1109.2629 (J. C. Phillips)

Self-Organized Criticality: A Guide to Water-Protein Landscape Evolution    [PDF]

J. C. Phillips

We focus here on the scaling properties of small interspecies differences
between red cone opsin transmembrane proteins, using a hydropathic elastic
roughening tool previously applied to the rhodopsin rod transmembrane proteins.
This tool is based on a non-Euclidean hydropathic metric realistically rooted
in the atomic coordinates of 5526 protein segments, which thereby encapsulates
universal non-Euclidean long-range differential geometrical features of water
films enveloping globular proteins in the Protein Data Bank. Whereas the
rhodopsin blue rod water films are smoothest in humans, the red cone opsins'
water films are optimized in cats and elephants, consistent with protein
species landscapes that evolve differently in different contexts. We also
analyze red cone opsins in the chromatophore-containing family of chameleons,
snakes, zebrafish and goldfish, where short- and long-range (BLAST and
hydropathic) aa correlations are found with values as large as 97-99%. We use
hydropathic amino acid (aa) optimization to estimate the maximum number Nmax of
color shades that the human eye can discriminate, and obtain 10^6 < Nmax <
10^7, in good agreement with experiment.

View original: http://arxiv.org/abs/1109.2629