Talk:WikiJournal of Science/The TIM barrel fold

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WikiJournal of Science
Wikipedia-integrated • Public peer review • Libre open access

WikiJournal of Science is an open-access, free-to-publish, Wikipedia-integrated academic journal for science, mathematics, engineering and technology topics. WJS WikiJSci Wiki.J.Sci. WikiJSci WikiSci WikiScience Wikiscience Wikijournal of Science Wikiversity Journal of Science WikiJournal Science Wikipedia Science Wikipedia science journal STEM Science Mathematics Engineering Technology Free to publish Open access Open-access Non-profit online journal Public peer review

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Article information

Authors: Deepesh Nagarajan[a][i]ORCID iD.svg , Neha Nanajkar[a]ORCID iD.svg 

Deepesh Nagarajan; Neha Nanajkar (2020), "The TIM barrel fold", WikiJournal of Science, 3 (1): 4, doi:10.15347/WJS/2020.004, ISSN 2470-6345, Wikidata Q87400003




 


Plagiarism checking

Pass. Report from WMF copyvios tool: 2.9% Plagiarism (trivial overlap), 97.1% Unique. HemachanderTBio (discusscontribs) 14:03, 10 April 2019 (UTC)

First peer reviewer

Review by Cristina Elisa Martina , Université de Liège
This review was submitted on , and refers to this previous version of the article


In general the review is well organized and complete, regarding structural and evolutionary features that characterize the TIM-barrel family. Also the chapter on the TIM-barrel design reports in detail all the works performed so far on the subject. Comments and few minor corrections are attached in the pdf file. The line number refers to the pdf version of the manuscript.

Line 10: fix “αhelices” in “α-helices”.

Response

Fixed to “α-helices” (line 10).

Lines 11-12: C-terminal loops are important for catalytic activity, while N-terminal loops are important for the stability of the TIM-barrels. This should be mentioned.

Response

“while N-terminal loops are important for the stability of the TIM-barrels” has now been mentioned in line 12.

Line 14: The reference #7 is not related to the statement.

Response

Reference 7 has been removed.

Line 14: There is a new EC classe (EC.7, translocases). Change “5 of 6” in “5 of 7”.

Response

“5 of 7” is now mentioned (line 14).

Lines 26-27: It is not correct to state that the shear number of 8 for the TIM-barrels is due to “their staggered nature”. Most of the β-barrels have a staggered nature, but their shear number is not 8.

Response

Agreed. We no longer claim that the shear number is 8 due to a staggered nature (lines 27-28).

Line 27: The reference #2 is imprecise. Wierenga did not defined himself the shear number of TIMbarrel proteins. Please check the 2 papers of Murzin AG, 1994, “Principle determining the structure of β-sheet barrels in proteins,” I and II, and the paper of Liu W, 1998, “Shear numbers of protein β- barrels: definition refinements and statistics”.

Response

We have now used and cited a definition similar to that provided by Murzin AG, 1994 (figure 1 caption) for shear number.

Murzin’s definition reads: On this part of the Figure we mark the number of strands in the B-sheet, n (6 here) and the measure of its stagger: the shear number S. S can be determined by starting from residue k in strand l, move around the barrel, in a direction perpendicular to the direction of the strand, until strand 1 is reached again. Because of the stagger the point of return will not be residue k but one displaced from it. The shear number is |Z-k| (in this example S = 8)

Our definition reads: The shear number is determined by picking a residue x on β-strand-1, and moving along the β-barrel, in a perpendicular direction to the direction of the strands, until residue y on the original β-strand-1 is reached. The number of residues between the start and end positions (| y-x|) is the shear number (lines 28-30).

Line 29: Again, it is not correct to state that the 4-fold geometric symmetry depends on the stagger. Since the number of strands (n) is equal to the Shear number (S), side-chains point alternatively towards the pore and the core, giving a 4-fold symmetry.

Response

Agreed. We have used the reviewer’s explanation for 4-fold symmetry (lines 30-31).

Line 37: “historically” is a bit exaggerated for a reference dated 2015, especially if it comes from the author itself. Find a true historic reference, or just mention that you defined the regions “core” and “pore”.

Response

Agreed. The line now reads: “We have previously referred to these regions as the 'core' and 'pore'” (line 39).

Line 43: “Consequently” is misleading. The fact that 11% of the core residues are polar does not depend by the fact that 95% of core residues are buried.

Response

We have now removed the word ‘consequently’ (line 45).

Lines 55-57: Reference #25 support the idea that the folding process is driven by hydrophobic interactions of branched aliphatic side-chains (leucine, isoleucine and valine). This theory is opposite to the one that you mention in lines 53-55 (polar residues stabilizing the foldons). Please make it clear that there are evidences for both theories.

Response

We now mention the difference between the two foldon hypotheses: “In this case however, the authors credited branched aliphatic amino acids (valine, leucine, and isoleucine) for foldon stability” (lines 61-62).

Line 64: There is an open parenthesis that is never closed. at the C-terminal of the β-barrel is now without parentheses (line 74). Lines 90-91: The fact that TIM-barrels evolved from a single ancestor, following gene duplication and fusion, is still a theory (the most supported, but still a theory). Please make it clear that it is a theory in this introductory sentence. Moreover pay attention to the sentence “forming an enzymatically active TIM-barrel”, it suggest that the half barrels have no functions and that only TIM-barrels became enzymes. Evolutionary speaking it is quite unlikely that the half-barrels had no function, however there are no evidences to support (or deny) this theory. I will simply use “forming the actual structure of the TIM-barrels” or something similar, without references to the function.

Response

We have rephrased this sentence: “The predominant theory for TIM barrel evolution involves gene duplication and fusion, starting with a half- barrel that eventually formed a full TIM barrel.” (lines 121-122)

Lines 118-124: You should re-organize this paragraph. Höcker et al. (reference #17) are the firsts that designed HisF-C*C in their paper of 2004, and should be mentioned at the beginning. Seitz et al. (reference #15) used the HisF-C*C designed by Höcker as basis to create HisF-C***C, which was then crystallized and its structure solved in 2009 (reference #16).

Response

We have reorganized the paragraph in the correct chronological order, putting Hocker’s work first (lines 150-158).

Second peer review

Review by Reinhard Sterner , University of Regensburg
This review was submitted on , and refers to this previous version of the article


This review on TIM barrels is timely and overall well organized. I have only some minor suggestions for the authors that might help them to further improve their manuscript:

Lines 8-10 and lines 24-26: the text is almost identical, please rephrase

Response

We have reworded lines 25-26:

“The TIM barrel gets its name from the enzyme triose phosphate isomerase (TIM), which was the first protein possessing the fold to be crystallized”

Figure 2: it is unclear what is meant by layer 1 and layer 2, please explain in the legend

Response

The legend now contains an explanation: “This symmetry is illustrated as two example "layers" in red and blue. Each layer contains 4 residues that point towards the pore, and lie on the same plane perpendicular to the barrel axis.”

Line64: “…in place of the ba loops at the C-terminal of the b-barrel.” Please state which ba loops have been replaced by a-helices.

Response

Positions of the ba loops replaced by a-helices have now been given: “residues 35-42, 89-91, 126-133, and 215-219” (lines 74-75)

Lines 70-71: the sentence is misleading; PriA does not catalyze the conversion of both ProFAR and PRA into CdRP. Instead, it catalyzes the conversion of ProFAR into PrFAR (HisA reaction), and the conversion of PRA into CdRP (TrpF reaction). Please correct.

Response

This has been corrected. The sentence now reads (lines 79-83):

Mycobacterium tuberculosis bifunctional histidine/tryptophan biosynthesis isomerase (PriA) (PDB ID: 2Y85, possesses the ability to catalyse two reactions: (i) HisA reaction: the conversion of N-[(5-phosphoribosyl) formimino]-5-aminoimidazole-4-carboxamide ribonucleotide (ProFAR) to N-[(5-phosphoribulosyl)formimino]-5-aminoimidazole-4-carboxamide ribonucleotide (PRFAR), and (ii) TrpF reaction: N-(5'-phosphoribosyl)-anthranilate (PRA) to 1-(O-carboxyphenylamino)-1'-deoxyribulose-5'-phosphate (CdRP)

Legend to Figure 4B: “The product CdRP is colored green.” should be replaced by “CdRP, the product of the TrpF reaction, is colored green.”

Response

We have made the change in the Figure 4B legend.

Figure 5 is shown before Figure 4. Please invert.

Response

Figure 4 is now placed before figure 5.

Line 127: the authors might wish to cite Carstensen et al. (2012) J. Am. Chem. Soc. 134, 12786-12791 along with Fortenberry et al. (ref. 21)

Response

We have cited the reference provided (line 158).

The format of the references is very heterogeneous and partially erroneous (For example ref. 24).

Response

We have fixed reference 24. It now reads:

Brändén, C.-I. The tim barrel—the most frequently occurring folding motif in proteins. 1: 978–983. Curr. Opin. Struct. Biol. 1, 978–983 (1991).

All other references are consistent with the Nature Referencing Style (part of the bibtex latex package used to generate this manuscript).

Followup comments

Review by Reinhard Sterner , University of Regensburg
This review was submitted on , and refers to this previous version of the article


There are two issues that need to be addressed by the authors:

1) The new references added by Robert Matthews have not been incorporated.

Response

We have added the references previously not incorporated.

2) The second paragraph of the chapter “Origin through gene duplication and gene fusion” is not entirely correct:

Response

We have used the corrected paragraph contributed by the reviewer.

Current version:

Interestingly, this evolutionary model has been experimentally validated using directed evolution and protein design techniques. Höcker et al. created the first chimeric HisA-HisF TIM barrel using HisA and HisF half-barrels. These experiments lead Höcker et al. to propose a novel means of diversification and evolution of TIM-barrel enzymes through the exchange of (βα)4 half-barrel domains amongst preexisting TIM barrels. Similarly, Seitz et al. constructed proteins HisF-C*C and HisF-C***C [28] from C-terminal HisF half-barrels. A salt-bridge cluster present in wild-type HisF was reconstructed, and random mutagenesis was performed to stabilize and solubilize the construct. The crystal structure [29] of HisF-C***C revealed a 2-fold symmetric TIM barrel, validating the possibility of natural domain fusion. Similar experiments were performed by Hocker et al. using HisA and HisF half-barrels, resulting in the successful creation of a chimeric HisA-HisF TIM barrel [30]. These experiments lead Hocker et al. to propose a novel means of diversification and evolution of TIM-barrel enzymes through the exchange of (βα)4 half-barrel domains amongst preexisting TIM barrels……

Suggestion for corrected version:

Interestingly, this evolutionary model has been experimentally validated using rational protein design and directed evolution. Höcker et al. first fused two C-terminal halves of HisF, yielding HisF-CC. This construct was then stabilized by the insertion of an internal salt bridge, yielding HisF-C*C (PNAS, 2004). Seitz et al. (JMB, 2007) and Höcker et al. (Biochemistry, 2009) then stepwise further stabilized and solubilized HisF-C*C by optimizing the half-barrel interface, generating HisF-C**C and HisF-C***C, respectively. The crystal structure of HisF-C***C revealed a 2-fold symmetric TIM barrel, validating the possibility of natural domain fusion. Moreover, Höcker created the first chimeric HisAF and HisFA TIM barrels using HisA and HisF half-barrels (PNAS, 2004). These experiments led to the proposal of a novel means of diversification and evolution of TIM-barrel enzymes through the exchange of (βα)4 half-barrel domains amongst preexisting TIM barrels. In accordance with this idea, Claren et al. established high catalytic activity on the HisAF construct (PNAS, 2009)……..

Third peer review

TIM review Robert Matthews .pdf

A

Reviewer-annotated pdf file.

Review by C. Robert Matthews , UMASS Medical School, University of Massachusetts, USA
This review was submitted on , and refers to this previous version of the article


With assistance of Yvonne Chan and Konstantin Zeldovich

Recommended additional content attached as PDF.

Response

We thank the reviewer for contributing additional information for this review. All new information provided has been incorporated into the manuscript. An acknowledgment for this contribution has also been added.