Protein domain swapping

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... 

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. 

D domain swapping shares several features with amyloid fibril formation. It is specific in that only one type of protein is contained in any given... 

Janowski, R., Kozak, M., Jankowska, E., Grzonka, Z., Grubb, A., Abrahamson, M., and Jaskolski, M. (2001). Human cystatin C, an amyloidogenic protein, dimerizes through three-dimensional domain swapping. Nat. Struct. Biol. 8, 316-320. 

Schlunegger, M. P., Bennett, M. J., and Eisenberg, D. (1997). Oligomer formation by 3D domain swapping A model for protein assembly and misassembly. Adv. Protein Chem. 50, 61-122. 

The following diagram, adapted from that first presented by Bennett et alC, describes a postulated pathway for evolution of a protein dimer from single-domain proteins. The scheme begins with the fusion of two singledomain polypeptides and proceeds through the evolution of interdomain contacts, and in the case of enzymes, development of an active site. These same interdomain contacts can also stabilize formation of a domain-swapped dimer which then undergoes further evolution into a present-day dimer. 

As illustrated in the diagram below, domain swapping can also result in indefinite polymerization to form linear supramolecular structures. These may correspond to present-day polymers of proteins such as microtubules, or they may represent abnormal structures, like the straight and paired-helical filaments in the neurofibrillary tangles observed in the brain tissue of those afflicted with Alzheimer s disease. 

A process that partially or fully restores the biological activity of two proteins, each lacking a functional domain or motif, through the formation of an oligomeric species. See Domain Swapping... 

SERPINS (INHIBITORY MECHANISM) PROTEIN COMPLEMENTATION DOMAIN SWAPPING PROTEIN DISULFIDE ISOMERASE... 

The first data concerning the structmal requirements for communication with the transcription apparatus came from domain swapping experiments with the GAL4 protein of yeast. 

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