Homology Modeling of Bacteriocins: From sequence alignments to structural models

Pranita Atri, Dipankar Sengupta, Sachi Verma, Sadaf Ali , Gargi Dey*

*Corresponding author for this work

Research output: Contribution to journalArticle

Abstract

Structural and functional characterizations of proteins have been one of the major problems in biological studies for a long time. The conventional methods of protein structure determination of NMR and X-Ray crystallography, though more accurate, are highly time consuming and tedious to carry out. Also, the instrumentation required is not that easily available. In the absence of proper structural information, like in the case of bacteriocins, which are anti-microbial proteins or protein complexes produced by lactic acid bacteria, comparative and homology modeling can be useful in predicting the structure based on the protein sequences and their alignment with one or more already known structures. The prediction process consists of fold assignment, target–template alignment, model building, and model evaluation. The present study focuses on the comparative protein-structure modelling of bacteriocins produced by five food starter cultures viz., Pediococcus acidilactici, Leuconostoc mesenteroids, Enterococcus mundtii, Lactobacillus plantarum and Lactobacillus sakei. The structures were modelled using MOE software and accuracy was evaluated based on the “errat” score.
All the bacteriocins belonged to Class IIA subclass with same structural motif. The results of the present study will find its application in the develepoment of synthetic bacteriocins especially in the absence of structural information of such proteins.
Original languageEnglish
Pages (from-to)123-126
Number of pages4
JournalInternational Journal of Scientific & Engineering Research
Volume5
Issue number5
Publication statusPublished - 05 May 2014

Keywords

  • Bacteriocins
  • Peptides
  • Homology modelling
  • MoE
  • Errat

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