It would appear to be much more useful to have a web-based interface for the targeted users. I also recommend the author to build interface to other IDP analysis tools besides IUPred, such as Rohit Pappu's CIDER and others.

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Reviewer #1: No

Reviewer #2: No

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idpr: A package for profiling and analyzing Intrinsically Disordered Proteins in R

PONE-D-21-38609R1

Dear Dr. Yanowitz,

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Kind regards,

Eugene A. Permyakov, Ph.D., Dr.Sci.

Academic Editor

PLOS ONE

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