Analyses of the Sequence and Structural Properties Corresponding to Pentapeptide and Large Palindromes in Proteins

Abstract

The analyses of 3967 representative proteins selected from the Protein Data Bank revealed the presence of 2803 pentapeptide and large palindrome sequences with known secondary structure conformation. These represent 2014 unique palindrome sequences. 60% palindromes are not associated with any regular secondary structure and 28% are in helix conformation, 11% in strand conformation and 1% in the coil conformation. The average solvent accessibility values are in the range between 0-155.28 Å2 suggesting that the palindromes in proteins can be either buried, exposed to the solvent or share an intermittent property. The number of residue neighborhood contacts defined by interactions ≤ 3.2 Ǻ is in the range between 0-29 residues. Palindromes of the same length in helix, strand and coil conformation are associated with different amino acid residue preferences at the individual positions. Nearly, 20% palindromes interact with catalytic/active site residues, ligand or metal ions in proteins and may therefore be important for function in the corresponding protein. The average hydrophobicity values for the pentapeptide and large palindromes range between -4.3 to +4.32 and the number of palindromes is almost equally distributed between the negative and positive hydrophobicity values. The palindromes represent 107 different protein families and the hydrolases, transferases, oxidoreductases and lyases contain relatively large number of palindromes.

Fig 1. Histogram showing distribution of PALINs (length ≥ 5) in representative proteins of known three-dimensional structure selected from the Protein Data Bank.

Fig 2. Pie-chart showing the secondary structure composition corresponding to (a) PALINs (length ≥ 5) in representative proteins of known three-dimensional structure and (b) non-PALINs.

Fig 3. Weblogos for PALINs of different sequence lengths; (a) 5, (b) 6, (c) 7, (d) 8, and (e) 9.

Fig 4. Weblogos for PALINs of length 5 in: (a) helix, (b) strand and (c) coil conformation.

Fig 5. (a-e) Range of average solvent accessibility values corresponding to different sequence lengths for PALINs (blue color) and non-PALINs (red color).

Fig 6. Average hydrophobicity values corresponding to the palindromes.

Fig 7. (a-d) Illustrative examples showing the structural overlay corresponding to the palindromes of same length, sequence and secondary structure in different proteins (brown and yellow colors).

The palindrome sequence and location in the corresponding PDB code are indicated in each panel. The side-chain orientations for at least one or more equivalent residues is different in each case suggesting that the ‘environment’ representing the complementary charge distribution and shape of the proteins characterized by these palindromes need not be the same.