Journal of Environmental Biology

Protein characterization and sequence analysis of ALLCE

antimicrobial peptide from Allium cepa 

Raid Al Akeel¹, Ayesha Mateen²*, V.C. Gupta² and K. Janardhan³

 ¹Department of Clinical Laboratory Sciences, College of Applied Medical Sciences.King Saud University, Riaydh, Saudi Arabia

²Central Research Institute for Unani Medicine, Opp. Employees' State Insurance, Hyderabad, India

³P.G. Department of Biotechnology, A.V. College, Hyderabad, India

*Corresponding Author E-mail: ayeshamateen@gmail.com

Publication Data

Paper received:

11 June 2015

Revised received:

14 September 2015

Re-revised received:

07 October 2015

Accepted:

28 October 2015

Abstract

Antimicrobial proteins/peptides produced by plant seeds participate in protection of seeds against pathogenic organisms. A study was carried out to investigate the in silico analysis of protein sequence localization, structure, homology modeling and 3D structure prediction of ALLCE-AMP in Allium cepa.? Primary structure prediction and physico-chemical characterization were performed by computing theoretical isoelectric point (pI), molecular weight, total number of positive and negative residues, extinction coefficient, instability index, aliphatic index and grand average hydropathy (GRAVY). In the present study, homology modeling, a high quality of peptide 3D structure, was predicted by submitting the peptide sequence (target) to ESYPred3D web server. The template (1T12 chain A) was found to share 18.2% identity with the Query (B2CZN8). The model was validated using protein structure checking tools PROCHECK and ERRAT VALUE (62.353). The present study would be useful in studying protein-protein interactions and drug designing.       

 Key words

Allium cepa, ALLCE-AMP, PROCHECK, Structure prediction, Subcellular localization

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