A tale of two symmetrical tails: Structural and functional characteristics of palindromes in proteins
1 Bioinformatics Group, School of Computer Science, Institute for Studies in Theoretical Physics and Mathematics (IPM), Tehran, Iran
2 Computer Engineering Department, Sharif University of Technology, Tehran, Iran
3 Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
4 National Institute of Genetic Engineering and Biotechnology, Tehran-Karaj Highway, Tehran, Iran
5 Center of Excellence in Biomathematics, School of Mathematics, Statistics and Computer Science, College of Science, University of Tehran, Tehran, Iran
6 Faculty of Mathematics, Shahid-Beheshti University, Tehran, Iran
7 IMPRS-CBSC, Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, Berlin, Germany
8 DFG-Research Center Matheon, FB Mathematik und Informatik, Freie Universität Berlin, Arnimallee 6, D-14195 Berlin, Germany
BMC Bioinformatics 2008, 9:274 doi:10.1186/1471-2105-9-274Published: 11 June 2008
It has been previously shown that palindromic sequences are frequently observed in proteins. However, our knowledge about their evolutionary origin and their possible importance is incomplete.
In this work, we tried to revisit this relatively neglected phenomenon. Several questions are addressed in this work. (1) It is known that there is a large chance of finding a palindrome in low complexity sequences (i.e. sequences with extreme amino acid usage bias). What is the role of sequence complexity in the evolution of palindromic sequences in proteins? (2) Do palindromes coincide with conserved protein sequences? If yes, what are the functions of these conserved segments? (3) In case of conserved palindromes, is it always the case that the whole conserved pattern is also symmetrical? (4) Do palindromic protein sequences form regular secondary structures? (5) Does sequence similarity of the two "sides" of a palindrome imply structural similarity? For the first question, we showed that the complexity of palindromic peptides is significantly lower than randomly generated palindromes. Therefore, one can say that palindromes occur frequently in low complexity protein segments, without necessarily having a defined function or forming a special structure. Nevertheless, this does not rule out the possibility of finding palindromes which play some roles in protein structure and function. In fact, we found several palindromes that overlap with conserved protein Blocks of different functions. However, in many cases we failed to find any symmetry in the conserved regions of corresponding Blocks. Furthermore, to answer the last two questions, the structural characteristics of palindromes were studied. It is shown that palindromes may have a great propensity to form α-helical structures. Finally, we demonstrated that the two sides of a palindrome generally do not show significant structural similarities.
We suggest that the puzzling abundance of palindromic sequences in proteins is mainly due to their frequent concurrence with low-complexity protein regions, rather than a global role in the protein function. In addition, palindromic sequences show a relatively high tendency to form helices, which might play an important role in the evolution of proteins that contain palindromes. Moreover, reverse similarity in peptides does not necessarily imply significant structural similarity. This observation rules out the importance of palindromes for forming symmetrical structures. Although palindromes frequently overlap with conserved Blocks, we suggest that palindromes overlap with Blocks only by coincidence, rather than being involved with a certain structural fold or protein domain.