title: Homology modeling and protein engineering of alkane monooxygenase in Burkholderia thailandensis MSMB121: in silico insights.
abstract: The degradation of hydrocarbons plays an important role in the eco-balancing of petroleum products, pesticides and other toxic products in the environment. The degradation of hydrocarbons by microbes such as Geobacillus thermodenitrificans, Burkhulderia, Gordonia sp. and Acinetobacter sp. has been studied intensively in the literature. The present study focused on the in silico protein engineering of alkane monooxygenase (ladA)-a protein involved in the alkane degradation pathway. We demonstrated the improvement in substrate binding energy with engineered ladA in Burkholderia thailandensis MSMB121. We identified an ortholog of ladA monooxygenase found in B. thailandensis MSMB121, and showed it to be an enzyme involved in an alkane degradation pathway studied extensively in Geobacillus thermodenitrificans. Homology modeling of the three-dimensional structure of ladA was performed with a crystal structure (protein databank ID: 3B9N) as a template in MODELLER 9v11, and further validated using PROCHECK, VERIFY-3D and WHATIF tools. Specific amino acids were substituted in the region corresponding to amino acids 305-370 of ladA protein, resulting in an enhancement of binding energy in different alkane chain molecules as compared to wild protein structures in the docking experiments. The substrate binding energy with the protein was calculated using Vina (Implemented in VEGAZZ). Molecular dynamics simulations were performed to study the dynamics of different alkane chain molecules inside the binding pockets of wild and mutated ladA. Here, we hypothesize an improvement in binding energies and accessibility of substrates towards engineered ladA enzyme, which could be further facilitated for wet laboratory-based experiments for validation of the alkane degradation pathway in this organism.
authors.affiliation: Department of Biotechnology, Jaypee Institute of Information Technology, A-10, Sector-62, NOIDA, Uttar Pradesh, 201307, India, ckj522@yahoo.com.
authors.forename: Chakresh Kumar
authors.initials: CK
authors.lastname: Jain
authors.forename: Money
authors.initials: M
authors.lastname: Gupta
authors.forename: Yamuna
authors.initials: Y
authors.lastname: Prasad
authors.forename: Gulshan
authors.initials: G
authors.lastname: Wadhwa
authors.forename: Sanjeev Kumar
authors.initials: SK
authors.lastname: Sharma
mesh_terms: D000473:Alkanes / Q000378:metabolism*; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D001665:Binding Sites; D019117:Burkholderia / Q000201:enzymology* / Q000235:genetics; D003460:Crystallization; D030562:Databases, Protein; D006899:Mixed Function Oxygenases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009154:Mutation; D011485:Protein Binding; D011487:Protein Conformation; D015202:Protein Engineering; D017385:Sequence Homology; D013329:Structure-Activity Relationship; D013379:Substrate Specificity
chemical_list: D000473:Alkanes; D001426:Bacterial Proteins; D006899:Mixed Function Oxygenases