The DOI matches its Crossref record; 107 of the 107 references it cites were found in a registry or an index; none of the 83 sources its claims cite is checked for support yet.
3D domain swapping: As domains continue to swap
Open accessAbstract
Three‐dimensional (3D) domain swapping creates a bond between two or more protein molecules as they exchange their identical domains. Since the term '3D domain swapping' was first used to describe the dimeric structure of diphtheria toxin, the database of domain‐swapped proteins has greatly expanded. Analyses of the now about 40 structurally characterized cases of domain‐swapped proteins reveal that most swapped domains are at either the N or C terminus and that the swapped domains are diverse in their primary and secondary structures. In addition to tabulating domain‐swapped proteins, we describe in detail several examples of 3D domain swapping which show the swapping of more than one domain in a protein, the structural evidence for 3D domain swapping in amyloid proteins, and the flexibility of hinge loops. We also discuss the physiological relevance of 3D domain swapping and a possible mechanism for 3D domain swapping. The present state of knowledge leads us to suggest that 3D domain swapping can occur under appropriate conditions in any protein with an unconstrained terminus. As domains continue to swap, this review attempts not only a summary of the known domain‐swapped proteins, but also a framework for understanding future findings of 3D domain swapping.
Overview
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Written from the paper’s full text.
TL;DR
This review summarizes about 40 structurally characterized 3D domain-swapped proteins, emphasizing diverse swapped domains, flexible hinge loops, and examples including RNase A, T7 helicase, human prion, and cystatin C. It proposes that 3D domain swapping can occur under appropriate conditions in any protein with an unconstrained terminus and may relate to oligomerization, allostery, and amyloid formation.
Key findings
- About 40 domain-swapped proteins have known structures; all swapped domains except one are from either the N or C terminus, and swapped domains vary widely in size, sequence, and secondary structure, with no specific sequence motif found.
- RNase A can swap both N- and C-terminal domains: structures include the N-terminal swapped dimer (2.1 Å), C-terminal swapped dimer (1.75 Å), and cyclic C-terminal swapped trimer (2.2 Å); RNase A is the first protein found to form both linear and cyclic domain-swapped oligomers.
- Blood coagulant factor IX/X-binding protein is the only known example of 3D domain swapping in the middle of the molecule and the only known domain-swapped heterodimer; T7 gene 4 ring helicase forms open oligomeric domain swapping along a six-fold screw axis and requires swapping for hexamerization and activity.
- Human prion and human cystatin C form domain-swapped dimers and are amyloidogenic, suggesting domain swapping and amyloid formation may share common intermediates; physiological relevance is supported for some proteins, such as RNase A dimerization at pH 6.5 and 37°C with a dissociation constant of ∼2 mM, but considered artifact for others such as barnase at pH 4.5 and truncated TrkA Domain 5.
Methods
- Review and structural synthesis of domain-swapped proteins, tabulating bona fide examples, quasi-domain-swapped proteins, and candidates in Tables 1–3 with PDB codes, residue counts, swapped domains, hinge loops, and functions.
- Compares crystal and NMR structures plus biochemical data from cited studies, with detailed discussion of six examples: IX/X-binding protein, RNase A trimers, glyoxalase I, T7 helicase, human prion, and human cystatin C.
- Main analysis is qualitative structural comparison and synthesis of a free-energy/mechanism model for 3D domain swapping.
Limitations
- The paper states that the mechanism of 3D domain swapping remains elusive, few studies have examined it, and it is unclear whether the domain-swapped dimer is the building block for amyloid fibers.
- The paper states that RNase A tetramer structures are unknown and models are hypothetical; glyoxalase I C-terminal domain swapping is ambiguous because there are two ways to define the monomer, and the crystal structure of the monomer is needed.
- Evident from the text: this is a review without new experimental data, and some hinge-loop residues in candidate proteins are speculative and marked with question marks.
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Claims the paper makes
66 Not checked yet · 36 Own interpretation · 5 No basis given · 2 Own result
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Analyses of the now about 40 structurally characterized cases of domain-swapped proteins reveal that most swapped domains are at either the N or C terminus”
- Also stated in: § Advances in 3D domain swapping · plain
“One common feature of these domain-swapped proteins is that all the swapped domains (except in one protein) are from either the N terminus or the C terminus.”
§ 3D domain swapping: As domains continue to swap > Abstract
plainn = 40- Asserted: passes — The authors put it forward as true.
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- Rests on an assumption: The set of about 40 structurally characterized domain-swapped proteins is representative of domain-swapped proteins generally.
- Also stated in: § Advances in 3D domain swapping · plain
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“the swapped domains are diverse in their primary and secondary structures”
- Also stated in: § Diversity of the swapped domains · plain
“The swapped domains have diverse sizes and sequences.”
- Also stated in: § Diversity of the swapped domains · plain
“The swapped domains also have diverse secondary struc-tures.”
§ 3D domain swapping: As domains continue to swap > Abstract
plainn = 40- Asserted: passes — The authors put it forward as true.
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- Rests on an assumption: The set of about 40 structurally characterized domain-swapped proteins is representative of domain-swapped proteins generally.
- Also stated in: § Diversity of the swapped domains · plain
None of the sources cited for this claim have been checked yet.
In the paper
“Several recent structural studies of 3D domain swapping further support the flexibility of the hinge loops.”
§ 3D domain swapping: As domains continue to swap > Flexibility and diversity of the hinge loops
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“A common feature is that when the hinge loop forms a -strand or an ␣-helix, the oligomeric form is favored over the monomer.”
§ 3D domain swapping: As domains continue to swap > Flexibility and diversity of the hinge loops
plaincorrelational- Asserted: passes — The authors put it forward as true.
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In the paper
“The only exception found to date is blood coagulant factors IX/X-binding protein (IX/X-bp, Mizuno et al. 1997).”
§ 3D domain swapping: As domains continue to swap > IX/X-binding protein
What the sources say
- Not checked yetcites Mizuno et al. 1997
plainSingle case- Asserted: passes — The authors put it forward as true.
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The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“No specific sequence motif can be found among these domains.”
§ 3D domain swapping: As domains continue to swap > Diversity of the swapped domains
plain- Asserted: passes — The authors put it forward as true.
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- Rests on an assumption: The set of about 40 structurally characterized domain-swapped proteins is representative of domain-swapped proteins generally.
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“IX/X-bp is the only known example of 3D domain swapping taking place in the middle of the molecule, in contrast to other domain-swapped proteins, in which domain swapping takes place at either the N or C terminus.”
§ 3D domain swapping: As domains continue to swap > IX/X-binding protein
plain- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“One advance in understanding 3D domain swapping is that more than one domain in a protein can swap.”
- Also stated in: § Swapping of more than one domain in a protein · boosted
“Thus, structural studies of 3D domain swapping in RNase A show that a protein can have domains swapped at both the N-and C-termini, and that these two types of swapping can occur simultaneously in one oligomer.”
§ 3D domain swapping: As domains continue to swap > Swapping of more than one domain in a protein
boostedSingle case- Asserted: passes — The authors put it forward as true.
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- Also stated in: § Swapping of more than one domain in a protein · boosted
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The present state of knowledge leads us to suggest that 3D domain swapping can occur under appropriate conditions in any protein with an unconstrained terminus.”
§ 3D domain swapping: As domains continue to swap > Abstract
hedgedconditionaln = 40- Asserted: passes — The authors put it forward as true.
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- Rests on an assumption: The set of about 40 structurally characterized domain-swapped proteins is representative of domain-swapped proteins generally.
In the paper
“RNase A forms a dimer during lyophilization in acetic acid (Crestfield et al. 1962).”
§ 3D domain swapping: As domains continue to swap > Swapping of more than one domain in a protein
What the sources say
- Not checked yetcites Crestfield et al. 1962
plaindirect- Asserted: passes — The authors put it forward as true.
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- Probably not a substantial claim. 3
- It may state two separate claims as one. 46
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In the paper
“To date, about 40 domain-swapped proteins have known structures.”
- Also stated in: § New examples of 3D domain swapping in proteins · plain
“To date, about 40 domain-swapped proteins have been reported.”
§ 3D domain swapping: As domains continue to swap > Advances in 3D domain swapping
plain- Asserted: passes — The authors put it forward as true.
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Probably not a substantial claim. The paper’s conclusions may not depend on it.
- Rests on an assumption: The set of about 40 structurally characterized domain-swapped proteins is representative of domain-swapped proteins generally.
- Also stated in: § New examples of 3D domain swapping in proteins · plain
The paper states this without a source or data behind it here, so there is nothing to check it against. The quote shows it is in the paper.
In the paper
“In addition, IX/X-bp is the only known example of a domain-swapped heterodimer; all other domain-swapped proteins are homooligomers.”
§ 3D domain swapping: As domains continue to swap > IX/X-binding protein
plain- Asserted: passes — The authors put it forward as true.
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- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
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It may state two separate claims as one.
- Rests on an assumption: The set of about 40 structurally characterized domain-swapped proteins is representative of domain-swapped proteins generally.
None of the sources cited for this claim have been checked yet.
In the paper
“Structures of both dimers (Fig. 2) reveal that the N-terminal helix is swapped in the less abundant dimer (the N-terminal swapped dimer, previously named the minor dimer) (Liu et al. 1998), whereas the Cterminal strand is swapped in the other dimer (the C-terminal swapped dimer, previously named the major dimer) (Liu et al. 2001).”
§ 3D domain swapping: As domains continue to swap > Swapping of more than one domain in a protein
What the sources say
- Not checked yetcites Liu et al. 1998
- Not checked yetcites Liu et al. 2001
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“Further studies showed that there are two types of dimers of RNase A, formed with one dimer more abundant than the other dimer (Libonati et al. 1996;Gotte et al. 1999).”
§ 3D domain swapping: As domains continue to swap > Swapping of more than one domain in a protein
What the sources say
- Not checked yetcites Libonati et al. 1996
- Not checked yetcites Gotte et al. 1999
plain- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In summary, the diversity of the swapped domains indicates that 3D domain swapping does not depend on the protein sequence or secondary structure.”
§ 3D domain swapping: As domains continue to swap > Diversity of the swapped domains
hedged- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Therefore, 3D domain swapping is required for the hexamerization and the activity of T7 helicase.”
§ 3D domain swapping: As domains continue to swap > Glyoxalase I
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“The dissociation constant for the dimer at this condition is ∼2 mM, which is about 20-fold greater than the concentration of RNase A in the bovine pancreas”
§ 3D domain swapping: As domains continue to swap > Physiological relevance
What the sources say
- Not checked yetcites Park and Raines 2000
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“These results suggest that 3D domain swapping in RNase A exists in vivo and may play some physiological role.”
§ 3D domain swapping: As domains continue to swap > Physiological relevance
hedgedconditional- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“By examining domain-swapped proteins, we conclude that domain swapping is physiologically relevant in some proteins, but not in others.”
§ 3D domain swapping: As domains continue to swap > Physiological relevance or crystallographic artifact?
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“T7 helicase provides the structural evidence for 3D domain swapping in a hexamer, supporting the proposal that 3D domain swapping is a mechanism for extended protein oligomerization (Bennett et al. 1995).”
§ 3D domain swapping: As domains continue to swap > Glyoxalase I
What the sources say
- Not checked yetcites Bennett et al. 1995
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Although it is unclear whether the domain-swapped dimer is the building block for these fibers, these studies show that domain swapping and amyloid formation may share common intermediates, and thus suggest that 3D domain swapping is a possible mechanism for amyloid formation.”
§ 3D domain swapping: As domains continue to swap > Glyoxalase I
hedgedconditional- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This diversity shows that 3D domain swapping does not require or prefer certain types of secondary structure.”
§ 3D domain swapping: As domains continue to swap > Diversity of the swapped domains
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“In the less abundant trimer, only the C-terminal strand is swapped, and the structure is cyclic (cyclic C-terminal swapped trimer, previously named the minor trimer, Fig. 2) (Liu et al. 2002).”
§ 3D domain swapping: As domains continue to swap > Swapping of more than one domain in a protein
What the sources say
- Not checked yetcites Liu et al. 2002
plain- Asserted: passes — The authors put it forward as true.
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It may state two separate claims as one.
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In the paper
“In summary, the”
§ 3D domain swapping: As domains continue to swap > Diversity of the swapped domains
plaincorrelational- Asserted: fails — The authors may not put it forward as true.
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Probably not a substantial claim. The authors may not put it forward as true. The paper’s conclusions may not depend on it. The paper may give no reason why it holds. It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Thus, RNase A oligomers display two basic types of 3D domain swapping, and show that with two types of swapping, a protein can form a variety of oligomers.”
§ 3D domain swapping: As domains continue to swap > Swapping of more than one domain in a protein
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Further biochemical studies support this model and indicate that the model belongs to the more abundant trimer (linear N-and C-terminal swapped trimer, previously named the major trimer).”
§ 3D domain swapping: As domains continue to swap > Swapping of more than one domain in a protein
What the sources say
- Not checked yetcites Liu et al. 2002
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
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None of the sources cited for this claim have been checked yet.
In the paper
“3D domain swapping in bovine seminal ribonuclease (BS-RNase, sharing 80% sequence identity with RNase A, Mazzarella et al. 1993) was reported to be necessary for its immunosuppression activity and allostery activity (Piccoli et al. 1988;Cafaro et al. 1995)”
§ 3D domain swapping: As domains continue to swap > Physiological relevance
What the sources say
- Not checked yetcites Piccoli et al. 1988
- Not checked yetcites Cafaro et al. 1995
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Cyanovirin-N (Yang et al. 1999) was also crystallized under low pH and was shown to be domain-swapped.”
§ 3D domain swapping: As domains continue to swap > Artifact
What the sources say
- Not checked yetcites Yang et al. 1999
plainSingle case- Asserted: passes — The authors put it forward as true.
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In the paper
“These proteins include BS-RNase (Mazzarella et al. 1993), T7 helicase (Singleton et al. 2000), cro repressor (Anderson et al. 1981), phosphoenolpyruvate mutase (Huang et al. 1999), T4 endonuclease VII (Raaijmakers et al. 1999), IX/X-binding protein (Mizuno et al. 1997), and bleomycin resistance protein (Dumas et al. 1994).”
§ 3D domain swapping: As domains continue to swap > Physiological relevance
What the sources say
- Not checked yetcites Mazzarella et al. 1993
- Not checked yetcites Singleton et al. 2000
- Not checked yetcites Anderson et al. 1981
plain- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“These studies provide evidence for 3D domain swapping as a mechanism for allostery and signal sensing in a macromolecule, and therefore for regulating biological functions of proteins.”
§ 3D domain swapping: As domains continue to swap > Physiological relevance
plaindirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The mutations that shift the equilibrium are distant from the hinge loop, suggesting that the strain at the hinge loop can be “sensed” by the remote mutation sites.”
§ 3D domain swapping: As domains continue to swap > Physiological relevance
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
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None of the sources cited for this claim have been checked yet.
In the paper
“3D domain swapping regulated by ligands was reported in glyoxalase I (Saint-Jean et al. 1998) and p13suc1 (Schymkowitz et al. 2001), where the equilibrium between the monomer and the dimer is regulated by glutathione and phosphopeptide, respectively”
§ 3D domain swapping: As domains continue to swap > Physiological relevance
What the sources say
- Not checked yetcites Saint-Jean et al. 1998
- Not checked yetcites Schymkowitz et al. 2001
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Macromolecular crowding increases protein local concentration and facilitates protein oligomerization (Cole and Ralston 1994;Lindner and Ralston 1995;Rivas et al. 1999).”
§ 3D domain swapping: As domains continue to swap > Physiological relevance
What the sources say
- Not checked yetcites Cole and Ralston 1994
- Not checked yetcites Lindner and Ralston 1995
- Not checked yetcites Rivas et al. 1999
plaindirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Several domain-swapped oligomers are obtained under nonphysiological low pH, and the biological functions of the oligomers are unknown.”
§ 3D domain swapping: As domains continue to swap > Artifact
plaindirect- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“these examples suggest that smaller domains form domain-swapped oligomers more easily than larger domains, and may do so under nonphysiological conditions.”
§ 3D domain swapping: As domains continue to swap > Artifact
hedgedconditional- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“However, the active forms of these proteins are domain-swapped, suggesting that their 3D domain swapping is related to their biological functions in vivo.”
§ 3D domain swapping: As domains continue to swap > Physiological relevance
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
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A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Thus, macromolecular crowding in cells increases the population of domain-swapped oligomers and thus in a general way adds support to the possible physiological relevance to 3D domain swapping.”
§ 3D domain swapping: As domains continue to swap > Physiological relevance
plaindirect- Asserted: passes — The authors put it forward as true.
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In the paper
“Therefore, domain swapping in Domain 5 is regarded as a consequence of the truncation of the whole protein (Ultsch et al. 1999) and is not of physiological significance.”
§ 3D domain swapping: As domains continue to swap > Artifact
What the sources say
- Not checked yetcites Ultsch et al. 1999
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“| T4 endonuclease VII dimer (Raaijmakers | 1EN7 | 157 | 60 | 63-72 (?) | Mismatch repair, Resolving | N-terminal helix |”
§ 3D domain swapping: As domains continue to swap > Summary
What the sources say
- Not checked yetcites Raaijmakers et al. 1999
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“| Dimer of one repeat of ␣-spectrin | 2SPC | 107 | 32 | 72-75 | Cytoskeletal protein | C-terminal ␣-helix |”
§ 3D domain swapping: As domains continue to swap > Summary
What the sources say
- Not checked yetcites Yan et al. 1993
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“| Designed coiled coil dimer (Ogihara | 1G6U | 48 | 14 | 33-34 (?) | Unknown | C-terminal ␣-helix |”
§ 3D domain swapping: As domains continue to swap > Summary
What the sources say
- Not checked yetcites Ogihara et al. 2001
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“| Cab-type  class carbonic anhydrase | 1G5C | 170 | 12 | 13-23 (?) | Catalyzing reversible hydration | N-terminal ␣-helix |”
§ 3D domain swapping: As domains continue to swap > Summary
What the sources say
- Not checked yetcites Strop et al. 2001
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In several proteins, 3D domain swapping is found in the active form of these proteins, whereas in other proteins, domain swapping seems an artifact of truncation of the whole molecules.”
§ 3D domain swapping: As domains continue to swap > Summary
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“| CesT dimer (Luo et al. 2001) | 1K3E | 156 | 32 | 33-36 | Molecular chaperone in type | N-terminal ␣-helix |”
§ 3D domain swapping: As domains continue to swap > Summary
What the sources say
- Not checked yetcites Luo et al. 2001
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“| dUTPase trimer (Larsson et al. 1996) | 1DUD | 136 | 10 | 125-126 (?) dUTP hydrolysis | C-terminal strand |”
§ 3D domain swapping: As domains continue to swap > Summary
What the sources say
- Not checked yetcites Larsson et al. 1996
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“| Citrate synthase dimer from chicken heart | 1CTS | 433 | 10 | 417-423 (?) Citrate synthesis | C-terminal helix |”
§ 3D domain swapping: As domains continue to swap > Summary
What the sources say
- Not checked yetcites Remington et al. 1982
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“| Heat shock protein 33 dimer | 1HW7 | 255 | 75 | 178-184 (?) Molecular chaperone | C-terminal helices |”
§ 3D domain swapping: As domains continue to swap > Summary
What the sources say
- Not checked yetcites Vijayalakshmi et al. 2001
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“| Bleomycin resistance protein dimer | 1BYL | 122 | 8 | 9-11 (?) | Bleomycin resistance | N-terminal -strand |”
§ 3D domain swapping: As domains continue to swap > Summary
What the sources say
- Not checked yetcites Dumas et al. 1994
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“| Grb2-SH2 domain dimer (Schiering | 1FYR | 93 | 27 | 121-123 | Binding phosphorylated | C-terminal ␣-helix |”
§ 3D domain swapping: As domains continue to swap > Summary
What the sources say
- Not checked yetcites Schiering et al. 2000
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“| BTB domain of PLZF (Ahmad et al. | 1BUO | 120 | 12 | 13-23 (?) | Evolutionarily conserved | N-terminal -strand |”
§ 3D domain swapping: As domains continue to swap > Summary
What the sources say
- Not checked yetcites Ahmad et al. 1998
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“| Phosphoenolpyruvate mutase dimer | 1PGM | 295 | 35 | 240-260 (?) Converting | C-terminal helices |”
§ 3D domain swapping: As domains continue to swap > Summary
What the sources say
- Not checked yetcites Huang et al. 1999
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“| T7 gene 4-ring helicase hexamer | 1E0J | 326 | 40 | 283-305 (?) Separation of nucleic acid | N-terminal ␣-helix |”
§ 3D domain swapping: As domains continue to swap > Summary
What the sources say
- Not checked yetcites Singleton et al. 2000
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“| SH3 domain of Eps8 (Kishan et al. | 1AOJ | 65 | 26 | 34-39 | Recognition of proline-rich | C-terminal |”
§ 3D domain swapping: As domains continue to swap > Summary
What the sources say
- Not checked yetcites Kishan et al. 1997
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The independence of 3D domain swapping from protein sequence, secondary structure and hinge loop suggests that any protein can be domain-swapped under appropriate conditions where the terminal domain of the protein is unconstrained.”
§ 3D domain swapping: As domains continue to swap > Summary
hedgedconditional- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: fails — The paper may give no reason why it holds.
Probably not a substantial claim. The paper may give no reason why it holds.
In the paper
“| Catalase dimer (beef liver) (Fita and | 7CAT | 500 | 65 | 66-70 (?) | H 2 O 2 hydrolysis | N-terminal helices |”
§ 3D domain swapping: As domains continue to swap > Summary
What the sources say
- Not checked yetcites Fita and Rossmann 1985
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“| Simian virus 40 oligomer (Stehle et al. | 1SVA | 361 | 61 | 296-300 (?) Virus coat protein | C-terminal helix |”
§ 3D domain swapping: As domains continue to swap > Summary
What the sources say
- Not checked yetcites Stehle et al. 1996
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“| RecA hexamer from E. coli (Story et al. | 2REB | 352 | 26 | 27-39 (?) | DNA recombination and repair | N-terminal ␣-helix |”
§ 3D domain swapping: As domains continue to swap > Summary
What the sources say
- Not checked yetcites Story et al. 1992
hedged- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“| T7 gene 4-ring helicase fragment | 1CR0 | 296 | 12 | 283-305 (?) Unknown | N-terminal ␣-helix |”
§ 3D domain swapping: As domains continue to swap > Summary
What the sources say
- Not checked yetcites Sawaya et al. 1999
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The paper relies on this without support.
The set of about 40 structurally characterized domain-swapped proteins is representative of domain-swapped proteins generally.
“Analyses of the now about 40 structurally characterized cases of domain-swapped proteins reveal that most swapped domains are at either the N or C terminus”
“To date, about 40 domain-swapped proteins have known structures.”
The paper relies on this without support.
The biochemical behavior of Pseudomonas putida Glx I (55% sequence identity to human Glx I) can be used to infer the active-site completeness and domain-swapping state of human Glx I.
“Biochemical data show an equilibrium of monomer and dimer in Glx I from Pseudomonas putida (55% sequence identity to human Glx I), and both the monomer and the dimer are active (Saint-Jean et al. 1998).”
“Based on these biochemical data, we regard human Glx I as a protein with two domains swapped, as proposed by Cameron et al. (1997).”
The paper relies on this without support.
Thermodynamic activity exceeds concentration.
“That is, thermodynamic activity exceeds concentration.”
The paper relies on this without support.
The greater entropy of the monomer makes it more favored thermodynamically.
“First, the greater entropy of the monomer makes it more favored thermodynamically.”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“This is an unusual target in that there are very extensive inter-subunit interactions, including a domain swap21 in which part of the fold of one monomer occupies the corresponding position of a neighboring one.”
From Critical assessment of methods of protein structure prediction (CASP)—Round XIV (2021) · cites this paper as [21]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
Each contradiction between two passages listed here was confirmed by an independent check.
Rated minor: it would not touch a result — a value no result rests on, a p-value that stays on the same side of the significance level, or a conflict that is clerical, resolved elsewhere in the paper, or outside its own findings.
In the paper
§ 3D domain swapping: As domains continue to swap > RNase A linear N-and C-terminal swapped trimer and cyclic C-terminal swapped trimer
“In addition, the crystal structure of the RNase A N-terminal swapped trimer shows that it is a cyclic molecule, with swapping of the C-terminal strands (Fig. 2; Liu et al. 2002).”
§ 3D domain swapping: As domains continue to swap > Swapping of more than one domain in a protein
“In the less abundant trimer, only the C-terminal strand is swapped, and the structure is cyclic (cyclic C-terminal swapped trimer, previously named the minor trimer, Fig. 2) (Liu et al. 2002).”
Citations
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Metadata
- Authors
- Liu, Y., & Eisenberg, D.
- Affiliations
- Howard Hughes Medical Institute (US)
- Corresponding author
- Eisenberg, David
- Venue
- Protein Science
- Publisher
- Wiley
- Published
- 2002-06
- Volume
- 11
- Issue
- 6
- Pages
- 1285-1299
- ISSN
- 0961-8368 (ISSN-L)
- 1469-896X
- PMC
- PMC2373619
- OpenAlex
- W2160082320
- Cited by
- 684
- References
- 106
- Citations by year
- 2026: 6 · 2025: 15 · 2024: 16 · 2023: 14 · 2022: 12 · 2021: 37 · 2020: 21 · 2019: 21 · 2018: 18 · 2017: 18 · 2016: 41 · 2015: 31 · 2014: 34 · 2013: 25 · 2012: 35
- FWCI
- 3.37
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Protein Science (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation
- National Institutes of Health
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Structural Characterization
- Keywords
- protein-protein interaction, diphtheria toxin, amyloid proteins, protein flexibility, protein structure
- MeSH terms
- Animals, Humans, Models, Molecular, Protein Binding, Proteins, Protein Structure, Tertiary, Dimerization
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