Thursday, August 15, 2013

Review of Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

The reviews for +Anders Steen Christensen's paper, submitted to PLoS ONE on 2013.07.24, are in.

There are 3 main points raised by the reviwer:

1. Do ProCS-predicted chemical shifts predicted using all high resolution structures of ubiquitin compare poorly with experiment?

That's not too tough to find out.

2. "Can the authors show improved structure validation characteristics when using more conventional evaluation criteria (e.g using the Protein Structure Validation Software (PSVS), or RDC Q factors)?"

The problem is were dealing with ensembles of 1000s of structures, so unless we can find an downloadable version of PSVS, this won't be possible.  Also, I don't believe PSVS scores report on anything directly associated with backbone amide hydrogen bonds, so I am not sure what the answer would tell us.

Wrt RDC Q factors, that'll take a while to write the code for questionable benefit.  Should we argue on this or try to do it?

3. Depositing the structures.  We need to find a place that'll accept 10-20 GB files.

From: PLOS ONE <>
Date: Wed, Aug 14, 2013 at 6:49 AM
Subject: PLOS ONE Decision: Revise [PONE-D-13-30410]
To: "Anders S. Christensen" <xxx>

Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

Dear Mr. S. Christensen,

Thank you for submitting your manuscript for review to PLOS ONE. After careful consideration, we feel that your manuscript will likely be suitable for publication if it is revised to address the points below. Therefore, my decision is "Minor Revision."

We invite you to submit a revised version of the manuscript that addresses the three points that reviewer #1 raises. The first point in particular concerning errors in chemical shifts due lack of ensemble sampling in x-ray structures may require considerable work but would be of serious benefit to thrills.

We encourage you to submit your revision within forty-five days of the date of this decision.

When your files are ready, please submit your revision by logging on to and following the Submissions Needing Revision link. Do not submit a revised manuscript as a new submission. Before uploading, you should proofread your manuscript very closely for mistakes and grammatical errors. Should your manuscript be accepted for publication, you may not have another chance to make corrections as we do not offer pre-publication proofs.

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Yours sincerely,

Academic Editor

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Journal requirements:

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1) Please ensure that you refer to Supplementary Figures S1, S4 and S5 in your text as, if accepted, production will need this reference to link the reader to the Figures.

2) Thank you for stating the following in the Financial Disclosure section:

ASC is funded by the Novo Nordisk STAR PhD program. MB is funded by the Danish Council for Independent Research (FTP, 09-066546). WB and K L-L are supported by a Hallas-Møller stipend (to K L-L) from the Novo Nordisk Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Partly

Please explain (optional).

Reviewer #1: The manuscript builds on earlier work for 1H chemical shift calculation using QM methods to parameterize a novel method (ProCS) to rapidly predict 1H chemical shifts by adding the various terms, assuming their additivity applies, which the authors demonstrate to be a good approximation within the errors that one has to deal with. The 1H chemical shift prediction errors with ProCS remain high compared to the empirical programs "on the market" today, but as the authors argue (probably correctly) these prediction errors are dominated by structural noise, and empirical methods have been optimized to be as insensitive as possible to errors in the input coordinates.

They then take advantage of this extreme sensitivity to structural errors by including the difference between ProCS and experimental shift as a "constraint" when refining the structure with their MCMC method, and validate the improvement in structural quality by showing improved agreement between experimental h3JNC' couplings and values predicted on the basis of H-bond geometry by the Barfield equation, showing dramatic improvements in agreement (i.e., presumably in H-bond geometry).

Although the method appears computationally more expensive than the popular CAMSHIFT program, it clearly offers a new and potentially more powerful approach for refining structures directly against amide 1H shifts.

I believe the work is potentially important and of suitable quality for publication in PLOS One, but would like to see the two minor issues raised below addressed prior to its publication (as I presume many readers will have the same questions).

1. The authors comment that the inability to reproduce the experimental chemical shifts by QM methods may be caused by the fact that X-ray structures represent merely one snapshot of what in real life is a statistical ensemble (p.4). If that is true, one would expect all high resolution structures of ubiquitin to agree rather poorly (there are at least a dozen with X-ray resolution <=1.8 A). Is this true? Is it also true that ensembles refined against the experimental h3JNC' couplings (e.g. 2K39 or 2KOX) fit better than single structures (e.g. 1D3Z)?

2. Both HN chemical shift and h3JNC' are dominated by H-bond length, and the improved fitting of chemical shifts after refinement is therefore perhaps a bit circular. Can the authors show improved structure validation characteristics when using more conventional evaluation criteria (e.g using the Protein Structure Validation Software (PSVS), or RDC Q factors)?

2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Please explain (optional).

Reviewer #1: (No Response)

3. Does the manuscript adhere to standards in this field for data availability?

Authors must follow field-specific standards for data deposition in publicly available resources and should include accession numbers in the manuscript when relevant. The manuscript should explain what steps have been taken to make data available, particularly in cases where the data cannot be publicly deposited.

Reviewer #1: No

Please explain (optional).

Reviewer #1: The atomic coordinates of the refined structures of the three proteins studied should be deposited.

4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors below.

Reviewer #1: Yes

Please explain (optional).

Reviewer #1: (No Response)

5. Additional Comments to the Author (optional)

Please offer any additional comments here, including concerns about dual publication or research or publication ethics.

Reviewer #1: (No Response)

6. If you would like your identity to be revealed to the authors, please include your name here (optional).

Your name and review will not be published with the manuscript.

Reviewer #1: (No Response)

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