Membrane proteins are intrinsically harder to study than soluble proteins due to them being surrounded by the lipid environment. They are harder to crystallize, they have different hydrophobicity, and their folding mechanism is also not as simple. Computational methods like MD(molecular dynamics) help us simulate such experimentally complex systems which can further guide the wet-lab work.

Ligand binding to the EmrE protein: I started by looking at the small bacterial multidrug resistance protein, EmrE. They are present in E. coli membrane and bind to toxins that could kill the bacteria. This toxin is then exported out of the cell, thus protecting the bacteria. I am interested in finding the free energy of ligand binding to the protein, and if there is any lipid contribution to this.

Lipid-metal forcefield developement: I am currently collecting experimental values of model lipid molecules with Be metal ion to adjust the parameters in the CHARMM forcefield. The idea is to first correct it for the CHARMM additive forecfield and then for the Drude polarizable forecfield.