Protein Tertiary Structure: A Prediction By the Knob-Socket Construct

The ability to identify tertiary protein structure based on a known sequence can provide avenues into understanding the relationship between amino acid sequence and biological function. The order in which amino acids are arranged in a polypeptide is called the primary structure, whereas the conformation of the protein backbone is known as secondary structure. The secondary structure can then be packed into three-dimensional structures based on the properties of their side chains referred to as tertiary structures. This study lays the experimental foundation for tertiary structure prediction starting from the protein KSα1.1, which was created de novo to be 27 amino acids in length with a purely alpha helical fold. This protein was predicted to have the folded structure it does using the packing motif known as the knob-socket model. The construct of KSα1.1 is insightful in the understanding of protein structure and protein design based on a novel characterization of side chain affinities and packing patterns. The knob-socket model further allows prediction towards the stabilization or destabilization of a helix in the presence of a mutation. By using KSα1.1 and its known properties, mutations can be introduced to change packing structure within the helix. From purification of KSα1.1 along with its mutants, helix stability can be characterized by CD and NMR spectroscopy, thus confirming the practicality of the knob-socket construct