Protein transport 4

Question 1

Membrane protein insertion

Answer 1

• Membrane proteins = 20-30% of euakaryotic proteome
• Initially assembled in ER
• Issues = hydrophobic TM needs to be shielded)
• Need route if transport past highly polar surface
• Ideal TMH = 20aa in hydrophobic section

Question 2

Determinants of TM domain integration

Answer 2

• Free E contribution of each aa = additive

- Assume TMD insertion approximates a thermodynamically driven eq btw aq environment + surrounding

Question 3

Determinants of topology

Answer 3

• 2 stage model: individual helices of polypeptide protein are stable separately as domains in a bilayer
• 1o sequence also influences topology of TM
• 2 theories: follow topology vs local determination
• Experiment = remove section of membrane + observe topology, +ve inside rule (most +ve residues = cytoplasmic side, experiment = change topology)

Question 4

Insertion

Answer 4

• Targeting + insertion machinery = conserved
• Protein directed to translocon, hydrophobicity
• Large energetic penalty when polar = charged aa near centre
• Close to polar head group
• Process:
  1. Hydrophobic segment emerges
  2. Recognised by SRP
  3. SRP = high affinity for ribosome
  4. Met-rich region of SRP54 perfectly poised to capture nascent protein
  5. SRP-bound ribosome-nascent chain targeted to receptor
  6. Complex released from SRP/Sec61 complex
  7. Sec61 positioned to recognise each TMD

Question 5

Lipid partitioning model

Answer 5

• Protein segments equilibrate according to their polarity
  1. aq lumen of translocon
  2. amphipathic ‘interface site’ btw bilayer interior + translocon lumen
  3. Interior of bilayer

Question 6

Accessory protein

Answer 6

• Membrane proteins usually contact accessory protein
• EMC = assists Sec w/ topogenesis
• TRAAM + TRAP
• YIDC = 5-6 helices, abundant, promote membrane insertion