We used molecular dynamics modeling to test the propensity of the bacteria-derived hydrophobic protein BslA in a biphasic system of organic solution and water. The organic solution we use is isobutanol solution, which is the organic solution we will use in the actual experiment.
The.PDB file of isobutanol was obtained from PubChem website. We're going to use that to create organic solutions. We also need the.top file for isobutanol. We can get topol files through many channels, here we choose to use the gromacs program to run the topol files, this is because through gromacs we can choose our own need force field.
By randomly adding molecules into the box, we successfully constructed an organic solvent box of isobutanol. In order to ensure that the organic molecules in the box were saturated, we added isobutanol molecules in different quantity gradients, and only stopped adding them when the number of molecules in the box converged.
In order to ensure the stability of the system, we first conducted an md simulation in this step to obtain a more stable organic solvent box.
After completing the md simulation of the organic solvent box, we will build the biphasic system we need.
First, we need to get the.pDB file of BslA on the RCSB website.
Second, we need to process the hexamer of BslA with pymol to get a single BslA file, which is a fragment of the source file.
We add the resulting BslA to the organic solution box we created earlier and inject water molecules into it. And then we get the biphasic system that we want to build.
To ensure charge balance in the system, we need to add counterbalance ions. We only need to add one CL ion to our system. In order to ensure the successful md simulation, we need to conduct energy minimization, nvt balance and npt balance before md simulation.
After that we can start the molecular dynamics simulation. Since the purpose of our simulation is not to verify the stability of BslA under the two solution systems, we do not need to analyze the pressure, temperature and other indicators of the system. As long as our simulation doesn't break down.
In order to observe whether the BslA will move from the aqueous solution to the organic solution, we need to observe the movement trajectory of the BslA using VMD.
By observing the picture, BslA has a clear trend of displacement. And we put BslA in an aqueous solution, so it's currently moving in the direction of the organic solution, the isobutanol solution. This means that BslA has a pattern of movement that tends to be isobutanol. This provides guidance for our experiments on the aqueous phase and makes us understand that BslA can indeed help us to complete the purification of the aqueous phase more quickly.
