title: Internal water molecules of pharaonis phoborhodopsin studied by low-temperature infrared spectroscopy.
abstract: In the Schiff base region of bacteriorhodopsin (BR), a light-driven proton-pump protein, three internal water molecules are involved in a pentagonal cluster structure. These water molecules constitute a hydrogen-bonding network consisting of two positively charged groups, the Schiff base and Arg82, and two negatively charged groups, Asp85 and Asp212. Previous infrared spectroscopy of BR revealed stretching vibrations of such water molecules under strong hydrogen-bonding conditions using spectral differences in D2O and D2(18O) [Kandori and Shichida (2000) J. Am. Chem. Soc. 122, 11745-11746]. The present study extends the infrared analysis to another archaeal rhodopsin, pharaonis phoborhodopsin (ppR; also called pharaonis sensory rhodopsin-II, psR-II), involved in the negative phototaxis of Natronobacterium pharaonis. Despite functional differences between ppR and BR, similar spectral features of water bands were observed before and after photoisomerization of the retinal chromophore at 77 K. This implies that the structure and the structural changes of internal water molecules are similar between ppR and BR. Higher stretching frequencies of the bridged water in ppR suggest that the water-containing pentagonal cluster structure is considerably distorted in ppR. These observations are consistent with the crystallographic structures of ppR and BR. The water structure and structural changes upon photoisomerization of ppR are discussed here on the basis of their infrared spectra.
authors.affiliation: Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan. kandori@ach.nitech.ac.jp
authors.forename: H
authors.initials: H
authors.lastname: Kandori
authors.forename: Y
authors.initials: Y
authors.lastname: Furutani
authors.forename: K
authors.initials: K
authors.lastname: Shimono
authors.forename: Y
authors.initials: Y
authors.lastname: Shichida
authors.forename: N
authors.initials: N
authors.lastname: Kamo
mesh_terms: D019843:Archaeal Proteins / Q000737:chemistry*; D001436:Bacteriorhodopsins / Q000737:chemistry; D002338:Carotenoids / Q000737:chemistry*; D018360:Crystallography, X-Ray; D017666:Deuterium Oxide / Q000737:chemistry; D005615:Freezing; D025602:Halorhodopsins; D006860:Hydrogen Bonding; D007536:Isomerism; D012545:Schiff Bases / Q000737:chemistry; D025603:Sensory Rhodopsins; D017550:Spectroscopy, Fourier Transform Infrared / Q000379:methods*; D014867:Water / Q000737:chemistry*
chemical_list: D019843:Archaeal Proteins; D025602:Halorhodopsins; D012545:Schiff Bases; D025603:Sensory Rhodopsins; C061508:sensory rhodopsin II protein, archaeal; D014867:Water; D002338:Carotenoids; D001436:Bacteriorhodopsins; D017666:Deuterium Oxide