Ribbon diagram
3D schematic representation of protein backbone structure.
Ribbon diagrams, also known as Richardson diagrams, are 3D schematic representations of protein structure. They depict the general course and organization of the protein backbone, with α-helices shown as coiled ribbons or thick tubes, β-sheets as arrows, and loops as lines or thin tubes. These diagrams are one of the most common methods of protein depiction used today, serving as a visual framework for understanding the overall organization of protein structures.
- creator
- Jane S. Richardson
- field
- Structural biology
- known_for
- First systematic 3D schematic of protein structure
Lore & Background
The first ribbon diagrams were hand-drawn by Jane S. They were created to illustrate a classification of protein structures for an article in Advances in Protein Chemistry. These drawings were outlined in pen on tracing paper over a printout of a Cα trace of the atomic coordinates, and shaded with colored pencil or pastels; they preserved positions, smoothed the backbone path, and incorporated small local shifts to disambiguate the visual appearance. Hand-drawn examples depicted triose isomerase, prealbumin, flavodoxin, and Cu,Zn superoxide dismutase. Lesk and co-workers first enabled the automatic generation of ribbon diagrams through a computational implementation that uses Protein Data Bank files as input. This algorithm fitted cubic polynomial B-spline curves to the peptide planes. Both hand-drawn and most computer ribbons are smoothed over about four successive guide points to produce a more visually pleasing representation. To give the right radius for helical spirals while preserving smooth β-strands, the splines can be modified by offsets proportional to local curvature, as first developed by Mike Carson for his Ribbons program. Since their inception, ribbon diagrams have been the single most common representation of protein structure and a common choice of cover image for a journal or textbook. Current computer programs for drawing ribbon diagrams include Molscript, Jmol, DeepView, MolMol, KiNG, UCSF Chimera, and PyMOL.
Reader's Guide
Ribbon diagrams are simple yet powerful, expressing the visual basics of a molecular structure (twist, fold and unfold). This method has successfully portrayed the overall organization of protein structures, reflecting their three-dimensional nature and allowing better understanding of these complex objects both by expert structural biologists and by other scientists, students, and the general public. The diagrams are generated by interpolating a smooth curve through the polypeptide backbone, with the direction of the polypeptide chain shown locally by arrows and may be indicated overall by a color ramp along the length of the ribbon. They serve as a visual framework for hanging details of the entire atomic structure, such as the balls for oxygen atoms attached to myoglobin's active site. Ribbon diagrams remain a standard tool for representing protein structure in research, education, and publication.
Did You Know?
- Ribbon diagrams are generated by interpolating a smooth curve through the polypeptide backbone.
- Ribbon diagrams have been the single most common representation of protein structure since their inception.
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