PMC

New and interesting coiled-coil structures. Each coiled coil is shown axially and from the side. Color indicates helix orientation: blue – N-terminus, red – C-terminus. A, B and D Show variants of a GCN4-derived coiled coil with altered hydrophobic-polar patterning. A When all e positions are mutated to Val, departing from the canonical 3–4 repeat and creating a 3-3-1 hydrophobic repeat, the resulting sequence gives a parallel tetramer []. B When all g positions are substituted with either Val or Ala, also producing a 3-3-1 repeat, the result is an anti-parallel tetramer []. C A right-handed parallel coiled-coil tetramer []. D A parallel heptamer is formed when both e and g positions of GCN4 are substituted with Ala []. E–F A coiled coil with phenylalanine at all a and d positions folds as a parallel pentamer (E), while if just one of these phenylalanines is substituted by methionine the resulting structure is a tetramer (F) []

Helical wheels for coiled coils of varying topology. Heptad positions are shown in small letters, with gray and orange circles indicating predominantly hydrophobic and predominantly polar/charged residues, respectively. A The canonical 3–4 heptad repeat, in which hydrophobic residues are 3 and 4 amino acids apart, is found for many coiled coils including dimers (shown in the figure), trimers and tetramers. Prime notation (e.g. a’) in this figure and throughout the main text is used to indicate a residue on the opposite chain. B An antiparallel tetramer with a 3-3-1 repeat, as in and reference []. C A parallel seven-helix coiled coil with a 3-1-2-1 hydrophobic pattern, as in and reference []. Note that these hydrophobic patterns do not uniquely specify these structures. Other features, including a-a’ asparagine hydrogen bonding, can be important. Helical wheels were made using DrawCoil 1.0 (http://www.gevorggrigoryan.com/drawcoil/)