Intrinsic Conformational Preferences of the Charged Amino Acids in Disordered Proteins

Abstract

Conformational equilibria in the unfolded states of proteins have many important biological roles, from regulating how some proteins fold and maintain structural stability, to describing the macromolecular details of intrinsically disordered proteins (IDPs), a protein class that does not adopt physiologically stable structures and instead utilizes unfolded states to facilitate their functions. Recently, to better understand the structural properties of IDPs, we analyzed both the sequence dependence to the mean hydrodynamic size of IDPs in water, as well as the impact of heat on the coil dimensions, showing that the sequence dependence and thermodynamic energies associated with intrinsic biases for the polyproline II (PPII) backbone conformation could be obtained. This result is important because PPII is used biologically for protein–protein and protein–nucleic acid interactions and thus has a role in molecular recognition. Experiments that evaluate how the hydrodynamic size changes with compositional changes in the IDP revealed amino acid-specific preferences for PPII that were in excellent quantitative agreement with calorimetry-measured values from small unfolded peptides and also those inferred by a survey of the protein coil library. Here, a set of charge-substitution experiments were used to measure the intrinsic preferences of the charged amino acids (i.e., lysine, arginine, glutamic acid, and aspartic acid) for the PPII backbone conformation, the results of which provide insight into how long-range charge-charge interactions and short-range effects, such as hydration and sterics, can modulate the structural and dynamical properties of IDPs, an increasingly important protein class in cell function.