Purification of Novel Protein Design Mutants

The close packing in the protein structure results from the interaction of amino acid side chains distant in sequence position. In an exhaustive analysis of packing in the Protein Data Bank, the knob-socket tetrahedral construct was identified as a fundamental principle underlying the packing in protein structure. Application of this knob-socket principle to the classification of protein structure reveals distinct amino acid preferences for specific knob-socket arrangements in protein packing. These preferences define a discrete amino acid code for the relative spatial arrangement of protein residues in secondary and tertiary structure. Amino acid composition of 3-residue sockets specifies secondary structure, while interaction of the 3-residue socket with a fourth residue indicates tertiary packing. This code for amino acid structure was applied in a completely novel approach to protein structure design in order to test its practicality and accuracy. The knob-socket principle was used to construct a specific protein helix that would interact with itself. This tests packing of at the levels of tertiary and quaternary structure. Experimental results for purification and characterization via CD and NMR are shown of the protein design. This approach represents a novel and significant advancement in the understanding of protein structure for prediction and design.