Ligand binding cavity encoded as a local hydrophobicity deficiency

The above diagram illustrates the specific deviation from the theoretical distribution of hydrophobicity which is associated with the presence of a ligand binding cavity

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)

Hypothetical in silico model of the early-stage intermediate in protein folding

This paper presents a method for determining the structure of the early stage (ES) intermediate in the multistage protein folding process. ES structure is modeled on the basis of a limited conformational subspace of the Ramachandran plot. The model distinguishes seven structural motifs corresponding to seven local probability maxima within the limited conformational subspace. Three of these are assigned to well-defined secondary structures, while the remaining four are found to represent various types of random coils. The presented heuristic approach also provides insight into the reasons behind incorrect predictions occurring when the folding process depends on external factors (e.g., ligands, ions or other proteins) rather than on the characteristics of the backbone itself. The accuracy of the presented method is estimated at around 48%