Calcium Binding Mechanism in TAT Rhodopsin.

TAT rhodopsin binds Ca near the Schiff base region, which accompanies deprotonation of the Schiff base. This paper reports the Ca-free and Ca-bound structures of TAT rhodopsin by molecular dynamics (MD) simulation launched from AlphaFold structures. In the Ca-bound TAT rhodopsin, Ca is directly coordinated by eight oxygen atoms, four oxygens of the side chains of E54 and D227, and four oxygens of water molecules. E54 is not involved in the hydrogen-bonding network of the Ca-free TAT rhodopsin, while flipping motion of E54 allows Ca binding to TAT rhodopsin with deformation of helices observed by FTIR spectroscopy. The hydrogen-bonding network plays a crucial role in maintaining the Ca binding, as mutations of E54, Y55, R79, Y200, E220, and D227 abolished the binding. Only T82V exhibited the Ca binding like the wild type among the mutants in this study. The molecular mechanism of Ca binding is discussed based on the present computational and experimental analysis.