An Amino Acid Code for the Rational Design and Investigation of Protein Packing Structure using the knob-socket Model

Abstract

The applications of protein design are limited by the ability to determine a protein's fold and function based solely on a given amino acid sequence. The novel knob-socket model accurately classifies protein tertiary packing structure and provides a code that aims to accurately describe the packing interactions of side-chain residues. It is able to classify protein structure based on distinct amino acid side-chain preferences, which then predict the knob-socket arrangement of the packed protein. From the frequency of appearance in known structures, the knob-socket model provides the basis for prediction of stabilizing and destabilizing mutations. This model was used to design a 27 amino acid sequence, KSalpha1.1, which has been shown to fold into a stable alpha-helix configuration and that oligomerizes. The effects of helix stability are characterized with CD spectroscopy and oligomerization with NMR. Using known correlations of amino acid composition to alpha-helix propensity from the knob-socket model specific amino acids in the KSalpha1.1 sequence are changed to predictively strengthened or weakened packing stability. Current work involves purification and characterization of these mutations in the KSalpha1.1 protein to demonstrate the accuracy of the knob-socket model for protein design. The results provide further proof of knob-socket's ability to correctly model the packing in protein structure and serve as a fundamental descriptor of higher order protein structure.