![]() PQR and RQP will be referred to as the "sides" of this palindrome, while S will be called the "linker" (see Methods). For example, the hypothetical protein sequence: In proteins, palindromes appear in a polypeptide chain. Palindromic sequences are known to have roles in DNA replication and RNA transcription. Several studies suggest that reverse palindromes (or for simplicity, "palindromes") are statistically under-represented in some genomes, presumably because of the existence of restriction endonucleases in the host cells. They are usually referred to as "reverse palindromes", because the sequence and polarity of both strands of the DNA molecule define their palindromic nature. Is an example of a palindromic sequence recognized by restriction enzyme Eco RI. Restriction enzymes recognition sites which exist in double-stranded and not single stranded DNA, are usually "palindromic". reverse palindrome, occur in DNA sequences. From the study of restriction endonucleases in the 60's and the early 70's, it became clear that a certain type of palindrome, i.e. With the progress of molecular biology in the 20th century, a new level of symmetry was discovered in nature. Since then, many other famous palindromic sentences have been constructed in different languages. Note that the word "tenet" is a palindrome itself. The Sator Square contains probably the oldest known palindrome, which shows the Latin sentence "SATOR AREPO TENET OPERA ROTAS". "palindromes") goes back to at least 20 centuries ago. Human beings have always been attracted to symmetrical properties of natural phenomena, and their interest is reflected in art.Ĭreation of symmetrical sentences (i.e. Symmetry of shapes is something that is found everywhere in nature. 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. This observation rules out the importance of palindromes for forming symmetrical structures. Moreover, reverse similarity in peptides does not necessarily imply significant structural similarity. 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. 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. Finally, we demonstrated that the two sides of a palindrome generally do not show significant structural similarities. It is shown that palindromes may have a great propensity to form α-helical structures. Furthermore, to answer the last two questions, the structural characteristics of palindromes were studied. However, in many cases we failed to find any symmetry in the conserved regions of corresponding Blocks. In fact, we found several palindromes that overlap with conserved protein Blocks of different functions. Nevertheless, this does not rule out the possibility of finding palindromes which play some roles in protein structure and function. Therefore, one can say that palindromes occur frequently in low complexity protein segments, without necessarily having a defined function or forming a special structure. 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. ![]() sequences with extreme amino acid usage bias). (1) It is known that there is a large chance of finding a palindrome in low complexity sequences (i.e. ![]() Several questions are addressed in this work. In this work, we tried to revisit this relatively neglected phenomenon. However, our knowledge about their evolutionary origin and their possible importance is incomplete. It has been previously shown that palindromic sequences are frequently observed in proteins.
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