Lecture 13: Principles of Membrane Structure

Question 1

What is the importance of membrane proteins?

Answer 1

• Gatekeepers in and outside of the cell
  
  • Downstream signaling effects: allow signals to transmit outside the cell into the cell
  • Allow ions to move thru their membranes in a selective fashion
  • Difficult to get a molecule into a cell [has to permeate the membrane]
    ○ Proteins decorate the membrane to make this process easier
  • Fundamental to mitochondrial processes
    Generating ATP

Question 2

Name 3 of the integral membrane proteins and their functions within biological membranes

Answer 2

• Single TM
  ○ Single alpha helix that goes across the membrane
  
  • Multi TM
    ○ Helix will go in n back out again
    ○ Loop-like domain
  • Oligomerization
    ○ Form larger n larger complexes
    ○ Tetrameric pores

Question 3

Name 3 of the membrane associated proteins and their functions within biological membranes

Answer 3

• Protein/protein
  ○ Green is not necessarily a membrane protein but a membrane associated protein (MAP)
  
  • Electrostatic
    ○ Positive patch on MAP drawn to negative
  • Hydrophobic
    ○ Within the core of the membrane region is a hydrophobic region
    ○ Attracted from outside
    ○ Drawn into the membrane but don’t necessarily span all the way across

Question 4

How are membranes classified?

Answer 4

• Classified into 4 different types
  
  • Based on whether the end terminus is on the outside/inside of the cell whether the anchoring of the membrane protein is by the C terminus
    ○ Inserted by a protein called translocon
    ○ Translocon operates predominantly to insert w the C terminus outside of the cell
  • Type I
    ○ C terminus inside
  • Type II
    ○ C terminus outside
    ○ Most abundant
  • Type III
    ○ C terminus inside
    ○ Single polypeptide chain
    ○ Multiple regions of it cross back n forth across the membrane (often to form channel)
  • Type IV
    ○ C terminus outside
    ○ Least abundant
    ○ Multi-polypeptide protein which ahas
  • Type I and type III are similar but the signal sequence is cleaved off in type III
  • Majority of membranes hv their N terminus embedded in the membrane [N is positive]

Question 5

How do peripheral membrane proteins interact with membranes, and what are some examples of these interactions?

Answer 5

• Negatively charged lipid on the membrane interacting w positively charged patches on a protein
  
  • PTEN when mutated causes cancer
    ○ Binds to PIP molecule engaging in a phosphate group to hv a favourable interaction b/w the protein n the membrane
  • BamC (outer membrane protein in bacteria)
    ○ 3 lipid tail anchor in the hydrophobic core
    ○ Soluble domain sits on the membrane surface

Question 6

Describe the bilayer environment

Answer 6

• Gray core region (hydrophobic)
  ○ 30 Angstrom thick
  
  • Any protein that spang the hydrophobic core needs to get all the way across this region to escape this hydrophobic core
  • Orange - negatively charged
  • Don’t want molecules diffusing from outside the cell
  • Hydrophobic greasy barrier prevents anyth from going across
  • Interface region (10A)
    ○ Generally negatively charged [phosphate group]
  • Different head group regions that determine whether it’s more positive/negative

Question 7

Why is the hydrophobicity important?

Answer 7

• Don’t want molecules diffusing from outside the cell
  
  • Polar molecule -> not going to diffuse into hydrophobic region
  • Hydrophobic greasy barrier prevents any molecules from going across
  • If bacteria, don’t want antibiotics going into cell

Question 8

Describe the challenges in studying membrane proteins experimentally and explain how techniques like nuclear magnetic resonance (NMR) and X-ray crystallography address these challenges.

Answer 8

• Functional studies
  ○ Membrane protein in native lipid environment
  § Required to put in detergent environment to get the 3D structure
  
  • NMR
    ○ Detergents that hv long micelle tails
    ○ Don’t sit as a bilayer
    ○ Spherical entity (polar regions on the outside, lipid tails will engage w the hydrophobic core of the membrane protein)
    ○ Extract protein from lipid like environment via micelle
    ○ Important to go from micelle to tight packing
  • X-ray
    ○ Crystal lattice
    Stack up the protein structures

Question 9

Describe the structural function of the inner membrane protein

Answer 9

• Composed of alpha helical domain
  
  • 7 transmembrane helices
  • 38A thickness
  • 20 AA that span the membrane
  • Continuous stretch of hydrophobic AA
    Most of the hydrogen bonds are held within the protein structure to allow it to go across the membrane

Question 10

Describe the structural function of the outer membrane protein

Answer 10

• Composed of beta strands
  
  • 8-10 resides to go across the membrane
  • Thinner thickness of 33 A [hydrophobic core is shorter [lipid tail length is thinner]]
    Shorter distance to go inside the cell than outside the cell

Question 11

Describe the process of TM helix formation and aggregation in the context of membrane protein insertion into the lipid bilayer.

Answer 11

• TM helix formation
  
  • Helix aggregation
    ○ Inserted by the Sec translocase
    ○ Done on a basis of the helix being inserted into the membrane
    ○ Folds into a helix
    ○ Inserted out into the membrane -> results in helix aggregation (single membrane protein)
    ○ Might also get the membrane protein associating directly w other membrane protein complexes

Question 12

What are the 6 different type of membrane protein structures within a membrane?

Answer 12

• 310 helix
  ○ Tighter coiling of the helix so that instead of It being 4 residues, there is a hydrogen bond b/w this residue below n residue abv
  ○ Fewer amino acids to span n go across the membrane
  
  • Pi bulge
    ○ TM helix that has a hydrogen bond b/w 1st n 5th AA round in the helix
  • Helix kinks
    ○ Caused by proline or glycine residues
    ○ Allow different features to emerge within the MP
    ○ Can be q dynamic, not just rigid rods
  • Glycine not having a side chain incorporates some flexibility
  • Proline residue bc its own sidechain is hooked back up to its own nitrogen -> increases rigidity of the helix -> breaks hydrogen bonding network -> allows a bit more flexibility within the membrane
  • Half-helix n loop
  • Amphipathic interfacial helix
    ○ Helix that engages w the membrane but doesn’t go all the way thru
    ○ Hydrophobic side chains are sitting within membrane core
  • Beta-barrels

Question 13

Explain the structural features and functions of α-helix bundles and β-barrels in membrane proteins and provide examples of membrane proteins that exhibit each architecture

Answer 13

• Membrane proteins features are to allow solute/signals to predominantly go across the membrane
  
  • α-helix bundles (predominant architecture for membrane proteins)
    ○ GlpF (water n glycerol pore)
    § Similar fold to aquaporin (how water seeps across membranes)
    § Water n glycerol pore
    ○ KscA (K+ channel)
    § Allows efflux of potassium of the membrane
  • β-barrels (bacterial outer membrane proteins)
    ○ OmpA (pore/structural protein)