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. | ||
<scene | <StructureSection load='' size='450' side='right' caption='' scene='59/599354/Helix/13'> | ||
==Protein Main Chain== | |||
<scene name='59/599354/Helix/ | 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}} | |||
{{Template:ColorKey_Element_H}} | |||
{{Template:ColorKey_Element_O}} | |||
{{Template:ColorKey_Element_N}}</font>. | |||
<scene name='59/599354/Helix/ | *First, we'll simplify by <scene name='59/599354/Helix/2'>hiding the hydrogen atoms</scene>. [[Hydrogen in macromolecular models|Hydrogen]] atoms make up almost exactly 50% of the atoms in proteins. | ||
<scene name='59/599354/Helix/ | *Next, we'll simplify by <scene name='59/599354/Helix/3'>hiding the amino acid side chains</scene>. 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 <scene name='59/599354/Helix/4'>hide the oxygen atoms</scene>, leaving only the atoms that are part of the '''main chain''', also called the backbone. | ||
==Protein Backbone Trace== | |||
<scene name='59/599354/Helix/ | <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/ | *<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>. | ||
==Backbone Trace== | ==Ribbon Backbone Trace== | ||
<scene name='59/599354/ | 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/ | *Here is the <scene name='59/599354/Helix/11'>ribbon alone</scene>. | ||
<scene name='59/599354/ | *Here the <scene name='59/599354/Helix/12'>ribbon is decorated with sticks representing all atoms in this helix</scene>. | ||
<scene name='59/599354/Domain/ | ==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/ | *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/7'>trace</scene> | *For comparison, here are <scene name='59/599354/Domain/9'>all the atoms in this domain</scene>. | ||
*Here are the <scene name='59/599354/Domain/4'>atoms alone</scene>, without the ribbon. | |||
*A simple <scene name='59/599354/Domain/5'>backbone</scene> for this small domain. | |||
*The domain <scene name='59/599354/Domain/6'>backbone plus the smoothed backbone 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]] | |||
Latest revision as of 20:45, 5 November 2020
Backbone representations are simplified 3D depictions of proteins or nucleic acids that enable the polymer chain structure to be seen. In proteins, a simple backbone trace connects alpha carbons (shown as balls in the ) but the backbone trace line does not coincide with any of the covalent bonds in the main chain.
Protein Main ChainLets begin with (15 amino acids)[1] The atoms and bonds are colored by element: C H O N.
Protein 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.
Smoothed Protein Backbone TraceA is another common backbone representation. Here, the smoothed backbone trace is green .
Ribbon Backbone TracePerhaps the most common protein backbone representation is the . 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.
Protein Domain ExampleNow lets look at a (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.
Alpha Helices, Beta Strands , Loops .
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See AlsoSee Also
- Introduction to molecular visualization
- Secondary structure which has links to other pages with details on alpha helices, beta sheets, and turns.