Investigation into the Amino Acid Characteristic of Intrinsically Disordered Proteins

Caulobacter crescentus, which belongs to the class of Alphaproteobacteria, has a highly organized cytoplasm that includes complex macromolecular structures at the cell poles. These polar complexes are assembled through the activity of a scaffolding protein, known as the Polar Organizing Protein Z (PopZ). PopZ interacts with other proteins via an N-terminal domain that is mostly intrinsically disordered, and contains, an abundance of proline, glutamte, and aspartate (P, E, and D) residues. Surprisingly, scrambling the order of amino acids in the PED region does not affect PopZ function, suggesting that binding affinity and specificity are not dependent on interactions with individual amino acids within this low-complexity region. The biochemical qualities of P,E and D promote intrinsic disorder, but they are not the only types of amino acids that are found in unstructured protein domains. By making targeted changes in the PopZ sequence, we are asking if binding affinity and specificity are dependent on qualities associated specifically with P, E, and D (for example, negative charge), or if any form of intrinsic disorder is sufficient to support a functional PopZ binding domain. One change we are making is to substitute all of the prolines for serine. While this will certainly affect the hydrophobicity of the protein, our in silico analyses predict that the change will preserve intrinsic disorder. Another change will be to substitute the asparate and glutamate residue for lysine, thus reversing the electrostatic charge with an amino acid that promotes intrinsic disorder.