Eukaryotic cells have different membrane-bound organelles with distinct protein requirements. The process by which proteins are targeted to a specific organelle is called protein sorting.

Protein sorting can be of two types: signal-based sorting and vesicle-based trafficking. In signal-based sorting, specific amino acid sequences called sorting signals target proteins to the proper location inside the cell either via gated transport or by protein translocation. In gated transport, folded proteins with exposed nuclear localization signals are recognized by soluble cytosolic receptors. The cytosolic receptor binds the cargo and transports it across the nucleus by passing through the nuclear pore complex embedded in the nuclear membrane.

In contrast, precursors of proteins are translocated or moved from the cytosol to different organelles such as mitochondria, chloroplast, Endoplasmic Reticulum (ER), and peroxisomes. During protein translocation, cytosolic chaperones bind and unfold the target protein to guide them to the organelle surface. Specific receptors on an organelle membrane recognize the signal sequences on the unfolded protein precursor and bind them. The unfolded peptide chain is threaded through specialized transporters called translocons to cross the lipid bilayer membrane and reach the lumen of the organelle.

Protein sorting by vesicular trafficking involves the movement of proteins in membrane-bound structures called transport vesicles. Soluble proteins in the ER lumen get packed onto the transport vesicles and are bud off from the ER membrane. Molecular markers displayed on the organelle membrane guide the proper delivery and fusion of the transport vesicles.