title: Functional analysis of the binding model of microbial inulinases using docking and molecular dynamics simulation.
abstract: Recently inulinase has regained interest due to its usage in the production of fructooligosaccharides, biofuels, and in pharmaceutical industries. Inulinases properties are experimentally reported by nomerous studies but their characteristics are just partially explained by only a few computational investigations. In the present study we have investigated exoinulinase and endoinulinase from different microbial sources toward their catalytic activity. Docking and molecular dynamic (MD) simulation were carried out for microbial endoinulinase and exoinulinase docked with 1-kestose and fructose-6-phosphate respectively. Pseudomonas mucidolens (-7.42 kcal mol(-1) binding energy), docked with fructose-6-phosphate, was recorded as the most favorable binding energy, Pseudomonas mucidolens made hydrogen bonds with fructose-6-phosphate and the amino acids involved were arginine 286, tryptophan 158, and isoleucine 87. After the simulation only tryptophan 158 remained bonded and additionally valine 156 made hydrogen bonds with fructose-6-phosphate. Aspergillus niger docked with 1-kestose was bonded with the involvement of threonine 271, aspartate 285, threonine 288, and proline 283, after the simulation aspartate 285 was retained till the end of the simulation. The present study thus refers to the indication of depicting binding analysis of microbial inulinases.
authors.affiliation: Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India.
authors.forename: Puneet Kumar
authors.initials: PK
authors.lastname: Singh
authors.affiliation: Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India.
authors.forename: Josmi
authors.initials: J
authors.lastname: Joseph
authors.affiliation: School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
authors.forename: Sukriti
authors.initials: S
authors.lastname: Goyal
authors.affiliation: School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
authors.forename: Abhinav
authors.initials: A
authors.lastname: Grover
authors.affiliation: Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, India. pratyoosh.shukla@gmail.com.
authors.forename: Pratyoosh
authors.initials: P
authors.lastname: Shukla
mesh_terms: D001234:Aspergillus niger / Q000737:chemistry / Q000201:enzymology; D001426:Bacterial Proteins / Q000737:chemistry*; D001665:Binding Sites; D005636:Fructosephosphates / Q000737:chemistry*; D005656:Fungal Proteins / Q000737:chemistry*; D006026:Glycoside Hydrolases / Q000737:chemistry*; D006860:Hydrogen Bonding; D007527:Isoenzymes; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011549:Pseudomonas / Q000737:chemistry / Q000201:enzymology; D013045:Species Specificity; D040681:Structural Homology, Protein; D013379:Substrate Specificity; D013816:Thermodynamics; D014312:Trisaccharides / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; D005636:Fructosephosphates; D005656:Fungal Proteins; D007527:Isoenzymes; D014312:Trisaccharides; C072433:1-kestose; C027618:fructose-6-phosphate; D006026:Glycoside Hydrolases; C023086:inulinase
keywords: 1-Kestose; Endoinulinase; Exoinulinase; Fructose-6-phosphate; Molecular docking; Molecular dynamic simulation