2nd of Feb 2018

Lecture 8

Protein Sorting

“Protein targeting or protein sorting is the biological mechanism by which proteins are transported to
the appropriate destinations in the cell or outside it.”

Unlike a bacterium, which generally consists of a single intracellular compartment surrounded by a plasma
membrane, a Eukaryotic cell is elaborately subdivided into functionally distinct membrane enclosed
compartments

organelles

Each organelle consist its own characteristics set of enzymes and other specialized molecules.

complex distribution system transport

Proteins can move between compartments in different ways. Synthesis of all protein begins on ribosomes in the
cytosol, except for the few that are synthesized on the robisomes on mitochondria and plastids

Theri subsequent fate depends on their Amino acid sequence, which can contain sorting signal that directs their
delivery to location outside the cytosole.

Most proteins don’t have a sorting signal and remain in the cytosol. Proteins with specified sorting signals are
transported from the cytosol into the nucleus, ER, mitochondria, plastids or peroxisomes.

1. Gated Transport - protein moves between the cytosol and the nuclear
2. Transmembrane transport - specific proteins are transported across the membrane from the cytosol to
a species that is topological different
3. Vascular transport - membrane enclosed transporter intermediates ferry proteins from one
compartment to another
 All of them are derived form ER, so all are
topologically equal. So fusion can be
occurred easily.

Vesicular transport

The transport vesicles become located with a cargo, a molecule is derived from the lumen (cavity) of one
compartment as they bud and pinch off from it membrane and they discharged their cargo into a second
compartment (target compartment) by fusing with the membrane enclosing that compartment.

The transfer of soluble protein from ER to Golgi bodies occurs in this way.
Because the transport proteins don’t possess a membrane, vesicles transport can move proteins that only
between compartments, that are topologically equivalent.

The membrane is also transported and the original orientation of both proteins and lipids in the donor
compartment membrane is preserved in the target compartment membrane.
Signal sequences directs proteins to the correct cell address. Most protein sorting signals reside ion a stretch of f
Amino acid sequence typically 15 to 60 residues long – often found at the N terminus. (sometime can be
internal)
Specialized signal peptidases remove the signal sequence from the finished protein once the sorting process in
complete.

Sometime signal sequences are composed of multiple internal Amino acid sequence that from a specific three-
dimensional arrangement of atoms on the protein surface - signal patch

Transport of Molecule between the nucleus and the cytosol

The inner nuclear membrane contains specific protein that act as an anchoring site for chromatin and for the
nuclear lamina.
Bidirectional traffic occurs continuously between the cytosol and the nucleus.
The many proteins that function in the nucleus, such as histone, DNA or RNA polymerase, RNA processing
proteins, gene regulatory proteins.
These are selectively imported to the nucleus (because they made in cytosol). At the same time, t-RNA and m-
RNA synthesis in the nucleus compartment are exported into the cytosol.

Ribosomal proteins are made in the cytosol and are imported into the nucleus, where they assemble within the
newly formed ribosomal RNA in the particles. There ribosomal particles are then exported into the cytosol,
where the assemble into ribosome.

Nuclear Pore Complex (NPC)

Large elaborate structures that perforate the nuclear envelope in all eukaryotes.
Composed of about 30 different NPC proteins (nucleoporins) which are present in multiple copies and are
arranged with a striking octagonal symmetry.
Each NPC can transport up to 500 macromolecules per second and can transport in both directions at the same
time.

Each NPC contains one or more aqueous passage through which small water-soluble molecules can diffuse
passively.

The larger a protein, they move slowly it passes through the NPC.

2nd of Feb 2018

Lecture 9

Npc have 4 structural building blocks.

1. Column: it forms a bulk of the wall

 2. Annulary Subunit: are centrally located
3. Luminal subunit contains transmembrane protein that anchor the complex to the nuclear membrane
4. The rings subunit: forms the cytosolic and nuclear face of the…….
in addition and ……………….

From the nuclear side the fibril concave to form basket like a structure.

The total number of NPCs found in the nucleus envelope of the typical mammalian cell is 3000 – 4000.
Therefore, the total traffic that passes through the NPC is enormous.

Anyway how and NPC coordinate the direction of flow of macromolecules to avoid conjusion and head on
collision is not properly know.
Many NPC protein that lying the central core contain expensive unstructured region with are through the form
disordered hanger. This blocks the central opening on the NPC, to the passage of large macromolecules, but
leaving small opening to allow the diffusion of smaller molecules.

Many cell proteins are too large to diffuse through the NPCs. Therefore, the nuclear compartment and the
cytosol can maintain different compartments of proteins.
Examples: Matured cytosolic ribosome are above 30nm in diameter. Therefore they cant go
through this to Nucleus. They can’t diffuse through NPCs. It cause……………….. protein structure in
cytosol.
but how does the nuclear export in newly made ribosomal ………. or import large molecules
such as DNA or RNA.

As many Cell protein are too large to diffuse passively. the nucleus compartment and the
cytosol maintained different compartment of protein
Example: Matured cytosolic ribosome

To intimate nuclear import, most nuclear localization signals must be recognized by nuclear import
receptors, which are solute cytosolic proteins that bind both to the nuclear localization signal on the protein and
to NPC proteins.

some proteins from the fibrils of the NPC that extended into the cytosol.

The cargo proteins 1, 2 and 3 contain different nuclear localization signals and, therefore each bind to different
nuclear import receptor.

These fibrils and many of the NPC proteins, that line the center of the NPC and contribute to the diffusion
barrier, include a large number of short amino acid repeats – FG repeats.

FG repeats binding site for the import receptors.

The receptor cargo complex move along the transport parth by repeatedly binding, dissociation and rebinding
to adjacent FG repeat sequences.

In this way the complex number of protein from one NPC protein another to transverse and tangled interior of
the NPC.

Inside the nucleus, the import receptors dissociate from there cargo and return to the cytosol.

Nuclear import receptors doesn’t always bind to nuclear proteins directly.

The adaptor protein are structurally relate to nuclear import receptors and recognize nuclear localization signal
on cargo protein. All also contain the nuclear localization signal that binds them and import receptors.

Nuclear export work like nuclear import, but in reverse.

Nuclear export of large molecules occurs through NPCS and also depends on a selective transport system.

Relies on nuclear export signals and on complementary nuclear export receptors.

The nuclear pores transport proteins in the fully folded confirmation and transfer ribosomal components as
assembled particles.

This distinguishes this mechanism from the mechanism that transport proteins into other organelles.
The Transport of proteins into Mitochondria and Chlorophylls