Residual colours: a proposal for aminochromography.

All 20 amino acids have pure spectral colours (those seen in the rainbow). Given this fundamental fact, it takes only a prescribed cyclic ordering of the acids and two fixed Keywords: amino acid colouring/protein multiple sequence points (say, North and East, as in the cardinal points of the alignments compass) to establish the absolute colour of all. The cyclic ordering of the acids, while not completely unambiguous, is relatively clear and can be found in the convergence of Aminochromatic blindness a number of different arguments derived from the genetic code, relative mutability and basic physics and chemistry 'No doubt you are aware that the winds have colour .... (See Taylor (1986) for a review). This ordering is dominated There are four winds and eight sub-winds, each of which by the two properties of amino acids (size and polarity) has its own colour. The wind from the east is a deep that are fundamental to the stability of protein structure. At purple, the south a fine shining silver. The north wind is opposite ends of the circle (say, North and South) lie the hard black and the west wind is amber. People in the old large and small acids, while orthogonal to this (say, East days had the power of perceiving these colours and could and West) lie the hydrophobic and hydrophilic acids. spend a day sitting quietly on a hillside watching the beauty of the winds, their fall and rise and changing hues, the To establish a unique orientation of the circle, both the magic of neighbouring winds when they inter-weaved like N-S and the E-W axes must be assigned colours. One ribbons at a wedding. It was a better occupation than gazing fixed point, that is seldom in dispute, is that cystine (cys, at newspapers. The sub-winds had colours of indescribable C) is yellow. This choice is inescapable, given the vivid delicacy, a reddish-yellow halfway between silver and purple, pure yellow colour of sulphur. The second required orthogonal a greyish-green that was related equally to black and brown. point is less obvious but hinges on the allocation of the What could be more exquisite than a countryside swept amino acids with charged side groups. The negatively lightly by cool rain reddened by the south-west breeze.' charged acidic groups (glutamate and aspartate) are often The gift of seeing these colours is very rare these days; coloured red, following the conventional colour for oxygen indeed, the last recorded observation was now many years in molecular models (originally from its visible manifestation ago in a small isolated community in Ireland. (The lives in fire). Similarly, the positively charged basic groups (lysine (or more accurately, deaths) of these people, centering and arginine) are coloured blue by extension from the blue around the local constabulary, was recorded by Flann colour of their charged nitrogen atoms (sky-blue to be O'Brien in The Third Policeman, from which the opening exact). Unfortunately, some who have lingered over-long in quotation is taken. (Some neglected aspects of atomic theory, physics laboratories reverse this convention and colour the of undoubted relevance to protein structure, can also be positively charged acids red, following the colour of the found in this work).) Lamentable as the loss of these powers positive terminal in electricity. This misconception forces is, a matter of even graver concern is the growing sign that black as the logical choice for the negatively charged many people appear unable to see the colours of the residues, but as black is not a proper colour for an amino amino acids. acid (which are all colours of the rainbow) this assignment In the days when protein sequence alignments were can be rejected immediately. published only in black-and-white, much of this aminochrom- The cardinal colours atic blindness passed unnoticed, but now, with plentiful Given the fixed points, the colours of the acids themselves