Domain swapping

A method for determining domain binding sites in proteins with swapped domains implications for PA3- and pB2- crystallins... 

In be complexes bci complexes of mitochondria and bacteria and b f complexes of chloroplasts), the catalytic domain of the Rieske protein corresponding to the isolated water-soluble fragments that have been crystallized is anchored to the rest of the complex (in particular, cytochrome b) by a long (37 residues in bovine heart bci complex) transmembrane helix acting as a membrane anchor (41, 42). The great length of the transmembrane helix is due to the fact that the helix stretches across the bci complex dimer and that the catalytic domain of the Rieske protein is swapped between the monomers, that is, the transmembrane helix interacts with one monomer and the catalytic domain with the other monomer. The connection between the membrane anchor and the catalytic domain is formed by a 12-residue flexible linker that allows for movement of the catalytic domain during the turnover of the enzyme (Fig. 8a see Section VII). Three different positional states of the catalytic domain of the Rieske protein have been observed in different crystal forms (Fig. 8b) (41, 42) ... 

DNA binding could result in a general conformational change that allows the bound protein to activate transcription, or these two functions could be served by separate and independent domains. Domain swap experiments suggest that the latter is the case. 

When one inspects the multiple channel protein sequences that have been derived, one readily recognizes that they have related primary sequences. This suggests that they have similar three-dimensional structures. The primary sequences can be subdivided into an amino-terminal, a core and a carboxy-terminal domain (see Fig. 5). Each domain seems to contribute separately to the structure and function of a given channel [49]. Following this hypothesis, it has been possible to carry out domain swapping experiments between Sh and RCK proteins [49] as well as between... 

Figure 3.4 Improvement of the activity of chimeric NRPSs using directed evolution. (1) A heterologous A domain is swapped into an NRPS, typically resulting in a significant loss of synthetase activity. (2) A library of chimeric synthetase mutants is constructed in which the heterologous A domain has been diversified (for example, by error-prone PCR). (3) The library is subjected to an in vivo screen for production of the unnatural nonribosomal peptide derivative. (4) Clones showing improved production are characterized and subjected to further rounds of diversification and screening...

Del Vecchio, F., Petkovic, H., Kendrew, S.G. et al. (2003) Active-site residue, domain and module swaps in modular polyketide synthases. Journal of Industrial Microbiology Biotechnology, 30, 489. 

FIGURE 22.2 Structure of NO synthases and domain swapping, [From U Siddhanta, A Presta, B Fa, D Wolan, DL Rousseau, DJ Stiehr. J Biol Chem 273 18950-18958, 1998. With permission.]... 

The earlier computational studies (151,152,175,184,185) considered both domain-swapped and contact dimers as equally possible mechanisms of GPCR oligomerization. In contrast, the later computational studies on GPCR oligomerization (186-189) take into account only the hypothesis of contact dimers, supported by the more recent experimental evidence. For the prediction of heterodimer interfaces, the recent studies use a modified CMA methodology, termed subtractive correlated mutation (SCM) analysis (187,188). A similar method for the identification of physically interacting protein pairs has recently been reported in the literature (180). 

Hadac, E. M., Ji, Z., Pinon, D. I., Henne, R. M., Lybrand, T. P., and Miller, L. J. (1999) A peptide agonist acts by occupation of a monomeric G protein-coupled receptor dual sites of covalent attachment to domains near TM1 and TM7 of the same molecule make biologically significant domain-swapped dimerization unlikely. J. Med. Chem. 42, 2105-2111. 

Gouldson, P. R. and Reynolds, C. A. (1997) Simulations on dimeric peptides evidence for domain swapping in G protein-coupled receptors Biochem. Soc. Trans. 25,1066-1071. 

Siddhanta U., Presta, A., Fan, B., Wolan, D., Rousseau, D. L., Stuehr, D.)., Domain swapping in inducible nitric-oxide synthase. Electron transfer occurs between flavin and heme groups located on adjacent subunits in the dimmer, J. Biol. Chem. 273 (1998), p. 18950-18958... 

Several /i-solenoid domains appear to promote the oligomerization of multidomain proteins. There are at least three types of /i-solenoid association. First, oligomers (dimers or trimers) are formed by lateral interaction of the solenoids. For example, the C-terminal domain of the bacterial cell division inhibitor MinC is a short right-handed T-type solenoid with an apolar lateral face that mediates homodimerization (Cordell et al., 2001). Trimers of several bacterial transferases are formed by lateral, in-register, interaction of left-handed T-type /1-solenoids (Fig. 5). Second, dimers may form via interactions of the open terminal coils of /1-solenoids as in the dimeric structure of iron transporter stabilizer SufD (Badger et al., 2005). Finally, dimerization may be mediated by swapping of /1-strands of the terminal coils, as in the CAP (Dodatko et al., 2004) (Fig. S). 

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