Collagen: Difference between revisions

<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>-<font color="gold">Hyp</font>.  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.

Looking down the axis of a tropocollagen displayed as wireframe, <font color="#ff0000">glycine</font> can be seen <scene name='Collagen/Gly_position_tropo/2'>positioned in the center</scene> of the triple helix.  The two types of helical turns consistently positions the Gly in the center of the triple helix. <span style="color:limegreen;background-color:black;font-weight:bold;">Proline</span> and the <font color="gold">hydroxyproline</font> are on the <scene name='Collagen/Pros_position_tropo/1'>outside</scene> of the triple helix.  With the hydroxyl group of Hyp extending to the surface of the triple helix, it can be involved in hydrogen bond formation, as will be seen in the next section. The cyclical side chains of Pro and Hyp are some what rigid, and this rigidity adds to the stability  of the collagen fiber. The primary structure of repeating Gly-Pro-Hyp along with the two types of helical turns determine the 3D positions of Gly, Pro and Hyp in the tropocollagen.  

In order to make a compact strong fiber the interior residues of the triple helix need to be close packed.  The <scene name='Collagen/Gly_no_hindrance/1'>Gly side chain</scene> is the only one small enough to accommodate this close packing in the interior of the triple helix. (Realize that in this model the hydrogen on the <font color="limegreen"> α carbon</font> is not displayed.) <scene name='Collagen/Glys_close_pack/1'>Three Gly</scene>, one on each of three different chains, are close packed together.  The gray atoms of the yellow and lime Gly are the α-carbons, and only a hydrogen could fit between these carbons and the atoms of the adjacent Gly.  <scene name='Collagen/Glys_pro_close/2'>A Pro</scene> on each of the 3 chains are shown close packed to the three Gly (lime, cyan, yellow). Adding the <scene name='Collagen/Glys_pro_hyp/1'>Hyp</scene> shows that Pro and Hyp are tightly positioned around the small interior Gly leaving no space for side chains longer than the single hydrogen of Gly.