Hydrophobicity and signal sequence binding to the Sec complex: A single molecule biophysical perspective

The Sec61 complex plays a critical role in protein translocation into the endoplasmic reticulum (ER), enabling the passage of soluble proteins into the lumen and the lateral insertion of membrane proteins. The Sec complex, comprising Sec61, Sec63, Sec62, and other auxiliary proteins, is especially important for the translocation of precursor proteins with inefficient signal sequences (SSs) that require additional assistance to trigger the opening of the Sec61 channel. In this study, we investigated how the hydrophobicity of SSs affects the interaction with the Sec complex at the single-molecule level using optical tweezers. We analyzed three SSs representing low, moderate, and high hydrophobicity in the h-regions. Our results show that the highly hydrophobic SS from DPAP-B pαF forms a less stable bond with the Sec complex, evidenced by shorter interaction time and reduced energy barrier to the unbound state. In contrast, SSs with lower hydrophobicity establish more stable interactions, characterized by extended interaction times, and elevated energy barriers to reach the unbound state. These findings suggest that the Sec complex may selectively recognize and interact with SSs based on their hydrophobicity, offering insights into the mechanisms by which defects in SS translocation contribute to ER-associated diseases.