-
What do loops do?
Connect secondary structures (helices, sheets etc)
-
Long loop β-hairpin
- Special case of Ω-loops
- Wide range of nonspecific conformations (random coil)
-
β-meander
- Consecutive antiparallel β-strands connected by long loop β-hairpin
- Supersecondary stucture
-
β-corner alternative definition
- β-hairpin with two-residue β-bulge
- Supersecondary structure
-
Long loop conformations
Large variety/many possibilities
-
αα-hairpin
Two antiparallel α helices connected by a long loop
-
Parallel and antiparallel helix interactions
- Hydrophobic strip
- One hydrophobic residue per turn
- (Amphipathic helices possible)
-
Shortest loops
- Two and three residues
- Single allowed conformation
-
2 Residue αα hairpin
- Residue 1: Bridging conf. (α-β) (ignore bold)
- Residue 2: Gly(Helix perpendicular)
-
3 Residue αα-hairpin
- Residue 1: Bridging conf. (α-β) [X]
- Residue 2: Left handed helix conf. [Gly]
- Residue 3: β-strand conf. [X](X-Gly-X)
-
Capping αα helices
- 2-Residue: Residue 1 caps first helix
- 3-Residue: Residues 2 & 3 cap terminii of both helices
-
4 Residue helix hairpin overview
- aka αα-hairpin
- Two possible conformations
- ~23° between helices
-
4 residue αα-hairpin conformation 1)
- Residue 1: Bridging
- Residue 2: Left-handed helix
- Residue 3: β-strand
- Residue 4: β-strand
-
4 residue αα-hairpin conformation 2)
- Residue 1: β-strand
- Residue 2: Bridging
- Residue 3: β-strand
- Residue 4: Bridging
-
αα-corner
- Two ~perpendicular α-helices connected by a short loop
- Chiral
-
3 Residue αα-corner
- Residue 1: Small (Gly, Ala; avoid steric conflict), cap first helix
- Residue 2: Hydrophobic
- Residue 3: Small polar (Ser, Asp), cap second helix
-
Handedness of helices
Right handed (left handers have steric clash)
-
EF hand
- Functional motif - Helix-loop-helix
- Occur in pairs
- Enclose calcium (carboxyl residues)
-
Structure of an EF hand
- 12 Residue long loop
- Invariant Gly at position 6
- Asp and Glu required in four positions
-
DNA-binding protein interactions
- Occur in pairs
- Helix one and loop position helix 2 in major groove (B-DNA)
|
|
