Trans-membrane proteins convert extra-cellular stimulation to intra-celluar signaling. In bacteriorhodopsin, opening of the proton uptake channel is a key event leading to the robust vectorial transportation of protons from cytosol. By molecular dynamics simulation, we show that D96, a key residue and a proton donor, plays crucial roles in this process. The simulations indicate that the proton uptake channel remains closed when D96 is protonated and opens quickly when D96 is deprotonated, making it possible for D96 to re-capture a proton from water molecules. In bovine rhodopsin, a G-protein coupled receptor, stability of the crucial ion-lock is examined through molecular dynamics simulations. Here, we illustrate that the ion-lock has been designed such that the conformational change of retinal would disrupt the ion-lock and trigger the subsequence conformational changes on the cytoplasmic side of the protein that eventually leads to the binding of the G-protein.
When: 5/10/12 4:10 PM
Where: 1005 GBSF