自组织临界性：水-蛋白质景观演化指南
Self-Organized Criticality: A Guide to Water-Protein Landscape Evolution
摘要：
在这里，我们专注于红锥视蛋白跨膜蛋白之间的小种间差异的缩放特性，使用亲水性弹性粗糙化工具先前应用于视紫红质杆跨膜蛋白。这个工具是基于一个非欧几里德亲水性度量现实植根于原子坐标的5526蛋白质片段，从而封装通用的非欧几里德远程微分几何特征的水膜包裹球状蛋白质的蛋白质数据库。虽然人类的视紫红质蓝棒水膜是最平滑的，但红锥视蛋白的水膜在猫和大象中是最优化的，这与在不同环境中进化不同的蛋白质物种景观一致。我们还分析了红锥视蛋白的变色龙，蛇，斑马鱼和金鱼，其中短期和长期（BLAST和亲水性）的相关性被发现的值高达97- 99%的含色素家族。我们使用亲水性氨基酸（aa）优化来估计人眼可以辨别的最大色调数Nmax，并且获得10^6 < Nmax < 10^7，与实验良好一致。
英文摘要：
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.
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