3D Domain Swapping : Structural features:
3D Domain Swapping : The structural phenomenon observed in a wide array of structures, where two or more chains form an oligomeric conformation by mutually sharing a structural segment between the chains.
Hinge Region : The residues(or short sequence) which connects the secondary minor and major region is called as hinge region. The hinge region can be a loop, sheet, helix or few residues.
Swapped region : A globular domain (or sometimes one or few elements of secondary structure) that is intertwined with an identical protein chain, is referred as the swapped segment. The swapped domain retains an environment essentially identical to that of the same domain in a protein monomer.
Secondary Minor Region : The entire domain or a part of one chain which is swapped with the other domain of the neighbouring chain is referred as "secondary minor region" or Guest. Secondary minor region is an alternate definition used to define hinge region to explain the secondary regions with more clarity.
Secondary Major Region * : The region which interacts with the secondary minor region is termed as Secondary major region or Host.
Quasi-Domain Swapping : Quasidomain swapping refers to the structures where some proteins form domain swapped oligomers without a known closed monomer. If these proteins have homologues known to be closed monomers, these oligomers are considered to be .quasidomain swapped. Examples of quasidomain swapping include crystallin, pheromone/odorant binding/transport proteins, RYMV (viral capsid protein) , human cystatin C (protease inhibitor) etc.
Bonafide Domain Swapping : Bonafide domain swapping refers to structures where both the monomer and the dimer of a molecule exist in stable forms, where the dimer adopts a domain-swapped conformation and the monomer adopts a closed conformation. Examples of Bonafide domain swapping includes diphtheria toxin, RNases, CD2 (T-cell adhesion), Spo0A (development regulation) etc.
Extent of swapping * : Extent of swapping is a new method developed to assess of the extent of swapping with respect to the protein chains involved in swapping. For example, for a protein with 2 chains X, Y, the extent of swapping is calculated using the formula given below:
Where RMI= Number of residues in secondary major interface, Rmi = Number of residues in secondary minor interface. RChain:1 = Number of residues in Chain 1 and RChain:2 = Number of residues in Chain 2. Based on the percentage of extent of swapping observed in different structures, we have classified the structures in to three major classes as ‘Extensive swapping’, ‘Moderate swapping’ and ‘Minimum swapping’. Extensive swapping refers to the oligomeric structures where the ‘Extent of Swapping’ is observed within the range of 35%-100% [Example: 1A64]. Moderate swapping refers to the oligomeric structures where the ‘Extent of Swapping’ is observed within the range of 15%-35% [Example: 1OQF]. Minimum swapping refers to the oligomeric structures where the ‘Extent of Swapping’ is observed within the range of 1-15% [Example: 1K6W].
3DSwap - Literature based Protein Structural Curation Method:
Protein structures presented in 3DSwap was curated using a new curation approach. We combined literature mining approach and manual structural analysis and visualization in an iterative fashion to identify hinge and swapped region features of 3D domain swapping to structures. We defined this approach as “literature based protein structural curation”. PDB ID, Chain ID, Oligomeric state, Hinge Regions, Swapped Region, Extent of Swapping, Sequence Data and Reference fields were curated and stored in the database.