Protein G Text

Overall Architecture of Protein G

The B1 domain of protein G from Streptococcus is used here to highlight several features of protein architecture that are found in many other proteins.
In addition, each of the Chime images and the buttons that modify them serve as starting points for making changes in the displays. In this way, most of the display and coloring options of RasMol can be explored and practiced before attempting to do so on a protein of your choice.
[If you can't see the entire image on the left, "Resize".]

This starting image shows Protein G in the Cartoons display. The elements of secondary structure are readily seen in this view; they are depicted with Structure coloring as follows:

a-helices are magenta-colored spirals;
b-strands are yellow-colored arrows (pointing from the N to C terminus);
regular turns are colored light blue;
unspecified (mostly connecting) segments are colored white.

Additional Display and Color combinations can be selected from the Chime menu. (Mac: click-and-hold in the image; Windows: right-click.) Some suggestions for this structure are:

Wireframe with CPK: the connections between atoms are shown as thin lines.
Sticks with Group: the connections between atoms are shown as thicker lines; the color spectrum is used trace the polypeptide from N-terminus (dark blue) to C-terminus (red).
Ball & Stick with Temperature: the atoms are shown as small spheres with thin connections; the color spectrum is used again, this time to indicate atomic motion (or disorder) in the crystal. Blue indicates the least mobility, and red the greatest.
Spacefill with CPK: the atoms are shown as spheres with their Van der Waals radii.
Backbone with Structure: the peptide units are connected; the coloring is the same in as the original image.
Restore the original view by choosing "Reload Frame" from the Netscape "View" menu.

From these views of protein G, we expect that (i) the space between the b-sheet and a-helix would be filled with hydrophobic side-chains and (ii) the surfaces of the b-sheet and a-helix exposed to solvent would be composed of hydrophilic R-groups. Both of these expectations are borne out by closer looks at these secondary structure elements.

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