A rapid transition in the unfolding of ubiquitin at high SDS concentrations

Protein interactions with surfactants are crucial in various contexts, from enzymatic applications in detergent formulations to the formulation of protein pharmaceuticals and industrial processes. Sodium dodecyl sulfate (SDS), an anionic surfactant, is a well-known denaturant capable of inducing changes in protein conformation. Understanding the intricacies of this interaction is crucial for unraveling the dynamics of protein-surfactant complexes.

This study focuses on ubiquitin (Ubi) as a model protein and employs small-angle X-ray Scattering (SAXS) and molecular dynamics (MD) simulations to investigate its behavior in the presence of SDS. Earlier controversies surrounding the nature of the Ubi-SDS complex have been resolved by these SAXS studies, confirming that Ubi conforms to the canonical core-shell model upon exposure to SDS.

We made the surprising observation that Ubi unfolding rate accelerates rapidly when crossing a certain SDS concentration threshold far above the critical micelle concentration of 5 mM SDS. At room temperature, Ubi unfolds slowly in the presence of SDS at concentrations from the cmc to around 60 mM, showing that it is kinetically stable against denaturation in SDS. However, within the concentration range of 60-70 mM SDS, there is a pronounced acceleration in unfolding, regardless of temperature and independent of ionic strength. A similar trend is observed in all-atom MD simulations performed at elevated temperatures (450K), which reveal the unfolding mechanisms to be the intercalation of SDS molecules inside the protein, resulting in the breakage of the secondary structure from the inside. In the concentration range above 50mM, the unfolding rate increases several times, as with higher concentrations, we observe a higher degree of clustering of SDS molecules inside the protein. It is worth noting that the resulting Ubi-SDS complexes after cooling down to 303.15K, closely resemble that of the canonical core-shell structures shown by previous SAXS studies.