Mechanism of Spectral Tuning in Green-Absorbing Proteorhodopsin

ABSTRACT: The absorption spectrum of green proteorhodopsin (GPR) is pH-dependent, exhibiting either red-shifted (low pH) or blue-shifted (high pH) absorption maxima. We examine the molecular basis of the pH-dependent spectral properties of green proteorhodopsin by using homology modeling and molecular orbital theory. Bacteriorhodopsin (BR) and sensory rhodopsin II (SRII) are compared as homology templates. The model of GPR generated by using BR as the homology parent is better than that generated by using SRII on the basis of the potential energy, relative stability to dynamics, and ability to rationalize pH effects. MNDO-PSDCI (molecular neglect of differential overlap with partial single- and double-configuration interaction) calculations provide insight into the spectroscopic properties of GPR and help rule out the viability of the SRII-based model. The proximity of His 75 to the quadrupole residues (LYR, D97, D227, and R94) in the BR-based model provides a good model for both the low- and high-pH spectral states of GPR. The observation that BR is a better structural model for GPR than SRII is in contrast to our previous study of BPR, which observed that SRII was the better homology parent [Hillebrecht, J. R. (2006) Biochemistry 45, 1579-1590]. The implications of this observation are discussed. Proteorhodopsin (PR)1 is a light-driven proton pump found in the cell membrane of an uncultivated marine bacteriu