Homology modeling and docking studies of a Δ9-fatty acid desaturase from a Cold-tolerant Pseudomonas sp. AMS8

Lawal Garba; Mohamad Ariff Mohamad Yussoff; Khairul Bariyyah Abd Halim; Siti Nor Hasmah Ishak; Mohd Shukuri Mohamad Ali; Siti Nurbaya Oslan; Raja Noor Zaliha Raja Abd Rahman

doi:10.7717/peerj.4347

Homology modeling and docking studies of a Δ9-fatty acid desaturase from a Cold-tolerant Pseudomonas sp. AMS8

PeerJ. 2018 Mar 19:6:e4347. doi: 10.7717/peerj.4347. eCollection 2018.

Authors

Lawal Garba^{1

2

3}, Mohamad Ariff Mohamad Yussoff⁴, Khairul Bariyyah Abd Halim⁴, Siti Nor Hasmah Ishak¹, Mohd Shukuri Mohamad Ali^{1

5}, Siti Nurbaya Oslan^{1

5}, Raja Noor Zaliha Raja Abd Rahman^{1

2}

Affiliations

¹ Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.
² Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.
³ Department of Microbiology, Faculty of Science, Gombe State University, Gombe, Gombe State, Nigeria.
⁴ Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia, Kuantan, Pahang Darul Makmur, Malaysia.
⁵ Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.

Abstract

Membrane-bound fatty acid desaturases perform oxygenated desaturation reactions to insert double bonds within fatty acyl chains in regioselective and stereoselective manners. The Δ9-fatty acid desaturase strictly creates the first double bond between C9 and 10 positions of most saturated substrates. As the three-dimensional structures of the bacterial membrane fatty acid desaturases are not available, relevant information about the enzymes are derived from their amino acid sequences, site-directed mutagenesis and domain swapping in similar membrane-bound desaturases. The cold-tolerant Pseudomonas sp. AMS8 was found to produce high amount of monounsaturated fatty acids at low temperature. Subsequently, an active Δ9-fatty acid desaturase was isolated and functionally expressed in Escherichia coli. In this paper we report homology modeling and docking studies of a Δ9-fatty acid desaturase from a Cold-tolerant Pseudomonas sp. AMS8 for the first time to the best of our knowledge. Three dimensional structure of the enzyme was built using MODELLER version 9.18 using a suitable template. The protein model contained the three conserved-histidine residues typical for all membrane-bound desaturase catalytic activity. The structure was subjected to energy minimization and checked for correctness using Ramachandran plots and ERRAT, which showed a good quality model of 91.6 and 65.0%, respectively. The protein model was used to preform MD simulation and docking of palmitic acid using CHARMM36 force field in GROMACS Version 5 and Autodock tool Version 4.2, respectively. The docking simulation with the lowest binding energy, -6.8 kcal/mol had a number of residues in close contact with the docked palmitic acid namely, Ile26, Tyr95, Val179, Gly180, Pro64, Glu203, His34, His206, His71, Arg182, Thr85, Lys98 and His177. Interestingly, among the binding residues are His34, His71 and His206 from the first, second, and third conserved histidine motif, respectively, which constitute the active site of the enzyme. The results obtained are in compliance with the in vivo activity of the Δ9-fatty acid desaturase on the membrane phospholipids.

Keywords: Cold-tolerant Pseudomonas sp. AMS8; Homology modeling; Molecular docking; Palmitic acid; δ9-fatty acid desaturase.

Grants and funding

The research was funded by the Putra grant, Universiti Putra Malaysia (GP-IPS/2016/9471000), FRGS2015-207-0448 and FRGS2015-208-0449. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.