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arXiv · 1102.2433

Self-Organized Criticality: A Magic Wand for Protein Physics

J. C. Phillips
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Abstract

Self-organized criticality (SOC) is a popular concept that has been the subject of more than 3000 articles in the last 25 years. Here we show that SOC may enable theory to connect standard Web-based (BLAST) short-range amino acid (aa) similarities to long-range aa roughening form factors that accurately describe evolutionary trends in water-membrane protein interactions. Our method utilizes a hydropathic aa metric based on 5526 protein segments and thereby encapsulates differential geometrical features of the Protein Data Bank. It easily organizes small aa sequence differences between humans and proximate species. For rhodopsin, the most studied transmembrane signaling protein associated with night vision, it shows that short- and long-range aa sequence properties correlate with 96% success for humans, monkeys, cats, mice and rabbits. Proper application of SOC promises unprecedented simplifications of exponentially complex protein sequence-structure-function problems, both conceptual and practical.

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J. C. Phillips. 2011-02-11. Self-Organized Criticality: A Magic Wand for Protein Physics. https://arxiv.org/abs/1102.2433

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