Protein targeting

Protein targeting, also known as protein sorting, is the biological mechanism that moves proteins to specific locations. Proteins are essential for life, but they must reach the right place to function. They may be sent to the inner space of an organelle or to different membranes. Some proteins move to the plasma membrane, while others are sent outside the cell through secretion. This precise delivery is vital for cellular health. If the sorting process fails or becomes dysfunctional, it can lead to various diseases.

How do these molecules find their way? The instructions are contained within the protein itself. Many proteins possess a short amino acid sequence known as a signal peptide. This sequence acts like a biological postal code. It directs the cell's transport machinery to a specific destination. Most signal peptides are located at the N-terminal end of the protein. Once the protein reaches its target, an enzyme called signal peptidase typically cleaves the peptide away. This is why most mature, finished proteins do not contain these signal sequences.

Scientists spent decades uncovering these rules. In 1970, Günter Blobel conducted landmark experiments on protein translocation. At the time, he was an assistant professor at Rockefeller University. He expanded upon the earlier research of his colleague, George Palade. Palade had shown that some proteins are made by free ribosomes in the cytosol. Other proteins are made by ribosomes attached to the endoplasmic reticulum, or ER. Blobel hypothesized that the targeting depended on the proteins themselves rather than the ribosomes. For discovering these intrinsic signal sequences, Blobel was awarded the 1999 Nobel Prize in Physiology.

Signal peptides often have a specific tripartite structure. They usually feature a positively charged, hydrophilic region near the N-terminal. This is followed by a middle span of 10 to 15 hydrophobic amino acids. Finally, there is a slightly polar region near the C-terminal. While most signal peptides are at the N-terminal, peroxisomes use a sequence on the C-terminal extension. Some proteins use signal patches instead of peptides. These are made of amino acids that are not next to each other in the main sequence. However, they become a functional unit when the protein folds into its final shape. Unlike peptides, signal patches are not cleaved after sorting is complete.

There are two primary ways proteins move through membranes. The first is co-translational translocation, which occurs during protein synthesis. This is the pathway used by most secretory and membrane-bound proteins. It begins when a signal recognition particle, or SRP, identifies an N-terminal signal peptide. The SRP binds to the ribosome and temporarily pauses protein synthesis. The entire complex is then transferred to an SRP receptor on the ER in eukaryotes. The protein is inserted into a translocon, which is a protein-conducting channel. In eukaryotes, this channel is the Sec61 complex.

Some proteins use post-translational translocation, which happens after synthesis is finished. In prokaryotes, this requires cofactors like SecA and SecB. In the ER, the Sec63 complex uses ATP hydrolysis to help slide the protein into the lumen. This method is also used for proteins heading to the nucleus, mitochondria, or chloroplasts. For example, proteins destined for the nucleus use a nuclear localization sequence (NLS). This sequence helps them pass through nuclear pores in the nuclear envelope.

Mitochondria have their own complex sorting systems. Most mitochondrial proteins are made in the cytosol as precursors. These proteins often have amphipathic sequences, meaning they have both water-loving and water-avoiding parts. These sequences often form an alpha-helix shape. To enter the mitochondria, proteins interact with the TOM complex, which stands for translocase of the outer membrane. The protein is handed off to the TOM40 general import core. It is then fed through the intermembrane space to the TIM17/23/44 complex in the inner membrane.

This movement is driven by an electrochemical gradient. During oxidative phosphorylation, the mitochondrion creates a negative potential inside its matrix. This negative charge helps pull the positively charged targeting sequences into the correct location. Some proteins are also destined for the mitochondrial inner membrane via a carrier pathway. These proteins use a stop-transfer-anchor sequence to embed themselves in the membrane. Understanding these pathways helps scientists learn how cells maintain their complex internal structures.