Information encoded in protein structure

Schematic depiction of variable quantities of information encoded as specific deformations in a protein “micelle” (of varying complexity), producing many different conformations – from spherical to ribbon-like. Except for the first and last structure, each form in the sequence encodes information in proportion to its deviation from the theoretical distribution of hydrophobicity. Such deviations may be regarded as a way to ensure the protein's specificity, (note, however that the first structure – i.e. a spherical micelle – and the last structure – a ribbonlike micelle – are devoid of information and therefore nonspecific)

Amyloid as a ribbon-like micelle

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Ligation site in proteins recognized in silico

Recognition of a ligation site in a protein molecule is important for identifying its biological activity. The model for in silico recognition of ligation sites in proteins is presented. The idealized hydrophobic core stabilizing protein structure is represented by a three-dimensional Gaussian function. The experimentally observed distribution of hydrophobicity compared with the theoretical distribution reveals differences. The area of high differences indicates the ligation site

Chaperonin Structure – The Large Multi-Subunit Protein Complex

The multi sub-unit protein structure representing the chaperonins group is analyzed with respect to its hydrophobicity distribution. The proteins of this group assist protein folding supported by ATP. The specific axial symmetry GroEL structure (two rings of seven units stacked back to back - 524 aa each) and the GroES (single ring of seven units - 97 aa each) polypeptide chains are analyzed using the hydrophobicity distribution expressed as excess/deficiency all over the molecule to search for structure-to-function relationships. The empirically observed distribution of hydrophobic residues is confronted with the theoretical one representing the idealized hydrophobic core with hydrophilic residues exposure on the surface. The observed discrepancy between these two distributions seems to be aim-oriented, determining the structure-to-function relation. The hydrophobic force field structure generated by the chaperonin capsule is presented. Its possible influence on substrate folding is suggested