Prediction of the three-dimensional structure of aflatoxin of Aspergillus flavus by homology modelling.

Aruna Kasoju,Charuvaka Muvva,M Lakshmi Narasu,Bathula V V Subbarao

doi:10.6026/97320630008684

Abstract

Aflatoxins are polyketide-derived secondary metabolites produced by Aspergillus spp. The toxic effects of aflatoxins have adverse consequences for human health and agricultural economics. The aflR gene, a regulatory gene for aflatoxin biosynthesis, encodes a protein containing a zinc-finger DNA-binding motif. AFLR-Protein three-dimensional model was generated using Robetta server. The modeled AFLR-Protein was further optimization and validation using Rampage. In the simulations, we monitored the backbone atoms and the C-α-helix of the modeled protein. The low RMSD and the simulation time indicate that, as expected, the 3D structural model of AFLR-protein represents a stable folding conformation. This study paves the way for generating computer molecular models for proteins whose crystal structures are not available and which would aid in detailed molecular mechanism of inhibition of aflatoxin.

Highlights

Aflatoxins are a group of mycotoxins with potent toxicity and carcinogenicity toward mammals
They are produced by some strains of Aspergillus flavus, Aspergillus parasiticus, Aspergillus nomius and Aspergillus tamarii and they can be found as contaminants in a wide variety of food and feed commodities
The constructed model was further validated by Ramachandran plot

Summary

Background

Aflatoxins are a group of mycotoxins with potent toxicity and carcinogenicity toward mammals. 3D-Structure of AFLR-Protein was performed using Robetta Server. Methodology: Sequence retrieval alignment and Protein structure prediction: 3D-Structure of AFLR-Protein was performed using Robetta Server. Geometric evaluations of the modeled 3D structure were performed using Rampage [7] by calculating the Ramachandran plot (Figure 2). The RMSD values of the modeled structure’s backbone atoms were plotted as a time-dependent function of the MD simulation. The time dependence of the RMSD of the backbone atoms of the modeled protein during a 10 ns simulation is shown in (Figure 3). The low RMSD and the simulation time indicate that, as expected, the 3D structural model of AFLR-protein represents a stable folding. Q-Site Finder [9] server was used to predict the structure based protein functional site

Discussion

Findings

Conclusion