Ribbon Diagram - History

History

Originally conceived by Jane S. Richardson in 1980 (influenced by some earlier individual illustrations, e.g., see), her hand-drawn ribbon diagrams were the first schematics of 3D protein structure to be produced systematically, to illustrate a classification of protein structures for an article in Advances in Protein Chemistry (now available in annotated form on-line at Anatax). These drawings were made in pen on tracing paper over a printout of a Cα trace of the atomic coordinates; they preserved positions, smoothed the backbone path, and incorporated small local shifts to disambiguate the visual appearance. As well as the TIM ribbon drawing at the right, other hand-drawn examples are for prealbumin, flavodoxin, and Cu,Zn superoxide dismutase.

In 1982, Arthur M. Lesk and co-workers first enabled automatic generation of ribbon diagrams through a computational implementation that uses Protein Data Bank files as input. This conceptually simple algorithm fit cubic polynomial B-spline curves to the peptide planes. Most modern graphics systems provide either B-splines or Hermite splines as a basic drawing primitive. One type of spline implementation passes through each Cα guide point, producing an exact but choppy curve. Both hand-drawn and most computer ribbons (such as those shown here) are smoothed over about 4 successive guide points (usually the peptide midpoint), to produce a more visually pleasing and understandable representation. In order 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 (figure at right) and later adapted by other molecular graphics software, such as the open-source Mage program for kinemage graphics that produced the ribbon image at top right (other examples: 1xk8 trimer and DNA polymerase).

Since their inception, and continuing in the present, a ribbon diagram is the single most common representation of protein structures and a very common choice of cover image for a journal or textbook.