Title: Mining amino acid association patterns in class B GPCRs

Authors: Tannu Kumari; Kamal Raj Pardasani

Addresses: Department of Bioinformatics, MANIT - Maulana Azad National Institute of Technology, Bhopal 462051, India ' Department of Mathematics, MANIT - Maulana Azad National Institute of Technology, Bhopal 462051, India

Abstract: Class B GPCR family is a small group of receptors which are activated by peptides of intermediate length that range from 30 to 40 amino acid residues including hormones, neuropeptides and autocrine factors that mediate diverse physiological functions. They are involved in physiological processes like glucose homeostasis (glucagon and glucagon-like peptide-1), calcium homeostasis and bone turnover (parathyroid hormone and calcitonin), and control of the stress axis (corticotropin-releasing factor). Most of the GPCR structures and their functions are still unknown. Thus, the study of amino acid association patterns can be useful in prediction of their structure and functions. In view of above, in this paper, an attempt has been made to explore amino acid association patterns in class B GPCRs and their relationships with secondary structures and physiochemical properties. The fuzzy association rule mining is employed to take care of uncertainty due to variation in length of sequences. The association rules have been generated with the help of patterns discovered in the sequences.

Keywords: GPCR; G-protein coupled receptors; extracellular loop; intracellular loop; cys-cysteine; fuzzy ARM; association rule mining; secretin; parathyroid hormone; N-frequent patterns; amino acids; association patterns; sequencing; bioinformatics.

DOI: 10.1504/IJBRA.2015.069193

International Journal of Bioinformatics Research and Applications, 2015 Vol.11 No.3, pp.219 - 232

Accepted: 03 Mar 2014
Published online: 05 May 2015 *

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