Untitled

Abstract

In the process of oligomeric structure formation through a mechanism of three-dimensional domain swapping, one domain of a monomeric protein is replaced by the same domain from an identical monomer. The swapped "domain" can represent an entire tertiary globular domain or an element of secondary protein structure, such as an alpha-helix or a beta-strand. Different examples of three-dimensional domain swapping are reviewed; the functional importance of this phenomenon and its role in the development of new properties by some proteins in the process of evolution are considered. The contribution of three-dimensional domain swapping to the formation of linear protein polymers and amyloids is discussed.

3DSwap: curated knowledgebase of proteins involved in 3D domain swapping

“…To generate a generic framework to understand swapping in protein structures, various key terminologies like ‘bona fide domain swapping’; ‘quasidomain swapping’, ‘swapped region’ and ‘hinge region’ were introduced earlier (27, 34). Protein structures involved in 3D domain swapping are classified into two major groups (15, 34): bona fide domain swapping and quasidomain swapping (55). Bona fide domain swapping refers to structures formed where while both the monomer and dimer of a molecule exist in stable forms, the dimer adopts a domain swapped conformation and the monomer adopts a closed conformation.…”

10.1007/s10541-008-3003-8

“…Dimer formation in preparations of HGF (hepatocyte growth factor) frag ment containing the kringle domain was described previ ously in the literature [30]. Dimer is likely to form as a result of intermolecular domain exchange [29]. Figure 5a shows one of the possible dimeric structures explain ing the presence of dimers and oligomers in ATF prepa rations.…”

“…It was demonstrated for a number of proteins that homopolymeric structures were formed by so called "mutual exchange" of domains interacting in the protein monomer [29]. Therefore, we proposed that under some conditions the KD and GFD of uPA might interact when being in different molecules.…”

Tah1 helix-swap dimerization prevents mixed Hsp90 co-chaperone complexes

“…Ultimately, the helix swap allows the fifth helix of Tah1 to be involved in roles not only observed for helix 5 but also for helix 7 in conventional TPR domains such as AIP and CHIP (Morgan et al, 2012;Zhang et al, 2005). Exchange of secondary structures or even whole domains as part of dimer formation is a well known phenomenon (Liu & Eisenberg, 2002;Nagradova, 2002) and indeed plays a role in the N-terminal domain association that occurs as part of the ATPase-coupled conformational cycle of Hsp90 itself .…”