Collagen
|
The collagen sequence is typically (Gly - Pro - hydroxy-Pro)n.
Each forms an elongated left-handed helix. Three of these chains are associated to a right-handed .
Every third amino acid is
Ribbon and Spacefilling Diagrams of the Collagen Triple HelixRibbon and Spacefilling Diagrams of the Collagen Triple Helix
(KineMage currently not supported)
Fibrous proteins are, for the most part, characterized by highly repetitive simple sequences. We shall examine here a trimer that forms a collagen-like triple helix. Collagen, the most abundant protein in vertebrates, is an extracellular protein that comprises the major protein component of such stress-bearing structures as bones, tendons, and ligaments. Collagen is characterized by a distinctive repeating sequence: (Gly-X-Y)n where X is often Pro, Y is often 5-hydroxyproline (Hyp), and n may be >300. This, as we shall see, causes each collagen chain to assume a left-handed helical conformation with 3.3 residues per turn and a pitch (rise per turn) of 10.0 Å. Three such chains associate in parallel to form a right-handed triple helix.
Here we study a model compound for naturally occurring collagen, a 30-residue synthetic polypeptide of sequence (Pro-Hyp-Gly)4-Pro-Hyp-Ala-(Pro-Hyp-Gly)5, three chains of which associate to form a collagen-like triple helix of parallel strands that is 87 Å long and ~10 Å in diameter.
View1 shows the triple helical molecule in ribbon form seen perpendicular to its triple helical axis and with its three parallel and identical chains, "Chain 1", "Chain 2", and "Chain 3", colored purple, gold, and white, respectively. View2 is down the triple helical axis, a perspective in which this ribbon diagram appears to have a hollow center. However, click the "ANIMATE" button to show the spacefilling form and prove to yourself that the center is not hollow. Return to the ribbon diagram by clicking the "ANIMATE" button again before continuing.
Go back to View1 and repeatedly click the "2ANIMATE" button. This "grows" Strand 1 from its N- to its C-terminus in differently colored 3-residue increments. Note how the molecule's three strands twist around each other and that the triple helix makes one turn every ~7 three-residue repeats.
Repeatedly click the "ANIMATE" button to alternately display the original ribbon diagram and a spacefilling diagram of the polypeptide chains together with their side chains. The chains of the spacefilling diagram, which are colored identically to those of the ribbon diagram, can be individually turned on and off. Displaying one or two chains as ribbons and the remainder in spacefilling form may better reveal the helical character of the triple helix.
Additional InformationAdditional Information
Another Jmol tutorialAnother Jmol tutorial
Tutorial which illustrates and describes the 3D structure of collagen