Backbone representations

Backbone representations are simplified 3D depictions of proteins or nucleic acids that enable the polymer Hydrogen structure to be seen. In proteins, a simple  backbone trace  connects alpha carbons (shown as balls in the initial scene) but the  backbone trace line  does not coincide with any of the covalent bonds in the main chain.

spinqualitylabelsall models Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Protein Main Chain Lets begin with all atoms of a small alpha helix (15 amino acids) The atoms and bonds are colored by element: C H O N. First, we'll simplify by hiding the hydrogen atoms. Hydrogen atoms make up almost exactly 50% of the atoms in proteins. Next, we'll simplify by hiding the amino acid side chains. What remains is called the main chain. Each amino acid's main chain atoms are N-C-C, where the first C is the alpha carbon (shown as a ball), and the second, the carboxyl carbon with its double-bonded oxygen (double bonds not shown). We could also hide the oxygen atoms, leaving only the atoms that are part of the main chain, also called the backbone. Protein Backbone Trace Backbone Trace: Now we'll draw a  yellow line  between alpha carbons (balls). This line is called a  backbone trace . Note that the backbone trace does not follow any actual covalent chemical bonds -- it simply connects alpha carbon positions, thereby simplifying the representation. Hiding all atoms except alpha carbons makes the backbone trace even clearer. Here is the backbone trace by itself. Smoothed Protein Backbone Trace A smoothed backbone trace is another common backbone representation. Here, the  smoothed backbone trace is green . Here is the smoothed backbone trace alone. Ribbon Backbone Trace Perhaps the most common protein backbone representation is the ribbon. Here the  ribbon is violet , the standard secondary structure color for alpha helices. As you can see, the ribbon is a smoothed backbone trace expanded in width. The arrowhead at one end points to the carboxyl terminus. Here is the ribbon alone. Here the ribbon is decorated with sticks representing all atoms in this helix. Protein Domain Example Now lets look at a small protein domain (1pgb). This domain contains the alpha helix used above, but also contains a small beta sheet made of four beta strands, plus loops (regions that are neither alpha helix nor beta strand) connecting the helices and strands. The helices and strands are represented as ribbons, while the "ropes" connecting them are smoothed backbone traces. This type of representation is properly called a secondary structure schematic, but is called a cartoon in Jmol and its family of ancestral visualization programs (RasMol, Chime). Arrowheads point towards the carboxy terminus. A useful way of coloring such a ribbon representation is with a spectral sequence of colors from the amino (N) terminus to the carboxy (C) terminus. (Proteins are synthesized by adding amino acids to the C terminus.) This color scheme is called N->C Rainbow. Notice how the arrowheads point towards the C terminus. N               C Next, lets color by secondary structure: Alpha Helices,  Beta Strands ,  Loops . For comparison, here are all the atoms in this domain. Here are the atoms alone, without the ribbon. A simple backbone for this small domain. The domain backbone plus the smoothed backbone trace. The smoothed backbone trace alone.

See Also

• standard secondary structure color
• 1pgb which has links to other pages with details on alpha helices, beta sheets, and turns.

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Margaret Franzen