Collagen: Difference between revisions

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=== Primary Structure of Peptide ===

<scene name='Collagen/One_peptide_wireframe/1'>Show side chains</scene> of the peptide in wireframe display. Identify the amino acids making up the peptide by resting the cursor on a residue and observing the name in the label (Toggling spin off will make this easier.). Which three amino acids are present in the peptide in a reocurring pattern? Collagen is characterized by a distinctive repeating sequence: (Gly-X-Y)n where X is often Pro, Y is usually 5-hydroxyproline (Hyp), and n may be >300. The model ([[4clg]]) being studied here contains a <scene name='Collagen/One_peptide_tricolored/1'>repeating sequence</scene> of residues - Gly-Pro-Hyp. This sequence produces a conformation which is a <scene name='Collagen/One_peptide_backbone/1'>left-handed helix</scene> with a rise 10.0 Å/turn or <scene name='Collagen/Peptide_3_residue_segments/1'>3.3 residues per turn</scene>, the peptide is colored in three residue segments. <scene name='Collagen/Peptide_helix_z_axis/1'>Looking down</scene> the center axis of a segment of the helix. Since a helix with a larger rise is superimposed on the helix described above, the entire center axis does not align for viewing. The <scene name='Collagen/Ramachandran/2'>Ramachandran plot</scene> shows that the psi and phi angles of the collagen helix are different from the α-helix, which has a rise of 3.6. The two clusters shown here are outside of the area expected for an α-helix. Review where you would expect a cluster of [[Ramachandran_Plots|α-helix]] residues to be located.

<scene name='Collagen/One_peptide_wireframe/1'>Show side chains</scene>(<scene name='Collagen/One_peptide_bs/1'>ball and stick</scene>) of the peptide in wireframe display. Identify the amino acids making up the peptide by resting the cursor on a residue and observing the name in the label (Toggling spin off will make this easier.). Which three amino acids are present in the peptide in a reocurring pattern? Collagen is characterized by a distinctive repeating sequence: (Gly-X-Y)n where X is often Pro, Y is usually 5-hydroxyproline (Hyp), and n may be >300. The model ([[4clg]]) being studied here contains a <scene name='Collagen/One_peptide_tricolored/1'>repeating sequence</scene> of residues - Gly-Pro-Hyp. This sequence produces a conformation which is a <scene name='Collagen/One_peptide_backbone/1'>left-handed helix</scene> with a rise 10.0 Å/turn or <scene name='Collagen/Peptide_3_residue_segments/1'>3.3 residues per turn</scene>, the peptide is colored in three residue segments. <scene name='Collagen/Peptide_helix_z_axis/1'>Looking down</scene> the center axis of a segment of the helix. Since a helix with a larger rise is superimposed on the helix described above, the entire center axis does not align for viewing. The <scene name='Collagen/Ramachandran/2'>Ramachandran plot</scene> shows that the psi and phi angles of the collagen helix are different from the α-helix, which has a rise of 3.6. The two clusters shown here are outside of the area expected for an α-helix. Review where you would expect a cluster of [[Ramachandran_Plots|α-helix]] residues to be located.

=== Other Levels of Structure ===

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 === Primary Structure of Peptide ===
-<scene name='Collagen/One_peptide_wireframe/1'>Show side chains</scene> of the peptide in wireframe display.  Identify the amino acids making up the peptide by resting the cursor on a residue and observing the name in the label (Toggling spin off will make this easier.). Which three amino acids are present in the peptide in a reocurring pattern?  Collagen is characterized by a distinctive repeating sequence: (Gly-X-Y)n where X is often Pro, Y is usually 5-hydroxyproline (Hyp), and n may be >300. The model ([[4clg]]) being studied here contains a <scene name='Collagen/One_peptide_tricolored/1'>repeating sequence</scene> of residues - <font color="#ff0000">Gly</font>-<span style="color:limegreen;background-color:black;font-weight:bold;">Pro</span>-<span style="color:gold;background-color:black;font-weight:bold;">Hyp</span>.  This sequence produces a conformation which is a <scene name='Collagen/One_peptide_backbone/1'>left-handed helix</scene> with a rise 10.0 Å/turn or <scene name='Collagen/Peptide_3_residue_segments/1'>3.3 residues per turn</scene>, the peptide is colored in three residue segments.  <scene name='Collagen/Peptide_helix_z_axis/1'>Looking down</scene> the center axis of a segment of the helix.  Since a helix with a larger rise is superimposed on the helix described above, the entire center axis does not align for viewing.  The <scene name='Collagen/Ramachandran/2'>Ramachandran plot</scene> shows that the psi and phi angles of the collagen helix are different from the α-helix, which has a rise of 3.6. The two clusters shown here are outside of the area expected for an α-helix. Review where you would expect a cluster of [[Ramachandran_Plots|α-helix]] residues to be located.
+<scene name='Collagen/One_peptide_wireframe/1'>Show side chains</scene>(<scene name='Collagen/One_peptide_bs/1'>ball and stick</scene>) of the peptide in wireframe display.  Identify the amino acids making up the peptide by resting the cursor on a residue and observing the name in the label (Toggling spin off will make this easier.). Which three amino acids are present in the peptide in a reocurring pattern?  Collagen is characterized by a distinctive repeating sequence: (Gly-X-Y)n where X is often Pro, Y is usually 5-hydroxyproline (Hyp), and n may be >300. The model ([[4clg]]) being studied here contains a <scene name='Collagen/One_peptide_tricolored/1'>repeating sequence</scene> of residues - <font color="#ff0000">Gly</font>-<span style="color:limegreen;background-color:black;font-weight:bold;">Pro</span>-<span style="color:gold;background-color:black;font-weight:bold;">Hyp</span>.  This sequence produces a conformation which is a <scene name='Collagen/One_peptide_backbone/1'>left-handed helix</scene> with a rise 10.0 Å/turn or <scene name='Collagen/Peptide_3_residue_segments/1'>3.3 residues per turn</scene>, the peptide is colored in three residue segments.  <scene name='Collagen/Peptide_helix_z_axis/1'>Looking down</scene> the center axis of a segment of the helix.  Since a helix with a larger rise is superimposed on the helix described above, the entire center axis does not align for viewing.  The <scene name='Collagen/Ramachandran/2'>Ramachandran plot</scene> shows that the psi and phi angles of the collagen helix are different from the α-helix, which has a rise of 3.6. The two clusters shown here are outside of the area expected for an α-helix. Review where you would expect a cluster of [[Ramachandran_Plots|α-helix]] residues to be located.
 === Other Levels of Structure  ===