Searching for Palindromic Sequences in Primary Structure of Proteins

Hoffmann, Marcin; Rychlewski, Jacek

doi:10.12921/cmst.1999.05.01.21-24

Cited by 6 publications

(3 citation statements)

References 19 publications

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“…Of these peptides sequences, 331 were equivalent to real peptides identified in the regular "forward" data base. The large overlap between the forward and "reversed" data bases was probably due to the presence of many palindromic sequences (39,40) and inversed sequence similarity of proteins (41). This leaves 64 peptides as true "false positives," which corresponds to 3.3% of the total 1919 peptides identified, well within the Using the reversed data base to estimate the rate of false positives has been shown to give good results, but the approach is not without problems.…”

Section: Improving Protein Identification Using Complementary Pairsmentioning

confidence: 99%

Improving Protein Identification Using Complementary Fragmentation Techniques in Fourier Transform Mass Spectrometry

Nielsen

Savitski

Zubarev

2005

Molecular & Cellular Proteomics

139

195

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Identification of proteins by MS/MS is performed by matching experimental mass spectra against calculated spectra of all possible peptides in a protein data base. The search engine assigns each spectrum a score indicating how well the experimental data complies with the expected one; a higher score means increased confidence in the identification. One problem is the false-positive identifications, which arise from incomplete data as well as from the presence of misleading ions in experimental mass spectra due to gas-phase reactions, stray ions, contaminants, and electronic noise. We employed a novel technique of reduction of false positives that is based on a combined use of orthogonal fragmentation techniques electron capture dissociation (ECD) and collisionally activated dissociation (CAD). Since ECD and CAD exhibit many complementary properties, their combined use greatly increased the analysis specificity, which was further strengthened by the high mass accuracy (Ϸ1 ppm) afforded by Fourier transform mass spectrometry. The utility of this approach is demonstrated on a whole cell lysate from Escherichia coli. Analysis was made using the data-dependent acquisition mode. Extraction of complementary sequence information was performed prior to data base search using in-house written software. Only masses involved in complementary pairs in the MS/MS spectrum from the same or orthogonal fragmentation techniques were submitted to the data base search. ECD/ CAD identified twice as many proteins at a fixed statistically significant confidence level with on average a 64% higher Mascot score. The confidence in protein identification was hereby increased by more than 1 order of magnitude. The combined ECD/CAD searches were on average 20% faster than CAD-only searches. A specially developed test with scrambled MS/MS data revealed that the amount of false-positive identifications was dramatically reduced by the combined use of CAD and ECD. Molecular & Cellular Proteomics 4:835-845, 2005.

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Section: Improving Protein Identification Using Complementary Pairsmentioning

confidence: 99%

Improving Protein Identification Using Complementary Fragmentation Techniques in Fourier Transform Mass Spectrometry

Nielsen

Savitski

Zubarev

2005

Molecular & Cellular Proteomics

139

195

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“…Since the original suggestion of the existence of important palindromic sequences in proteins [ 13 - 15 ], or simply "palindromic peptides", relatively little effort has been made to find the significance of such sequences. Inverse sequence similarity of proteins is not an exception by any means [ 16 , 17 ], and some studies suggest that palindromes may appear in protein sequences more frequently than is expected by chance [ 18 , 19 ]. Many have tried to find a relationship between palindromic sequences and protein structure.…”

Section: Introductionmentioning

confidence: 99%

A tale of two symmetrical tails: Structural and functional characteristics of palindromes in proteins

et al. 2008

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BackgroundIt 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.ResultsIn 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.ConclusionWe 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.

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“…Palindromic sequences are observed in various classes of proteins like histones (Cheng et al 1989), prion proteins (Sulkowski 1992;Kazim 1993), DNA-binding proteins (Suzuki 1992;Ohno 1993;Giel-Pietraszuk et al 2003), Rhodopsin family (Ohno 1990), metal-binding proteins (Pan et al 1999), sugar-metabolizing proteins (Ohno 1992) and receptors (Jaseja et al 2005). In proteins, short palindromic sequences occur more frequently than long palindromic sequences (Hoffmann and Rychlewski 1999), which are generally composed of amino acids like tryptophan, cysteine, histidine and methionine (Ohno 1992). A comprehensive study (Ohno 1992) shows that histones are rich in palindromes (>50%), whereas sugarmetabolizing proteins exhibit low composition of palindromes (<18%).…”

Section: Introductionmentioning

confidence: 99%

An algorithm to find all palindromic sequences in proteins

2013

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A palindrome is a set of characters that reads the same forwards and backwards. Since the discovery of palindromic peptide sequences two decades ago, little effort has been made to understand its structural, functional and evolutionary significance. Therefore, in view of this, an algorithm has been developed to identify all perfect palindromes (excluding the palindromic subset and tandem repeats) in a single protein sequence. The proposed algorithm does not impose any restriction on the number of residues to be given in the input sequence. This avant-garde algorithm will aid in the identification of palindromic peptide sequences of varying lengths in a single protein sequence.

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Searching for Palindromic Sequences in Primary Structure of Proteins

Cited by 6 publications

References 19 publications

Improving Protein Identification Using Complementary Fragmentation Techniques in Fourier Transform Mass Spectrometry

Improving Protein Identification Using Complementary Fragmentation Techniques in Fourier Transform Mass Spectrometry

A tale of two symmetrical tails: Structural and functional characteristics of palindromes in proteins

An algorithm to find all palindromic sequences in proteins

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