The Knob-Socket Model: A Novel Method for Predicting Protein Tertiary Structure

The novel knob-socket model provides a basis for defining how sequence determines protein structure. This model describes a four-residue tetrahedral motif: a single amino acid residue “knob” from one secondary structure element that packs into a three amino acid residue “socket” from another piece of secondary structure. Specifically, we analyzed the capabilities of the knob-socket construct in ⍺-helical protein packing. The knob-socket model provides a method of predicting intra- and inter-helical interactions based on amino acid side chains. Sockets can be categorized into three different groups: (1) free, unpacked and favoring intra-helical interactions, (2) filled, packed with a knob, and favoring inter-helical interactions, and (3) non, disfavoring alpha-helical packing. Using the PDB database, free and filled propensity libraries were developed to assign numerical probabilities to each combination of 3 amino acids in a socket. The propensities of the three residue sockets then served as an amino acid sequence code for alpha-helical packing interactions. This amino acid code allowed for the de novo design of an ⍺-helical antiparallel homodimer called KS⍺1.1. The structure of KS⍺1.1 and its dimerization was investigated using point mutations via site-directed mutagenesis. Based on propensities from the knob-socket model, we were able to predict how the point mutations will affect helix stability. These predictions were then confirmed via analysis with circular dichroism spectroscopy