Determination of specificity and affinity of the Lactose permease (LacY) protein of Escherichia coli through application of molecular dynamics simulation

Sammanfattning: Proteins are essential in all living organisms. They are involved in various critical activities and are also structural components of cells and tissues. Lactose permease a membrane protein has become a prototype for the major facilitator super family and utilises an existing electrochemical proton gradient to shuttle galactoside sugars to the cell. Therefore it exists in two principle states exposing the internal binding site to either side of the membrane. From previous studies it has been suggested that protonation precedes substrate binding but it is still unclear why this has to occur in the event of substrate binding. Therefore this study aimed to bridge this gap and to determine the chemical characteristics of the transport pathway. Molecular dynamics simulation methods and specialised simulation hardware were employed to elucidate the dependency of substrate binding on the protonation nature of Lactose permease. Protein models that differed in their conformation as well as their protonation states were defined from their respective X-ray structures. Targeted molecular dynamics was implemented to drive the substrate to the binding site and umbrella sampling was used to define the free energy of the transport pathway. It was therefore suggested that protonation for sugar binding is due to the switch-like mechanism of Glu325 in the residue-residue interaction (His322 and Glu269) that leads to sugar binding only in the protonated state of LacY. Furthermore, the free energy profile of sugar transport path way was lower only in the protonated state which indicates stability of sugar binding in the protonated state.