Which amino acids orient toward the hydrophobic interior?
V, L, I, M, F (non-polar no G, A, P “weird ones”)
Which amino acids tend to H-bond with the protein interior?
Y, W, (non-polar)
S, T, N, Q (polar no C)
Which amino acids tend to display on the protein surface/ active site?
H, K, R, D, E (acids + bases)
Linus Pauling’s secondary structure rules
- bond length and angles should conform to predetermined
- Steric restrictions (bond rotation around peptide backbone via VDW of atom radii)
- backbone, 6 carbons remain coplanar
- H-bonds are key to secondary structure stabilization
How many atoms define each?
- torsion
- bond angle
- bond length
- 4
- 3
- 2
What is the name and symbol for the N-terminal angle? Draw the structure in line and Newman projection.
Phi (O/) - between N and alpha carbon
= Look for ss
What is the name and symbol for the C-terminal angle? Draw the structure in line and Newman projection.
Psi (Y/) - between alpha carbon and C
= Look for ss
What is the plot name that combines the phi and psi angles to determine the most favourable orientations? Roughly draw it out.
Ramachandra plot
find ss
When describing helices
- n =
- p =
- direction =
n = number of residues per turn
p = distance between turns
direction = right hand / left hand
Details for alpha helix
- phi angle
- psi angle
- n
- p
phi = -57º
psi = -47º
n = 3.6 residues/turn
p = 5.4 Å/turn
Details of other helices (3^10 and pi)
- n
- p
- h-bond angle
3^10
n = 3.0
p = 6.0 Å
angle = 120º (i+3)
pi
n = 4.4
p = 5.2 Å
angle = not coplanar (i+5)
How to draw a helical wheel?
- build 4 square coordinates
- place the first amino acid at 0º
- add next amino acid ___º away (360/n)
- keep adding from the previous amino acid
- connect with line
Details for peptide II helix
- n
- p
Does not satisfy Pauling (no H-bonds)
- made of glycine and proline
n = 3
p = 9.4Å
Difference in h-bonds in helix and sheet
helix - between 1 strand of polypeptide
sheet - between 2 strands of polypeptide
Beta sheets
- classification
- bond angle
- h-bond strength
- abundance
- phi-psi angles
- antiparallel vs parallel
- 180º vs ≠ 180º
- strong vs weak
- 80% vs 20%
- (-139º,135º) vs (-119º, 113º)
Two types of beta turns, draw them. What is the difference between beta and gamma turns?
type 1 - cis-pro at position 2 (4 residues)
type 2 - gly at position 3(4 residues)
gamma - cis pro (3 residues)
3 characteristics that make loops good protein identifiers
- irregular and unique to amino acid sequence
- at the surface, accessible to other proteins
- charged or polar
3 types of loops, draw them
- simple turn
- left-handed crossover
- right-handed crossover
4 types of supersecondary motifs
= aa
= BB
= BBBB motif - greek key
= BaB (parallel B sheet, right-handed)
3 types of alpha-alpha structures
- hairpin (<4 residues) - gamma turn
- helix-turn-helix (~4 residues) - 1/2 turn
- helix-loop-helix (~12 residues) - loop
Another name for helix-loop-helix
the loop is also known as the leucine-zipper
= cationic Lys or Arg create salt bridges with anionic phosphate backbone of DNA
Rossman fold Motif
- bind cofactors like NAD+ or FAD
- BaB - a - BaB
= two helix-loop-helix motifs bonded by alpha helix
Disulfide bond
intrachain covalent linkage
- oxidation of two Cystein-thiols
- very stable
Draw out a melting curve
heat applied to a given protein, the % denatured (native state vs unfolded) and is compared to a protein property that changes with unfolding (light)
Tm (melting temp) = temperature at which 50% denatured
