Signal Sequence in Protein Synthesis

Signal Sequence and SRP

• A signal sequence is internally located in terminal or integral membrane proteins.
• The sequence is recognized by the signal recognition particle (SRP), a large protein-RNA complex, as soon as it is translated.

SRP-Nascent Peptide Chain Association

• Translation arrests, allowing time for the SRP-nascent peptide chain to associate with the SRP receptor on the ER membrane.
• The SRP receptor associates with a translocon (ER membrane channel).

Signal Sequence Orientation and Insertion

• The translocon checks the signal sequence of the peptide and inserts the nascent peptide in the appropriate orientation.
• The orientation of the peptide cannot be altered later.

SRP Release and Protein Synthesis

• The SRP is released to be re-used, and protein synthesis resumes, threading the growing protein through the translocon.

Translocon and Hydrophobic Residues

• The translocon continues to survey the growing protein, looking for stretches of hydrophobic residues that will form membrane-spanning domains.
• These hydrophobic residues are retained in the translocon until all TMDs are fully assembled, then they pass into the ER membrane.

Protein Modifications in ER Lumen

• The growing peptide is scrutinized by further enzymes in the ER lumen.
• Protease cleaves any N-terminal signal sequence.
• Oligosaccharyl transferase identifies asparagine residues within the sequence Asn-X-Ser/Thr and adds pre-assembled sugar residues (N-linked glycosylation).
• Chaperone proteins (e.g., BiP) help the growing peptide fold and pull it into the ER lumen.
• Other enzymes make additional modifications, including catalyzing the formation of disulphide bonds.

Protein Quality Control in the ER

• Damaged proteins in the ER lumen are removed to prevent clogging and aggregation of the system.
• ER-associated degradation (ERAD) is a process that transports misfolded ER proteins to the cytosol for degradation.
• Ubiquitin ligase attaches ubiquitin to lysine residues on the protein, marking it for degradation.

ERAD Pathway

• Over 30% of all ER proteins are marked for degradation via the ERAD pathway.
• A subunit of ubiquitin ligase is encoded by the Parkin gene, which is defective in Parkinson's disease.

Disease Association

• The delta 508F mutation causes CFTR (a plasma membrane chloride channel) to enter the ERAD pathway, leading to cystic fibrosis (affects 1 in 2500 UK births).
• Human cytomegalovirus (CMV) diverts MHC (major histocompatibility complex) for degradation, allowing the virus to remain hidden from the immune system.
• Normally, MHC displays antigens, which mark an infected cell, but CMV's diversion of MHC prevents this.