Analysis and comparison of lignin peroxidases between fungi and bacteria using three different modes of Chou's general pseudo amino acid composition.
Lignin peroxidases (LiPs) are important enzymes in the degradation process of lignin which are presented in different species of fungi and bacteria. In the present study, sequence and structure-based properties of LPs in fungi and bacteria are compared. These properties include pseudo amino acid composition (PseAAC), physicochemical properties and the secondary structure. Autodock 4 has been used for docking between LiPs and lignan. The motifs of LiP were predicted by MEME tool. Statistical analysis and Multinomial Naïve Bayes (MNB) algorithm were used for the classification of two LiP protein groups. The results demonstrated that molecular weight, isoelectric point, aliphatic, extinction coefficient and random coil percentage of LiPs in fungi and bacteria were significantly different between these two groups. The classification of these two groups based on the concept of PseAAC showed over 80% accuracy. The binding free energy between bacterial LiPs and lignan is significantly more than fungi LiP and ligand. The aliphatic and instability of most important motifs of bacteria and fungi were significantly different. In conclusion, the results indicated that computational techniques could provide useful information for comparing fungal and bacterial LiPs. These results can also explain that there is a relationship between efficacy and physicochemical properties of LiPs.
Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran.
Mandana
M
Behbahani
Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran. Electronic address: h.mohabatkar@ast.ui.ac.ir.
Hassan
H
Mohabatkar
Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan, Isfahan, Iran.
Mokhtar
M
Nosrati
D020816:Amino Acid Motifs / Q000235:genetics; D000596:Amino Acids / Q000737:chemistry / Q000235:genetics*; D001419:Bacteria / Q000201:enzymology / Q000235:genetics; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D005656:Fungal Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D005658:Fungi / Q000201:enzymology / Q000235:genetics; D008957:Models, Genetic; D010544:Peroxidases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D011485:Protein Binding; D017433:Protein Structure, Secondary
D000596:Amino Acids; D001426:Bacterial Proteins; D005656:Fungal Proteins; D010544:Peroxidases; C042858:lignin peroxidase
Binary classification; Bioremediation; Lignin peroxidase