Protein trafficking refers to the process by which proteins are transported within a cell or between different cellular compartments. It is a fundamental cellular mechanism that ensures proteins are delivered to their appropriate destinations within the cell and perform their specific functions. This process is essential for maintaining cell structure and function, as well as for carrying out various cellular processes. Here's an overview of protein trafficking: Protein Synthesis: The journey of a protein typically begins in the ribosomes, where it is synthesized based on the instructions provided by the cell's DNA. Targeting Signals: Proteins have specific targeting signals or sequences that direct them to their intended destinations. Nuclear transport, also known as nucleocytoplasmic transport, is a vital process that regulates the movement of molecules such as proteins and RNA between the cell's nucleus and cytoplasm. The nucleus is a membrane-bound organelle within eukaryotic cells that contains genetic material in the form of DNA. Proper nuclear transport is essential for a variety of cellular functions, including gene expression, DNA replication, and regulation of cell cycle processes. Here's an overview of nuclear transport: Nuclear Pores: The nuclear envelope, which separates the nucleus from the cytoplasm, is perforated by specialized structures called nuclear pores. These nuclear pores act as gatekeepers, allowing selective passage of molecules in and out of the nucleus. Nuclear Localization Signal (NLS): Proteins that need to enter the nucleus typically contain a specific amino acid sequence known as a nuclear localization signal (NLS). This NLS is recognized by transport proteins called importins, which facilitate the import of the protein into the nucleus. Export Signals: Conversely, proteins or RNA molecules that need to exit the nucleus carry a nuclear export signal (NES). Exportins are responsible for recognizing these NES-containing molecules and facilitating their export from the nucleus to the cytoplasm. Ran-GTP System: The transport of molecules through nuclear pores is regulated by the Ran-GTP system. Ran is a small GTPase protein that exists in two forms: Ran-GTP (guanosine triphosphate-bound) and Ran-GDP (guanosine diphosphate-bound). The direction of transport (import or export) is determined by the nucleotide-bound state of Ran. Importins and exportins are sensitive to Ran-GTP levels, which helps ensure proper cargo transport. Transport Mechanism: During nuclear import, importins bind to cargo proteins containing NLS sequences in the cytoplasm. This complex is then translocated through the nuclear pore. Inside the nucleus, Ran-GTP binds to the importin, causing it to release the cargo. Conversely, during nuclear export, exportins bind to cargo molecules with NES sequences inside the nucleus.

1. Cell Biology:
Vesicular Transportation
Dr. Amit Joshi
HOD & Assistant Professor
Biochemistry Department
KALINGA UNIVERSITY
Naya Raipur, CG, INDIA-492101

10. COP-I Vesicle Formation
A B

11. COP-II Vesicle Formation

12. Clathrin Coat Vesicle Formation

14. ER: KDEL & KKXX SIGNATURE
SEQUENCE
• The KKXX and KDEL sequences are signal sequences found in proteins that are involved
in the regulation of protein trafficking within the cell, particularly in the context of
vesicular transport between the endoplasmic reticulum (ER) and the Golgi apparatus.
These sequences play a crucial role in targeting and retaining proteins within the ER or in
retrieving them from the Golgi apparatus back to the ER.
KKXX Sequence:
• The KKXX sequence is a retrieval signal found at the C-terminus of some ER-resident
membrane proteins or soluble ER proteins. The most well-known KKXX-containing
protein is the KDEL receptor (These are present on Transmembrane proteins of RER).
• The KKXX sequence functions as a retrieval signal that helps maintain ER-resident
proteins within the ER. It interacts with COPI (Coat Protein I) vesicles, which are
involved in retrograde transport from the Golgi apparatus back to the ER.
• When a protein containing the KKXX signal is transported to the Golgi apparatus, COPI
vesicles recognize the KKXX sequence and transport the protein back to the ER,
preventing its accumulation in the Golgi.

15. KDEL Sequence:
• The KDEL sequence is a retrieval signal found at the C-terminus of
soluble ER-resident proteins, such as chaperone proteins like BiP
(Binding immunoglobulin Protein).
• Proteins containing the KDEL sequence are typically enzymes or
chaperones that need to be retained within the ER for proper protein
folding and quality control.
• The KDEL sequence interacts with the KDEL receptor, a
transmembrane protein in the Golgi apparatus. When KDEL-
containing proteins escape from the ER and reach the Golgi, they are
recognized by the KDEL receptor.
• The KDEL receptor binds to KDEL-containing proteins and directs
them back to the ER via retrograde transport vesicles, such as COPI-
coated vesicles.

16. Resident proteins that escape the ER are captured by the KDEL receptor
and retrieved in a COPI dependent process

17. KKXX Sequence:
• Proteins with the KKXX sequence also have it encoded in their amino acid sequence.
• The COPI complex recognizes the KKXX sequence and, when a protein bearing this
signal reaches the Golgi apparatus, COPI-coated vesicles are formed around it.
• These vesicles transport the protein back to the ER, where they fuse with the ER
membrane, releasing the protein into the ER lumen.
• The protein can then be sorted or folded within the ER or continue on to other
destinations if needed.
KDEL Sequence:
• Proteins that are meant to carry the KDEL sequence usually have it encoded in their
amino acid sequence. This sequence is recognized by the KDEL receptor (ERD2) as
the protein exits the Golgi apparatus.
• The KDEL receptor binds to the KDEL sequence, allowing the protein to be
transported back to the ER via vesicles budding from the Golgi apparatus.
• Once in the ER, the protein is released from the receptor and can continue to perform
its functions within the ER.

18. • The high resolution of the crystal structures obtained using lipid cubic
phase crystallisation revealed that KDEL binding results in the
formation of a very short hydrogen bond, an extremely rare intra
molecular interaction.
• This bond only forms when the pH of the binding site is acidic and helps
to explain how pH changes between the ER and Golgi help to drive
protein trafficking in one direction. (In Cis Golgi Low pH and High
affinity between KDEL and KDEL receptor exist, while in ER High pH
• Binding of the KDEL signal peptide in the lumen of the Golgi results in
structural changes in the cytoplasmic face of the receptor, which signals
to COPI coatomer to bind and initiate trafficking back to the ER

31. Cell Biology:
Vesicular Fusion
Dr. Amit Joshi
HOD & Assistant Professor
Biochemistry Department
KALINGA UNIVERSITY
Naya Raipur, CG, INDIA-492101

35. Cell Biology:
Nuclear Transport
Dr. Amit Joshi
HOD & Assistant Professor
Biochemistry Department
KALINGA UNIVERSITY
Naya Raipur, CG, INDIA-492101

40. Cell Biology:
ABO Blood Group
Biochemistry
Dr. Amit Joshi
HOD
BIOCHEMISTRY DEPARTMENT
KALINGA UNIVERSITY
Naya Raipur, CG, INDIA-492101

46. Cell Biology:
Ubiquitinization of Proteins
Dr. Amit Joshi
HOD
BIOCHEMISTRY DEPARTMENT
KALINGA UNIVERSITY
Naya Raipur, CG, INDIA-492101

50. •Questions