A Ramachandran plot is a way to examine the backbone conformation of each residue in a protein. It was first used by G.N. Ramachandran et al. in 1963 to describe stable arrangements of individual residues of a protein. Today, a Ramachandran plot is frequently used by crystallographers to identify protein models with an unrealistic backbone.
As many of you may recall, each residue of a protein has two rotatable bonds, which we designate φ and ψ. If we take a protein structure and measure the rotations about these bonds (between -180 and 180 degrees), then we can plot each residue with respect to its φ (x-axis) and ψ (y-axis). The result is a Ramachandran plot, where each black point is a residue of the protein:
Certain rotations are more stable than others: white areas of the Rama plot are unstable, and a residue in this space will have a bad backbone score; colored areas of the Rama plot are more stable, and a residue in this space will have a better backbone score.
The stable areas of the Rama Map in Foldit are divided into four regions, called ABEGO regions, and are colored accordingly:
- Red: Right-handed helix (characteristic of α-helix)
- Blue: Right-handed strand (characteristic of β-strand)
- Green: Left-handed helix (uncommon, except for GLY)
- Yellow: Left-handed strand (very uncommon, except for GLY)
Because the 20 different amino acid types have different properties, each amino acid type has a slightly different Rama profile. For example, most amino acids have a side chain that would clash with the backbone in a left-handed helix, so maps of these residues have only a faint green region. However, glycine has no side chain and can easily adopt a left-handed helix conformation, so its map has a large, intense green region.
Mouse over a point in the Rama Map to see its residue type and number in the upper right corner.
Click on a point to see the specific Rama profile for its amino acid type; this also selects the residue in Selection Mode.
Click and drag a point to change the φ and ψ rotations of a single residue's backbone.
The viewport at the top of the Rama Map will focus on a selected residue, and simply shows the local configuration of the protein backbone around the selected residue. Each residue in the viewport is colored according to the ABEGO region in which it lies. The ABEGO coloring scheme can also be applied to the main Foldit console in the View Options with View->AbegoColor.
When designing a protein, there are usually a number of different loop backbones that can connect α-helices and β-strands. However, we've found that certain types of loops occur frequently in native proteins, and that these "ideal" loops can be distinguished by ABEGO patterns. For example, the most common way to connect two β-strands is by a short hairpin, with two residues in left-handed helix (green) conformation.
The Foldit Rama Map includes a gallery of ideal loops, located in the drop menus in the upper right corner. Each drop menu displays a handful of ideal loops that can be used to connect some combination of α-helices and β-strands. These are provided as a reference for Foldit players, and we encourage players to try to incorporate these loop structures in their designs. Within each drop menu, the most common loops are listed at the top, but a less common loop may be preferred depending on the precise layout of α-helices and β-sheets in a design!
The Rama Map will be available to use in selected design puzzles. It can be accessed from the Actions menu in the Original Interface; or from the Main menu in Selection Interface. Try out the new Rama Map in the latest design puzzle!( Posted by bkoep 80 1005 | Wed, 03/16/2016 - 01:53 | 10 comments )