PH EFFECT STUDY ON THE CONFORMACIONAL ENSEMBLE OF INTRINSICALLY DISORDERED PROTEINS

Intrinsically Disordered Proteins (IDPs) are proteins, or large portions of your sequence, that do not have a well-defined three-dimensional  structure at its functional native state. An IDPs fundamental feature is their larger number of polar and charged amino acid residues compared with proteins that bend in a well-defined structure. Besides the amino acid composition, the charge specific pattern of the sequence determines the chain compaction and the dimension dependence of intrinsically disordered proteins with the solution conditions. Thus, the pH variation, and consequently of protein’s charge density and ionic strength, that modules the electrostatics interactions, becomes decisive for macromolecule behavior. Using a continuous polymeric chain model with a specific charge distribution given by the protein's primary sequence, a Hamiltonian was written considering the excluded volume interactions, electrostatic interactions, and three-body repulsion [J. Chem. Phys. 148, 123305 (2018); J. Chem. Phys. 152, 161102 (2020)]. With this model, a charge regulation mechanism was used, in order to obtain the ionizable residues depending on pH and on the interaction with each other. From this, it was possible to determine the average distance between all residue pairs, providing a distance profile map which allows us to analyze how variations in the primary sequence affect the set of conformations. Additionally, it was analyzed how charge regulation modulates the distance profile map and the charge distribution. This model was applied to the protein Uniprot ID P0A8H9, also known as YacG. This protein is found in the cytoplasm of Escherichia coli (a bacterium primarily found in the intestines of warm-blooded animals) and functions to inhibit DNA gyrase. This model was also applied to determine the pKa values of ionizable residues in Nuclear Protein 1, which were then compared against experimental results.