The Anatomy and Taxonomy of Protein Structure

Ribbon representation of Triosephosphate isomerase by Prof. Jane Richardson (Image Source: Wikipedia)

So, here goes my first post of structural bioinformatics. 🙂

In college when I was flipping the pages of a biochemistry textbook, I remember getting completely mesmerized by the amazing images of proteins, which I learnt later were the ribbon representation of proteins. Digging for more information I came across the name Prof. Jane Richardson, who pioneered this particular representation of proteins.

In my opinion, the publication The Anatomy and Taxonomy of Protein Structure in 1981 is an important milestone in Structural Bioinformatics. (I know that I am not going chronologically). I have heard from my PI that there used to a coloring book or proteins made available from her lab, where we could color the proteins by hand and understand the topology. I am sure it would have been an interesting thing to do, while waiting for a script to finish its job!

Scientific importance of the work

  • An easy way to represent protein structures

    What do I understand from this blob? (Image source: http://kinemage.biochem.duke.edu/teaching/anatax/images/fig003.72.png)

  • One can understand the topology of the protein easily (directionality shown in beta-strands)
  • It is not hard on the eyes to see the detail and at the same to understand the protein structure

The publication also classified proteins on the basis of structure and thus taxonomy of proteins form the second part of the publication. In her own words

 a suitable view was chosen (consistent for each subcategory of structure), and plotter output was obtained at a consistent scale (approximately 20Å per inch on the final drawings as reproduced here). The schematic was drawn on top of the plotter output for accuracy, with continual reference to the stereo for the third dimension. Loops, and to some extent β strands, were smoothed for comprehensibility, and shifts of 1 or 2Å were sometimes necessary in order to avoid ambiguity at crossing points. A uniform set of graphical conventions was adopted (see Section III,A,3 for explanation) in which β strands are shown as arrows, helices as spiral ribbons, and nonrepetitive structure as ropes. Location and extent of β strands and helices are sometimes based on published descriptions and hydrogen-bonding diagrams, but often must be judged from the stereo view itself. Very short β interactions are shown as arrows when they form part of a larger sheet but may be left out if they are isolated. Foreshortening, overlaps, edge appearance, and relative size change are used to provide depth cues.

So now if you are thinking of coloring a protein structure, print this image and the other images in the link above and use your imagination to fill in the colors. 🙂

FIG. 76. Parallel α/β: classic doubly wound β sheets.
Image source: http://kinemage.biochem.duke.edu/teaching/anatax/html/anatax.3a3.76.html

 

References:

http://kinemage.biochem.duke.edu/teaching/anatax/index.html
ResearchBlogging.org
Jane S. Richardson (1981). The Anatomy and Taxonomy of Protein Structure Advances in Protein Chemistry, 34, 167-339 DOI: 10.1016/S0065-3233(08)60520-3

 

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