10.1: Targeting membrane proteins to where they need to be

What determines where a polypeptide (protein) ends up? As you might suspect, there are signals and receptors involved. Signals are typically part of the polypeptide’s primary (amino acid) sequence and receptors are proteins encoded by other genes. The receptors that are present in the living cell, they are part of what is inherited from a cell's progenitor, part of the continuity of life. We begin our description of polypeptide targeting with prokaryotes, because they are simpler. We will consider how a newly synthesized polypeptide comes to end up in the cytoplasm, the plasma membrane, or outside of the plasma membrane.

In prokaryotes, the genomic DNA is located in the cytoplasm; there is no barrier between a newly synthesized RNA molecule and the ribosomes, tRNAs, and the other components involved in RNA-dependent polypeptide synthesis. Newly synthesized mRNA molecules can interact with the small and large ribosomal subunits, assemble with them to form a functional ribosome and direct polypeptide synthesis. For a water-soluble cytoplasmic polypeptide, as opposed to a polypeptide that resides in, or passes through the membrane, no further “signals” are necessary. The ribosomal complex moves along the mRNA, the polypeptide is synthesized, passes through the ribosomal channel, and emerges into the cytoplasm. When the ribosome reaches a stop codon, release factor binds, leading to the disassembly of the ribosomal-mRNA-polypeptide complex. The ribosomal components, as well as the mRNA can then initiate a new mRNA-ribosome complex, to produce another polypeptide. The released (newly synthesized) polypeptide may fold on its own or associate with other polypeptides to form a functional protein. Some of these folding steps may involve interactions with chaperones.

What is going on with a polypeptide destined for insertion into a membrane? Clearly it has a different structure than a water-soluble protein; differences you should be able to predict. The first step in delivering a membrane protein to or through a membrane is to recognize that it as a membrane protein or a protein that needs to pass through the cell membrane. The general mechanism (and the only one we will consider) involves what is known as a signal sequence (↓). A signal sequence is composed primarily of hydrophobic amino acids; the typical signal sequence is between 8 to 12 amino acids in length and generally located near the polypeptide’s N-terminus, the first part of the polypeptide to be synthesized. The presence of such a signal sequence marks the polypeptide as a membrane protein. As the nascent polypeptide emerges from the ribosomal tunnel, the signal sequence is recognized through its binding of a cytoplasmic receptor, the signal recognition particle (SRP). SRP is composed of polypeptides and a structural RNA. The binding of a SRP to a signal sequence causes translation to halt, although the mRNA-ribosome-nascent polypeptide-SRP complex remains intact. The complex diffuses within the cell until it engages an SRP-receptor located on the cytoplasmic surface of the plasma membrane. The SRP receptor is associated with a transmembrane polypeptide translocator protein (↑). When the mRNA-ribosome-nascent polypeptide-SRP+SRP Receptor complex forms, SRP disassociates from the ribosome-nascent polypeptide complex, translation resumes and the nascent polypeptide interacts with the translocator protein and either folds to become embedded within the membrane, or passes through the membrane, and is released (secreted) on the other side. Typically, if the polypeptide is secreted, the signal sequence is removed by proteolysis during the process.

Now consider the situation in eukaryotic cells. Although topologically more complex the same basic process applies. The difference is that the SRP receptor is not located in the plasma membrane, it is located in the ER membrane. A protein with a signal sequence will be delivered to the ER membrane or released into the lumen of the ER. From there other signals will determine whether the protein stays in the ER, moves to the Golgi apparatus, where it is post-translationally modified, and may then move to the plasma membrane, or to some other membrane compartment within the cell. A protein in the lumen of the ER is effectively outside of the cytoplasm, and can be retained within a membrane compartment (such as the ER) or secreted from the cell. At this point, we will not concern ourselves with further details, except to say that whenever a protein is targeted to a specific cellular compartment, we can assume that the protein contains signals that are recognized by receptors that lead to its localization.

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