pH-Dependent Binding and Releasing Mechanism of Acetate in the Inner Water Cavity of Heliorhodopsin

The high-resolution structure of heliorhodopsin crystallizedatlow pH reveals the presence of a planar triangle molecule, acetate,in the inner water cavity. Here, we investigate how the acetate moleculeis stabilized at the counterion Glu107 moiety, using molecular dynamics(MD) simulations and a quantum mechanical/molecular mechanical (QM/MM)approach. QM/MM calculations indicate that the density is best describedas acetate among triangle acids, including nitric acid and bicarbonate.The calculated protonation state indicates that protonated acetatedonates an H-bond to deprotonated Glu107 in the low-pH crystal structure.The observed red-shift of & SIM;30 nm in the absorption wavelengthwith pK (a) & AP; 4 is likely due to theHis23/His80 protonation, rather than the Glu107 protonation. MD simulationsalso show that acetate can exist at the Glu107 moiety only when itis protonated. When ionized, acetate is released from the Glu107 moietyvia Asn101 at the channel bottleneck and Arg91 on the intracellularprotein surface. These observations could explain how acetate bindsat low pH and releases at high pH.

Automated summary

This article investigates how the acetate molecule is stabilized at the counterion Glu107 moiety in a low-pH environment using molecular dynamics simulations and quantum mechanical/molecular mechanical calculations. The results show that the protonation state of acetate determines its hydrogen bonding with deprotonated Glu107. Additionally, the red-shift of the absorption wavelength at low pH is attributed to the protonation of His23/His80. MD simulations reveal that acetate is released from Glu107 via Asn101 and Arg91 when ionized, explaining its binding and release under different pH conditions.