Proteins are biological macromolecules made up of a long polypeptide chain of amino acids linked by peptide bonds (put together by the ribosome, according to the genetic code as stored in DNA genes, transcribed into messenger RNA, and then translated by the ribosome into the amino-acid sequence of the protein). Each amino acid has one of 20 types of side chains, functional groups of different sizes and chemistries, which branch off from the backbone. Once synthesized, a protein molecule folds up by interactions of those sidechains: 1) making hydrogen bonds between backbone peptides to form α-helix and β-sheet secondary structures, and 2) burying the hydrophobic or non-polar sidechains on the inside away from water. The 3D shape of the folded protein produces its functional, biological properties such as enzyme catalysis or specific binding of other molecules.
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 copper and zinc atoms at the active site of superoxide dismutase 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.[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 both by the expert structural biologists and also by other scientists, students,[2] and the general public.
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Originally conceived by Jane S. Richardson in 1980 (influenced by some earlier individual illustrations, e.g., see[3]), her hand-drawn ribbon diagrams were the first schematics of 3D protein structure to be produced systematically,[3][4] to illustrate a classification of protein structures for an article in Advances in Protein Chemistry[5] (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.[4] 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.[6] 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[7] (figure at right) and later adapted by other molecular graphics software, such as the open-source Mage program for kinemage graphics[8] 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.
One popular program used for drawing ribbon diagrams 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 Arthur M. Lesk, Karl Hardman, and John Priestle.[9] Jmol is an open-source Java-based viewer for browsing molecular structures on the web; it includes a simplified "cartoon" version of ribbons. Other graphics programs such as DeepView (example: urease) and MolMol (example: SH2 domain) also produce ribbon images. KiNG[10] is the Java-based successor to Mage (examples: α-hemolysin top view and side view).
UCSF Chimera is a powerful molecular modeling program that also includes visualizations such as ribbons, notable especially for the ability to combine them with contoured shapes from cryo-electron microscopy data.[11] PyMOL, by Warren DeLano,[12] is a very popular and flexible molecular graphics program (based on Python) that operates in interactive mode and also produces presentation-quality 2D images for ribbon diagrams and many other representations (see figure at right, and also mabinlin and TNF-alpha).
| Secondary Structure[4][5] | ||
|---|---|---|
| α-Helices | Cylindrical spiral ribbons, with ribbon plane approximately following plane of peptides. | |
| β-Strand | 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. β-sheets are seen as unified, because neighboring strands twist in unison. | |
| Loops and miscellaneous | ||
| Nonrepetitive loops | Round ropes that are fatter in the foreground and thinner towards the back, following smoothed path of Cα trace. | |
| 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 stylized lightning stroke | |
| Prosthetic groups or inhibitors | Stick figures, or ball&stick. | |
| Metals | Spheres (e.g., see top image). | |
| 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. |
