Membrane Proteins (Baker) Flashcards
What are the major classes of membrane proteins?
- Peripheral
- Integral
- Lipid-Anchored
What is a requirement of membrane spanning helices?
Main chain C=O and N=H must be hydrogen bonded to neutralise their charges.
On the Kyte and Doolittle Scale (from Arg = -4.5 - Ile =+4.5), what is the minimum number that predicts a transmembrane helix?
+1.6
How many residues are used in the window on a hydropathy plot, and why?
19, as this is the number of residues in a typical transmembrane helix.
On a hydropathy plot, what value must peaks be above to be a transmembrane helix?
+1.6
Can Kyte Doolittle analysis be performed on transmembrane ß-barrels?
No - as the residues alternate between hydrophobic-hydrophilic
What are three kinds of hydrophobic protein anchors?
- Acylated
- Prenylated
- GPI Anchor
What is myristoylation?
An amide bond to an N-terminal glycine
Where is myristoylation typically found?
The inner leaflet of eukaryotes
What is prenylation?
A thioester link to C-terminal cysteine
When does prenylation occur?
Post-translationally
What is a thioesterase?
An enzyme that reversibly cleaves thioester lipid anchors.
What is GPI?
Glycosyl phophatidylinositol
Where do GPI anchors face?
Exoplasm
What is the general structure Aquaporin?
- 6 transmembrane helices + 2 short helices per subunit
- Aquaporin is a tetramer
- Each subunit has a pore
How wide is the aquaporin pore?
2.8Å
Which two highly conserved residues form the gate?
Arg195 and His180
Is the pore lined with hydrophobic or hydrophilic residues?
Hydrophobic
What happens in the aquaporin channel if an uninterrupted chain of water molecules forms?
The chain becomes a ‘proton conducting wire’, co-translating protons from one side of the membrane to another, forming hydronium ions
What mechanism stops proton co-translation in aquaporin?
Water is stabilised by two highly conserved Asn residues.
They hydrogen bond the lone pairs on the O on water.
What is the general structure of the Potassium Channel?
- Four identical subunits
- Each subunit has two membrane spanning helices
- One channel per tetramer
- P segment (selectivity filter)
What the are key features of the potassium channel p segment?
- Selectivity filter to allow only potassium
- Homologous in all potassium channels
- Mutations stop selectivity
- Functional even if bacterial segment replaced with mammalian segment
What is the rate of transport of the potassium channel?
108 ions/second
What is the diameter of the potassium channel selectivity filter?
3Å
What is the diameter of the potassium channel vestibule?
10Å
What form of potassium travels through the selectivity filter?
Desolvated potassium
Since potassium is larger than sodium, how is it selected?
It is transported as the desolvated ion - the desolvation energy is matched by specific coordination by the filter.
What part of the selectivity filter coordinates the desolvated potassium ion?
The main chain carbonyl groups that line the channel.
What is the difference in activation energy that favours potassium transport over sodium transport in the potassium channel?
1000X
How many potassium binding sites are there in the selectivity filter?
4
Which potassium binding sites can be occupied similtaneously, and why?
1 & 3 or 2 & 4, this prevents electrostatic repulsion.
What is the purpose of the potassium channel vestibule?
It limits the hydrophobic distance that the ions have to travel through.
