PROTEOME-2 (Part 1)

Molecular biocoding of Prot P62258 14-3-3 protein epsilon, Homo sapiens

Abstract:This paper discusses cyberinformation studies of the amino acid composition of 14-3-3 protein epsilon, in particular the identification of scientific terminology that could describe this phenomenon, ie, the study of genetic information, as well as the relationship between the genetic language of proteins and theoretical aspect of this system and cybernetics. The result of this research show that there is a matrix code for proteome. It also shows that the coding system within the amino acidic language gives detailed information, not only on the amino acid „record“, but also on its structure, configuration and its various shapes. The issue of the existence of an proteome code and coding of the individual structural elements of this protein are discussed. Answers to the following questions are sought. Does the matrix mechanism for biosynthesis of this protein function within the law of the general theory of information systems, and what is the significance of this for understanding the genetic language of proteome? What is the essence of existence and functioning of this language? Is the genetic information characterized only by biochemical, or also by cyberinformation principles? The potential effects of physical and chemical, as well as cybernetic and information ptinciples, on the biochemical basis of proteome are also investigated.This paper discusses new methods for developing genetic technologies, in particular more advanced digital technology based on programming, cybernetics, and informational laws and systems, and how this new technology could be useful in medicine, bioinformatics, genetics, biochemistry, and other natural sciences.

Keywords
Protein attributes, proteome, human, P31946, protein code, tahonomy, gene ontology, enzyme class, patway, beta/alpha

Introduction

The biologic role of any given protein in essential life processes, eg, 14-3-3 protein epsilon, depends on the positioning of its component amino acids, and is understood by the „positioning of letters forming words“. Each of these words has its biochemical base. If this base is expressed by corresponding discrete numbers, it can be seen that any given base has its own program, along with its own unique cybernetics and information characteristics.

Indeed, the sequencing of the molecule is determined not only by distin biochemical features, but also by cybernetic and information principles. For this reason, research in this field deals more with the quantitative rather than qualitative characteristcs of genetic information and its biochemical basis. For the purposes of this paper, specific physical and chemical factors have been selected in order to express the genetic information for 14-3-3 protein epsilon. Numerical values are them assigned to these factors, enabling them to be measured. In this way it is possible to determine oif a connection really exists between the quantitative ratios in the process of transfer of genetic information and the qualitative appearance of the 14-3-3 protein epsilon molecule. To select these factors, preference is given to classical physical and chemical parameters, including the number of atoms in the relevant amino acids, their analog values, the position in these amino acids in the peptide chain, and their frenquencies.There is a arge numbers of these parameters, and each of their gives important genetic information. Going through this process, it becomes clear that there is a mathematical relationship between quantitative ratios and the qualitative appearance of the biochemical „genetic processes“ and that there is a measurement method that can be used to describe the biochemistry of 14-3-3 protein epsilon.

Methods

14-3-3 protein epsilon can be represented by two different forms, ie, a discrete form and a sequential form. In the discrete form, a molecule of 14-3-3 protein epsilon is represented by a set of discrete codes or a multiple dimension vector. In the sequential form, an 14-3-3 protein epsilon molecule is represent by a series of amino acids according to the order of their position in the 14-3-3 protein epsilon.

Therefore, the sequential form can naturally reflect all the information about the sequence order and lenght of an 14-3-3 protein epsilon molecule. The key issue is whether we can develop a different discrete method of representing an 14-3-3 protein epsilon molecule that will allow accomodation of partial, if not all sequence order information? Because a protein sequence is usually represented by a series of amino acids should be assigned to these codes in order to optimally convert the sequence order information into a series of numbers for the discrete form representation?

Expression of 14-3-3 protein epsilon

The matrix mechanism of 14-3-3 protein epsilon, the evolution of biomacromolecules and, especially, the biochemical evolution of 14-3-3 protein epsilon language, have been analyzed by the application of cybernetic methods, information theory and system theory, respectively. The primary structure of a molecule of 14-3-3 protein epsilon is the exact specification of its atomic composition and the chemical bonds connecting those atoms.

SQ   SEQUENCE   255 AA;  29174 MW;  07817CCBD1F75B26 CRC64;

     MDDREDLVYQ AKLAEQAERY DEMVESMKKV AGMDVELTVE ERNLLSVAYK NVIGARRASW

     RIISSIEQKE ENKGGEDKLK MIREYRQMVE TELKLICCDI LDVLDKHLIP AANTGESKVF

     YYKMKGDYHR YLAEFATGND RKEAAENSLV AYKAASDIAM TELPPTHPIR LGLALNFSVF

     YYEILNSPDR ACRLAKAAFD DAIAELDTLS EESYKDSTLI MQLLRDNLTL WTSDMQGDGE

     EQNKEALQDV EDENQ

//

Fragment of sequence 255 AA:

Number of atoms

M	D	D	R	E	D	L	V	Y	Q	.	.	D	E	N	Q	Sum
20	16	16	26	19	16	22	19	24	20	.	.	16	19	17	20	4828
1	2	3	4	5	6	7	8	9	10	.	.	252	253	254	255	32640

Amino acid 1 (AC1) = 20 atoms; AC2=16 atoms; AC3= 16 atoms, etc.

Figure 1. Group of amino acids from 1 to 255

Notes: Aforementioned aminoacids are positioned from number 1 to 255. Numbers 1, 2, 3, n... present the position of a certain aminoacid. This positioning is of the key importance for understanding of programmatic, cybernetic and information principles in this protein. The scientific key for interpretation of bio chemical processes is the same for 14-3-3 protein epsilon and as well as for the other proteins and other sequences in biochemistry.

The first aminoacid in this example has 20 atoms, the second one 16, the third one 16, etc. They have exactly these numbers of atoms because there are many codes in the 14-3-3 protein epsilon, analog codes, and other voded features. In fact, there is a cybernetic algorithm which it is „recorded“ that the firs amino acid has to have 20 atoms, the second one 16, the third one 16, etc. The first amino acid has its own biochemistry, as does the second and the third, etc. The obvious conclusion is that there is a concrete relationship between quantitative ratios in the process of transfer of genetic information and qualitative appearance, ie, the characteristcs of the organism.