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Paper Title
Analysing Amino Acids in Galanin Graph Theoretical Approach
Authors
Suresh Singh G., Akhil C. K.
Abstract
Graph theoretical analysis is an important area of the research in biological networks. Here first we introduce Pt-graph of peptide/protein based on physicochemical properties and adjacency of amino acids in the corresponding peptide/protein. Based on the Pt-graph, we introduce the graph of species which containing the peptide/protein named as SPt-graph. Finally, we analyze graph theoretically Pt-graphs of fourteen species of animals containing Galanin, a neuropeptide and their SPt-graph. From the graph theoretical analyses of Pt-graph and SPt-graph we get some observations about the relations among the amino acids, physicochemical properties of amino acids, peptide/protein and species containing peptide/protein and it may help in the field of evolution of peptide/protein and drug design in future.
Keywords
Amino acid, Galanin, Graph, Pt-graph, SPt-graph, biological networks
Citation/Export
MLA
Suresh Singh G., Akhil C. K., “Analysing Amino Acids in Galanin Graph Theoretical Approach”, June 17 Volume 5 Issue 6 , International Journal on Recent and Innovation Trends in Computing and Communication (IJRITCC), ISSN: 2321-8169, PP: 342 – 346
APA
Suresh Singh G., Akhil C. K., June 17 Volume 5 Issue 6, “Analysing Amino Acids in Galanin Graph Theoretical Approach”, International Journal on Recent and Innovation Trends in Computing and Communication (IJRITCC), ISSN: 2321-8169, PP: 342 – 346

Paper Title
Analysing Amino Acids in Galanin Graph Theoretical Approach
Authors
Suresh Singh G., Akhil C. K.
Abstract
Graph theoretical analysis is an important area of the research in biological networks. Here first we introduce Pt-graph of peptide/protein based on physicochemical properties and adjacency of amino acids in the corresponding peptide/protein. Based on the Pt-graph, we introduce the graph of species which containing the peptide/protein named as SPt-graph. Finally, we analyze graph theoretically Pt-graphs of fourteen species of animals containing Galanin, a neuropeptide and their SPt-graph. From the graph theoretical analyses of Pt-graph and SPt-graph we get some observations about the relations among the amino acids, physicochemical properties of amino acids, peptide/protein and species containing peptide/protein and it may help in the field of evolution of peptide/protein and drug design in future.
Keywords
Amino acid, Galanin, Graph, Pt-graph, SPt-graph, biological networks
Citation/Export
MLA
Suresh Singh G., Akhil C. K., “Analysing Amino Acids in Galanin Graph Theoretical Approach”, June 17 Volume 5 Issue 6 , International Journal on Recent and Innovation Trends in Computing and Communication (IJRITCC), ISSN: 2321-8169, PP: 342 – 346
APA
Suresh Singh G., Akhil C. K., June 17 Volume 5 Issue 6, “Analysing Amino Acids in Galanin Graph Theoretical Approach”, International Journal on Recent and Innovation Trends in Computing and Communication (IJRITCC), ISSN: 2321-8169, PP: 342 – 346

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_______________________________________________________________________________________________

Analysing Amino Acids in Galanin

Graph Theoretical Approach

Department of Mathematics Department of Mathematics

University of Kerala, Kariavattom, University of Kerala, Kariavattom,

Thiruvananthapuram 695581, Kerala, India, Thiruvananthapuram 695581, Kerala, India,

E-mail: sureshsinghg@yahoo.co.in E-mail: redakhil87@gmail.com

Abstract Graph theoretical analysis is an important area of the research in biological networks. Here first we introduce Pt-graph of

peptide/protein based on physicochemical properties and adjacency of amino acids in the corresponding peptide/protein. Based on the Pt-graph,

we introduce the graph of species which containing the peptide/protein named as SPt-graph. Finally, we analyze graph theoretically Pt-graphs of

fourteen species of animals containing Galanin, a neuropeptide and their SPt-graph. From the graph theoretical analyses of Pt-graph and SPt-

graph we get some observations about the relations among the amino acids, physicochemical properties of amino acids, peptide/protein and

species containing peptide/protein and it may help in the field of evolution of peptide/protein and drug design in future.

Keywords- Amino acid, Galanin, Graph, Pt-graph, SPt-graph, biological networks.

__________________________________________________*****_________________________________________________

observations about the relations among the amino acids,

I. INTRODUCTION physicochemical properties of amino acids, peptide/protein

Proteins [3] are the most abundant biological and species containing peptide/protein and it may help in the

macromolecules, occurring in all cells and all parts of cells. field of evolution of peptide/proteins and drug design in

Their building blocks are called amino acids and they are future.

organic compounds which contain at least one amino group (-

NH2) and a carboxyl (-COOH) group. They have some II. BASIC CONCEPTS OF GRAPH THEORY

physicochemical properties [1] (Hydrophobicity,

Hydrophilicity, Polarity, Non-polarity, Aliphaticity, A Graph [5] is a pair = (, ) consisting of a finite set

Aromaticity and Charge (Positive and Negative)). The V of vertices and a set of 2-element subsets of . The

sequence of amino acids [3] in a protein is characteristic of elements of are called vertices [5] and elements of are

that protein and is called its primary structure. called edges [5]. The set is known as the vertex set of and

Peptides/proteins are the compounds of amino acids in which a as the edge set of . Two vertices and of are said to

carboxyl group of one is united with an amino group of be adjacent [5], if an edge join and , and two edges are

another. Neuropeptides are peptides formed and released by adjacent if they have common vertex.

neurons.They are often localized in axon terminals at synapses 2.1. Centralities in Graphs [2]. In graph theory, centrality

and are classified as putative neurotransmitters, although some measure of a vertex represents its relative importance within

are also hormones. the graph. A centrality is a real-valued function on the vertices

Galanin [6] is a peptide widely distributed in the central of a graph. More formally a centrality is a function which

and peripheral nervous systems and the endocrine system. It assigns every vertex of a given graph a value

was first identified from porcine intestinal extracts in 1978 by () . In the following we have discussed four most

Professor Viktor Mutt and colleagues at the Karolinska commonly used centrality measures.

Institute, Sweden. It is a peptide consisting of a chain of 2.1.1. Degree of Centrality [2]. The most simple centrality

29 amino acids (30 amino acids in humans). Galanin is so- measure is degree of centrality, (). It is defined as the

called because it contains an N-terminal glycine residue and a number of vertices to which the vertex is directly connected.

C-terminal alanine. The vertices directly connected to a given vertex are also

Graph theory [5] has so many applications in biology. called first neighbours of the given vertex. Degree centrality

Amino acid network [4] with in protein was studied by S. shows that an important vertex is involved in a large number

Kundu. Graph theoretic approach to analyze amino acid of interactions. The interaction gives the immediate

network [1] was studied by Adil Akthar and Nisha Gohan. importance or risk of the vertex in the corresponding network.

Centralities in amino acid networks [2] were used by Adil Mathematically it is defined as

Akhtar and Tazid Ali. By using the concept of amino acid = deg . (1)

network we define new graphs called Pt-graph and SPt-graph However in real world problem the degree of centrality is not

of peptide/protein. Here we analyze graph theoretically Pt- an actual measurement for finding important vertex may be

graphs of fourteen species of animals containing Galanin, a connected indirectly with other vertices.

neuropeptide and their SPt-graph. Finally, we get some

342

IJRITCC | June 2017, Available @ http://www.ijritcc.org

_______________________________________________________________________________________

International Journal on Recent and Innovation Trends in Computing and Communication ISSN: 2321-8169

Volume: 5 Issue: 6 342 346

_______________________________________________________________________________________________

2.1.2. Eigenvector Centrality [2]. Another important III. Pt-GRAPH AND SPt-GRAPH OF PEPTIDES/

measure of centrality is eigenvector centrality. An eigenvalue PROTEINS

of a square matrix is a value for which ( ) =

0 , where is the identity matrix of the same order as . In the amino acid network [1], a vertex set was defined as

Eigenvector centrality is defined as the principal eigenvector collection of all twenty natural amino acids and the edge set is

of the adjacency matrix of corresponding graph. In matrix- defined as the connection between two amino acids having at

vector notation we can write least one (two in another case) common properties. Using the

= , (2) concepts of amino acid networks we define a new graph called

where is the adjacency matrix of the graph, is a constant Pt-graph of peptide/protein.

(the eigenvalue), and is the eigenvector. In general, there

will be different eigenvalues for which an eigenvector Definition 3.1: A Pt-graph is defined as a graph =

solution exists. However eigenvector of the greatest (, ) of a peptide/protein in which the vertex set, is the

eigenvalue is the eigenvector centrality. Eigenvector centrality collection of all different amino acids presented in the

gives the direct as well as indirect importance of a vertex in a peptide/protein and weight of a vertex in is the number of

network. times it appears in the sequence of the peptide/protein. Two

2.1.3. Closeness Centrality [2]. The closeness centrality is vertices are said to be adjacent in if they are consecutive

the idea how a vertex is close to all other vertices not only to elements in the sequence and also have at least one common

the first neighbor but also in global scale. Generally a vertex is physicochemical property.

central; then it is close to all other vertices. If a vertex is close

to other vertices, then it can quickly interact with all other Remark 3.2: Weight of a vertex implies the frequency of

vertices. In general closeness centrality is defined as the occurrence of a specific amino acid in a sequence. Obviously

inverse of the sum of the shortest path distances between each greater the weight of a vertex of a Pt-graph implies greater the

vertex and every other vertex in the network. The closeness characteristics of those particular amino acid can be attributed

centrality of a vertex depicts an important vertex that can to the peptide/protein.

easily reach or communicate with other vertex of the network.

Mathematically it is defined as Remark 3.3: Centrality Measures of a Pt-graph help us to

( 1) identify the quantity of related amino acids by direct or

= , (3)

(, ) indirect with neighbor amino acids in the sequence of

where is the number of vertices of the network and (, ) corresponding peptide/protein which shares at least one

is the shortest path distance between the pair of vertices and common physicochemical property.

. From the above definition it is clear that if a vertex has

minimum cumulative shortest path distance, then that vertex Definition 3.3: SPt-graph is a graph derived from the Pt-

has maximum closeness centrality. And maximum closeness graphs of a peptide/protein. It is defined as a graph = (, )

centrality vertex is very well connected to all other verties. of a peptide/protein in which the vertex set, V is the collection

2.1.4. Betweenness Centrality [2]. Another well-known of species containing the given peptide/protein. Two vertices

centrality measure is the betweenness centrality. Betweenness 1 and 2 in SPt-graph are said to be adjacent if in both Pt-

centrality interactions between two nonadjacent vertices graphs of species, the highest value of at least one centrality

depend on the other vertex, generally on those on the paths measures must be received by the same vertex.

between the two. The betweenness centrality of a vertex is

the number of shortest paths going through . Mathematically IV. GRAPH THEORETICAL ANALYSIS OF Pt-

it is defined as GRAPH AND SPt-GRAPH OF GALANIN

()

= , (4)

Here we construct and analyze graph theoretically the Pt-

graph and SPt-graph of Galanin. For the construction, we

where is the number of shortest paths from vertex to

consider fourteen species of animals. They are American

and () is the number of shortest paths from to that pass

alligator (Alligator mississipiensis), Bowfin (Amia calva),

through . Betweenness centrality depicts identifying vertices

Brown rat (Rattus norvegicus), House mouse (Mus

that make most information flow of the network. An important

musculus), Cattle (Bos Taurus), Ciona intestinalis (Ciona

vertex will lie on a large number of paths between other

intestinalis), Human (Homo sapiens), Japanese quail

vertices in the network. From this vertex we can control the

(Coturnix japonica), Red junglefowl (Gallus gallus), Marsh

information of the network. Without these vertices, there

frog (Pelophylax ridibundus), Rainbow trout (Oncorhynchus

would be no way for two neighbors to communicate with each

mykiss), Sheep (Ovis aries), Small-spotted catshark

other. In general the high degree vertex has high betweenness

(Scyliorhinus canicula) and Wild boar (Sus scrofa). Table 1

centrality because many of the shortest paths may pass through

gives the amino acid sequences of Galanin in fourteen

that vertex. However a high betweenness centrality vertex

species of animals.

need not always be high degree vertex.

343

IJRITCC | June 2017, Available @ http://www.ijritcc.org

_______________________________________________________________________________________

International Journal on Recent and Innovation Trends in Computing and Communication ISSN: 2321-8169

Volume: 5 Issue: 6 342 346

_______________________________________________________________________________________________

Table 1: Amino acid sequences of Galanin contained in Table 2: Amino acids and corresponding centrality measures

fourteen species of animals of Pt-graph of Galanin of Human

Different species Amino acid sequences Centrality measures

Amino Closeness Betweeness Eigenvector

GWTLN SAGYL LGPHA Degree

1 American alligator Acids Centrality Centrality Centrality

IDNHR SFNEK HGIA

GWTLN SAGYL LGPHA 5 7 0.58 31.83 1

2 Bowfin 2 3 0.52 8.5 0.58

VDNHR SLNDK HGLA

GWTLN SAGYL LGPHA 1 2 0.44 0 0.42

3 Cattle

LDSHR SFQDK HGLA 1 2 0.45 1.33 0.40

4 Ciona intestinalis

GWTLN SAGYL LGPHA 4 4 0.52 7 0.75

IDSHR SLGDK RGVA 1 1 0.37 0 0.20

GWTLN SAGYL LGPHA 1 1 0.37 0 0.27

5 Japanese quail

VDNHR SFNDK HGFT

1 2 0.4 0 0.47

GWTLN SAGYL LGPHA

6 Red junglefowl

VDNHR SFNDK HGFT 4 6 0.58 34.67 0.74

GWTLN SAGYL LGPHA 2 3 0.48 7 0.51

7 Human 3 5 0.61 28.33 0.84

VGNHR SFSDK NGLTS

GWTLN SAGYL LGPHA 1 2 0.40 2 0.29

8 House mouse 1

IDNHR SFSDK HGLT 2 0.41 2.17 0.31

GWTLN SAGYL LGPHG 2 2 0.41 2.17 0.31

9 Rainbow trout

IDGHR TLSDK HGLA 1 2 0.40 2 0.30

GWTLN SAGYL LGPHA

10 Sheep

IDNHR SFHDK HGLA By proceeding like this we can construct all Pt-graphs

GWTLN SAGYL LGPHA

11 Marsh frog of Galanin in fourteen species of animals. Table 3 represents

IDNHR SFNDK HGLA

the vertices which receive the highest values of centrality

GWTLN SAGYL LGPHA

12 Brown rat measures of Pt-graphs of Galanin.

IDNHR SFSDK HGLT

Small-spotted GWTNL SAGYL LGPHA

13 Table 3: Vertices which receive the highest value of centrality

catshark VDNHR SLNDK HGLA

GWTLN SAGYL LGPHA measure for Pt-graphs

14 Wild boar

IDNHR SFHDK YGLA Centrality Measures

Species Degree Closeness Betweeness Eigenvector

By using the sequences of Galanin we construct fourteen American

Pt-graphs of species of animals. For the construction we 1 4 ,3 3 3 4

alligator

consider the Pt-graph of Galanin of Human as an example.

2 Bowfin 5 5 5 5

Here the amino acids 5 , 2 , 1 , 1 , 4 , 1 , 1 , 1 , 4 , 2 , 3 , 1 ,

1 , 2 and 1 are the vertices. Table 2 represents the amino 3 Brown rat 4 , 4 2 , 3 3 4

acids and corresponding centrality measures of Pt-graph of

4 House mouse 4 , 4 2 , 3 3 4

Galanin of Human.

5 Cattle 3 3 3 3

Ciona

6 5 5 5 5

intestinalis

7 Human 5 3 4 5

8 Japanese quail 4 , 3 3 , 2 3 3

Red

9 4 , 3 3 , 2 3 3

junglefowl

10 Marsh frog 4 4 3 3

11 Rainbow trout 6 , 5 6 6 5

12 Sheep 4 4 4 4

Small-spotted

13 4 , 5 5 5 5

catshark

14 Wild boar 4 , 4 4 4 4

Galanin we get some observations.

value of degree centrality for American alligator, Japanease

Fig 1: Pt-graph of Galanin of Human quail and Red junglefowl are same having the same weight.

(that is 4 and 3 ).

344

IJRITCC | June 2017, Available @ http://www.ijritcc.org

_______________________________________________________________________________________

International Journal on Recent and Innovation Trends in Computing and Communication ISSN: 2321-8169

Volume: 5 Issue: 6 342 346

_______________________________________________________________________________________________

Observation 4.2: The amino acids which receive the highest

value of degree centrality for Brown rat, House mouse and

wild boar are same having the same weight. (that is 4 and

4 ).

value of degree centrality for Ciona intestinalis and Human are

same having the same weight. (that is 5 ).

value of degree centrality for Marsh frog and Sheep are same

having the same weight. (that is 4 ).

value of closeness centrality for American alligator and

Human are same having the same weight. (that is 3 ).

value of closeness centrality for Bowfin, Marsh frog, Sheep,

Small-spotted catshark and Wild boar are same (that is ).

Fig 2: SPt-graph of Galanin of fourteen species of animals

Observation 4.7: The amino acids which receive the highest

value of closeness centrality for Ciona intestinalis and Table 4: Species and corresponding centrality measures of

Rainbow trout are same (that is ). SPt-graph of Galanin

Centrality Measures

Observation 4.8: The amino acids which receive the highest Label Species Degree Closeness Betweeness Eigenvector

value of betweenness centrality for American alligator, American

Japanese quail, Red junglefowl and Marsh frog are same 1 12 0.93 2.09 0.95

alligator

having the same weight (that is 3 ). 2 Bowfin 7 0.68 0.09 0.59

3 Brown rat 13 1 3.31 1

Observation 4.9: The amino acids which receive the highest

4 House mouse 13 1 3.31 1

value of betweenness centrality for Bowfin, Sheep, Small-

5 Cattle 4 0.59 0 0.34

spotted catshark and Wild boar are same (that is ).

Ciona

6 11 0.87 0.09 0.92

intestinalis

Observation 4.10: The amino acids which receive the highest

value of betweenness centrality for Brown rat, House mouse 7 Human 12 0.93 2.09 0.95

and Cattle are same having same weight (that is 3 ). 8

Japanese

11 0.87 0.09 0.92

quail

Red

Observation 4.11: The amino acids which receive the highest 9 11 0.87 0.09 0.92

junglefowl

value of Eigenvector centrality for American alligator, Ciona 10 Marsh frog 12 0.93 0.81 0.97

intestinalis and Human are same (that is ). Rainbow

11 12 0.93 0.81 0.97

trout

Observation 4.12: The amino acid which receive the highest 12 Sheep 12 0.93 0.81 0.97

value of all centrality measures for Bowfin is and that for Small-

Cattle is . 13 spotted 11 0.87 0.71 0.90

catshark

Next we construct and analyze graph theoretically the 14 Wild boar 12 0.87 0.71 0.90

SPt-graph of Galanin from fourteen Pt-graphs of Galanin.

Here the vertices of SPt-graphs are the fourteen species of

From the graph theoretical analyses of SPt-graph of

animals containing Galanin. Table 4 represents the species of

Galanin we get some observations.

animals and corresponding centrality measures of SPt-graph of

Galanin.

Observation 4.13: Brown rat and House mouse receive the

same value of amino acids having highest among all the

centrality measures in SPt-graph of Galanin.

receive the same amino acids which have the same values for

all centrality measures in SPt-graph of Galanin.

345

IJRITCC | June 2017, Available @ http://www.ijritcc.org

_______________________________________________________________________________________

International Journal on Recent and Innovation Trends in Computing and Communication ISSN: 2321-8169

Volume: 5 Issue: 6 342 346

_______________________________________________________________________________________________

REFERENCES

[1] Adil Akhtar and Nisha Gohain, Graph theoretic

approach to analyze amino acid network, Int. J. Adv.

Appl. Math. And Mech. 2(3) (2015) 31-37.

[2] Adil Akhtar and Tazid Ali, Analysis of Unweighted

Amino Acids Network, Hindawi Publishing

Corporation, Vol. 2014, Article ID 350276 (2014) 6

pages.

[3] David L. Nelson and Michael M. Cox, Lehninger

Principles of Biochemistry, W. H Freeman and

Company (2008).

[4] S. Kundu, Amino acid network with in protein,

Physica A, 346 (2005) 104-109.

[5] G. Suresh Singh, Graph Theory, PHI Learning Private

Limited (2010).

[6] Yang Wang, Mingnia Wang, Sanwen Yin, Richard

Jang, Jian Wang, Zhidong Xue and Tao Xu,

Neoropep: a comprehensive Resource of

Neuropeptides, Database (Oxford) 2015 Apr 29.

doi:10.1093/ database/ bar038.

346

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