Analysis of Dopamine D2 Receptor with Multiple Sequence Alignment

This project presents a Multiple Sequence Alignment (MSA) analysis of the Dopamine D2 receptor. The student utilizes the ClustalW tool to align multiple sequences, including the D2 receptor and its associated partners from the STRING database. The analysis involves setting parameters like gap p...Read More

Multiple Sequence Alignment (MSA) of Mutated Dopamine D2 receptor in Human
Multiple sequence Alignment is use to align more than two sequences for finding phylogenetic relation
among them. Many tools are available like ClustalW and Clustal omega[1 ] Here I take Dopamine D2
receptor sequence [2] from Genbank as query along with their highly associated partners from STRING
database. After that I perform MSA through ClustalW tool by applying some parametes like Gap
penalities (gap-open: 15 and gap extension:6.66) for optimal alignment [3].
Number of input sequences :4 (given in file)
Aligned score among all sequence are shown below:
Sequences (1:2) Aligned-Score: 19.1296
Sequences (1:3) Aligned-Score: 19.9215
Sequences (1:4) Aligned-Score: 20.1722
Sequences (2:3) Aligned-Score: 19.2561
Sequences (2:4) Aligned-Score: 20.8249
Sequences (3:4) Aligned-Score: 18.8602
Dendogram tree:
(
(
NC_000011.10_c113475279-113409595:0.39743,
NM_001160226.1:0.40336)
:0.01019,
NM_001044.4:0.39749,
NM_001128826.1:0.39426)
Rooted Phylogenetic tree with branch length generated.
Analysis: From result of MSA ,I found that DRD2 (Dopamine D2 receptor) sequence is very much
nearest to SLC6A3(Sodium-dependent dopamine transporter; Amine transporter); terminate the action of
dopamine by its high-affinity metal-dependent uptake into the presynaptic vessels and
D2DR(Cannabinoid receptor 1; G-protein coupled receptor ) have aligning score of 19.12696 and

19.9215 respectively. To find evolutionary relation between them Phylogenetic tree are drawn and shown
in above figure by their accession numbers; how these genes are linked to each other evolutionarly.
References:
1. Sievers, Fabian, Andreas Wilm, David Dineen, Toby J. Gibson, Kevin Karplus, Weizhong Li, Rodrigo
Lopez et al. "Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal
Omega." Molecular systems biology 7, no. 1 (2011): 539.
2. Gluskin, B. S., and B. J. Mickey. "Genetic variation and dopamine D2 receptor availability: a systematic
review and meta-analysis of human in vivo molecular imaging studies." Translational psychiatry 6, no. 3
(2016): e747.
3. Bawono, Punto, Maurits Dijkstra, Walter Pirovano, Anton Feenstra, Sanne Abeln, and Jaap Heringa.
"Multiple sequence alignment." In Bioinformatics, pp. 167-189. Humana Press, New York, NY, 2017.