Correlating Knob-Socket Model Propensities with Alpha-Helicity and Stability

The Knob-Socket (KS) model provides a basis for the description of a protein’s packing structure. The KS model describes secondary and tertiary packing based on a three amino acid residue “socket” which provides a space on one secondary structure element for the interaction with a single residue “knob”, which comes from another piece of secondary structure. Using the KS model, it has been shown that the socket propensities, as well as the amino acid sequence, are related to protein secondary structure and stability. For alpha-helical structure, the KS model can be used to accurately predict the change in alpha-helicity upon introduction of point mutations as well as indicate the direction of the change in stability using a hexagon of six sockets (Rabara) directly affected by that single point mutation. As a primary test to this relationship between Rabara frequency with secondary structure propensity and stability, a survey of the literature was made to collate point mutations in helical peptides along with their respective changes in secondary structure and/or thermodynamic stability. Previous data collected about the propensity and stability of the alpha-helical protein KSα1.1 and its mutant variants will provide another main data resource. The results plot across a wide range of helical sequences the correlation between the six socket Rabara hexagon construct and helical content as well as stability