A molecular modeling study of the interaction between SRP-receptor complex and peptide translocon

The signal recognition particle (SRP) mediated protein translocation pathway is universal and highly conserved in all kingdoms of life. Significant progresses have been made to understand its molecular mechanism, yet many open questions remain. A structure model, showing how nascent peptide inserts into peptide translocon with the help of SRP protein Ffh and its receptor FtsY, is desired to facilitate our studies. In this work, we presented such a model derived by computational docking of the Ffh-FtsY complex onto the translocon. This model was compatible with most available experiments. It suggested that the Ffh-FtsY complex approached the translocon with its G domains and was locked up by the cytoplasmic loop of SecG and the C5/C6 loops of SecY. Several residues were expected to play important roles in regulating GTP hydrolysis. Additionally, a hypothesis on the yet ambiguous function of FtsY A domain was proposed. These interesting results invite experimental investigations.