Identification of sequence repetitions in immunoglobulin folds

Abstract

A lot of evidence suggests that many proteins with the symmetric structures have evolved by internal duplication and fusion. Meanwhile many internal sequence repeats correspond to functional and structural units. These proteins, which have internal structural symmetry, this means that their sequences should be made up of identical repeats. However, many of these repeat signals can only be seen at the structural level yet. We have developed a de novo algorithm, modified recurrence correlation analysis, to detect the symmetries in the primary sequences of immunoglobulin folds (Ig folds), which adopt highly symmetrical tertiary structures while their sequences appear nearly random. Using this method, we show that the internal repetitions of the immunoglobulin folds could be identified directly at the sequence level. These results may give us some help to study the hypotheses about the origin of Ig folds by duplication of simpler fragments and it may also give us some helps to understand the relationship between the sequences and their tertiary structures.