Molecular docking simulation of Aspergillus flavus AlmA like protein binding with long chain alkanes (C16-C40)

Abstract

Introduction: AlmA is a bacterial enzyme known to initiate the degradation of long-chain alkanes. Although efficient degradation of alkanes has been observed in fungi, their mechanisms and the enzymes involved are poorly understood. The objective of this study was to identify the binding capability of AlmA like protein in A.flavus using in-silico methods. Methods: A putative AlmA homolog protein sequence similar to the Acinetobacter sp. was identified from Aspergillus flavus and its 3D structure was modelled and validated using bioinformatics techniques. The 3D structures of Alkanes and the cofactors required for AlmA (FAD and NADP), were optimised using Orca Version 4.2.1 and molecules were docked stepwise using AutoDock Vina 1.2.0. The cofactors were initially docked on to the AlmA. The AlmA homolog bound to co-factors were then docked with alkanes (C16-C40). The RMSD value and binding affinity of molecules were evaluated. Hydrophobic interactions and docking site analysis of the A. flavus AlmA like protein and AlmA of Acinetobacter sp. were conducted using Chimera, Protein Ligand Interaction Profiler (PLIP), and ProteinsPlus and results were compared and analysed for ubiquity of similar interactions.