lec8 - super secondary structure - motifs

super secondary structure (motif): Associations of secondary structural elements through sidechain interactions. (almost like domains).

eg alpha-alpha, beta-alpha-beta, beta-beta


a turn states that the α-carbons of residues i and i+3 must be within 7.0 Å.

90 degree corners, beta-corner and alpha-alpha corner, because of Gly

Simplest Motif with a Specific function:

• helix-turn-helix: DNA binding
• helix-loop-helix (EF domain): Ca2+ (binds to loop) binding eg troponinC in muscles
• coiled-coil - very strong, insoluble, 2 amphipathic parallel helices interacts with hydrophobic edge in the middle, eg. alpha-keratin in hair
• helix bundle - 4 anti-parallel helix bundle, hydrophobic in the middle

Motifs with no function

• beta-hairpin turn (2-5 res), simples motif involving strands eg bovine trypsin inhibitor
  
• beta-meander (up-and-down) - 4 anti-parallel strands, order of sequence is the same order as strands/connection
• greek-key - 4 strand anti-parallel, looks like a loop that was bended

beta-sandwich - highly twisted

beta-alpha-beta - parallel beta-strands, right-handed, helix forms a shield