Helix

The helix is one of three basic structure types used in FoldIt. In its ideal form, it appears like a coiled cylindrical spring with all sidechains directed outward. Ideal helices usually have hydrogen bonds between every third amino acid in the chain; this bonding is not visible in the helix representation, but it can be informative to change the helix to sheets to see the hydrogen bond pattern.

The helix structure is used to represent the real protein structure called an alpha helix. An ideal alpha helix will have one coil for every 3.6 amino acids. The closer a particular series of amino acids in your FoldIt puzzle is to that ratio, the more helpful it may be to define it as helix using Structure Mode.

Certain amino acids have a tendency to form helices, while others tend not to. Those that often (but not always) form helices are Methionine, alanine, leucine, uncharged glutamate, and lysine ("MALEK" in the amino-acid 1-letter codes). Those that do not easily form helices include proline, glycine, and aspartic acid. Proline, however, may be found at the beginning of a helix.

Helices as Part of Larger Structures

Coiled-coil α helices are highly stable forms in which two or more helices wrap around each other in a "supercoil" structure. Coiled coils contain a highly characteristic sequence motif known as a heptad repeat, in which the motif repeats itself every seven residues along the sequence. The first and especially the fourth residues (known as the a and d positions) are almost always hydrophobic (the fourth residue is typically leucine) and pack together in the interior of the helix bundle. In general, the fifth and seventh residues (the e and g positions) have opposing charges and form a salt bridge stabilized by electrostatic interactions. Fibrous proteins such as keratin and myosin often adopt coiled-coil structures, as do several dimerizing proteins. A pair of coiled-coils - a four-helix bundle - is a very common structural motif in proteins. For example, it occurs in human growth hormone and several varieties of cytochrome. The Rop protein, which promotes plasmid replication in bacteria, is an interesting case in which a single polypeptide forms a coiled-coil and two monomers assemble to form a four-helix bundle.