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Title

Insights from the analysis of conserved motifs and permitted amino acid exchanges in the human, the fly and the worm GPCR clusters

 

Authors

Balasubramanian Nagarathnam1, Sankar Kannan2, Varadhan Dharnidharka3, Veluchamy Balakrishnan4, Govindaraju Archunan5, Ramanathan Sowdhamini1*

 

Affiliation

1National Center for Biological Sciences (TIFR), UAS-GKVK Campus, Bellary Road, Bangalore 560 065, India; 2Birla Institute of Technology and Science, Pilani, India; 3R.V. College of Engineering, Mysore Road, Bangalore, India; presently in : Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, USA; 4Department of Biotechnology, K. S. Rangasamy College of Technology, KSR. Kalvi Nagar, Tiruchengode - 637215, Tamilnadu, India; 5Department of Animal Science, Bharathidasan University Trichirapalli, Tamil Nadu, 620 024, India

 

Email

mini@ncbs.res.in; *Corresponding author

 

Phone

+91-080-23666001

 

Fax

+91-080-23636421

 

Article Type

Hypothesis

 

Date

Received August 05, 2011; Accepted August 08, 2011; Published August 20, 2011

 

Abstract

G-protein coupled receptors (GPCRs) belong to biologically important and functionally diverse and largest super family of membrane proteins. GPCRs retain a characteristic membrane topology of seven alpha helices with three intracellular, three extracellular loops and flanking Ní and Cí terminal residues. Subtle differences do exist in the helix boundaries (TM-domain), loop lengths, sequence features such as conserved motifs, amino acid patterns and their physiochemical properties amongst these sequences (clusters) at intra-genomic and inter-genomic level. In the current study, we employ prediction of helix boundaries and scores derived from amino acid substitution exchange matrices to identify the conserved amino acid residues (motifs) as consensus in aligned set of homologous GPCR sequences. Co-clustered GPCRs from human and other genomes, organized as 32 clusters, were employed to study the amino acid conservation patterns and species-specific or cluster-specific motifs. Critical analysis on sequence composition and properties provide clues to connect functional relevance within and across genome for vast practical applications such as design of mutations and understanding of disease-causing genetic abnormalities.

 

Keywords

Transmembrane Helices, Membrane Topology, Amino acid conservation and substitutions, GPCR cluster association.

 

Citation

Nagarathnam et al. Bioinformation 7(1): 15-20 (2011)
 

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

Copyright

Publisher

 

Copyright Transfer Agreement

The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes.

 

License

This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.