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.

An Alkaline Protease from Bacillus pumilus MP 27: Functional Analysis of Its Binding Model toward Its Applications As Detergent Additive

“…Serine-type endopeptidase activity was found in the translated sequence, the total length of conserve domain was 57 amino acids with total alignment score of 223 and Identities of 44/53 (83%), Positives of 48/53 (90%) with the target domain when submitted in the ProDom server. Such studies were also done in inulinases ( Singh and Shukla, 2011 ; Singh et al, 2011 , 2016 ), Xylanses ( Karthik and Shukla, 2012 ).…”

Computational investigation on the binding modes of Rimonabant analogs with CB1 and CB2

“…With the development of computer‐aid drug discovery methods, the molecular modeling and dynamics simulation are becoming perfect complements in explaining experimental results and guiding further experiments . The homology modeling is an important approach to get accurate 3D structures in the absence of experimental structures; the molecular docking is widely used in predicting the binding affinities of ligands and binding modes between ligands and receptors; the molecular dynamics simulations can provide detailed information about conformation changes and molecular mechanisms of ligand–receptor interaction . In this work, the integration of homology modeling, automated molecular docking, and molecular dynamics simulation were used to uncover the differences of binding modes and selectivity of four CB1/CB2 inverse agonists/antagonists (Rimonabant, MJ08, MJ15, and AM630) with CB1 and CB2.…”

Molecular dynamics provides insight into how N251A and N251Y mutations in the active site of Bacillus licheniformis RN-01 levansucrase disrupt production of long-chain levan

“…Molecular dynamics (MD) simulations is widely used to elucidate conformational changes of enzymes over a period of time and to gain insights into the interactions between enzymes and substrates that may not be accessible by experiments [ 15 – 20 ]. This method can also be used to calculate the binding free energy of ligand binding in macromolecules [ 17 , 21 ].…”