Entropy of Protein Sequences: An Integral Approach

Abstract

Several classifications of protein spatial structures and their structural elements are known. This makes revealing of the relation between these structural elements and sequence fragments rather topical. The most important move in this direction would be the determination of positional sensitivity levels and ranges between the residues in protein sequences. In this work the Shannon-Weaver informational entropy was used as a disorder criterion for solving this problem. This entropy was computed as function of the distance between the amino acid residues in different sets of unhomological protein sequences. Similarity of this function for different sets of protein sequences was shown. Analysis of informational entropy allows detecting a long-range positional correlation (> or =30) between the amino acid residues and oscillations with periods of 3.6 and 2.9. These oscillation periods correspond to periodicity of alpha- and 3(10)-helices.

Is crab duplex-specific nuclease a member of the Serratia family of non-specific nucleases?

“…To establish the region encompassing the complete functional catalytic domain of Par_DSN, we analyzed the protein information structure, as described by Nekrasov (2002Nekrasov ( , 2004. This analysis allows the detection of the spatial structural units of the protein in which residues relate more to each other than in a casual amino acid sequence (so-called IDIC-associations).…”

“…Briefly, the Par_DSN amino acid sequence was presented as "information units" (IU) composition, whereby IU is a short (up to 6 residues) overlapping fragments. A profile of information content was generated for the Par_DSN sequence on the basis of previously obtained statistic parameters (Nekrasov, 2002(Nekrasov, , 2004. Sites of increased degree of information coordination between residues (IDIC-sites) were detected by decomposing the information content profile into Gaussian curves, and locating maxima of the decomposition (Gaussian) functions with the greatest values for the protein sequence in question.…”

Selection of Cryptic B-Cell Epitopes Using Informational Analysis of Protein Sequenses

“…(iv) "Information content" profile of the protein sequence was generated using parameters of residue frequencies obtained earlier. 8,9 Characteristics of residue frequencies were analyzed earlier for three different sets of non-homologous protein data sets. 8,9 (v) To determine IDIC-sites the "information content" profile of the protein sequence, obtained at the step 2, was decomposed into Gaussian curves with a Closely located IDIC-branches of low hierarchic level are of a special interest in IS.…”

The definition of life in the context of its origin

“…Decoding starts from the point of identification of an amino acid residue (AA) itself and its position in the protein tape and in relation to its close (molecular, atomic) surroundings. The information content of the latter kind was investigated in the example of protein structure (see, for instance, Nekrasov, 2002, and references therein). There is a great difference between communicatory and decoding mechanisms.…”