Beta endorphin is a neurotransmitter and is involved in functions like enhancement of immune system, deceleration of cancer cell growth and induction of euphoria and relaxation. It is an opioid like neuropeptide synthesized in neurons of hypothalamus and pituitary gland. The study of its structure and its interaction with opioid receptors can throw light on its neuropsychopharmacology. Protein data bank does not contain the structural information of beta endorphin and mu opioid receptor. Hence, in the present study, we aimed at predicting their three dimensional structures. Owing to homologues with low sequence identity and unsatisfactory results from threading methods, we resorted to ab initio modelling. Quark algorithm was used for beta endorphin structure prediction. The structure of mu opioid receptor was modelled by I TASSER simulations. The quality of the protein models were evaluated with PROCHECK server. Functionally important regions in beta endorphin were located using ConSurf web server. Docking studies were performed on beta endorphin with three opioid receptors mu, kappa and gamma to anticipate residues important for binding.
Key words: Ab initio modelling, homology, docking, beta endorphin, opioid receptors, threading, QUARK, PROCHECK, AUTODOCK, template, binding sites.
ACTH, Adrenocorticotropic hormone; CASP, critical assessment of techniques for protein structure prediction; GRAMM, global range molecular matching; JCSG, joint centre for structural genomics; NCBI, National Centre for Biotechnology Information; PDB, protein data bank;PSI Blast, position specific iterated blast; RMS, root mean square distance.
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