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Quantitative deciphering of local mutation in protein structures of human olfactory receptors

Satya Ranjan Dash

School of Computer Application, KIIT University, Bhubaneswar 751024, India

E-mail : sdashfca@kiit.ac.in

Satchidananda Dehuri

Department of Information & Communication Technology, F.M. University, Balasore, Odisha, India

Sk. Sarif Hassan

Department of Mathematics, University of Petroleum and Energy Studies, Dehradun, India

DOI: 10.15761/FGNAMB.1000127

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Abstract

In Human, Odors are detected by a large family of Olfactory Receptors (ORs) proteins. A sequence of Human ORs database has been proposed by D. Lancet et al. (2000, 2006) based on divergence of evolutionary model. In our earlier work, we have reckoned many important features (viz. Fractal dimension of Indicator matrix, DNA walk, Hurst exponent of 2-adic and 4-adic representations, codon compositions) of DNA sequences and their corresponding amino acid sequences of human ORs and also after making local changes we have calculated the same and found significant quantitative variations between the original and edited sequences. But it is a fact that two same sequences may function different and two different sequences may function same due their specific protein structure. So for complete understanding the effect of mutation we need to study the structure of proteins of those DNA sequences. In this article, an effort has been made to understand the effect of local mutations in the amino acid sequences as well as their tertiary protein structures of Human ORs. The significant changes are resulted through the present analysis through Fractals and standard Bioinformatics tools.

Key words

human olfactory receptors (ORs), protein sequences, fractal dimension & protein structure

Introduction

ORs is the basis for the sense of smell, and they constitute the largest gene super family in the Human genome [1]. In Human genome, there are about 25000 protein-coding genes and out of which only 700 approximately ORs present [2,3]. However, these genes are more complex, with more alternative splicing generation of larger number of protein products.

Mutation is a biological process which are essentially an arbitrary insertion/ deletion/ replacement in the genomic DNA sequences. Effect of mutations occur in enzymes that do not function, abnormal protein structure or changes in protein conformation that result in a non-functioning or differently functioning protein.

In our earlier work, we have taken a class of human ORs sequences and their mutated sequences which are analyzed using Fractal we have been able to understand effect of edition (mutation) in DNA level. Some of the sequences are entirely been tracked out as per fractal observations and some of them still in the ranges. But through these analysis what we have lost to conclude is that whether they are at all functioning or malfunctioning. Essentially only syntactical changes in DNA are being encountered. So for complete understanding the effect of mutation we need to study the structure of proteins of those DNA sequences.

In this article, we have deciphered a quantitative details of effect of local mutation in protein through fractal analysis and standard Bioinformatics1.

Current state of the art and review of fundamentals

Point mutations in a protein sequence may result in a change or loss of the native structure, which in turn may cause a change or loss of function [4], and ultimately yields different phenotypes. In addition to the natural variations among the individuals, researchers frequently introduce single amino acid residue replacements by misdirected mutagenesis in the laboratory to explore structural and functional features of proteins.

Experimental exploration of different positions in a protein structure with various residue types is a time consuming and expensive process. Such an exploration is generally facilitated by three dimensional (3D) modeling of side-chain mutations [5-9]. While the modeling of a single side chain in a given atomic environment seems to be one of the easiest of all protein structure prediction problems, it is still unsolved [10]. Seemingly insignificant change of a side-chain may lead to a significant change or loss of protein function [11]. This observation implies that side-chain conformation prediction is useful only if it is highly accurate, which makes it a challenging problem. Two simplifications are frequently applied in the modeling of side-chain conformations. First, amino acid residue replacements often leave the backbone conformation almost unchanged [12]. As a consequence, many algorithms x the backbone during the search for the best side-chain conformations. Second, it was observed that most side-chains in high-resolution crystallographic structures can be represented by a limited number of conformers that comply with stereo chemical and energetic constraints [13]. This observation motivated Ponder and Richards to develop the first library of side-chain rotamers for the 17 types of residues with dihedral angle degrees of freedom in their side-chains, based on 10 high-resolution protein structures determined by X-ray crystallography [14].

1 Data Used: We have taken a list of OR sequences of namely OR13G1, OR10K1, OR10T2, ,OR10R2, OR6Y1, OR10K2, OR2T1, OR2T4, OR2T5, OR2T6, OR6P1, OR10Z1, OR6K2, OR6K3, OR6K6, OR6N1, OR2L2, OR6N2, OR2L8, OR5AX1, OR5AY1, OR2G2, OR6F1, OR2G3, OR5AV10, OR11L1, OR10J1, OR2T3, OR1C1 and OR10J5 from OR database .

However, it seems difficult to directly apply traditional pattern matching algorithms [15-17] to 3D protein structure data. There are several qualitative bio-physical/chemical techniques through which we can analyze protein structures [18].

There are several methods to analyse and to compare tertiary protein structures. A method for matching curves that accommodates large and small deformations was implemented by Karp and Rabin [19]. This method preserves geometric similarities in the case of small deformation, and decreases geometric constraints when large deformations occur.

The approach is based on the computation of a set of geodesic paths connecting the curves. These two curves are defined as a source area and a destination area that can have an arbitrary number of connected components and different topologies.

In the present work, in understanding local mutation effect(s) on protein structures and functions, fractal geometric techniques have been employed [20]. We took a list of human olfactory receptors amino acid sequences and corresponding protein structures for this study. Before entering into the main work. Let us have a very brief look into fractals.

Fractal and fractal dimension

Our artificial world can be described easily through Euclidean geometric shapes. But there are many things in nature. Such as shape of cloud, geometry of lightening etc. could not be described through Euclidean geometry [21]. Many mathematicians descended the challenge for a fair enough description of natural objects. But after a long period in 1975, B. Mandelbrot took the challenge and gave the birth of a new geometry to describe nature which is known to us as Fractal Geometry in short Fractal. The precise definition of "Fractal" according to Benoit Mandelbrot is as a set for which the Hausdroff Besicovitch dimension strictly exceeds the topological dimension. To gain a quantitative insight of Fractal, some fractal parameters, namely Fractal dimension, Hurst exponent, succolarity, lacunarity etc. is also introduced in the literature. A brief discussion follows about one of the well-known methods of calculating fractal dimension, namely Box-Counting method [22].

Box-counting method

This method computes the number of cells required to entirely cover an object, with grids of cells of varying size. Practically, this is performed by superimposing regular grids over an object and by counting the number of occupied cells. The logarithm of N(r), the number of occupied cells, versus the logarithm of 1/r, where r is the size of one cell, gives a line whose gradient corresponds to the box dimension.

Methods and results

Here we took thirty two protein sequences of Human ORs and their corresponding tertiary protein structures through Protein Structure Prediction Server ((PS)2) server [23].

Methods

After DNA sequence taken from ORDB [2] we have calculated the number of A,T,C and G occurrence in a single DNA sequence which has given in Tables 2 and 3, then we have edited the sequence to get a new sequence, after finding the position of each sequence. Before and after local editing in the sequences the detail account of frequencies of singletone nucleotide and polytone nucleotides is given in the Table 1. Using Bioinformatics toolbox of Matlab, we have determined the some of the graphs of fundamental protein properties, namely % of accessible residues (AR), Buried resides (BR), Alpha helix (Chou & Fasman) (AH), Amino acid composition (%)) (AC), Beta sheet (Chou & Fasman) (BS), Beta turn (Chou & Fasman) (BT), Coil (Deleage & Roux) (C), Hydrophobicity (Aboderin) (H), codon frequencies (CF) [24,25]. Corresponding to each of such graph we have evaluated the fractal dimension using the fractal analysis tools [21]. We have also found the 3D structure of those original and edited sequences. Then we have calculated the fractal dimension of the 3D protein structures given in Table 4 and compared both the FD value through DaliLite Pairwise comparison of protein structures to nd the Z-scores [26] and then find the difference between these two values [27-31].

Table 1. Details of protein Sequence Mutation where in from column we have no. of consecutive current nucleotides and in to column no. of edited nucleotides along with their Position has mentioned.

 

Protein Name: OR10K1

Protein Name: OR6Y1

Protein Name: OR2T4

Edited

From

To

Position

From

To

Position

From

To

Position

 

1T

1G

34

4T

4G

557

4G

4C

841

 

1C

1G

7

4T

4C

106

4T

4A

644

 

3T

3A

83

 

 

 

 

 

 

 

Protein Name: OR1C1

Protein Name: OR2G2

Protein Name: OR2G3

Edited

From

To

Position

From

To

Position

From

To

Position

 

4T

4A

766

4T

4A

775

4T

4G

96

 

3T

3A

92

3C

3A

884

5C

5G

861

 

3T

3C

107

2C

2A

139

3T

3C

833

 

Protein Name: OR2L2

Protein Name: OR2L8

Protein Name: OR2T1

Edited

From

To

Position

From

To

Position

From

To

Position

 

5T

5A

147

4T

4G

344

4G

4C

126

 

5T

5C

606

2T

2G

9

4G

4A

287

 

4A

4G

5

2C

2G

9

5C

5G

485

 

Protein Name: OR2T3

Protein Name: OR2T5

Protein Name: OR2T6

Edited

From

To

Position

From

To

Position

From

To

Position

 

4T

4G

527

5T

5A

334

5T

5A

539

 

5C

5G

503

4C

4G

792

4G

4A

772

 

4C

4T

890

3C

3A

155

 

 

 

 

4C

4A

653

2C

2A

5

 

 

 

 

3C

3A

338

 

 

 

 

 

 

 

Protein Name: OR5AT1

Protein Name: OR5AV1P

Protein Name: OR5AX1

Edited

From

To

Position

From

To

Position

From

To

Position

 

5C

5G

851

5T

5G

144

5T

5G

533

 

5A

5T

56

3T

3C

60

5T

5A

719

 

4T

4A

636

3G

3C

20

 

 

 

 

3T

3C

760

 

 

 

 

 

 

 

3T

3A

177

 

 

 

 

 

 

 

3T

3G

303

 

 

 

 

 

 

 

2T

2G

536

 

 

 

 

 

 

 

Protein Name: OR5AY1

Protein Name: OR5BF1

Protein Name: OR6F1

Edited

From

To

Position

From

To

Position

From

To

Position

 

5T

5A

504

4T

4G

720

5C

5G

520

 

4G

4A

284

1C

1G

88

4C

4G

25

 

 

 

 

3T

3G

28

3T

3G

34

 

Protein Name: OR6K2

Protein Name: OR6K3

Protein Name: OR6K6

Edited

From

To

Position

From

To

Position

From

To

Position

 

4T

4G

759

4T

4C

96

4T

4G

823

 

4C

4G

878

4A

G

715

4T

4A

701

 

3T

3G

309

 

 

 

3T

3G

156

 

 

 

 

 

 

 

2C

2A

15

 

 

 

 

 

 

 

2G

2A

901

 

Protein Name: OR6N1

Protein Name: OR6N2

Protein Name: OR6P1

Edited

From

To

Position

From

To

Position

From

To

Position

 

3T

3G

427

4G

4A

680

4C

4T

555

 

4T

4A

608

4T

4C

726

5T

5C

491

 

4C

G

520

2T

2G

28

5T

5A

184

 

 

 

 

 

 

 

1C

1G

183

 

 

 

 

 

 

 

1T

1G

75

 

Protein Name: OR10J1

Protein Name: OR10J5

Protein Name: OR10K2

Edited

From

To

Position

From

To

Position

From

To

Position

 

4T

4G

38

5T

5G

629

5T

5G

725

 

4T

4A

722

4T

4A

249

3T

3A

280

 

3C

3A

78

3T

3G

880

 

 

 

 

Protein Name: OR10R2

Protein Name: OR10T2

Protein Name: OR10Z1

Edited

From

To

Position

From

To

Position

From

To

Position

 

4T

4G

753

5T

5C

316

4T

4A

497

 

4A

4C

187

4T

4G

229

4G

41

709

 

3T

3G

677

3T

3A

500

 

 

 

 

2T

2A

10

2C

2A

691

 

 

 

 

Protein Name: OR11L1

Protein Name: OR13G1

 

 

 

Edited

From

To

Position

From

To

Position

From

To

Position

 

4C

4A

403

4T

4C

170

 

 

 

 

3T

3G

90

3T

3A

634

 

 

 

 

2C

2A

626

2T

2A

402

 

 

 

Table 2.

 

 

(Before) Protein Name: OR10K1

 

 

(After)Protein Name: OR10K1

 

occurrences

1

 

2

3

4

5

6

7

 

8

1

 

2

3

4

5

6

7

 

8

A

116

28

4

0

1

0

0

 

0

116

29

4

0

1

0

0

 

0

T

172

41

13

1

0

0

0

 

0

173

40

12

1

0

0

0

 

0

G

98

23

5

1

0

0

0

 

0

98

24

5

1

0

0

0

 

0

C

138

54

12

2

0

0

0

 

0

138

54

12

2

0

0

0

 

0

Total number of Characters : 957

 

 

 

Total number of Characters : 957

 

 

 

(Before) Protein Name: OR6Y1

 

 

 

(After)Protein Name: OR6Y1

 

occurrences

1

 

2

3

4

5

6

7

 

8

1

 

2

3

4

5

6

7

 

8

A

145

25

5

1

0

0

0

 

0

145

25

5

1

0

0

0

 

0

T

164

39

10

4

1

1

0

 

0

164

39

10

2

1

1

0

 

0

G

107

29

4

2

0

0

0

 

0

107

29

4

3

0

0

0

 

0

C

143

56

6

1

0

0

0

 

0

143

55

6

1

0

1

0

 

0

Total number of Characters : 994

 

 

 

Total number of Characters : 994

 

 

 

(Before) Protein Name: OR2T4

 

 

 

(After)Protein Name: OR2T4

 

occurrences

1

 

2

3

4

5

6

7

 

8

1

 

2

3

4

5

6

7

 

8

A

142

24

3

0

2

0

0

 

0

141

24

3

0

3

0

0

 

0

T

189

26

9

2

3

0

0

 

0

189

26

9

1

3

0

0

 

0

G

104

33

9

0

1

0

0

 

0

104

33

9

1

1

0

0

 

0

C

129

60

6

4

1

0

0

 

0

129

60

6

3

1

0

0

 

0

Total number of Characters : 1009

 

 

 

Total number of Characters : 1009

 

 

 

(Before) Protein Name: OR10Z1

 

 

(After)Protein Name: OR10Z1

 

occurrences

1

 

2

3

4

5

6

7

 

8

1

 

2

3

4

5

6

7

 

8

A

138

14

3

0

0

0

0

 

0

136

14

3

0

2

0

0

 

0

T

162

39

8

4

0

0

1

 

0

162

39

8

3

0

0

1

 

0

G

106

24

10

3

0

0

1

 

0

106

24

10

2

0

0

1

 

0

C

129

53

8

1

1

1

0

 

0

129

53

8

1

1

1

0

 

0

Total number of Characters : 957

 

 

 

Total number of Characters : 957

 

 

 

(Before) Protein Name: OR6N2

 

 

 

(After)Protein Name: OR6N2

 

occurrences

1

 

2

3

4

5

6

7

 

8

1

 

2

3

4

5

6

7

 

8

A

129

30

6

1

1

0

0

 

0

129

30

6

1

1

0

0

 

0

T

155

45

14

4

1

0

0

 

0

155

44

14

4

1

0

0

 

0

G

104

29

4

2

0

0

0

 

0

103

29

5

1

0

0

0

 

0

C

135

44

6

1

0

0

0

 

0

134

44

6

1

0

0

0

 

0

Total number of Characters : 970

 

 

 

Total number of Characters : 970

 

 

 

(Before) Protein Name: OR5BF1

 

 

(After)Protein Name: OR5BF1

 

occurrences

1

 

2

3

4

5

6

7

 

8

1

 

2

3

4

5

6

7

 

8

A

135

21

4

2

0

0

0

 

0

135

21

4

2

0

0

0

 

0

T

165

35

11

4

1

1

0

 

1

165

35

10

3

1

1

0

 

1

G

103

32

3

0

1

0

0

 

0

104

32

4

1

1

0

0

 

0

C

140

40

9

2

0

0

0

 

0

139

40

9

2

0

0

0

 

0

Total number of Characters : 954

 

 

 

Total number of Characters : 954

 

 

(Before) Protein Name: OR5AV1P

 

 

(After)Protein Name: OR5AV1P

 

occurrences

1

 

2

3

4

5

6

7

 

8

1

 

2

3

4

5

6

7

 

8

A

128

26

4

1

1

0

0

 

0

128

26

4

1

1

0

0

 

0

T

149

40

10

3

5

1

0

 

0

149

40

9

3

4

1

0

 

0

G

96

26

6

1

0

0

0

 

0

96

26

5

1

0

1

0

 

0

C

110

32

3

3

1

1

0

 

0

110

32

5

3

1

1

0

 

0

Total number of Characters : 896

 

 

 

Total number of Characters : 896

 

 

 

(Before) Protein Name: OR5AT1

 

 

(After)Protein Name: OR5AT1

 

occurrences

1

 

2

3

4

5

6

7

 

8

1

 

2

3

4

5

6

7

 

8

A

124

24

8

1

2

0

0

 

0

122

24

8

2

2

0

0

 

0

T

148

48

20

5

0

0

0

 

0

146

47

17

4

0

0

1

 

0

G

102

21

3

3

0

0

0

 

0

101

22

4

3

0

1

0

 

0

C

133

33

5

1

2

0

0

 

0

132

32

5

1

1

1

0

 

0

Total number of Characters : 945

 

 

 

Total number of Characters : 945

 

 

 

(Before) Protein Name: OR11L1

 

 

(After)Protein Name: OR11L1

 

occurrences

1

 

2

3

4

5

6

7

 

8

1

 

2

3

4

5

6

7

 

8

A

126

19

6

1

0

0

0

 

0

125

20

6

1

1

0

0

 

0

T

164

35

11

3

0

0

1

 

0

165

35

11

2

0

0

1

 

0

G

111

33

5

3

0

0

0

 

0

111

33

6

3

0

0

0

 

0

C

126

60

8

5

0

0

0

 

0

126

59

8

4

0

0

0

 

0

Total number of Characters : 985

 

 

 

Total number of Characters : 985

 

 

 

(Before) Protein Name: OR6K6

 

 

 

(After)Protein Name: OR6K6

 

occurrences

1

 

2

3

4

5

6

7

 

8

1

 

2

3

4

5

6

7

 

8

A

132

19

6

0

1

0

0

 

0

132

19

6

2

1

0

0

 

0

T

147

39

11

5

2

1

0

 

0

147

39

10

3

2

1

0

 

0

G

108

31

6

0

0

0

0

 

0

106

30

6

1

1

0

0

 

0

C

115

54

6

2

0

0

0

 

0

115

53

6

2

0

0

0

 

0

Total number of Characters : 942

 

 

 

Total number of Characters : 942

 

 

 

(Before) Protein Name: OR2T6

 

 

 

(After)Protein Name: OR2T6

 

occurrences

1

 

2

3

4

5

6

7

 

8

1

 

2

3

4

5

6

7

 

8

A

131

19

6

2

0

0

0

 

0

130

19

6

3

1

0

0

 

0

T

163

31

7

2

2

0

0

 

0

163

31

7

2

1

0

0

 

0

G

98

27

6

7

1

0

0

 

0

98

27

6

6

1

0

0

 

0

C

137

40

9

2

2

0

0

 

0

137

40

9

2

2

0

0

 

0

Total number of Characters : 942

 

 

 

Total number of Characters : 942

 

 

 

(Before) Protein Name: OR2G2

 

 

(After)Protein Name: OR2G2

 

occurrences

1

 

2

3

4

5

6

7

 

8

1

 

2

3

4

5

6

7

 

8

A

132

21

7

1

0

0

0

 

0

129

20

7

2

2

0

0

 

0

T

161

33

13

5

1

0

0

 

0

161

33

13

4

1

0

0

 

0

G

109

30

9

3

0

0

0

 

0

109

30

9

3

0

0

0

 

0

C

117

45

14

1

0

0

0

 

0

117

44

13

1

0

0

0

 

0

Total number of Characters : 970

 

 

 

Total number of Characters : 970

 

 

 

(Before) Protein Name: OR2T3

 

 

 

(After)Protein Name: OR2T3

 

occurrences

1

 

2

3

4

5

6

7

 

8

1

 

2

3

4

5

6

7

 

8

A

139

17

3

1

0

0

0

 

0

137

17

3

3

2

0

1

 

0

T

172

21

7

4

0

1

0

 

0

171

21

7

3

0

2

0

 

0

G

126

24

9

0

0

0

0

 

0

125

24

9

0

2

0

0

 

0

C

137

54

11

3

4

0

0

 

0

137

54

10

3

1

0

0

 

0

Total number of Characters : 973

 

 

 

Total number of Characters : 973

 

Table 3. Detail no. of nucleotides (A, T, C, and G) consecutively present before and after mutation occurs, along with total no. of nucleotides present in the given amino acid sequences.

 

 

(Before) Protein Name: OR6F1

 

 

 

(After)Protein Name: OR6F1

 

occurrences

1

 

2

3

4

5

6

7

8

1

 

2

3

4

5

6

7

8

A

128

14

7

2

0

0

0

0

128

14

7

2

0

0

0

0

T

157

31

10

4

1

0

0

0

157

31

10

4

1

0

0

0

G

113

34

5

1

0

0

0

0

111

33

5

1

1

0

0

1

C

142

42

7

3

2

0

0

0

142

42

7

2

1

0

0

0

Total number of Characters : 942

 

 

Total number of Characters : 942

 

 

 

(Before) Protein Name: OR10J1

 

 

(After)Protein Name: OR10J1

 

occurrences

1

 

2

3

4

5

6

7

8

1

 

2

3

4

5

6

7

8

A

142

27

5

1

0

0

0

0

141

27

5

3

0

0

0

0

T

152

39

6

4

1

1

0

0

152

39

6

2

1

1

0

0

G

121

22

7

0

1

0

0

0

120

22

7

0

2

0

0

0

C

130

38

9

2

1

0

0

0

130

38

8

2

1

0

0

0

Total number of Characters : 945

 

 

Total number of Characters : 945

 

 

 

(Before) Protein Name: OR10K2

 

 

(After)Protein Name: OR10K2

 

occurrences

1

 

2

3

4

5

6

7

8

1

 

2

3

4

5

6

7

8

A

125

23

4

1

0

0

0

0

124

23

4

2

0

0

0

0

T

171

45

13

1

2

0

0

0

171

45

12

1

1

0

0

0

G

100

21

8

1

0

0

0

0

100

21

8

1

1

0

0

0

C

142

47

7

2

0

0

0

0

142

47

7

2

0

0

0

0

Total number of Characters : 954

 

 

Total number of Characters : 954

 

 

 

(Before) Protein Name: OR6K2

 

 

 

(After)Protein Name: OR6K2

 

occurrences

1

 

2

3

4

5

6

7

8

1

 

2

3

4

5

6

7

8

A

144

20

4

1

0

1

0

0

144

20

4

1

0

1

0

0

T

156

48

17

4

0

0

1

0

156

48

16

3

0

0

1

0

G

123

26

3

0

0

0

0

0

123

26

4

2

0

0

0

0

C

132

43

7

3

1

0

0

0

132

43

7

2

1

0

0

0

Total number of Characters : 991

 

 

Total number of Characters : 991

 

 

(Before) Protein Name: OR5AX1

 

 

(After)Protein Name: OR5AX1

 

occurrences

1

 

2

3

4

5

6

7

8

1

 

2

3

4

5

6

7

8

A

130

30

6

2

0

0

0

0

130

30

6

2

1

0

0

0

T

155

45

15

5

4

0

0

0

155

45

15

5

2

0

0

0

G

98

30

2

1

0

0

0

0

97

30

2

1

0

1

0

0

C

118

40

7

1

0

0

0

0

118

40

7

1

1

0

0

0

Total number of Characters : 960

 

 

Total number of Characters : 960

 

 

 

(Before) Protein Name: OR5AY1

 

 

(After)Protein Name: OR5AY1

 

occurrences

1

 

2

3

4

5

6

7

8

1

 

2

3

4

5

6

7

8

A

127

23

5

1

0

0

0

0

126

22

5

2

0

0

0

1

T

177

41

10

3

2

0

0

0

177

41

10

3

1

0

0

0

G

135

21

4

4

0

0

0

0

135

21

4

3

0

0

0

0

C

138

39

3

1

1

0

0

0

138

39

3

1

1

0

0

0

Total number of Characters : 960

 

 

Total number of Characters : 960

 

 

 

(Before) Protein Name: OR2T1

 

 

 

(After)Protein Name: OR2T1

 

occurrences

1

 

2

3

4

5

6

7

8

1

 

2

3

4

5

6

7

8

A

139

21

7

0

0

0

0

0

139

21

7

1

0

0

0

0

T

144

41

13

2

1

0

0

0

144

41

13

2

1

0

0

0

G

110

27

9

5

0

0

0

0

110

27

9

3

1

0

0

0

C

118

51

11

0

2

0

0

0

118

51

11

1

1

0

0

0

Total number of Characters : 973

 

 

Total number of Characters : 973

 

 

 

(Before) Protein Name: OR1C1

 

 

 

(After)Protein Name: OR1C1

 

occurrences

1

 

2

3

4

5

6

7

8

1

 

2

3

4

5

6

7

8

A

134

22

2

1

0

1

0

0

133

22

3

1

1

1

0

0

T

166

37

13

3

1

0

0

0

166

37

11

2

1

0

0

0

G

122

22

4

2

0

0

0

0

122

22

4

2

0

0

0

0

C

145

43

4

3

1

1

0

0

145

43

5

3

1

1

0

0

Total number of Characters : 960

 

 

Total number of Characters : 960

 

 

 

(Before) Protein Name: OR2G3

 

 

(After)Protein Name: OR2G3

 

occurrences

1

 

2

3

4

5

6

7

8

1

 

2

3

4

5

6

7

8

A

122

28

9

1

0

0

0

0

122

28

9

1

0

0

0

0

T

154

38

12

3

1

1

0

0

154

38

11

2

1

1

0

0

G

84

37

6

0

0

0

0

0

84

37

6

1

1

0

0

0

C

138

38

7

2

2

0

0

0

138

38

8

2

1

0

0

0

Total number of Characters : 945

 

 

Total number of Characters : 945

 

 

 

(Before) Protein Name: OR6K3

 

 

 

(After)Protein Name: OR6K3

 

occurrences

1

 

2

3

4

5

6

7

8

1

 

2

3

4

5

6

7

8

A

140

25

4

3

1

1

0

0

140

25

4

2

1

1

0

0

T

148

45

12

5

1

0

0

0

148

45

12

4

1

0

0

0

G

104

28

2

1

0

0

0

0

104

27

2

1

0

1

0

0

C

132

38

11

1

0

1

0

0

130

38

11

1

0

2

0

0

Total number of Characters : 963

 

 

Total number of Characters : 963

 

 

 

(Before) Protein Name: OR2L2

 

 

 

(After)Protein Name: OR2L2

 

occurrences

1

 

2

3

4

5

6

7

8

1

 

2

3

4

5

6

7

8

A

144

25

6

4

0

0

0

0

144

25

6

3

1

0

0

0

T

158

41

10

2

3

1

0

0

158

41

9

2

1

1

0

0

G

107

19

5

1

1

0

0

0

107

18

6

1

1

1

0

0

C

129

38

9

2

0

0

0

0

129

38

9

2

1

0

0

0

Total number of Characters : 954

 

 

Total number of Characters : 954

 

Table 4. Fractal Dimension of 3D Structures Before and After Mutation of nucleotides (A, T, C, G) of the Protein Sequences

Protin Name

Fractal Value (Before)

Fractal Value After

Di erence

OR13G1

1.18132

1.06183

0.11949

OR10K1

1.04287

1.09353

0.05066

OR10T2

1.10484

1.16372

0.05888

OR10R2

1.16588

1.1053

0.06058

OR6Y1

1.07644

0.93621

0.14023

OR10K2

1.06859

1.12591

0.05732

OR2T1

1.21768

1.22402

0.00634

0R2T4

1.03177

1.14265

0.11088

OR2T5

1.20664

1.19132

0.01532

OR2T6

1.23737

1.20839

0.02898

OR6P1

1.11079

0.93621

0.17458

OR10Z1

1.12791

1.00266

0.12525

OR6K2

1.03983

1.05646

0.01663

OR6K3

1.04208

1.03747

0.00461

OR6K6

1.03636

0.93444

0.10192

OR6N1

1.10593

1.04295

0.06298

OR2L2

0.97866

1.20928

0.23062

OR6N2

1.20545

1.18611

0.01934

OR2L8

0.96544

0.98279

0.01735

OR5BF1

1.09345

1.06988

0.02357

OR5AX1

1.17028

1.14738

0.0229

OR5AY1

1.23445

1.17678

0.05767

OR2G2

1.14891

1.0137

0.13521

OR6F1

1.05202

1.07362

0.0216

OR2G3

1.06231

0.98389

0.07842

OR5AV1

1.02043

0.96039

0.06004

OR11L1

1.18718

1.04259

0.14459

OR10J1

1.1283

1.08652

0.04178

OR2T3

1.06912

0.98635

0.08277

OR1C1

1.0842

1.04096

0.04324

OR10J5

1.11492

1.17187

0.05695

Results

In this section, we have selected some of OR proteins through which we have studied the effect of local mutation in protein properties as stated above. We have given the accessible residue and alpha helix properties of OR2T6 amino acid sequence before and after mutation in Figures 1 and 2. We have also other amino acid sequences detail has given in Tables 1-3. We have evaluated their fractal dimension of each of its properties. We have given the 3D structure of OR2T6 sequence after and before mutation in Figure 3, also marked the changes in 3D structure of before and after mutation. We have also generated 3D structure of each of the amino acid sequence, and also evaluate the fractional dimension of each of the structures before and after mutation.

Figure 1. Protein Properties of OR2T6 protein sequence ORs

Figure 2. Edited Protein Properties of OR2T6 protein sequence ORs

Figure 3. Change in structure of OR2T6 protein sequence before and after mutation

Discussion

In the previous section a set of 32 OR sequences has been experimented through Fractal dimensional analysis. Mainly we are intended to observe the similarities or dissimilarities in the original and edited (mutated) OR sequences. We have found out the fractal dimension of the different graphs and their corresponding fractal dimension of the protein properties as mentioned earlier.

It is obvious that if the percentage of Accessible Residues (AR) is less than the percentage of Buried Residues (BR) must be higher as these two protein properties are complementary to each other. Accordingly, the other protein properties also get affected due to the decrement of percentage of AR in an OR protein. In other words, all such protein properties are interlinked for a protein. This particular detail has been wide-opened in the Table 1.

Here we have considered 13 OR sequences out of those 31 sequences for which a detail analysis has been made in the Tables 5 and 6.

Table 5. AR - Accessible residue BR- Buried residue Properties AA - Amino Acid AH - Alpha Helix properties

 

 

AR

 

 

BR

 

 

AH

 

 

AA

 

 

 

 

 

 

 

 

 

 

 

 

 

 

protein

A

B

R

A

B

R

A

B

R

A

B

R

 

 

 

 

 

 

 

 

 

 

 

 

 

OR10K1

1.94359

1.94361

B=A

1.94266

1.94331

B<A

1.9427

1.94318

B<A

1.94289

1.94358

B<A

OR10Z1

1.94373

1.94284

B>A

1.94281

1.9432

B<A

1.94253

1.94298

B<A

1.94331

1.94303

B>A

OR2G3

1.94264

1.94372

B<A

1.94283

1.94315

B<A

1.94266

1.94299

B<A

1.94247

1.94366

B<A

OR2T6

1.94346

1.9431    B>A

1.94263

1.94317

B<A

1.94314

1.94269

B<A

1.94324

1.94299

B>A

OR2T1

1.94293

1.9433    B<A

1.9426

1.94308

B>A

1.94179

1.94269

B<A

1.94325

1.9431

B<A

OR6N2

1.94274

1.9436    B<A

1.94265

1.94324

B<A

1.94367

1.94326

B>A

1.94284

1.94389

B<A

OR6P1

1.9431

1.94313

B=A

1.94232

1.94333

B<A

1.94303

1.94297

B=A

1.94215

1.94378

B<A

OR13G1

1.94248

1.94283

B<A

1.94251

1.9434    B<A

1.94319

1.94306

B<A

1.94325

1.94259

B>A

OR6K2

1.94279

1.94315

B<A

1.9424

1.94309

B<A

1.9431

1.94336

B<A

1.94282

1.94355

B<A

OR2T5

1.94302

1.94346

B<A

1.94248

1.94357

B<A

1.9427

1.9432

B<A

1.94292

1.94342

B<A

OR10J5

1.94305

1.94333

B<A

1.94182

1.94332

B<A

1.94294

1.94341

B<A

1.94331

1.9435

B<A

OR6Y1

1.94263

1.94321

B<A

1.94215

1.94283

B<A

1.94279

1.94317

B<A

1.94237

1.94334

B<A

OR1C1

1.94271

1.94321

B<A

1.94173

1.94304

B<A

1.94244

1.94273

B<A

1.94225

1.94333

B<A

 

 

 

 

 

 

 

 

 

 

 

 

 

Table 6. BS- Beta sheet BT-Beta turn HPC - Hydrophobicity coil, codon properties, and A, B , R used for After , Before and Result respectively

11

 

 

BS

 

 

BT

 

 

Coil

 

 

HPC

 

 

codons

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

protein

A

B

R

A

B

R

A

B

R

A

B

R

A

B

R

 

 

OR10K1

1.94326

1.94386

B<A

1.94292

1.94295

B=A

1.9447

1.94411

A>B

1.9428

1.94275

B<A

1.94279

1.94336

B<A

 

 

OR10Z1

1.94289

1.94243

B>A

1.94337

1.94271

B>A

1.94379

1.94409

B<A

1.94266

1.94276

B<A

1.94319

1.942298

B>A

 

 

OR2G3

1.94239

1.94389

B<A

1.94295

1.94247

B>A

1.94407

1.94395

B>A

1.94263

1.94239

B>A

1.94278

1.94331

B<A

 

 

OR2T6

1.94233

1.9439

B<A

1.94289

1.94252

B>A

1.94407

1.94398

B=A

1.94289

1.94305

B<A

1.94307

1.94279

B>A

 

 

OR2T1

1.94279

1.94307

B<A

1.94216

1.94254

B<A

1.94374

1.94401

B<A

1.94267

1.94299

B<A

1.94319

1.94302

B>A

 

 

OR6N2

1.94281

1.94385

B<A

1.94367

1.94291

B>A

1.94423

1.94408

B>A

1.943

1.94276

B>A

1.94238

1.94295

B<A

 

 

OR6P1

1.94243

1.94387

B<A

1.94305

1.94279

B>A

1.94407

1.94414

B<A

1.944266

1.94276

B<A

1.94231

1.94362

B<A

 

 

OR13G1

1.94236

1.94273

B<A

1.94336

1.94327

B>A

1.94409

1.94444

B<A

1.9425

1.94307

B>A

1.94359

1.94289

B>A

 

 

OR6K2

1.94289

1.94243

B>A

1.9427

1.94261

B>A

1.94379

1.94412

B<A

1.94253

1.94278

B<A

1.94284

1.94331

B<A

 

 

OR2T5

1.94287

1.9432

B<A

1.94303

1.94268

B>A

1.94407

1.94405

B=A

1.9428

1.94316

B<A

1.94242

1.94321

B<A

 

 

OR10J5

1.94231

1.94381

B<A

1.94289

1.9428

B=A

1.94417

1.944

B>A

1.94187

1.94323

B<A

1.94315

1.94352

B<A

 

 

OR6Y1

1.94273

1.94373

B<A

1.9426

1.94367

B>A

1.944

1.94389

B>A

1.94334

1.94281

B>A

1.94263

1.94281

B<A

 

 

OR1C1

1.94246

1.94389

B<A

1.94296

1.94256

B>A

1.94413

1.94408

B=A

1.94211

1.94259

B<A

1.94179

1.94361

B<A

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Let us illustrate the above fact by taking one example.

In case of OR2T6, the mutated sequence differs from the original OR2T6 in two positions at 539 and 772 of the sequence. The poly-string of 5Ts has been changed into 5As in the position 539 in the edited sequence and in position 772, 4Gs has been changed into 4As. Consequently the frequency of 1As is decreases by 1, 4As increased by 1, 5As increased by 1, 5Ts decreased by 1 and 4Gs decreased by 1 ,but the other frequencies of poly-strings has been remain unchanged even though the above changes in the poly-string frequencies of 5Ts and 4Gs.

As a result, the Fractal Dimension (FD) of the Accessible Residues (AR) in the mutated sequences is less than that of the original OR2T6. As a result, the FD of Buried Residues (BR) for the mutated OR2T6 is greater than that of the original, the FD of Alpha helix is greater than the and even after mutation the FD coil are almost same as it was in original OR2T6 whereas the FD of Amino Acid Composition (AA), Codon frequency (C) and Beta Turn (BT) of the mutated OR2T6 is less than that of the OR2T6. The FD of Beta Sheet and Hydrophobicity (HPC) is greater than that of the original OR2T6. Also the tertiary structures of the protein for the OR2T6 and corresponding edited sequence have been changed. The fractal dimension of those tertiary structure of proteins are 1:23737 and 1:20839 respectively.

Conclusion

In this study, we have considered a few OR sequences to understand the local mutation in the protein level. The detail account of poly-string frequencies have been made for each of the ORs and corresponding edited sequences. We then saw the effect of those local changes in poly-string frequency through the protein properties and tertiary structure of the protein of each of the ORs and edited sequences. As we illustrated through the example of OR2T 6 and its edited sequence in the discussion, we found that the edited sequence is almost same with the original OR2T 6 in the sense of ordering of the nucleotide bases except for the frequency change in case of 1As, 4As, 5As, 5Ts and 4Gs. Here we have found that the edited sequence of OR2T 6 is almost sequentially similar and also the tertiary structure is almost similar to the original tertiary structure of the protein OR2T6. Hence, it is our strong conviction that these kinds of mutation can be allowed in making the function of OR2T6 un-altered. Of course, the biological experiment is left to make us assured about its original functionality of OR2T6. Similar kind of analysis is also applicable for the other sequences in accordance with the change and their effect in protein properties and their tertiary structures.

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Editorial Information

Editor-in-Chief

Bianciardi Giorgio
University of Siena

Article Type

Research Article

Publication history

Received date: January 12, 2016
Accepted date: April 27, 2016
Published date: April 30, 2016

Copyright

© 2016 Dash SR. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Citation

Dash SR (2016) Quantitative deciphering of local mutation in protein structures of human olfactory receptors. Fractal Geometry and Nonlinear Anal in Med and Biol 1: DOI: 10.15761/FGNAMB.1000127.

Corresponding author

Satya Ranjan Dash

School of Computer Application, KIIT University, Bhubaneswar 751024, India.

E-mail : sdashfca@kiit.ac.in

Figure 1. Protein Properties of OR2T6 protein sequence ORs

Figure 2. Edited Protein Properties of OR2T6 protein sequence ORs

Figure 3. Change in structure of OR2T6 protein sequence before and after mutation

Table 1. Details of protein Sequence Mutation where in from column we have no. of consecutive current nucleotides and in to column no. of edited nucleotides along with their Position has mentioned.

 

Protein Name: OR10K1

Protein Name: OR6Y1

Protein Name: OR2T4

Edited

From

To

Position

From

To

Position

From

To

Position

 

1T

1G

34

4T

4G

557

4G

4C

841

 

1C

1G

7

4T

4C

106

4T

4A

644

 

3T

3A

83

 

 

 

 

 

 

 

Protein Name: OR1C1

Protein Name: OR2G2

Protein Name: OR2G3

Edited

From

To

Position

From

To

Position

From

To

Position

 

4T

4A

766

4T

4A

775

4T

4G

96

 

3T

3A

92

3C

3A

884

5C

5G

861

 

3T

3C

107

2C

2A

139

3T

3C

833

 

Protein Name: OR2L2

Protein Name: OR2L8

Protein Name: OR2T1

Edited

From

To

Position

From

To

Position

From

To

Position

 

5T

5A

147

4T

4G

344

4G

4C

126

 

5T

5C

606

2T

2G

9

4G

4A

287

 

4A

4G

5

2C

2G

9

5C

5G

485

 

Protein Name: OR2T3

Protein Name: OR2T5

Protein Name: OR2T6

Edited

From

To

Position

From

To

Position

From

To

Position

 

4T

4G

527

5T

5A

334

5T

5A

539

 

5C

5G

503

4C

4G

792

4G

4A

772

 

4C

4T

890

3C

3A

155

 

 

 

 

4C

4A

653

2C

2A

5

 

 

 

 

3C

3A

338

 

 

 

 

 

 

 

Protein Name: OR5AT1

Protein Name: OR5AV1P

Protein Name: OR5AX1

Edited

From

To

Position

From

To

Position

From

To

Position

 

5C

5G

851

5T

5G

144

5T

5G

533

 

5A

5T

56

3T

3C

60

5T

5A

719

 

4T

4A

636

3G

3C

20

 

 

 

 

3T

3C

760

 

 

 

 

 

 

 

3T

3A

177

 

 

 

 

 

 

 

3T

3G

303

 

 

 

 

 

 

 

2T

2G

536

 

 

 

 

 

 

 

Protein Name: OR5AY1

Protein Name: OR5BF1

Protein Name: OR6F1

Edited

From

To

Position

From

To

Position

From

To

Position

 

5T

5A

504

4T

4G

720

5C

5G

520

 

4G

4A

284

1C

1G

88

4C

4G

25

 

 

 

 

3T

3G

28

3T

3G

34

 

Protein Name: OR6K2

Protein Name: OR6K3

Protein Name: OR6K6

Edited

From

To

Position

From

To

Position

From

To

Position

 

4T

4G

759

4T

4C

96

4T

4G

823

 

4C

4G

878

4A

G

715

4T

4A

701

 

3T

3G

309

 

 

 

3T

3G

156

 

 

 

 

 

 

 

2C

2A

15

 

 

 

 

 

 

 

2G

2A

901

 

Protein Name: OR6N1

Protein Name: OR6N2

Protein Name: OR6P1

Edited

From

To

Position

From

To

Position

From

To

Position

 

3T

3G

427

4G

4A

680

4C

4T

555

 

4T

4A

608

4T

4C

726

5T

5C

491

 

4C

G

520

2T

2G

28

5T

5A

184

 

 

 

 

 

 

 

1C

1G

183

 

 

 

 

 

 

 

1T

1G

75

 

Protein Name: OR10J1

Protein Name: OR10J5

Protein Name: OR10K2

Edited

From

To

Position

From

To

Position

From

To

Position

 

4T

4G

38

5T

5G

629

5T

5G

725

 

4T

4A

722

4T

4A

249

3T

3A

280

 

3C

3A

78

3T

3G

880

 

 

 

 

Protein Name: OR10R2

Protein Name: OR10T2

Protein Name: OR10Z1

Edited

From

To

Position

From

To

Position

From

To

Position

 

4T

4G

753

5T

5C

316

4T

4A

497

 

4A

4C

187

4T

4G

229

4G

41

709

 

3T

3G

677

3T

3A

500

 

 

 

 

2T

2A

10

2C

2A

691

 

 

 

 

Protein Name: OR11L1

Protein Name: OR13G1

 

 

 

Edited

From

To

Position

From

To

Position

From

To

Position

 

4C

4A

403

4T

4C

170

 

 

 

 

3T

3G

90

3T

3A

634

 

 

 

 

2C

2A

626

2T

2A

402

 

 

 

Table 2.

 

 

(Before) Protein Name: OR10K1

 

 

(After)Protein Name: OR10K1

 

occurrences

1

 

2

3

4

5

6

7

 

8

1

 

2

3

4

5

6

7

 

8

A

116

28

4

0

1

0

0

 

0

116

29

4

0

1

0

0

 

0

T

172

41

13

1

0

0

0

 

0

173

40

12

1

0

0

0

 

0

G

98

23

5

1

0

0

0

 

0

98

24

5

1

0

0

0

 

0

C

138

54

12

2

0

0

0

 

0

138

54

12

2

0

0

0

 

0

Total number of Characters : 957

 

 

 

Total number of Characters : 957

 

 

 

(Before) Protein Name: OR6Y1

 

 

 

(After)Protein Name: OR6Y1

 

occurrences

1

 

2

3

4

5

6

7

 

8

1

 

2

3

4

5

6

7

 

8

A

145

25

5

1

0

0

0

 

0

145

25

5

1

0

0

0

 

0

T

164

39

10

4

1

1

0

 

0

164

39

10

2

1

1

0

 

0

G

107

29

4

2

0

0

0

 

0

107

29

4

3

0

0

0

 

0

C

143

56

6

1

0

0

0

 

0

143

55

6

1

0

1

0

 

0

Total number of Characters : 994

 

 

 

Total number of Characters : 994

 

 

 

(Before) Protein Name: OR2T4

 

 

 

(After)Protein Name: OR2T4

 

occurrences

1

 

2

3

4

5

6

7

 

8

1

 

2

3

4

5

6

7

 

8

A

142

24

3

0

2

0

0

 

0

141

24

3

0

3

0

0

 

0

T

189

26

9

2

3

0

0

 

0

189

26

9

1

3

0

0

 

0

G

104

33

9

0

1

0

0

 

0

104

33

9

1

1

0

0

 

0

C

129

60

6

4

1

0

0

 

0

129

60

6

3

1

0

0

 

0

Total number of Characters : 1009

 

 

 

Total number of Characters : 1009

 

 

 

(Before) Protein Name: OR10Z1

 

 

(After)Protein Name: OR10Z1

 

occurrences

1

 

2

3

4

5

6

7

 

8

1

 

2

3

4

5

6

7

 

8

A

138

14

3

0

0

0

0

 

0

136

14

3

0

2

0

0

 

0

T

162

39

8

4

0

0

1

 

0

162

39

8

3

0

0

1

 

0

G

106

24

10

3

0

0

1

 

0

106

24

10

2

0

0

1

 

0

C

129

53

8

1

1

1

0

 

0

129

53

8

1

1

1

0

 

0

Total number of Characters : 957

 

 

 

Total number of Characters : 957

 

 

 

(Before) Protein Name: OR6N2

 

 

 

(After)Protein Name: OR6N2

 

occurrences

1

 

2

3

4

5

6

7

 

8

1

 

2

3

4

5

6

7

 

8

A

129

30

6

1

1

0

0

 

0

129

30

6

1

1

0

0

 

0

T

155

45

14

4

1

0

0

 

0

155

44

14

4

1

0

0

 

0

G

104

29

4

2

0

0

0

 

0

103

29

5

1

0

0

0

 

0

C

135

44

6

1

0

0

0

 

0

134

44

6

1

0

0

0

 

0

Total number of Characters : 970

 

 

 

Total number of Characters : 970

 

 

 

(Before) Protein Name: OR5BF1

 

 

(After)Protein Name: OR5BF1

 

occurrences

1

 

2

3

4

5

6

7

 

8

1

 

2

3

4

5

6

7

 

8

A

135

21

4

2

0

0

0

 

0

135

21

4

2

0

0

0

 

0

T

165

35

11

4

1

1

0

 

1

165

35

10

3

1

1

0

 

1

G

103

32

3

0

1

0

0

 

0

104

32

4

1

1

0

0

 

0

C

140

40

9

2

0

0

0

 

0

139

40

9

2

0

0

0

 

0

Total number of Characters : 954

 

 

 

Total number of Characters : 954

 

 

(Before) Protein Name: OR5AV1P

 

 

(After)Protein Name: OR5AV1P

 

occurrences

1

 

2

3

4

5

6

7

 

8

1

 

2

3

4

5

6

7

 

8

A

128

26

4

1

1

0

0

 

0

128

26

4

1

1

0

0

 

0

T

149

40

10

3

5

1

0

 

0

149

40

9

3

4

1

0

 

0

G

96

26

6

1

0

0

0

 

0

96

26

5

1

0

1

0

 

0

C

110

32

3

3

1

1

0

 

0

110

32

5

3

1

1

0

 

0

Total number of Characters : 896

 

 

 

Total number of Characters : 896

 

 

 

(Before) Protein Name: OR5AT1

 

 

(After)Protein Name: OR5AT1

 

occurrences

1

 

2

3

4

5

6

7

 

8

1

 

2

3

4

5

6

7

 

8

A

124

24

8

1

2

0

0

 

0

122

24

8

2

2

0

0

 

0

T

148

48

20

5

0

0

0

 

0

146

47

17

4

0

0

1

 

0

G

102

21

3

3

0

0

0

 

0

101

22

4

3

0

1

0

 

0

C

133

33

5

1

2

0

0

 

0

132

32

5

1

1

1

0

 

0

Total number of Characters : 945

 

 

 

Total number of Characters : 945

 

 

 

(Before) Protein Name: OR11L1

 

 

(After)Protein Name: OR11L1

 

occurrences

1

 

2

3

4

5

6

7

 

8

1

 

2

3

4

5

6

7

 

8

A

126

19

6

1

0

0

0

 

0

125

20

6

1

1

0

0

 

0

T

164

35

11

3

0

0

1

 

0

165

35

11

2

0

0

1

 

0

G

111

33

5

3

0

0

0

 

0

111

33

6

3

0

0

0

 

0

C

126

60

8

5

0

0

0

 

0

126

59

8

4

0

0

0

 

0

Total number of Characters : 985

 

 

 

Total number of Characters : 985

 

 

 

(Before) Protein Name: OR6K6

 

 

 

(After)Protein Name: OR6K6

 

occurrences

1

 

2

3

4

5

6

7

 

8

1

 

2

3

4

5

6

7

 

8

A

132

19

6

0

1

0

0

 

0

132

19

6

2

1

0

0

 

0

T

147

39

11

5

2

1

0

 

0

147

39

10

3

2

1

0

 

0

G

108

31

6

0

0

0

0

 

0

106

30

6

1

1

0

0

 

0

C

115

54

6

2

0

0

0

 

0

115

53

6

2

0

0

0

 

0

Total number of Characters : 942

 

 

 

Total number of Characters : 942

 

 

 

(Before) Protein Name: OR2T6

 

 

 

(After)Protein Name: OR2T6

 

occurrences

1

 

2

3

4

5

6

7

 

8

1

 

2

3

4

5

6

7

 

8

A

131

19

6

2

0

0

0

 

0

130

19

6

3

1

0

0

 

0

T

163

31

7

2

2

0

0

 

0

163

31

7

2

1

0

0

 

0

G

98

27

6

7

1

0

0

 

0

98

27

6

6

1

0

0

 

0

C

137

40

9

2

2

0

0

 

0

137

40

9

2

2

0

0

 

0

Total number of Characters : 942

 

 

 

Total number of Characters : 942

 

 

 

(Before) Protein Name: OR2G2

 

 

(After)Protein Name: OR2G2

 

occurrences

1

 

2

3

4

5

6

7

 

8

1

 

2

3

4

5

6

7

 

8

A

132

21

7

1

0

0

0

 

0

129

20

7

2

2

0

0

 

0

T

161

33

13

5

1

0

0

 

0

161

33

13

4

1

0

0

 

0

G

109

30

9

3

0

0

0

 

0

109

30

9

3

0

0

0

 

0

C

117

45

14

1

0

0

0

 

0

117

44

13

1

0

0

0

 

0

Total number of Characters : 970

 

 

 

Total number of Characters : 970

 

 

 

(Before) Protein Name: OR2T3

 

 

 

(After)Protein Name: OR2T3

 

occurrences

1

 

2

3

4

5

6

7

 

8

1

 

2

3

4

5

6

7

 

8

A

139

17

3

1

0

0

0

 

0

137

17

3

3

2

0

1

 

0

T

172

21

7

4

0

1

0

 

0

171

21

7

3

0

2

0

 

0

G

126

24

9

0

0

0

0

 

0

125

24

9

0

2

0

0

 

0

C

137

54

11

3

4

0

0

 

0

137

54

10

3

1

0

0

 

0

Total number of Characters : 973

 

 

 

Total number of Characters : 973

 

Table 3. Detail no. of nucleotides (A, T, C, and G) consecutively present before and after mutation occurs, along with total no. of nucleotides present in the given amino acid sequences.

 

 

(Before) Protein Name: OR6F1

 

 

 

(After)Protein Name: OR6F1

 

occurrences

1

 

2

3

4

5

6

7

8

1

 

2

3

4

5

6

7

8

A

128

14

7

2

0

0

0

0

128

14

7

2

0

0

0

0

T

157

31

10

4

1

0

0

0

157

31

10

4

1

0

0

0

G

113

34

5

1

0

0

0

0

111

33

5

1

1

0

0

1

C

142

42

7

3

2

0

0

0

142

42

7

2

1

0

0

0

Total number of Characters : 942

 

 

Total number of Characters : 942

 

 

 

(Before) Protein Name: OR10J1

 

 

(After)Protein Name: OR10J1

 

occurrences

1

 

2

3

4

5

6

7

8

1

 

2

3

4

5

6

7

8

A

142

27

5

1

0

0

0

0

141

27

5

3

0

0

0

0

T

152

39

6

4

1

1

0

0

152

39

6

2

1

1

0

0

G

121

22

7

0

1

0

0

0

120

22

7

0

2

0

0

0

C

130

38

9

2

1

0

0

0

130

38

8

2

1

0

0

0

Total number of Characters : 945

 

 

Total number of Characters : 945

 

 

 

(Before) Protein Name: OR10K2

 

 

(After)Protein Name: OR10K2

 

occurrences

1

 

2

3

4

5

6

7

8

1

 

2

3

4

5

6

7

8

A

125

23

4

1

0

0

0

0

124

23

4

2

0

0

0

0

T

171

45

13

1

2

0

0

0

171

45

12

1

1

0

0

0

G

100

21

8

1

0

0

0

0

100

21

8

1

1

0

0

0

C

142

47

7

2

0

0

0

0

142

47

7

2

0

0

0

0

Total number of Characters : 954

 

 

Total number of Characters : 954

 

 

 

(Before) Protein Name: OR6K2

 

 

 

(After)Protein Name: OR6K2

 

occurrences

1

 

2

3

4

5

6

7

8

1

 

2

3

4

5

6

7

8

A

144

20

4

1

0

1

0

0

144

20

4

1

0

1

0

0

T

156

48

17

4

0

0

1

0

156

48

16

3

0

0

1

0

G

123

26

3

0

0

0

0

0

123

26

4

2

0

0

0

0

C

132

43

7

3

1

0

0

0

132

43

7

2

1

0

0

0

Total number of Characters : 991

 

 

Total number of Characters : 991

 

 

(Before) Protein Name: OR5AX1

 

 

(After)Protein Name: OR5AX1

 

occurrences

1

 

2

3

4

5

6

7

8

1

 

2

3

4

5

6

7

8

A

130

30

6

2

0

0

0

0

130

30

6

2

1

0

0

0

T

155

45

15

5

4

0

0

0

155

45

15

5

2

0

0

0

G

98

30

2

1

0

0

0

0

97

30

2

1

0

1

0

0

C

118

40

7

1

0

0

0

0

118

40

7

1

1

0

0

0

Total number of Characters : 960

 

 

Total number of Characters : 960

 

 

 

(Before) Protein Name: OR5AY1

 

 

(After)Protein Name: OR5AY1

 

occurrences

1

 

2

3

4

5

6

7

8

1

 

2

3

4

5

6

7

8

A

127

23

5

1

0

0

0

0

126

22

5

2

0

0

0

1

T

177

41

10

3

2

0

0

0

177

41

10

3

1

0

0

0

G

135

21

4

4

0

0

0

0

135

21

4

3

0

0

0

0

C

138

39

3

1

1

0

0

0

138

39

3

1

1

0

0

0

Total number of Characters : 960

 

 

Total number of Characters : 960

 

 

 

(Before) Protein Name: OR2T1

 

 

 

(After)Protein Name: OR2T1

 

occurrences

1

 

2

3

4

5

6

7

8

1

 

2

3

4

5

6

7

8

A

139

21

7

0

0

0

0

0

139

21

7

1

0

0

0

0

T

144

41

13

2

1

0

0

0

144

41

13

2

1

0

0

0

G

110

27

9

5

0

0

0

0

110

27

9

3

1

0

0

0

C

118

51

11

0

2

0

0

0

118

51

11

1

1

0

0

0

Total number of Characters : 973

 

 

Total number of Characters : 973

 

 

 

(Before) Protein Name: OR1C1

 

 

 

(After)Protein Name: OR1C1

 

occurrences

1

 

2

3

4

5

6

7

8

1

 

2

3

4

5

6

7

8

A

134

22

2

1

0

1

0

0

133

22

3

1

1

1

0

0

T

166

37

13

3

1

0

0

0

166

37

11

2

1

0

0

0

G

122

22

4

2

0

0

0

0

122

22

4

2

0

0

0

0

C

145

43

4

3

1

1

0

0

145

43

5

3

1

1

0

0

Total number of Characters : 960

 

 

Total number of Characters : 960

 

 

 

(Before) Protein Name: OR2G3

 

 

(After)Protein Name: OR2G3

 

occurrences

1

 

2

3

4

5

6

7

8

1

 

2

3

4

5

6

7

8

A

122

28

9

1

0

0

0

0

122

28

9

1

0

0

0

0

T

154

38

12

3

1

1

0

0

154

38

11

2

1

1

0

0

G

84

37

6

0

0

0

0

0

84

37

6

1

1

0

0

0

C

138

38

7

2

2

0

0

0

138

38

8

2

1

0

0

0

Total number of Characters : 945

 

 

Total number of Characters : 945

 

 

 

(Before) Protein Name: OR6K3

 

 

 

(After)Protein Name: OR6K3

 

occurrences

1

 

2

3

4

5

6

7

8

1

 

2

3

4

5

6

7

8

A

140

25

4

3

1

1

0

0

140

25

4

2

1

1

0

0

T

148

45

12

5

1

0

0

0

148

45

12

4

1

0

0

0

G

104

28

2

1

0

0

0

0

104

27

2

1

0

1

0

0

C

132

38

11

1

0

1

0

0

130

38

11

1

0

2

0

0

Total number of Characters : 963

 

 

Total number of Characters : 963

 

 

 

(Before) Protein Name: OR2L2

 

 

 

(After)Protein Name: OR2L2

 

occurrences

1

 

2

3

4

5

6

7

8

1

 

2

3

4

5

6

7

8

A

144

25

6

4

0

0

0

0

144

25

6

3

1

0

0

0

T

158

41

10

2

3

1

0

0

158

41

9

2

1

1

0

0

G

107

19

5

1

1

0

0

0

107

18

6

1

1

1

0

0

C

129

38

9

2

0

0

0

0

129

38

9

2

1

0

0

0

Total number of Characters : 954

 

 

Total number of Characters : 954

 

Table 4. Fractal Dimension of 3D Structures Before and After Mutation of nucleotides (A, T, C, G) of the Protein Sequences

Protin Name

Fractal Value (Before)

Fractal Value After

Di erence

OR13G1

1.18132

1.06183

0.11949

OR10K1

1.04287

1.09353

0.05066

OR10T2

1.10484

1.16372

0.05888

OR10R2

1.16588

1.1053

0.06058

OR6Y1

1.07644

0.93621

0.14023

OR10K2

1.06859

1.12591

0.05732

OR2T1

1.21768

1.22402

0.00634

0R2T4

1.03177

1.14265

0.11088

OR2T5

1.20664

1.19132

0.01532

OR2T6

1.23737

1.20839

0.02898

OR6P1

1.11079

0.93621

0.17458

OR10Z1

1.12791

1.00266

0.12525

OR6K2

1.03983

1.05646

0.01663

OR6K3

1.04208

1.03747

0.00461

OR6K6

1.03636

0.93444

0.10192

OR6N1

1.10593

1.04295

0.06298

OR2L2

0.97866

1.20928

0.23062

OR6N2

1.20545

1.18611

0.01934

OR2L8

0.96544

0.98279

0.01735

OR5BF1

1.09345

1.06988

0.02357

OR5AX1

1.17028

1.14738

0.0229

OR5AY1

1.23445

1.17678

0.05767

OR2G2

1.14891

1.0137

0.13521

OR6F1

1.05202

1.07362

0.0216

OR2G3

1.06231

0.98389

0.07842

OR5AV1

1.02043

0.96039

0.06004

OR11L1

1.18718

1.04259

0.14459

OR10J1

1.1283

1.08652

0.04178

OR2T3

1.06912

0.98635

0.08277

OR1C1

1.0842

1.04096

0.04324

OR10J5

1.11492

1.17187

0.05695

Table 5. AR - Accessible residue BR- Buried residue Properties AA - Amino Acid AH - Alpha Helix properties

 

 

AR

 

 

BR

 

 

AH

 

 

AA

 

 

 

 

 

 

 

 

 

 

 

 

 

 

protein

A

B

R

A

B

R

A

B

R

A

B

R

 

 

 

 

 

 

 

 

 

 

 

 

 

OR10K1

1.94359

1.94361

B=A

1.94266

1.94331

B<A

1.9427

1.94318

B<A

1.94289

1.94358

B<A

OR10Z1

1.94373

1.94284

B>A

1.94281

1.9432

B<A

1.94253

1.94298

B<A

1.94331

1.94303

B>A

OR2G3

1.94264

1.94372

B<A

1.94283

1.94315

B<A

1.94266

1.94299

B<A

1.94247

1.94366

B<A

OR2T6

1.94346

1.9431    B>A

1.94263

1.94317

B<A

1.94314

1.94269

B<A

1.94324

1.94299

B>A

OR2T1

1.94293

1.9433    B<A

1.9426

1.94308

B>A

1.94179

1.94269

B<A

1.94325

1.9431

B<A

OR6N2

1.94274

1.9436    B<A

1.94265

1.94324

B<A

1.94367

1.94326

B>A

1.94284

1.94389

B<A

OR6P1

1.9431

1.94313

B=A

1.94232

1.94333

B<A

1.94303

1.94297

B=A

1.94215

1.94378

B<A

OR13G1

1.94248

1.94283

B<A

1.94251

1.9434    B<A

1.94319

1.94306

B<A

1.94325

1.94259

B>A

OR6K2

1.94279

1.94315

B<A

1.9424

1.94309

B<A

1.9431

1.94336

B<A

1.94282

1.94355

B<A

OR2T5

1.94302

1.94346

B<A

1.94248

1.94357

B<A

1.9427

1.9432

B<A

1.94292

1.94342

B<A

OR10J5

1.94305

1.94333

B<A

1.94182

1.94332

B<A

1.94294

1.94341

B<A

1.94331

1.9435

B<A

OR6Y1

1.94263

1.94321

B<A

1.94215

1.94283

B<A

1.94279

1.94317

B<A

1.94237

1.94334

B<A

OR1C1

1.94271

1.94321

B<A

1.94173

1.94304

B<A

1.94244

1.94273

B<A

1.94225

1.94333

B<A

 

 

 

 

 

 

 

 

 

 

 

 

 

Table 6. BS- Beta sheet BT-Beta turn HPC - Hydrophobicity coil, codon properties, and A, B , R used for After , Before and Result respectively

11

 

 

BS

 

 

BT

 

 

Coil

 

 

HPC

 

 

codons

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

protein

A

B

R

A

B

R

A

B

R

A

B

R

A

B

R

 

 

OR10K1

1.94326

1.94386

B<A

1.94292

1.94295

B=A

1.9447

1.94411

A>B

1.9428

1.94275

B<A

1.94279

1.94336

B<A

 

 

OR10Z1

1.94289

1.94243

B>A

1.94337

1.94271

B>A

1.94379

1.94409

B<A

1.94266

1.94276

B<A

1.94319

1.942298

B>A

 

 

OR2G3

1.94239

1.94389

B<A

1.94295

1.94247

B>A

1.94407

1.94395

B>A

1.94263

1.94239

B>A

1.94278

1.94331

B<A

 

 

OR2T6

1.94233

1.9439

B<A

1.94289

1.94252

B>A

1.94407

1.94398

B=A

1.94289

1.94305

B<A

1.94307

1.94279

B>A

 

 

OR2T1

1.94279

1.94307

B<A

1.94216

1.94254

B<A

1.94374

1.94401

B<A

1.94267

1.94299

B<A

1.94319

1.94302

B>A

 

 

OR6N2

1.94281

1.94385

B<A

1.94367

1.94291

B>A

1.94423

1.94408

B>A

1.943

1.94276

B>A

1.94238

1.94295

B<A

 

 

OR6P1

1.94243

1.94387

B<A

1.94305

1.94279

B>A

1.94407

1.94414

B<A

1.944266

1.94276

B<A

1.94231

1.94362

B<A

 

 

OR13G1

1.94236

1.94273

B<A

1.94336

1.94327

B>A

1.94409

1.94444

B<A

1.9425

1.94307

B>A

1.94359

1.94289

B>A

 

 

OR6K2

1.94289

1.94243

B>A

1.9427

1.94261

B>A

1.94379

1.94412

B<A

1.94253

1.94278

B<A

1.94284

1.94331

B<A

 

 

OR2T5

1.94287

1.9432

B<A

1.94303

1.94268

B>A

1.94407

1.94405

B=A

1.9428

1.94316

B<A

1.94242

1.94321

B<A

 

 

OR10J5

1.94231

1.94381

B<A

1.94289

1.9428

B=A

1.94417

1.944

B>A

1.94187

1.94323

B<A

1.94315

1.94352

B<A

 

 

OR6Y1

1.94273

1.94373

B<A

1.9426

1.94367

B>A

1.944

1.94389

B>A

1.94334

1.94281

B>A

1.94263

1.94281

B<A

 

 

OR1C1

1.94246

1.94389

B<A

1.94296

1.94256

B>A

1.94413

1.94408

B=A

1.94211

1.94259

B<A

1.94179

1.94361

B<A