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Three‐dimensional domain swapping in the protein structure space
Author(s) -
Huang Yongqi,
Cao Huaiqing,
Liu Zhirong
Publication year - 2012
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.24055
Subject(s) - domain (mathematical analysis) , protein domain , hinge , protein structure , b3 domain , hamp domain , cyclic nucleotide binding domain , computer science , egf like domain , computational biology , immunoglobulin domain , protein folding , biology , peptide sequence , physics , genetics , microbiology and biotechnology , dna binding protein , mathematics , biochemistry , mathematical analysis , classical mechanics , gene , transcription factor
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. Proteins 2012. © 2012 Wiley Periodicals, Inc.