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Protein evolution driven by symmetric structural repeats
BMC Bioinformatics volume 9, Article number: P3 (2008)
Duplications play a major role in the evolution of genomes by creating and modifying molecular functions. Repeats are created at the DNA level, but when they are intragenic they affect protein sequence and structure. Moreover, as sequences evolve faster than 3D structures, some ancient repeats cannot be detected at the sequence level. Therefore, an understanding of the evolutionary and functional role of repeats requires tracking them at the three levels.
Materials and methods
For this task we have developed a program (SWELFE) to find repeats in DNA, amino acid sequences and 3D protein structures (available at http://bioserv.rpbs.jussieu.fr/swelfe) . Repeats were searched independently at all three levels using dynamic programming (SIM algorithm) and we adapted scoring matrices for each level. 3D structures were encoded as strings of α angles (dihedral angle between four consecutive Cα) so that the same algorithm can be used at the three levels. We verified the validity of our approach by superimposing the 3D repeats. We made a statistical evaluation of the repeats we found.
As there is currently no connection between 3D structures and the corresponding DNA sequences, we built a databank where we associate a PDB structure with its best match among the genes in TREMBL. The databank has 85 845 entries corresponding to ~85% of the unique chains of the PDB databank after removing entries with very small peptides or many undefined residues. We could then compare directly the results of repeat identification at the three levels.
In our analyses we were surprised to find that many of the large structural repeats are symmetrical (2-fold symmetry): one copy of the repeat can be superimposed with the other copy by a simple rotation of 180° around an axis (some repeats have 3-fold symmetry or higher). An example of a symmetrical repeat is shown on Figure 1. Then structures containing such repeats resemble to homodimers combined into one unit.
Abraham A-L, Rocha EPC, Pothier J: Swelfe : a detector of internal repeats in sequences and structures. Bioinformatics 2008. doi: 10.1093/bioinformatics/btn234
This work was supported by grants from Region Ile-de-France to ALA, ACI IMPBIO to EvolRep and ANR-06-CIS to project PROTEUS.
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Abraham, AL., Pothier, J. & Rocha, E.P. Protein evolution driven by symmetric structural repeats. BMC Bioinformatics 9, P3 (2008). https://doi.org/10.1186/1471-2105-9-S10-P3
- Dynamic Programming
- Dihedral Angle
- Combinatorial Library
- Small Peptide
- Protein Evolution