Ribbon diagram

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. The ribbon shows the overall path and organization of the protein backbone in 3D, and serves as a visual framework on which to hang details of the full atomic structure, such as the balls for the oxygen atoms bound to the active site of myoglobin in the image at the right. 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 non-repetitive coils or loops. The direction of the polypeptide chain is shown locally by the arrows, and may be indicated overall by a colour ramp along the length of the ribbon.

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 both by the expert structural biologists and also by other scientists, students, and the general public.

Originally conceived by Jane S. Richardson in 1980 (influenced by earlier individual illustrations), 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.

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