3D domain swapping: As domains continue to swap

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.”

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.”

In the paper

“Several recent structural studies of 3D domain swapping further support the flexibility of the hinge loops.”

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.”

In the paper

“The only exception found to date is blood coagulant factors IX/X-binding protein (IX/X-bp, Mizuno et al. 1997).”

What the sources say

• Not checked yetcites Mizuno et al. 1997

In the paper

“No specific sequence motif can be found among these domains.”

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.”

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.”

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.”

In the paper

“RNase A forms a dimer during lyophilization in acetic acid (Crestfield et al. 1962).”

What the sources say

• Not checked yetcites Crestfield et al. 1962

In the paper

“suggesting that a small amount of RNase A dimer does exist in vivo (Park and Raines 2000).”

What the sources say

• Not checked yetcites Park and Raines 2000

In the paper

“Therefore, the diverse sizes and sequences of the swapped domains suggest that the activation energy for 3D domain swapping varies among domain-swapped proteins.”

In the paper

“Single point mutations at the closed interface of the suppressor of cyclin dependent kinase 1 (p13suc1) shifted the equilibrium between monomer and dimer (Schymkowitz et al. 2001).”

What the sources say

• Not checked yetcites Schymkowitz et al. 2001

In the paper

“Therefore, the same hinge loop adopts different conformations in the monomer, the C-terminal swapped dimer, and the cyclic C-terminal swapped trimer of RNase A, showing the great flexibility of this hinge loop.”

In the paper

“RNase A was reported to dimerize at pH 6.5 and 37°C, similar to the physiological conditions.”

What the sources say

• Not checked yetcites Park and Raines 2000

In the paper

“Because domain swapping takes place in the middle of IX/ X-bp, there are two hinge loops in each subunit.”

In the paper

“Thus, IX/X-bp is quasidomainswapped.”

In the paper

“Based on these biochemical data, we regard human Glx I as a protein with two domains swapped, as proposed by Cameron et al. (1997).”

What the sources say

• Not checked yetcites Cameron et al. 1997
• Not checked yetcites Saint-Jean et al. 1998

In the paper

“Based on the structures of the N-and C-terminal swapped dimers, a trimeric model with both types of swapping (Fig. 2) was proposed (Liu et al. 2001).”

What the sources say

• Not checked yetcites Liu et al. 2001

In the paper

“RNase A also forms tetramers (Gotte et al. 1999).”

What the sources say

• Not checked yetcites Gotte et al. 1999

In the paper

“Thus, RNase A represents the first protein found to form both linear and cyclic domain-swapped oligomers.”

In the paper

“RNase A forms dimers and trimers during lyophilization in acetic acid (Crestfield et al. 1962;Gotte et al. 1999).”

What the sources say

• Not checked yetcites Crestfield et al. 1962
• Not checked yetcites Gotte et al. 1999

In the paper

“RNase A also forms trimers (Gotte et al. 1999).”

What the sources say

• Not checked yetcites Gotte et al. 1999

In the paper

“Therefore, based on its sequence, a protein cannot be predicted to be domain-swapped or not.”

In the paper

“The structures of the RNase A trimers support the earlier proposal that a protein can form a linear or cyclic oligomer by 3D domain swapping.”

In the paper

“RNase A oligomers display higher enzyme activity on double-strand RNA than does the monomer (Gotte et al. 1999).”

What the sources say

• Not checked yetcites Gotte et al. 1999

In the paper

“more direct evidence of the physiological relevance of 3D domain swapping in DT comes from the crystal structure of the complex of DT and a domain of its receptor showing that DT forms domain-swapped dimer upon binding to its receptor at neutral pH (Louie et al. 1997).”

What the sources say

• Not checked yetcites Louie et al. 1997

In the paper

“Since high concentration of a protein favors 3D domain swapping, macromolecular crowding may facilitate 3D domain swapping in vivo.”

In the paper

“This energy barrier can be reduced under certain circumstances, such as change of pH, change of temperature, mutation in the protein, presence of denaturants, and binding of a ligand.”

In the paper

“These four domains may block the swapping of the N-terminal strand of Domain 5 and result in a monomer of the intact molecule.”

In the paper

“Macromolecular crowding also stabilizes protein oligomers (Eggers and Valentine 2001).”

What the sources say

• Not checked yetcites Eggers and Valentine 2001

In the paper

“Diphtheria toxin (DT), which enters cells by endocytosis, was first found to form a domain-swapped dimer upon lowering pH (Carroll et al. 1986;Bennett et al. 1994a).”

What the sources say

• Not checked yetcites Carroll et al. 1986
• Not checked yetcites Bennett et al. 1994a

In the paper

“It was reported that there is a strain at the hinge loop of suc1 which controls the equilibrium of the monomer and the dimer through 3D domain swapping (Rousseau et al. 2001).”

What the sources say

• Not checked yetcites Rousseau et al. 2001

In the paper

“Therefore, there is a high energy barrier between the closed monomer and the domain-swapped oligomer.”

In the paper

“However, when this domain is phosphorylated, it exists as a monomer.”

What the sources say

• Not checked yetcites Lewis et al. 2000

In the paper

“In addition, several domain-swapped proteins are fragments of their complete molecules, whereas the intact molecule is a monomer.”

In the paper

“Second, hinge loops may form new interactions in the domain-swapped dimer, which favor dimerization.”

In the paper

“Therefore, by changing the hinge loop or engineering the open interface, one can change the equilibrium between the monomer and the domain-swapped oligomer.”

In the paper

“Third, new interactions at the open interface make the domain-swapped oligomer more favorable thermodynamically (Kuhlman et al. 2001;Liu et al. 2001;Rousseau et al. 2001;Schymkowitz et al. 2001).”

What the sources say

• Not checked yetcites Kuhlman et al. 2001
• Not checked yetcites Liu et al. 2001
• Not checked yetcites Rousseau et al. 2001

In the paper

“However, the domain-swapped dimer is incapable of binding to the natural ligand (Urfer et al. 1995).”

What the sources say

• Not checked yetcites Urfer et al. 1995

In the paper

“suggesting that ligand binding may regulate the functions of its receptor through 3D domain swapping.”

In the paper

“After the hinge loop is shortened, Domain 1 of CD2 (Murray et al. 1995), staphylococcal nuclease (Green et al. 1995), and single chain Fv (Kortt et al. 1994;Perisic et al. 1994) form domain-swapped dimers.”

What the sources say

• Not checked yetcites Murray et al. 1995
• Not checked yetcites Green et al. 1995
• Not checked yetcites Kortt et al. 1994

In the paper

“First, the greater entropy of the monomer makes it more favored thermodynamically.”

In the paper

“Domain 5 alone is domainswapped at its N-terminal strand (Ultsch et al. 1999).”

What the sources say

• Not checked yetcites Ultsch et al. 1999

In the paper

“The contradictory fact is that the phosphorylated whole Spo0A is a dimer in solution (Lewis et al. 2000).”

What the sources say

• Not checked yetcites Lewis et al. 2000

In the paper

“Based on the monomeric and dimeric structures of DT and the conditions to form its dimer, a free energy diagram was proposed for the pathways of 3D domain swapping (Bennett et al. 1995).”

What the sources say

• Not checked yetcites Bennett et al. 1995

In the paper

“Therefore, even though the dissociation constant for the dimer of RNase A is greater than the concentration of RNase A in bovine pancreas, the amount of dimers formed in vivo may be higher than the amount calculated from the dissociation constant, due to macromolecular crowding.”

In the paper

“The N-terminal domain of sporulation response regulator Spo0A forms a domain-swapped dimer at pH 4.0.”

What the sources say

• Not checked yetcites Lewis et al. 2000

In the paper

“Ligand binding to suc1, which is distant from the hinge loop, also shifted the equilibrium”

What the sources say

• Not checked yetcites Schymkowitz et al. 2001

In the paper

“This effect was seen during the crystallization of the RNase A minor trimer, which is stabilized by polyethylene glycol (PEG) 10,000 even at pH 3.5 (Liu et al. 2002).”

What the sources say

• Not checked yetcites Liu et al. 2002

In the paper

“At pH 4.5, it forms a domain-swapped trimer (Zegers et al. 1999).”

What the sources say

• Not checked yetcites Zegers et al. 1999

In the paper

“| chimera (Canals et al. 2001) | | | | | RNase A and BS-RNase) | |”

What the sources say

• Not checked yetcites Canals et al. 2001

In the paper

“| SigE dimer (Luo et al. 2001) | 1K3S | 113 | | | Molecular chaperone in type | |”

What the sources say

• Not checked yetcites Luo et al. 2001

In the paper

“| Fyn-SH3 monomer (Musacchio | 1FYN | 62 | | 112-118 | Signal transduction | |”

What the sources say

• Not checked yetcites Musacchio et al. 1994

In the paper

“These two prolines control the balance of the monomeric and the dimeric forms by the strains at the hinge loop.”

What the sources say

• Not checked yetcites Rousseau et al. 2001

In the paper

“| Monomer of two repeats of | 1CUN | 211 | | | Cytoskeletal protein | |”

What the sources say

• Not checked yetcites Grum et al. 1999

In the paper

“In this review, we have summarized structures showing that 3D domain swapping takes place in proteins involved in diverse biological functions.”

In the paper

“However, studies on p13suc1, CD2, and Protein L suggest that these proteins are completely unfolded on the pathway to 3D domain swapping (Hayes et al. 1999;Kuhlman et al. 2001;Rousseau et al. 2001).”

What the sources say

• Not checked yetcites Hayes et al. 1999
• Not checked yetcites Kuhlman et al. 2001
• Not checked yetcites Rousseau et al. 2001

In the paper

“| Grb2 adaptor (SH2 + SH3) | 1GR1 | 217 | | | Signal transduction | |”

What the sources say

• Not checked yetcites Maignan et al. 1995

In the paper

“On the other hand, lengthening the hinge loop of the domainswapped dimer of cro repressor leads to the monomer formation (Albright et al. 1996).”

What the sources say

• Not checked yetcites Albright et al. 1996

In the paper

“Structural studies of DT and RNase A suggest that 3D domain swapping occurs in these proteins through partial unfolding of the monomer, to a core whose structure remains intact and to intact terminal domains free to move and to swap (Bennett et al. 1995;Liu et al. 2001).”

What the sources say

• Not checked yetcites Bennett et al. 1995
• Not checked yetcites Liu et al. 2001