Informational Way to Protein Alphabet: Entropic Classification of Amino Acids

Biology – Quantitative Biology – Biomolecules

Scientific paper

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13 p. 6 Tabs, 3 Figs, Reduced version with additional study of membrane and globular proteins

Scientific paper

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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