Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery: Bridging Experiments and Computations - September 10-14, 2014, Istanbul, Turkey

Modeling of Biomolecular Systems Interactions, Dynamics, and Allostery Poster Session II

94-POS Board 47 The Investigation of Activation Mechanism of BTL2 in Non-Aqueous Solvents through MD Simulations Asli Yenenler 1 , Osman Ugur Sezerman 1 , Alessandro Venturini 2 . 1 Sabanci University, Istanbul, Turkey, 2 ISOF Institue, ISOF, Bologna, Italy. Microbial lipases are one of the largest classes of biocatalyst and are involved in hydrolysis, transesterification and esterification reactions . Microbial lipases offer new possibilities in industry with shift of thermodynamic equilibria by solvent engineering . In our project, bacterial thermoalkoliphilic lipase from Bacillus thermocatenulatus (pdb:2w22) is chosen to be used as biocatalyst in non-aqueous solvents. Overcoming change in destabilization of enzyme are essential to handle lipases in non-aqueous solvents. Before applying protein engineering approaches such as enzyme modification through site-directed mutagenesis, MD simulations have been performed to investigate the activation mechanism of BTL2 in non-aqueous solvents. Then, in-silico mutagenesis will be performed to strengthen the structurally vulnerable parts of the lipase .Up to now, 10ns of MD runs were performed for BTL2-toluene and BTL2- toluene/water complexes. Before 10ns simulations, 2000 steps of conjugate gradient minimization followed by 1ns equilibration run are performed at 310K. According to analysis of 10ns, it has been revealed that calcium coordination and lid domain of BTL2 moved more in toluene (2Å, 2.5Å backbone-rmsd) compared to toluene-water (50/50 v/v) (0.8Å, 1.5Å backbone-rmsd). Also, some buried parts of BTL2, playing crucial role in activation mechanism, are moving around 0.8Å (backbone-rmsd) towards the surface of the protein and trying to interact with toluene molecules which may lead to the destabilization. Moreover, surface exposed ligand binding part of the protein is less flexible in toluene (0.6Å backbone-rmsd) compare to toluene/water (1.6Å backbone-rmsd) and low flexibility creates problems for the function of the protein. To observe more conformational change, these simulations have been extended to 50ns and performed at 450K with 3 repeats. We believe the analysis of these runs will provide valuable insights about the stability and the functionality of this enzyme in toluene- water environment.

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