Membranes Extra Flashcards
1
Q
Types of fold
A helix
A
- A-helix bundle protein = 20-25% of genes of most organisms
- H bonds form btw N-H group of aa and C=O of aa 4 residues earlier, satisfied requirement
- 20 residue stretch
- Antiparallel association
- 3o and 4o structure
2
Q
Types of fold
B barrel
A
- Largely found in OM of gram -ve bacteria + mitochondria
- Antiparallel B sheets, H bonds satisfied
- Even no.
- Alternating polar + hydrophilic aa so favourable
- E.g. porin = 16-18 B-strands
- Structurally harder to keep
- Longer loops on outside
3
Q
Types of fold
Other
A
- Some have both
- E.g. new fold in bacteria = combination of 2a-helical + B-barrel folds → a-helical barrel
4
Q
Membrane protein vs water soluble protein structure
A
- Membrane proteins = hydrophobic + relatively insoluble
- Water soluble also fold into bundles of a-helices similar to membrane
- But, outer section of water have hydrophilic aa but hydrophobic aa are buried (opposite in membrane)
- Membrane proteins hard to purify
- Some hydrophobic aa have similar structure to hydrophilic ones
- Keep interior residues the same so overall structure maintained
- Could cause subtle changes = drawback
5
Q
Topology + structure prediction
A
- Hard to get 3D structure (crystallisation, native environment)
- Hydropathy plot: taken window of 20aa and calculate mean hydrophobicity, shift across 1 and repeat
6
Q
Issue w/ B-barrel
A
- B-strands are shorter and less conspicuous than a-helices
- Also ↑ structural variants, barrels = 8-36 strands
- Other B-sheet rich regions like pre-barrel region
- Use neural networks: training set of proteins answer Y/N proteins
7
Q
Issues w/ structure prediction
A
- Hard to discriminate btw TM helices + other hydrophobic features
- TMH in single-spanning proteins = ↑ hydrophobic than polytopic membrane, can disrupt topology if x taken into account
- Some structures too complicated to fit into simple models e.g. 310 helix
8
Q
Potassium channel structure extra
A
- Common feature = pore forming domain + regulatory domain
- Tetramer w/ 4 single domain that have 2 helices (M1+2) w/ short loop, central pore that runs down centre of channel of M2
- Pore region has selectivity filter, water-filled cavity + closed gate
- Selectivity filter = TVGYG, O of which point into centre (S1-4)
- S1-4 form VSD
- S5-6 = like M1/2 = pore forming domain
- S4 = +ve Arg, connected to S4/5 linker
- Glycine wings
- Lipids btw S1-4 voltage domain
9
Q
Selectivity potassium channel extra
A
- The potassium ion radius = 1.33A, sodium = 0.95A, size not enough to discriminate
- Thought to do with dipoles (The magnitude of the repulsive interaction btw 2 ligands coordinating an ion is sensitive to the electrostatic properties of the ligands)
- Ligand-ligand repulsion
10
Q
Gating
A
- IC gate includes helix-bundle crossing, EC = selectivity filter
- Resting = both gates closed
- +ve S4 helix pulled down to attract -ve charge in cell
- Membrane depolarised → S4 moves up → transient bridges formed → 310 conformation→ S6 interacts w/ linker
Closing
- S4 moves inward, ions move out of pore → hydrophobic collapse → S4/5 moves fully down
11
Q
Sodium structure channel
A
- Less known
- Single polypeptide chain folds into 4 homologous repeats (each of 6TM repeats)
- Can have other subunits like B
- DEKA selectivity in eukaryotes, EEEE in prokaryotes
- Bacteria + human = only 25% sequence homology, x know structure
12
Q
Sodium selectivity
A
- Domains contribute asymmetrically (III and IV contribute more than I and II)
- Selectivity depends on field strength of binding site, high field strength ion like Glu needed to ↑ Na+ selectivity
13
Q
Sodium gating
A
- Unkown
- Also due to TM movement changes due to S4 → S4/5 linker opening IC gate
- Prokaryotes also interactions w/ CTD
- Eukaryotic sodium channels have short IC loop connecting S6 of III to S1 of IV = inactivation gate
14
Q
Calcium channel structure
A
- Similar to sodium
- a subunit = also 4 domains each of 6 TM helices
15
Q
Calcium selectivity
A
- EEEE sequence near sodium channel EDEKA motif
