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Informational Way to Protein Alphabet: Entropic Classification of Amino Acids

A. N. Gorban·M. Kudryashev·T. Popova
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Abstract

What are proteins made from, as the working parts of the living cells protein machines? To answer this question, we need a technology to disassemble proteins onto elementary func-tional details and to prepare lumped description of such details. This lumped description might have a multiple material realization (in amino acids). Our hypothesis is that informational approach to this problem is possible. We propose a way of hierarchical classification that makes the primary structure of protein maximally non-random. The first steps of the suggested research program are realized: the method and the analysis of optimal informational protein binary alphabet. The general method is used to answer several specific questions, for example: (i) Is there a syntactic difference between Globular and Membrane proteins? (ii) Are proteins random sequences of amino acids (a long discussion)? For these questions, the answers are as follows: (i) There exists significant syntactic difference between Globular and Membrane proteins, and this difference is described; (ii) Amino acid sequences in proteins are definitely not random.

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A. N. Gorban, M. Kudryashev, T. Popova. 2007-11-05. Informational Way to Protein Alphabet: Entropic Classification of Amino Acids. https://arxiv.org/abs/q-bio/0501019

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