protein targeting and trafficking
A big city works only because mail, deliveries, and people end up at the right addresses. A eukaryotic cell is just such a city, full of separate compartments — the nucleus, mitochondria, the endoplasmic reticulum, the cell surface, and more — and it makes thousands of proteins that must each find their correct compartment. Protein targeting and trafficking is the whole system of address labels and delivery routes that gets every protein where it belongs.
The trick is that the destination is written into the protein itself, usually as a short stretch of amino acids that acts like a postal code. Different codes route to different places: an ER signal peptide sends a protein into the secretory pathway; a nuclear localization signal, a patch of positively charged residues, marks a protein to be pulled through the pores of the nuclear envelope; a mitochondrial targeting sequence, which tends to form a particular kind of helix, directs a protein into the mitochondrion. Proteins with no such tag stay in the cytoplasm by default. Beyond getting in the door, trafficking continues: once a protein enters the ER, it can be packaged into little membrane bubbles (vesicles) that bud off, travel to the Golgi for further sorting, and shuttle on to the cell surface, a lysosome, or back again — a busy internal courier network. The reading of each address is done by dedicated receptor proteins that recognize that specific code.
Targeting matters because location is destiny for a protein: an enzyme meant for the mitochondrion is useless adrift in the cytoplasm, and a protein in the wrong place can be harmful. Sorting errors cause real disease — in one condition enzymes that should go to the lysosome are mis-shipped and secreted, so the lysosome cannot do its cleanup. Two honest notes worth keeping: not every protein is targeted the same way (some routes thread the protein in as it is being made, others move a finished protein), and a single protein can carry more than one signal or even be sent to two different places depending on the situation.
A protein destined for the nucleus carries a short cluster of positively charged amino acids — its nuclear localization signal. A shuttle protein recognizes that patch, grabs the cargo, and carries it through a nuclear pore. Tag a normally cytoplasmic protein with that same signal and it, too, ends up in the nucleus.
A nuclear localization signal is a postal code the cell obeys.
Default destination is the cytoplasm — a protein with no targeting tag simply stays there. The various destinations use distinct signals, distinct receptors, and sometimes distinct timing (during versus after synthesis).