The assembly of a living cell requires precise organization concerning the thousands of proteins that perform specific tasks inside or outside various compartments. Proteins are initially built by cellular machines called ribosomes, but many must be delivered to a specific destination, such as an organelle membrane or the outside of the cell. This delivery process is controlled by a short stretch of amino acids known as the signal sequence, which acts like a built-in shipping label. This sequence is typically found at the beginning of the protein chain and directs the newly synthesized molecule to the correct location.
Defining the Signal Sequence Structure
A typical signal sequence is a short peptide, ranging from 15 to 30 amino acids in length, most often located at the N-terminus of the protein chain. Despite variation in the exact amino acid makeup, all cleavable signal sequences share a characteristic tripartite structure. This structure begins with an N-terminal region, called the n-region, which usually contains one or more positively charged amino acids like arginine or lysine.
Following the n-region is the central hydrophobic core, known as the h-region, composed of 7 to 15 nonpolar amino acids such as leucine and isoleucine. This highly water-repellent section drives the delivery process through interaction with lipid membranes and targeting machinery. The sequence concludes with the C-terminal region, or c-region, a short, more polar segment that contains the recognition site for the enzyme that will ultimately remove the signal.
The Role in Protein Targeting
The primary function of the signal sequence is to act as a molecular address label, ensuring a protein arrives at its correct cellular destination. Without this specific sequence, proteins would remain in the cytoplasm where they were synthesized. Different signal sequences correspond to different cellular compartments, such as the mitochondria, chloroplasts, or the nucleus.
The sequence communicates with specialized receptor proteins embedded in the membrane of the target organelle or floating in the cytoplasm. This recognition step is the first stage in protein translocation, which involves moving the protein across a membrane barrier. This mechanism ensures proper cellular organization by sorting proteins destined for the internal membrane system or secretion away from those intended to stay in the cytosol. The most common destination is the endoplasmic reticulum (ER), which serves as the entry point for proteins destined for secretion or other parts of the endomembrane system.
Mechanism of ER Translocation
The process of delivering a protein to the ER membrane is a co-translational event, occurring while the protein is still being manufactured by the ribosome. As the ribosome translates the messenger RNA, the signal sequence is one of the first parts of the new protein to emerge from the ribosomal tunnel. The Signal Recognition Particle (SRP), a cytosolic ribonucleoprotein complex, recognizes and binds to this newly exposed hydrophobic signal sequence.
Binding of the SRP to the signal sequence and the ribosome temporarily halts further protein synthesis, a mechanism called translation arrest. This pause prevents the protein from folding completely in the cytoplasm before reaching the ER membrane. The entire complex (ribosome, mRNA, polypeptide chain, and SRP) then moves to the ER membrane, where it docks with the SRP receptor.
The SRP receptor is an integral membrane protein located near the Sec61 translocon, the protein-conducting channel in the ER membrane. The interaction between the SRP and its receptor is controlled by the binding and hydrolysis of Guanosine Triphosphate (GTP) on both complexes. Once docked, the SRP is released, translation resumes, and the ribosome transfers the nascent polypeptide chain directly to the Sec61 translocon channel. The signal sequence is then inserted into the translocon, often in a loop-like fashion, and the growing protein chain is threaded through the pore into the ER lumen.
Final Destination and Cleavage
Once the signal sequence has initiated translocation, it is frequently removed from the rest of the protein. Cleavage is performed by an enzyme complex called Signal Peptidase (SPase), which is positioned on the luminal side of the ER membrane. This enzyme recognizes the specific amino acid sequence at the C-terminal end of the signal sequence, which typically has small, neutral amino acids at positions -1 and -3 relative to the cleavage site.
The removal of the signal sequence results in a mature, functional protein inside the ER lumen. The cleaved signal peptide is released into the membrane and rapidly degraded by other proteases. However, not all signal sequences are cleaved; in some transmembrane proteins, the hydrophobic sequence functions as a signal-anchor sequence. This non-cleavable sequence initiates translocation but remains permanently embedded in the ER membrane, acting as a fixed transmembrane domain that anchors the protein in place.