Domain swapping: entangling alliances between proteins.

Abstract

The comparison of monomeric and dimeric diphtheria toxin (DT) reveals a mode for protein aciation which we call domain swapping. The structure of dimeric DT has been extensively refined against data to 2.0-A resoutin and a three-residue loop has been co d as compared with our published 2.5-A-resolution s re. The monomeric DT structure has also been determined, at 2.3-A resolution. Monomeric DT is a Y-shaped molecule with three domains: catalytic (C), transmembrane (T), and receptor binding (R). Upon fwzing in phosphate buffer, DT forms a long-lived, metstable dimer. The protein chain tracing doses that upon dim tion an unprecedented conformational rerangement occurs: the entire R domain from each molecule of the dimer is excag for the R domain from the other. This involves breaking the noncovalent interactions between the R domain and the C and T domai, rotating the R domain by 180°with atomic movements up to 65 A, and re-forming the same noncovalent interactions between the R domain and the C and T do of the other chain of the dimer. This conformational in exa the long life and metastability of the DT dimer. Several other intrtwined, dimeric protein strucres sadisf our definition of domain swapping and suggest that domain swapping may be the molecular mechanism for evolution of these oligomers and possibly of oligomeric proteins in general.

3D domain swapping: A mechanism for oligomer assembly

“…We first described 3D domain swapping as it occurs in metastable dimers of diptheria toxin (DT) formed by freezing in phosphate buffer (Bennett et al, 1994b) (Kinemage 2). However, the structures of other proteins that undergo domain swapping have also been reported (Table 1; Fig.…”

“…3, middle). The open monomers form domain-swapped dimers and higher oligomers at the high concentration of the mixture as the pH returns to normal during thawing (Bennett et al, 1994b).…”

“…We estimate ; 1 value for Act, the activation energy of converting dimer to open monomer, of 27 t 1 kcal/mol of dimer from the measured rate of dimer dissociation to monomers (Carroll et al, 1986) and the Eyring rate equation, assuming first-order kinetics and that the transmission coefficient is unity. Reprinted in modified form from Bennett et al (1994b).…”

“…3D domain swapping (Bennett et al, 1994b) provides an alternative pathway from protein monomers to dimers, in which dimers are formed by exchanging domains. A central feature of the 3D domain swapping model is that it exploits a pre-evolved, tightly binding interface at every stage of oligomer evolution, rather than requiring the gradual accumulation of several random mutations or yielding dimers that are only stable at high protein concentration.…”

“…Then a large aggregate is formed, which would be expected to precipitate in the test tube or cell. DT (Bennett et al, 1994b), single-chain Fv molecules (Raag & Whitlow, 1995), RNase A (Crestfield et al, 1962), tryptophan synthetase 01 subunit (Jackson & Yanofsky, 1969), and several other proteins form oligomers higher than dimers, and there appears to be no reason that very large open-ended oligomers of proteins could not be formed by domain swapping. Even though such large domain-swapped aggregates would be difficult to characterize in terms of molecular structure, it may be useful to keep in mind that the protein molecules of precipitates and amyloid deposits may be held together by domain swapping.…”