Detection Of Internal Sequence Repeats With Single-stranded Left-handed Beta-helix Fold

Detecting internal sequence repeats within proteins has become a hotspot in the field of sequence analysis since they have wide-ranging relations with the structures and functions of proteins, as well as the protein evolution pathways. It is evident that many proteins have evolved from gene duplication and fusion into functional oligomers so that they contain repeating structure units with similar functions. A classical example is chymotrypsin. In respect of deletions, insertions, and mutations, repeat units have diverged, and often they are separated by large loops, which made the detecting of the periodicity and repeat boundaries much more difficult.In this paper, we analyzed the sequences of proteins with single-stranded left-handed beta-helix fold, in the hope of finding the internal sequence repeat of these proteins. The tertiary structures of the proteins with this fold have obvious two-fold symmetries while their sequences do not. This seems contradictive with Anfinsen's proposal that the tertiary structure is exclusively determined by the primary sequence. Here we show that the internal two-fold sequence repetition in these proteins can be detected by using a modified recurrence analysis method. Our results demonstrate two points,(1)The sequences of these proteins do contain internal repeats corresponding with their tertiary structures. This detection indicates that the symmetric signals of the tertiary structures may come directly from their primary sequences. Symmetric sequences can fold into symmetric tertiary structures.(2)Based on the fact that all the sequences of these proteins have a two-fold symmetric pattern which is also consistent with their tertiary structure, we proposed that these proteins may share a common model of evolvement. They may evolve by two fold gene duplication and gene fusion from a common helix ancestor.