Ribbon diagram
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Ribbon diagrams, also known as Richardson Diagrams, are 3D schematic representations of protein structure and are one of the most common methods of protein depiction used today. Ribbon diagrams are generated by interpolating a smooth curve through the polypeptide backbone. α-helices are shown as coiled ribbons or thick tubes, β-strands as arrows, and lines or thin tubes for random coils. The direction of the polypeptide chain may be indicated by a colour ramp along the length of the ribbon.[1]
Ribbon diagrams are simple, yet powerful, in expressing the visual basics of a molecular structure (twist, fold and unfold). This method has successfully portrayed the overall organization of the protein structure, reflecting its 3-dimensional information, and allowing for better understanding of a complex object by structural biologists.
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[edit] History
Originally conceived by Jane S. Richardson, her hand-drawn sketches of the ribbon diagrams were the first schematic diagrams to be produced.[2] In 1982, Arthur M. Lesk and coworkers enabled automatic generation of ribbon diagrams through a computational implementation that uses Protein Data Bank files as input.[3] This conceptually simple algorithm fit cubic polynomial B-spline curves to the peptide planes. Most modern graphics systems provide B-splines as a basic drawing primitive. B-Splines are well suited to fitting between data points but not necessarily interpolating through each of those points. To create a line that intersects all data points, Hermite splines work better.
[edit] Current computer programs
A popular program used for drawing ribbon diagrams today is Molscript. Molscript utilizes hermite splines to create coordinates for coils, turns, strands and helices. The curve passes through all its control points (Cα atoms) guided by direction vectors. The program was built on the basis of traditional molecular graphics by Jane S. Richardson, Arthur M. Lesk & Karl Hardman, and John Priestle.[4]
Other programs such as PyMOL also produce ribbon diagrams.
[edit] Features of ribbon diagrams
| Secondary Structure | ||
|---|---|---|
| α-Helices | Cylindrical spiral ribbons | |
| β-Sheet | Arrows with thickness, about one-quarter as thick as they are wide, shows direction and twist of the strand from amino to the carboxy end | |
| Loops and miscellaneous | ||
| Nonrepetitive loops | Round ropes that are fatter in the foreground and thinner towards the back. | |
| Junctions between loops and helices | Round rope that gradually flattens out into a thin helical ribbon. | |
| Other features | ||
| Polypeptide direction,
NH2 and COOH termini |
Small arrows on one or both of the termini or by letters. For β-strands, the direction of the arrow is sufficient. Today, the direction of the polypeptide chain is often indicated by a colour ramp. | |
| Disulfide bonds | Interlocked SS symbol or a zigzag, like a lightning stroke | |
| Prosthetic groups or inhibitors | Stick figures. | |
| Metals | Spheres. | |
| Shading and colour | Shading or colour adds dimensionality to the diagram. Generally, the features at the front are the darkest while, becoming lighter and lower in contrast towards the back. |
[edit] References
- ^ Thomas J. Smith
- ^ Richardson, Jane S. Schematic Drawings of Protein Structures. Methods in Enzymology 115:359-380, 1985.
- ^ Arthur M. Lesk, Karl D. Hardman. Computer-Generated Schematic Diagrams of Protein Structures. Science 216:539-540, 1982.
- ^ MolScript v2.1: About the program
