Collagen: Difference between revisions
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<StructureSection load=' | <StructureSection load='4clg' size='500' side='right' caption='Structure of Collagen (PDB entry [[4clg]] or [[1cag]])'>__NOTOC__ | ||
Collagen, the most abundant protein in vertebrates, is an extracellular, inextensible fibrous protein that comprises the major protein component of such stress-bearing structures as bones, tendons, and ligaments. As with all fibrous proteins collagen is, for the most part, characterized by highly repetitive simple sequence. Here we study two model compounds (The structure of | Collagen, the most abundant protein in vertebrates, is an extracellular, inextensible fibrous protein that comprises the major protein component of such stress-bearing structures as bones, tendons, and ligaments. As with all fibrous proteins collagen is, for the most part, characterized by highly repetitive simple sequence. Here we study two model compounds (The structure of [[4clg]]<ref>J.M. Chen, C.E. Kung, S.H. Feairheller, E.M. Brown, AN ENERGETIC EVALUATION OF A "SMITH" COLLAGEN MICROFIBRIL MODEL, <I>J. Protein Chem., </I>'''10''', 535, 1991</ref> is shown in the applet to the right.) for naturally occurring collagen, in order to develop an understanding of the fibrous portion of collagen and to show how the different levels of protein structure come together and form a highly ordered and stable fiber. Collagen's properties of rigidity and inextensibility are due to this highly ordered structure. The part of collagen without structural order is not illustrated in this model. This part of the protein complex having a different amino acid composition, lysine and hydroxylysine are particularly important residues, is globular in nature and not as structurally organized. Lysine and hydroxylysine form covalent crosslinks in the protein complex, thereby adding strength and some flexibility to the fiber. This covalent crosslinking continues throughout life and produces a more rigid collagen and brittle bones in older adults. Go to [[Collagen Structure & Function]] for information on the functions and disorders of collagen and a link in the External Links section of this page for assembly movies of the triple helix of types I and IV. | ||
== Structure of a Segment == | == Structure of a Segment == | ||
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=== Primary Structure of Peptide === | === 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 ( | <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>-<font color="limegreen">Pro</font>-<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. | ||
=== Other Levels of Structure === | === Other Levels of Structure === | ||
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== Effect of a Mutation == | == Effect of a Mutation == | ||
The mutation being considered is an Ala replacing a Gly. Synthetic model PDB ID: [[1cag]]<ref>J.BELLA,M.EATON,B.BRODSKY,H.M.BERMAN, CRYSTAL AND MOLECULAR STRUCTURE OF A COLLAGEN-LIKE PEPTIDE AT 1.9 A RESOLUTION. ''SCIENCE'', '''266''', 75, 1994</ref> is <scene name='Collagen/1cag/7'>tropocollagen</scene> whose peptides contain thirty residues and have a <scene name='Collagen/Collagen_chain_1cag/4'>sequence</scene> of (Pro-Hyp-Gly)4-Pro-Hyp-Ala-(Pro-Hyp-Gly)5 (Ala displayed as large wireframe and colored as {{Template:ColorKey_Element_C}} {{Template:ColorKey_Element_O}} {{Template:ColorKey_Element_N}}). Viewing | The mutation being considered is an Ala replacing a Gly. Synthetic model PDB ID: [[1cag]]<ref>J.BELLA,M.EATON,B.BRODSKY,H.M.BERMAN, CRYSTAL AND MOLECULAR STRUCTURE OF A COLLAGEN-LIKE PEPTIDE AT 1.9 A RESOLUTION. ''SCIENCE'', '''266''', 75, 1994</ref> is <scene name='Collagen/1cag/7'>tropocollagen</scene> whose peptides contain thirty residues and have a <scene name='Collagen/Collagen_chain_1cag/4'>sequence</scene> of (Pro-Hyp-Gly)4-Pro-Hyp-Ala-(Pro-Hyp-Gly)5 (Ala displayed as large wireframe and colored as {{Template:ColorKey_Element_C}} {{Template:ColorKey_Element_O}} {{Template:ColorKey_Element_N}}). Viewing [[1cag]] from the side of the fiber shows: the <scene name='Collagen/1cag1/1'>Gly</scene> is only partially visible because it is buried in the interior, <scene name='Collagen/1cag2/1'>Pro</scene> being much more visible is positioned closer to the surface, <scene name='Collagen/1cag3/1'>Hyp</scene> being entirely on the surface is clearly visible, and <scene name='Collagen/1cag4/1'>Ala</scene> being a substitute for Gly is only partially visible. | ||
The <scene name='Collagen/1cag_surface/4'>surface</scene> of the tropocollagen is shown with the Ala appearing as olive and the Pro and Hyp adjacent to the Ala appearing as dark brown. Notice that the surface at these Pro and Hyp bulges slightly. This protrusion is due to the fact that the packing about the Ala side chains is not as close as it is about the Gly. In the two side-by-side scenes shown below compare the amount of open space between the chains in the area of the scene center. In the | The <scene name='Collagen/1cag_surface/4'>surface</scene> of the tropocollagen is shown with the Ala appearing as olive and the Pro and Hyp adjacent to the Ala appearing as dark brown. Notice that the surface at these Pro and Hyp bulges slightly. This protrusion is due to the fact that the packing about the Ala side chains is not as close as it is about the Gly. In the two side-by-side scenes shown below compare the amount of open space between the chains in the area of the scene center. In the [[1cag]] scene in the area of the Ala the distance between the chains is slightly greater than that of [[4clg]] scene. | ||
</StructureSection> | </StructureSection> | ||
<table width='100%' align='left' cellpadding='5'><tr><td rowspan='2'> </td><td bgcolor='#eeeeee'><Structure load=' | <table width='100%' align='left' cellpadding='5'><tr><td rowspan='2'> </td><td bgcolor='#eeeeee'><Structure load='4clg' size='400' frame='true' align='left' name='id1' scene='Collagen/Glys_close_wf/1' /></td><td bgcolor='#eeeeee'><Structure load='1cag' size='400' frame='true' align='right' name='id2' scene='Collagen/1cag_ala_pack_wf/1' /></td></tr><tr><td bgcolor='#eeeeee'><center>'''Gly Packing in [[4clg]]''' (<scene name='Collagen/Glys_close_wf/1'> Initial scene</scene>)</center></td><td bgcolor='#eeeeee'><center>'''Ala Packing in [[1cag]] (Mutated Collagen)''' (<scene name='Collagen/1cag_ala_pack_wf/1'> Initial scene</scene>)</center></td></tr></table> | ||
__NOTOC__ | __NOTOC__ | ||
