Protein Trafficking Mechanisms

Study Notes

There are four fundamentally different ways a protein is moved from one compartment to another.

Transmembrane protein translocators directly transport specific proteins from the cytosol into a topologically distinct space.
The transported protein molecule usually must unfold to snake through the translocator.
The initial transport of selected proteins from the cytosol into the ER lumen, the ER membrane, or mitochondria occurs in this way.

Proteins and RNA molecules move between the cytosol and the nucleus through nuclear pore complexes in the nuclear envelope.
The nuclear pore complexes function as selective gates that support the active transport of specific macromolecules and macromolecular assemblies between the two topologically equivalent spaces.

Membrane-enclosed transport intermediates ferry proteins from one topologically equivalent compartment to another.
The transport intermediate becomes loaded with a cargo of molecules derived from the lumen and membrane of the originating compartment as it buds and pinches off.
At the destination compartment, the transport intermediate fuses with the compartment's enclosing membrane to discharge its cargo.

Double membrane sheets wrap around portions of the cytoplasm, often including fragments of organelles or even entire organelles.
This membrane structure then seals by membrane fusion to enclose a separate compartment, the autophagosome.

Sorting signals are usually composed of amino acid side chains in a protein and come in two general varieties: signal sequence and batch sequence.
Signal patch: a specific three-dimensional arrangement of amino acids.
Signal sequence: a linear sequence of about 5–10 predominantly hydrophobic amino acids.
The linear signal sequences for protein translocation are often found at the N-terminus of the polypeptide chain.
These N-terminal signal sequences are usually removed from the finished protein by specialized signal peptidases once the sorting process is complete.

Proteins destined for mitochondria have signal sequences that include positively charged amino acids.
The signal for protein import into the nucleus is composed primarily of positively charged amino acids.
Proteins for peroxisomes have a signal sequence of three characteristic amino acids at their C-terminus.

The membrane of the ER typically constitutes more than half of the total membrane of an average animal cell.
The ER is organized into a netlike labyrinth of branching tubules and flattened sacs that extend throughout the cytosol.
The tubules and sacs interconnect, and their membrane is continuous with the outer nuclear membrane.
ER in most eukaryotic cells is to sequester Ca2+ from the cytosol.

Signal sequences were discovered in secreted water-soluble proteins that are first translocated across the ER membrane.
The signal hypothesis was formulated to explain these observations.

The ER signal sequence is guided to the ER membrane by at least two components: a signal-recognition particle (SRP), which binds to the signal sequence, and an SRP receptor in the ER membrane.

Post-translational translocation: proteins are completely synthesized in the cytosol as precursors before they are imported into the ER.
Post-translational protein translocation is more common across the yeast ER membrane and the evolutionarily related bacterial plasma membrane.

The signal peptide of a precursor directly engages the Sec61 translocator to open the channel.
To pull proteins into the ER lumen, eukaryotic cells use accessory proteins called Sec62 and Sec63 that associate with the Sec61 translocator and position an hsp70-like chaperone protein (called BiP) adjacent to the lumenal opening of the translocation channel.