Chameleon sequences reveal structural effects in proteins representing micelle-like distribution of hydrophobicity

The fundamental principle for protein structuring is that the 3D structure is determined by the amino acid sequence. An important phenomenon in this regard is the presence of a differentiated secondary structure for chain fragments of identical sequence-referred to as chameleons. In the present work, individual chain fragments were shown to constitute components of a system with specific physicochemical properties of the overall structure, adapting the secondary structure to the superior role assigned to the protein. The proteins (domains) represent the construction with a centrally located hydrophobic core and a polar surface (described by 3D Gauss function) representing a favourable arrangement in contact with water-the standard environment for the activity of most proteins. The fuzzy oil drop model (FOD-M), which takes into account the presence of a non-water environment for the active protein, was used to assess this condition. The proteins present in the ChSeq database are the object of analysis. The criterion for qualifying a pair of proteins for the analysis presented herein is the presence of a structuring-a hydrophobicity distribution consistent with a 3D Gaussian distribution representing a micelle-like system. The analysis shows that an appropriate secondary structure is not an aim by itself, but a means to achieve a hydrophobicity distribution appropriate for the status represented by the structural unit with its defined biological activity. The mathematical model for in silico simulation of protein folding process as environment dependent is also presented.