A novel approach to predicting aminoacids and proteins by relation Even-Odd (Second part)

A novel approach to predicting aminoacids and proteins by relation Even-Odd

(Second part)

Lutvo Kurić

Independent Researcher

Bosnia and Herzegovina

72290 Novi Travnik

Kalinska 7

Tel. 061 763 917

lutvokuric@yahoo.com

Distance 7 in digital genetic code matrix

An even genetic code matrix An odd genetic code matrix

36	38	38	38	40	40	40	270		37	37	37	39	39	39	39	267
38	38	38	40	40	40	40	274		37	37	39	39	39	39	41	271
38	38	40	40	40	40	40	276		37	39	39	39	39	41	41	275
38	40	40	40	40	40	40	278		39	39	39	39	41	41	41	279
40	40	40	40	40	40	40	280		39	39	39	41	41	41	41	281
40	40	40	40	40	40	40	280		39	39	41	41	41	41	41	283
x	x	x	x	X	x	x	0		x	x	x	x	X	x	x	0
x	x	x	x	X	x	x	0		x	x	x	x	X	x	x	0
x	x	x	x	X	x	x	0		x	x	x	x	X	x	x	0
44	44	44	44	44	44	44	308		43	43	43	43	43	45	45	305
44	44	44	44	44	44	44	308		43	43	43	43	45	45	45	307
44	44	44	44	44	44	46	310		43	43	43	45	45	45	45	309
44	44	44	44	44	46	46	312		43	43	45	45	45	45	47	313
44	44	44	44	46	46	46	314		43	45	45	45	45	47	47	317
44	44	44	46	46	46	48	318		45	45	45	45	47	47	47	321
1070	1078	1084	1092	1100	1106	1114	7644		1068	1076	1084	1092	1100	1108	1116	7644

(270+274+276+278+280+280+280+282+284+286+288+290+292+296+298+300+302+304+306+308+

+308+308+310+312+314+318) = 7644;

(267+271+275+279+281+283+285+287+287+287+289+291+293+295+297+299+301+301+301+303+305+307+309+313+317+321) = 7644;

Therefore, groups with 7 triplets in digital tables of even genetic code have 7644 atoms. Triplets in distance 7 on opposite sides are muttualy attracted, respectively they mathematicaly gravitate towards each other. Here are some examples:

(1070+1114) = (1078+1106) = (1084+1100) = (1092 x 2) = 2184;

2184 = [(19 + 7) x Y];

(270+318) = (274+314) = (276+312)…, + (296+292);

Codes 19 and 7 in even code matrix

(D1+D2+D3…, + D19) + (D29+D28+D27..., + D11) = 11172 = [(7x19 x 7) x Y]

(D2+D2+D4…, + D20) + (D28+D27+D26…, + D10) = 11172 = [(7x19 x 7) x Y]

(D3+D2+D5…, + D21) + (D27+D26+D25…, + D9) = 11172 = [(7x19 x 7) x Y]

etc.

Codes 19 and 7 in odd code matrix

(D1+D2+D3…, + D19) + (D29+D28+D27..., + D11) = 11172 = [(7x19 x 7) x Y]

(D2+D2+D4…, + D20) + (D28+D27+D26…, + D10) = 11172 = [(7x19 x 7) x Y]

(D3+D2+D5…, + D21) + (D27+D26+D25…, + D9) = 11172 = [(7x19 x 7) x Y]

etc.

Distance 19 in digital genetic code matrih

An even genetic code matrix

36	38	38	38	40	40	40	40	40	40	40	40	40	42	42	42	42	42	42	762
38	38	38	40	40	40	40	40	40	40	40	40	42	42	42	42	42	42	44	770
38	38	40	40	40	40	40	40	40	40	40	42	42	42	42	42	42	44	44	776
38	40	40	40	40	40	40	40	40	40	42	42	42	42	42	42	44	44	44	782
40	40	40	40	40	40	40	40	40	42	42	42	42	42	42	44	44	44	44	788
40	40	40	40	40	40	40	40	42	42	42	42	42	42	44	44	44	44	44	792
40	40	40	40	40	40	40	42	42	42	42	42	42	44	44	44	44	44	44	796
40	40	40	40	40	40	42	42	42	42	42	42	44	44	44	44	44	44	44	800
40	40	40	40	40	42	42	42	42	42	42	44	44	44	44	44	44	44	44	804
40	40	40	40	42	42	42	42	42	42	44	44	44	44	44	44	44	44	44	808
40	40	40	42	42	42	42	42	42	44	44	44	44	44	44	44	44	44	46	814
40	40	42	42	42	42	42	42	44	44	44	44	44	44	44	44	44	46	46	820
40	42	42	42	42	42	42	44	44	44	44	44	44	44	44	44	46	46	46	826
42	42	42	42	42	42	44	44	44	44	44	44	44	44	44	46	46	46	48	834
552	558	562	566	570	572	576	580	584	588	592	596	600	604	606	610	614	618	624	11172

Codes 19 and 7 in even code matrix

(D1+D2+D3+D4+D5+D6+D7) + (D14+D13+D12+D11+D10+D9+D8) = 11172 = [(7x19 x 7) x Y]

(D2+D3+D4+D5+D6+D7+D8) + (D13+D12+D11+D10+D9+D8+D7) = 11172 = [(7x19 x 7) x Y]

(D3+D4+D5+D6+D7+D8+D9) + (D12+D11+D10+D9+D8+D7+D6) = 11172 = [(7x19 x 7) x Y]

etc.

Codes 19 and 7 in odd code matrix

(D1+D2+D3+D4+D5+D6+D7) + (D14+D13+D12+D11+D10+D9+D8) = 11172 = [(7x19 x 7) x Y]

(D2+D3+D4+D5+D6+D7+D8) + (D13+D12+D11+D10+D9+D8+D7) = 11172 = [(7x19 x 7) x Y]

(D3+D4+D5+D6+D7+D8+D9) + (D12+D11+D10+D9+D8+D7+D6) = 11172 = [(7x19 x 7) x Y]

etc.

An odd genetic code matrix

37	37	37	39	39	39	39	41	41	41	41	41	41	41	41	41	43	43	43	765
37	37	39	39	39	39	41	41	41	41	41	41	41	41	41	43	43	43	43	771
37	39	39	39	39	41	41	41	41	41	41	41	41	41	43	43	43	43	43	777
39	39	39	39	41	41	41	41	41	41	41	41	41	43	43	43	43	43	43	783
39	39	39	41	41	41	41	41	41	41	41	41	43	43	43	43	43	43	43	787
39	39	41	41	41	41	41	41	41	41	41	43	43	43	43	43	43	43	43	791
39	41	41	41	41	41	41	41	41	41	43	43	43	43	43	43	43	43	43	795
41	41	41	41	41	41	41	41	41	43	43	43	43	43	43	43	43	43	45	801
41	41	41	41	41	41	41	41	43	43	43	43	43	43	43	43	43	45	45	805
41	41	41	41	41	41	41	43	43	43	43	43	43	43	43	43	45	45	45	809
41	41	41	41	41	41	43	43	43	43	43	43	43	43	43	45	45	45	45	813
41	41	41	41	41	43	43	43	43	43	43	43	43	43	45	45	45	45	47	819
41	41	41	41	43	43	43	43	43	43	43	43	43	45	45	45	45	47	47	825
41	41	41	43	43	43	43	43	43	43	43	43	45	45	45	45	47	47	47	831
554	558	562	568	572	576	580	584	586	588	590	592	596	600	604	608	614	618	622	11172

Therefore, groups with 19 triplets in digital tables of genetic code have 11172 atoms. And also in this example groups of triplets on opposite sides mutually attract forces of genetic gravitation.

Here are some examples:

(552+624) = (558+618) = (562+614) = (566+610)…, etc.

(762+834) = (770+826) = (776+820)…, etc.

11172 = [(7 x 19 x 7) x Y]; Y = 12;

Codes 19 and 7 in even code matrix

(D1+D2+D3+D4+D5+D6+D7) + (D14+D13+D12+D11+D10+D9+D8) = 11172 = [(7x19 x 7) x Y]

(D2+D3+D4+D5+D6+D7+D8) + (D13+D12+D11+D10+D9+D8+D7) = 11172 = [(7x19 x 7) x Y]

(D3+D4+D5+D6+D7+D8+D9) + (D12+D11+D10+D9+D8+D7+D6) = 11172 = [(7x19 x 7) x Y]

etc.

Codes 19 and 7 in odd code matrix

(D1+D2+D3+D4+D5+D6+D7) + (D14+D13+D12+D11+D10+D9+D8) = 11172 = [(7x19 x 7) x Y]

(D2+D3+D4+D5+D6+D7+D8) + (D13+D12+D11+D10+D9+D8+D7) = 11172 = [(7x19 x 7) x Y]

(D3+D4+D5+D6+D7+D8+D9) + (D12+D11+D10+D9+D8+D7+D6) = 11172 = [(7x19 x 7) x Y]

etc.

Distances in digital genetic code matrix

Number of atoms in triplets

		An even code Matrix										An odd code matrix
D1			1344		D17	11424				D1			1344		D17	11424
D2			2604		D18	11340				D2			2604		D18	11340
D3			3780		D19	11172				D3			3780		D19	11172
D4			4872		D20	10920				D4			4872		D20	10920
D5			5880		D21	10584				D5			5880		D21	10584
D6			6804		D22	10164				D6			6804		D22	10164
D7			7644		D23	9660				D7			7644		D23	9660
D8			8400		D24	9072				D8			8400		D24	9072
D9			9072		D25	8400				D9			9072		D25	8400
D10			9660		D26	7644				D10			9660		D26	7644
D11			10164		D27	6804				D11			10164		D27	6804
D12			10584		D28	5880				D12			10584		D28	5880
D13			10920		D29	4872				D13			10920		D29	4872
D14			11172		D30	3780				D14			11172		D30	3780
D15			11340		D31	2604				D15			11340		D31	2604
D16			11424		D32	1344				D16			11424		D32	1344

D1=D32; D2=D31; D3=D30; etc.

In previously mentioned examples forces of mathematical gravitation are interconnected groups with different number of triplets.

C O N C L U S I O N

It is a rewarding work to translate the biochemical language of amino acids into a digital language because it may be very useful for developing new methods for predicting protein sub cellular localization, membrane protein type, protein structure secondary prediction or any other protein attributes. 

This is because ever since the concept of Chou's pseudo amino acid composition was proposed [1,2], many efforts have been made trying to use various digital numbers to represent the 20 native amino acids in order to better reflect the sequence-order effects through the vehicle of pseudo amino acid composition. Some investigators used complexity measure factor [3], some used the values derived from the cellular automata [4-7], some used hydrophobic and/or hydrophilic values [8-16], some were through Fourier transform [17, 18], and some used the physicochemical distance [19]. 

In view of this, we finding might have a series of impacts to the aforementioned work. (33) We devoted to provide a digital code for each of 20 native amino acids. These digital codes should more complete and better reflect the essence of each of the 20 amino acids. Therefore, it might stimulate a series of future work by using the author’s digital codes to formulate the pseudo amino acid composition for predicting protein structure class [20-22], subcellular location [23, 24], membrane protein type [9, 25], enzyme family class [26, 27], GPCR type [28, 29], protease type [30], protein-protein interaction [31], metabolic pathways [32], protein quaternary structure [33], and other protein attributes.

Now, it is going to be possible to use the completely new strategy of research in genetics. However, observation of all these relations which are the outcome of the periodic law (actually, of the law of binary coding) is necessary, because it can be of great importance for decoding conformational forms and stereo-chemical and digital structure of proteins.

R E F E R E N C E S

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