The Identification of Hydrophobicity and Side Chain Charge Distribution in the Primary Structure of Polypeptides by Fractal Analysis

We investigated the distribution of amino acids in proteins of two functional groups: membrane-bound and DNA-binding proteins, from gram-positive and gram-negative bacteria. We applied the multifractal detrended fluctuation analysis (MF-DFA) for hydrophobicity, polarity and side chain charge of amino acids. We found that (i) clustering of amino acids with similar properties in membrane-bound proteins is significantly more pronounced in gram-positive bacteria compared to gram-negative ones, especially for hydrophobicity; (ii) multifractal features have been observed only in side chain charge studies. Probably this is an effect of different structure of membrane in gram-positive and gram-negative bacteria. In contrast, while studying DNA-binding proteins no significant differences between gram-positive and gram-negative bacteria has been observed.