Molecular Dynamics Simulation of Lipase

To study the protein structure at the molecule level, an MD simulation was performed on the GROMAS 2018 software package (http://www.gromacs.org/, accessed on 1 January 2020). The CHARMM36 force field was used for the MD simulation. The crystal structure of lipase NS 40086 (PDB ID: 3TGL) was obtained from the Protein Data Bank as the initial structure in a closed conformation for the simulation. The protein was dissolved in an explicit solvent. Considering that the primary TAGs in the reaction are triolein and tricaprylin, as for the water-free system, 44 triolein molecules (PubChem CID: 5497163) and 47 tricaprylin molecules (PubChem CID: 10850) were added to the simulation box. In the simulation of the PE system, a certain proportion of water molecules (about 9056) was added in the box, the TIP3P water model was selected, and 55 triolein molecules and 39 tricaprylin molecules acted as the oil phase. The model was placed in a cubic box. Energy minimization was performed using the steepest descent method. Furthermore, the system was first equilibrated for 100 ps under an isothermal-isochoric (NVT) system and then for 100 ps under an isothermal-isobaric (NPT) system using a leap-frog integrator and reached the corresponding simulated temperature (298.15 K) and pressure (0.1 MPa). The balanced system was simulated under the NPT system for 5 ns of all-atom molecular dynamics. The LINCS algorithm was used for all the key constraints in the system. Long-range electrostatic interactions were calculated using the Particle Mesh Ewald method with a time step of 2 fs. The root mean square deviation (RMSD) was studied to make sure that the protein structure was fully relaxed. Protein structure characterization and pertinent images were obtained using standard tools supplied by the Gromacs package, PyMol (Schrödinger, Inc., LLC, New York, NY, USA), VMD (University of Illinois, Champaign, IL, USA). The Caver web online server was used to conduct the tunnel analysis of lipase in the water-free system and the PE system [29 (link)].