Abstract
Domain-domain interactions in multi-domain proteins play an important role in the combined function of individual domains for the
overall biological activity of the protein. The functions of the tethered domains are often coupled and hence, limited numbers of domain
architectures with defined folds are known in nature. Therefore, it is of interest to document the available fold-fold combinations and their
preference in multi-domain proteins. Hence, we analyzed all multi-domain proteins with known structures in the protein databank and
observed that only about 860 fold-fold combinations are present among them. Analyses of multi-domain proteins represented in sequence
database result in recognition of 29,860 fold-fold combinations and it accounts for only 2.8% of the theoretically possible 1,036,080 (1439C2)
fold-fold combinations. The observed preference for fold-fold combinations in multi-domain proteins is interesting in the context of
multiple functions through structural adaptation by gene fusion.
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