Native Nanodiscs and the Convergence of Lipidomics, Metabolomics, Interactomics and Proteomics
Round 1
Reviewer 1 Report
Overduin and Esmaili provide a timely and well-written review of polymer-based nanodiscs and bring together some loose ends from different -omics approaches. The latter quality is what distinguishes the present manuscript from (too) many other reviews in the still relatively young but rapidly advancing field of polymer-mediated membrane protein extraction. Overall, the authors succeed in giving a fair account of many diverse contributions and in offering a fresh view of this field. Hence, I recommend this manuscript for publication, provided that the authors address the following minor issues.
- This is a question of taste, but the contracted word “memtein” is a pain not only to people fluent in Greek and Latin.
- “cEM” is a very unusual abbreviation for what is more commonly called “cryo-EM”.
- The paragraph starting on line 88 (“Both MS and NMR play key roles…”) is a bit misleading because it suggests that MS and NMR play similar roles in metabolomics and lipidomics. This is not the case, however, as the two methods play rather complementary roles, with MS affording much higher throughput and NMR furnishing more in-depth information.
- Line 116: The statement that “there is a memory of the original arrangement” seems questionable in light of the fast lipid transfer mentioned later.
- Line 305: “THE largest…” (not “A largest…”)
- Line 322: “binds to…” (not “binds two…”)
Author Response
Overduin and Esmaili provide a timely and well-written review of polymer-based nanodiscs and bring together some loose ends from different -omics approaches. The latter quality is what distinguishes the present manuscript from (too) many other reviews in the still relatively young but rapidly advancing field of polymer-mediated membrane protein extraction. Overall, the authors succeed in giving a fair account of many diverse contributions and in offering a fresh view of this field. Hence, I recommend this manuscript for publication, provided that the authors address the following minor issues.
- This is a question of taste, but the contracted word “memtein” is a pain not only to people fluent in Greek and Latin.
This term concisely describes a new concept that has been previously accepted and published,and referes to a complex of a protein and a bound shell of biological lipid. We would prefer to continue to use this term for conceptual clarity and consistency.
- “cEM” is a very unusual abbreviation for what is more commonly called “cryo-EM”.
This term has been replaced as suggested.
- The paragraph starting on line 88 (“Both MS and NMR play key roles…”) is a bit misleading because it suggests that MS and NMR play similar roles in metabolomics and lipidomics. This is not the case, however, as the two methods play rather complementary roles, with MS affording much higher throughput and NMR furnishing more in-depth information.
This has been amended as suggested.
- Line 116: The statement that “there is a memory of the original arrangement” seems questionable in light of the fast lipid transfer mentioned later.
This has been amended to be clearer.
- Line 305: “THE largest…” (not “A largest…”)
This has been corrected.
- Line 322: “binds to…” (not “binds two…”)
This has been corrected.
Reviewer 2 Report
line 23: The usual acronym for cryo-electron microscopy is cryo-EM (with or without dash) and for X-ray crystallography is XRD (for X-ray diffraction). The authors will make their work more accessible if they kept that convention.
line 33: ..."should be accurate and reproducible"... This applies to all scientific reporting
line 35: ..."due to their frequent low abundance"... is hard to read, I would remove frequent.
Overall Section 1 can use more citations.
p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 10.0px Times} span.s1 {font: 11.5px 'Times New Roman'}
line 70 ..."The problems that current detergent-based protocols confront proteomics and structural biology experts with are being addressed by development of native nanodiscs to separate memteins."... This sentence is very hard to read.
Author Response
line 23: The usual acronym for cryo-electron microscopy is cryo-EM (with or without dash) and for X-ray crystallography is XRD (for X-ray diffraction). The authors will make their work more accessible if they kept that convention.
These terms have been replaced as suggested.
line 33: ..."should be accurate and reproducible"... This applies to all scientific reporting
This sentence has been clarified.
line 35: ..."due to their frequent low abundance"... is hard to read, I would remove frequent.
This sentence has been clarified.
Overall Section 1 can use more citations.
Citations have been added to section 1.
line 70 ..."The problems that current detergent-based protocols confront proteomics and structural biology experts with are being addressed by development of native nanodiscs to separate memteins."... This sentence is very hard to read.
This sentence has been clarified.
Reviewer 3 Report
The authors present an interesting and well written review about the usage of polymer-based nanodiscs (from simplicity SMALPs in the following). I have only a few suggestions the authors may or may not include:
While the first part of the review nicely describes the potential of SMALPs as combined platform for omics approaches, the second part is more of a general review of SMALPs diverse applications. As such I felt a bit disappointed at the end because I was expecting more focus on the omics applications also in the second part. In case there are currently none to fill a full review, I would suggest to change the title to something like: Potential of native nanodiscs to converge …
While there are clearly some advantages of the method there are also downsides of using SMALPs. The authors address some limiting aspects in a rather short manner. I would suggest to include a separate heading about potential disadvantages and future challenges. In any case the authors should include a few more sentences discussing downsides. In my opinion in particular the heterogeneity as well as the very high charge density of the polymers have very strong disadvantages. E.g. in our case (GPCR with peptide ligands) we see that basically all tested proteins and peptides display a very strong (unwanted) interaction with the SMA polymer (often comparable to the specific binding to the receptor), making any binding assay very unreliable (this is probably also true for a number of published results, which did not check this properly). In respect to heterogeneity, in particular some insect cell membranes can only be solubilized in a very heterogenous particle distribution (8-100 nm). Unspecific binding and heterogeneity will clearly also be challenging for omics applications.
Author Response
The authors present an interesting and well written review about the usage of polymer-based nanodiscs (from simplicity SMALPs in the following). I have only a few suggestions the authors may or may not include:
While the first part of the review nicely describes the potential of SMALPs as combined platform for omics approaches, the second part is more of a general review of SMALPs diverse applications. As such I felt a bit disappointed at the end because I was expecting more focus on the omics applications also in the second part. In case there are currently none to fill a full review, I would suggest to change the title to something like: Potential of native nanodiscs to converge …
A new title is suggested: “Native nanodiscs and the convergence of lipidomics, metabolomics, interactomics and proteomics”
While there are clearly some advantages of the method there are also downsides of using SMALPs. The authors address some limiting aspects in a rather short manner. I would suggest to include a separate heading about potential disadvantages and future challenges. In any case the authors should include a few more sentences discussing downsides. In my opinion in particular the heterogeneity as well as the very high charge density of the polymers have very strong disadvantages. E.g. in our case (GPCR with peptide ligands) we see that basically all tested proteins and peptides display a very strong (unwanted) interaction with the SMA polymer (often comparable to the specific binding to the receptor), making any binding assay very unreliable (this is probably also true for a number of published results, which did not check this properly). In respect to heterogeneity, in particular some insect cell membranes can only be solubilized in a very heterogenous particle distribution (8-100 nm). Unspecific binding and heterogeneity will clearly also be challenging for omics applications.
A few sentences on the pros and cons have been added to the conclusion.
