2D (2-dimensional) Diagrams For Representing α-helices
Three differently arranged styles of 2D diagrams are used to represent different aspects of the sequence ad structure relationships that confer specific physical and interaction properties on individual α-helices. Two of these emphasize circular placement around the cylindrical cross-section: the first-developed such diagram is called the "helical wheel", and a more recent version is called the "wenxiang diagram". The latter name came from the fact that it resembles a coil-like incense used in China to repel mosquitos; Chinese 蚊香 (pronounced as "wenxiang").
The helical wheel represents a helix by a projection of the Cα backbone structure down the helix axis, while the wenxiang diagram represents it more abstractly as a smooth spiral coiled on the plane of the page. Both label the sequence with one-letter amino-acid code (see amino acid) at each Cα position, using different colors or symbols to code the amino-acid properties. Hydrophobic vs hydrophilic amino acids are always distinguished, as the most important property governing helix interactions. Sometimes positively vs negatively charged hydrophilics are distinguished, and sometimes ambiguous amino acids such as glycine (G) are distinguished. Color-coding conventions are various. The helical wheel does not change representation along the helix, while the wenxiang diagram is able to show the relative locations of the amino acids in an α-helix regardless of how long it is.
Either circular style of diagram can provide an intuitive and easily visualizable 2D picture that characterizes the disposition of hydrophobic and hydrophilic residues in α-helices, and can be used to study helix-helix interactions, helix-membrane interactions as quantified by the helical hydrophobic moment, or protein-protein interactions. Various utilities and web sites are available to generate helical wheels, such as the page by Kael Fischer . Recently, a web-server called "Wenxiang" was established to draw the wenxiang diagram for any α-helix sequence.
The third style of 2D diagram is called a "helical net". It is generated by opening the cylindrical surface of each helix along a line parallel to the axis and laying the result out vertically. The helix net is not suitable for studying helix-helix packing interactions, but it has become the dominant means of representing the sequence arrangement for integral membrane proteins because it shows important relationships of the helical sequence to vertical positioning within the membrane even without knowledge of how the helices are arranged in 3D.
Read more about this topic: Alpha Helix, Structure
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