The cost of exposing a hydrophobic loop and implications for the functional role of 4.5 S RNA in the Escherichia coli signal recognition particle

The signal recognition particle (SRP) is an RNA-protein complex that direct s ribosomes to the rough endoplasmic reticulum membrane by binding to targe ting signals found on the nascent chain of proteins destined for export to the endoplasmic reticulum. We found evidence from studies with fragments of the protein component of the Escherichia coli SRP that a long hydrophobic loop (the so-called "finger loop") is detrimental to the stability of its s ignal peptide-binding domain, the M domain. This hydrophobic loop is highly conserved and thus may have a critical role in the function of the SRP. Gi ven our previously reported evidence that 4.5 S RNA stabilizes the tertiary fold of the M domain (Zheng, N., and Gierasch, L. M. (1997) Mol. Cell 1, 7 9-87), we now propose that the functional requirement for 4.5 S RNA resides in its ability to counteract the destabilizing influence of the finger loo p.