Abstract
Most proteins adopt an approximate structural symmetry. However, they have no symmetry detectable in their sequences and it is unclear for most of these proteins whether their structural symmetry originates from duplication. As one of the six popular folds (super-folds) possessing an approximate structural symmetry, the triosephosphate isomerase barrel (TIM-barrel) domain has been widely studied. Using modified recurrent quantification analysis of primary sequences, we identified the same 2-, 3-, and 4-fold symmetry pattern as their tertiary structures. This result indicates that the symmetry in tertiary structure is coded by symmetry in the primary sequence and that the TIM-barrel adopts a 2-, 3-, or 4-fold repeat pattern during evolution. This discovery will be useful for understanding the evolutionary mechanisms of this protein family and the symmetry pattern that may be a clue into the ancient origin of duplication of half-barrels or the β a unit.
Highlights
Proteins are amino acid polymers that can adopt a wide range of structures uniquely determined by sequence
In order to understand the evolution of the (β/α)8-barrel family, here we propose a fast and sensitive modified quantification analysis method to detect the hidden symmetries in the primary sequence of nonhomologous sequences with CATH [29] Code 3.20.20
We used typical proteins of eight-stranded β/α barrel family as examples to demonstrate the effectiveness of our methods for detecting symmetries in protein sequence
Summary
Proteins are amino acid polymers that can adopt a wide range of structures uniquely determined by sequence. It is well-known that the information regarding structure formation is contained within their amino acid sequences [1]. Many proteins exhibit obvious symmetry at the level of tertiary structures and yet seldom show periodicity in their primary sequences [2] [3]. A detailed analysis of the repeats in protein sequences may. How to cite this paper: Ji, X.F., Zheng, Y., Wang, Z.P. and Sheng, J. (2016) Hidden Sequence Repeats: Additional Evidence for the Origin of TIM-Barrel Family.
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