title: Three-dimensional domain swapping in the protein structure space.
abstract: Since the proposal of three-dimensional (3D) domain swapping, many 3D domain-swapped structures have been reported. However, when compared with the vast protein structure space, it is still unclear whether 3D domain swapping is a general mechanism for protein assembly. Here, we investigated this possibility by constructing a dataset consisting of more than 500 domain-swapped structures. The domain-swapped structures were mapped into the protein structure space. We found that about 10% of protein folds and 5% of protein families contain domain-swapped structures. When comparing the domain-swapped structures in a family/superfamily, we found that proteins within a family/superfamily can swap in different ways. Interface analysis revealed that the hinge loops contributed more than half of the open interface in 70% of bona fide domain-swapped dimers, indicating that the hinge loops play an important role in stabilizing the domain-swapped conformations. Our study supports the suggestion that domain swapping is a general property of all proteins and will facilitate further understanding the mechanism of 3D domain swapping.
authors.affiliation: College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
authors.forename: Yongqi
authors.initials: Y
authors.lastname: Huang
authors.forename: Huaiqing
authors.initials: H
authors.lastname: Cao
authors.forename: Zhirong
authors.initials: Z
authors.lastname: Liu
mesh_terms: D000818:Animals; D002417:Cattle; D030562:Databases, Protein; D011487:Protein Conformation; D017510:Protein Folding; D054730:Protein Interaction Domains and Motifs; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins