Backbone representations: Difference between revisions
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Backbone representations are simplified 3D depictions of proteins or nucleic acids that enable the polymer [[chain]] structure to be seen. In proteins, a simple <font style="background:black;color:yellow;"> backbone trace </font> connects alpha carbons (shown as '''balls''' in the <scene name='59/599354/Helix/13'>initial scene</scene>) but the <font style="background:black;color:yellow;"> backbone trace line </font> does not coincide with any of the covalent bonds in the main chain. | |||
<StructureSection load='' size='450' side='right' caption='' scene='59/599354/Helix/13'> | |||
==Protein Main Chain== | ==Protein Main Chain== | ||
Lets begin with <scene name='59/599354/Helix/1'>all atoms of a small alpha helix</scene> (15 amino acids)<ref>Residues 23-37 from [[1pgb]].</ref> The atoms and bonds are colored by element: | |||
<font style="font-size:150%;">{{Template:ColorKey_Element_C}} | <font style="font-size:150%;">{{Template:ColorKey_Element_C}} | ||
{{Template:ColorKey_Element_H}} | {{Template:ColorKey_Element_H}} | ||
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==Protein Backbone Trace== | ==Protein Backbone Trace== | ||
<scene name='59/599354/Helix/5'>Backbone Trace</scene>: Now we'll draw a <font style="background:black;color:yellow;"> yellow line </font> between alpha carbons (balls). This line is called a <font style="background:black;color:yellow;"> backbone trace </font>. Note that the backbone trace does not follow any actual covalent chemical bonds -- it simply | |||
connects alpha carbon positions, thereby simplifying the representation. | |||
*<scene name='59/599354/Helix/6'>Hiding all atoms except alpha carbons</scene> makes the backbone trace even clearer. | |||
<scene name='59/599354/Helix/ | *Here is the <scene name='59/599354/Helix/7'>backbone trace by itself</scene>. | ||
==Smoothed Protein Backbone Trace== | |||
<scene name='59/599354/Helix/ | A <scene name='59/599354/Helix/8'>smoothed backbone trace</scene> is another common backbone representation. Here, the <font style="background:black;color:#00ff00;"> smoothed backbone trace is green </font>. | ||
<scene name='59/599354/Helix/ | *Here is the <scene name='59/599354/Helix/9'>smoothed backbone trace alone</scene>. | ||
==Ribbon Backbone Trace== | |||
<scene name='59/599354/Helix/10'> | Perhaps the most common protein backbone representation is the <scene name='59/599354/Helix/10'>ribbon</scene>. Here the <font style="color:#ff0080;"> ribbon is violet </font>, the [[DRuMS#Element|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. | ||
<scene name='59/599354/Helix/ | *Here is the <scene name='59/599354/Helix/11'>ribbon alone</scene>. | ||
<scene name='59/599354/Helix/ | *Here the <scene name='59/599354/Helix/12'>ribbon is decorated with sticks representing all atoms in this helix</scene>. | ||
== | ==Protein Domain Example== | ||
Now lets look at a <scene name='59/599354/Domain/1'>small protein domain</scene> ([[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. | |||
<scene name='59/599354/Domain/ | *A <scene name='59/599354/Domain/10'>useful way of coloring</scene> 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. | ||
{{Template:ColorKey_N2CRainbow}} | |||
<scene name='59/599354/Domain/2'> | *Next, lets <scene name='59/599354/Domain/2'>color by secondary structure</scene>: | ||
{{Template:ColorKey_Helix}}, | |||
{{Template:ColorKey_Strand}}, | |||
{{Template:ColorKey_Loop}}. | |||
<scene name='59/599354/Domain/ | *For comparison, here are <scene name='59/599354/Domain/9'>all the atoms in this domain</scene>. | ||
<scene name='59/599354/Domain/4'> | *Here are the <scene name='59/599354/Domain/4'>atoms alone</scene>, without the ribbon. | ||
<scene name='59/599354/Domain/5'>backbone</scene> | *A simple <scene name='59/599354/Domain/5'>backbone</scene> for this small domain. | ||
<scene name='59/599354/Domain/6'>backbone | *The domain <scene name='59/599354/Domain/6'>backbone plus the smoothed backbone trace</scene>. | ||
<scene name='59/599354/Domain/7'>trace</scene> | *The <scene name='59/599354/Domain/7'>smoothed backbone trace alone</scene>. | ||
</StructureSection> | </StructureSection> | ||
== See Also == | |||
*[[Introduction to molecular visualization]] | |||
*[[Secondary structure]] which has links to other pages with details on alpha helices, beta sheets, and turns. | |||
== References == | == References == | ||
<references/> | <references/> | ||
[[Category: BioMolViz]] | |||
[[Category: Alternate Renderings]] | |||