Calcium Binding Mechanism in TAT Rhodopsin.

TAT rhodopsin binds Ca 2+ near the Schiff base region, which accompanies deprotonation of the Schiff base. This paper reports the Ca 2+ -free and Ca 2+ -bound structures of TAT rhodopsin by molecular dynamics (MD) simulation launched from AlphaFold structures. In the Ca 2+ -bound TAT rhodopsin, Ca 2+ 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 2+ -free TAT rhodopsin, while flipping motion of E54 allows Ca 2+ binding to TAT rhodopsin with deformation of helices observed by FTIR spectroscopy. The hydrogen-bonding network plays a crucial role in maintaining the Ca 2+ binding, as mutations of E54, Y55, R79, Y200, E220, and D227 abolished the binding. Only T82V exhibited the Ca 2+ binding like the wild type among the mutants in this study. The molecular mechanism of Ca 2+ binding is discussed based on the present computational and experimental analysis.