Abstract
Three-dimensional domain swapping is a unique protein structural phenomenon where two or more protein chains in a protein oligomer share a common structural segment between individual chains. This phenomenon is observed in an array of protein structures in oligomeric conformation. Protein structures in swapped conformations perform diverse functional roles and are also associated with deposition diseases in humans. We have performed in-depth literature curation and structural bioinformatics analyses to develop an integrated knowledgebase of proteins involved in 3D domain swapping. The hallmark of 3D domain swapping is the presence of distinct structural segments such as the hinge and swapped regions. We have curated the literature to delineate the boundaries of these regions. In addition, we have defined several new concepts like ‘secondary major interface’ to represent the interface properties arising as a result of 3D domain swapping, and a new quantitative measure for the ‘extent of swapping’ in structures. The catalog of proteins reported in 3DSwap knowledgebase has been generated using an integrated structural bioinformatics workflow of database searches, literature curation, by structure visualization and sequence–structure–function analyses. The current version of the 3DSwap knowledgebase reports 293 protein structures, the analysis of such a compendium of protein structures will further the understanding molecular factors driving 3D domain swapping.Database URL: http://caps.ncbs.res.in/3dswap
Highlights
IntroductionStructural properties of proteins can be comprehensively explained using the concept of primary, secondary, teritiary and quaternary structures [1,2,3,4,5]
Protein structures are elementary units of form and function in living organisms
Search and browse utilities in 3DSwap Users can browse within 3DSwap using ‘Full list of entries in 3DSwap’, which provides a dynamic table of protein structures available in the current version of 3DSwap
Summary
Structural properties of proteins can be comprehensively explained using the concept of primary, secondary, teritiary and quaternary structures [1,2,3,4,5]. Proteins accomplish their specific functions by interacting with a wide variety of micro- and macromolecules within the cell. Some of these interactions are mediated by oligomerization in proteins [6,7,8,9,10]. Several key molecular functions rely on molecular interactions facilitated by such protein oligomers with other molecular players in the cell [11,12,13]
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