Structural insights into the camel milk lactoperoxidase: Homology modeling and molecular dynamics simulation studies

Ishfaq A. Sheikh*, Essam H. Jiffri, Ghulam Md Ashraf, Mohammad A. Kamal

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

9 Citations (Scopus)

Abstract

Lactoperoxodase (LPO) is a heme peroxidase enzyme present in mammalian milk. It is an antimicrobial protein with wide range of industrial applications. Although the three dimensional structure of LPO from various mammalian species has been reported, but its structure from camel source is still unknown. So far, the crystallization attempts have not been successful in determining camel LPO (cLPO) structure. Herein, we developed the three dimensional structure of cLPO by homology modeling approach using prime module available in Schrodinger suite. The developed model in complex with ligand hypothiocyanate (OSCN) was further validated by Ramachandran plot followed by molecular dynamics (MD) simulation studies using Desmond module of Schrodinger. cLPO model exhibited overall structural similarity with template crystal structure, however, it displayed different interaction pattern of amino acid residues with ligand OSCN in comparison to template crystal structure. Moreover, the ligand binding site environment in cLPO is more polar, less hydrophobic, and harbours more number of charged residues than template crystal structure. The substrate binding pocket environment of cLPO shows a considerable difference from template crystal structure. This subsequently resulted in dissimilar behaviour of ligand during the course of MD simulation studies.

Original languageEnglish
Pages (from-to)43-51
Number of pages9
JournalJournal of Molecular Graphics and Modelling
Volume86
DOIs
Publication statusPublished - Jan 2019
Externally publishedYes

Keywords

  • Camel lactoperoxidase
  • Homology modeling
  • Molecular dynamics
  • Substrate binding site
  • Three dimensional structure

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