Collagen: Difference between revisions
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=== Primary Structure of Peptide === | === Primary Structure of Peptide === | ||
<scene name='Collagen/One_peptide_wireframe/4'>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/3'>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:yellow;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/4'>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/3'>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:yellow;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. | ||
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==3D structures of collagen== | ==3D structures of collagen== | ||
''Update | ''Update January 2013'' | ||
[[3hqv]], [[3hr2]] – Col I – rat – fiber diffraction<br /> | [[3hqv]], [[3hr2]] – Col I – rat – fiber diffraction<br /> | ||
[[1q7d]] - hCol I α1 integrin-binding domain – human<br /> | [[1q7d]] - hCol I α1 integrin-binding domain – human<br /> | ||
[[1u5m]] - hCol II α1 (mutant) <br /> | [[1u5m]] - hCol II α1 (mutant) <br /> | ||
[[3dmw]] - hCol III | [[3dmw]] - hCol III α1residues 1158-1199 (mutant)<br /> | ||
[[4ae2]] - hCol III residues 1222-1466<br /> | |||
[[4aej]], [[4ak3]] - hCol III residues 1222-1466 (mutant)<br /> | |||
[[1kth]] - hCol III α3 Kunitz type domain<br /> | |||
[[1kun]] - hCol III α3 Kunitz type domain – NMR<BR /> | |||
[[1li1]] - hCol IV α Nc1 domain<br /> | [[1li1]] - hCol IV α Nc1 domain<br /> | ||
[[1t60]], [[1t61]], [[1m3d]] - Col IV α Nc1 domain – bovine<br /> | [[1t60]], [[1t61]], [[1m3d]] - Col IV α Nc1 domain – bovine<br /> | ||
[[2knt]], [[1knt]] - hCol VI Kunitz type domain<br /> | [[2knt]], [[1knt]] - hCol VI Kunitz type domain<br /> | ||
[[1o91]] - mCol VIII α1 Nc1 domain - mouse<br /> | [[1o91]] - mCol VIII α1 Nc1 domain - mouse<br /> | ||
