Domain rearrangement of SRP protein Ffh upon binding 4.5S RNA and the SRP receptor FtsY

Abstract

The signal recognition particle (SRP) mediates membrane targeting of translating ribosomes displaying a signal-anchor sequence. In Escherichia coli, SRP consists of 4.5S RNA and a protein, Ffh, that recognizes the signal peptide emerging from the ribosome and the SRP receptor at the membrane, FtsY. In the present work, we studied the interactions between the NG and M domains in Ffh and their rearrangements upon complex formation with 4.5S RNA and/or FtsY. In free Ffh, the NG and M domains are facing one another in an orientation that allows cross-linking between positions 231 in the G domain and 377 in the M domain. There are binding interactions between the two domains, as the isolated domains form a strong complex. The interdomain contacts are disrupted upon binding of Ffh to 4.5S RNA, consuming a part of the total binding energy of 4.5S RNA-Ffh association that is roughly equivalent to the free energy of domain binding to each other. In the SRP particle, the NG domain binds to 4.5S RNA in a region adjacent to the binding site of the M domain. Ffh binding to FtsY also requires a reorientation of NG and M domains. These results suggest that in free Ffh, the binding sites for 4.5S RNA and FtsY are occluded by strong domain–domain interactions which must be disrupted for the formation of SRP or the Ffh-FtsY complex.

Keywords

• protein targeting
• translation
• protein export
• bimane cross-linking
• fluorescence resonance energy transfer
• Alx, Alexa Fluor
• Bpy, BODIPY Fl
• FRET, fluorescence resonance energy transfer
• mBrB and dBrB, mono- and dibromobimane
• OG, Oregon Green
• RNC, ribosome nascent-chain complex
• SRP, signal recognition particle.