Helical Wheel Projections for Proteins

A helical wheel is a type of plot or visual representation used to illustrate the properties of alpha helices in proteins. The sequence of amino acids that make up a helical region of the protein's secondary structure are plotted in a rotating manner where the angle of rotation between consecutive amino acids is 100°, so that the final representation looks down the helical axis. The plot reveals whether hydrophobic amino acids are concentrated on one side of the helix, usually with polar or hydrophilic amino acids on the other. This arrangement is common in alpha helices within globular proteins, where one face of the helix is oriented toward the hydrophobic core and one face is oriented toward the solvent-exposed surface. Specific patterns characteristic of protein folds and protein docking motifs are also revealed, as in the identification of leucine zipper dimerization regions and coiled coils. This projection diagram is often called and "Edmondson wheel" after its inventor.

What its inventor says?

Edumudosn mentioned in his classical paper

“The three-dimensional structures of alpha-helices can be represented by two-dimensional projections which we call helical wheels. Initially, the wheels were employed as graphical restatements of the known structures determined by Kendrew, Perutz, Watson, and their colleagues at the University of Cambridge and by Phillips and his coworkers at The Royal Institution. The characteristics of the helices, discussed by Perutz et al. (1965), and Blake et al. (1965), can be readily visualized by examination of these wheels. For example, the projections for most helical segments of myoglobin, hemoglobin, and lysozyme have distinctive hydrophobic arcs. Moreover, the hydrophobic residues tend to be clustered in the n +/- 3, n, n +/- 4 positions of adjacent helical turns. Such hydrophobic arcs are not observed when the sequences of nonhelical segments are plotted on the wheels. Since the features of these projections are also distinctive, however, the wheels can be used to divide sequences into segments with either helical or nonhelical potential. The sequences of insulin, cytochrome c, ribonuclease A, chymotrypsinogen A, tobacco mosaic virus protein, and human growth hormone were chosen for application of the wheels for this purpose” .

Refer http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1368002/ for full-text of this paper.

How to read a helical wheel

From the basic understanding of alpha helical structures determined by corey, Pauling and Ramachandran, we know that a complete helical turn (which means 360 degree rotation) is obtained within a span of 3.6 residues (and this is the reason alpha helix is also called as 3.613 helix). Now imagine looking and alpha helix from top. Any helix from the top would appear like a wheel. But in order to determine a sequence one must note the angles at which which subsequent amino acids will be observed. So from above information we can say that a new amino acid addition to a peptide in alpha helix will take place at 100 degrees ( 360 degrees divided by 3.6). Also one should remember that in case of right handed alpha helix, reading will be done clockwise, while in left handed alpha helix reading will be done anticlockwise.

Example of a helical wheel

Following figure depicts a simple helical wheel projection, for alpha helical peptide with sequence ADITYAARYA , You may note that this helix is a right handed helix so one need to begin from amino acids marked A1, then move clockwise to obtain complete sequence. If it was left handed helix (or helix made up of D-amino acids instead of L-amino acids) we would read it in anticlockwise direction.

Some more examples of helical wheel projection

Wish to draw helical wheel yourself?

Based on the method developed by Edumudosn et al, several computer programs have been developed which can assist us to develop the helical wheel of any desired peptide by simply entering the sequence. of the peptide. Most of these platforms are based on java and therefore are platform independent and easy to run. Links to some common tools available publicly for helical wheel formation are as below.  http://rzlab.ucr.edu/scripts/wheel/wheel.cgi Created by Don Armstrong and Raphael Zidovetzki.

http://www.grigoryanlab.org/drawcoil/ Departments of Computer Science and Biological Sciences, Dartmouth College

http://www-nmr.cabm.rutgers.edu/bioinformatics/Proteomic_tools/Helical_wheel/ by john K Everett.

http://cti.itc.virginia.edu/~cmg/Demo/wheel/wheelApp.html by Edward K. O'Neil and Charles M. Grisham (University of Virginia in Charlottesville, Virginia). http://www.bioinformatics.nl/cgi-bin/emboss/pepwheel : Pepwheel by Alan Bleasby European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Cited text:

Mount DM (2004). Bioinformatics: Sequence and Genome Analysis (2 ed.). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. Schiffer M, Edmundson AB.. Use of helical wheels to represent the structures of proteins and to identify segments with helical potential. Biophys J. 1967 Mar;7(2):121-35.