The role of protein-bound water molecules in microbial rhodopsins.
Protein-bound internal water molecules are essential features of the structure and function of microbial rhodopsins. Besides structural stabilization, they act as proton conductors and even proton storage sites. Currently, the most understood model system exhibiting such features is bacteriorhodopsin (bR). During the last 20 years, the importance of water molecules for proton transport has been revealed through this protein. It has been shown that water molecules are as essential as amino acids for proton transport and biological function. In this review, we present an overview of the historical development of this research on bR. We furthermore summarize the recently discovered protein-bound water features associated with proton transport. Specifically, we discuss a pentameric water/amino acid arrangement close to the protonated Schiff base as central proton-binding site, a protonated water cluster as proton storage site at the proton-release site, and a transient linear water chain at the proton uptake site. We highlight how protein conformational changes reposition or reorient internal water molecules, thereby guiding proton transport. Last, we compare the water positions in bR with those in other microbial rhodopsins to elucidate how protein-bound water molecules guide the function of microbial rhodopsins. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.
Department of Biophysics, University of Bochum, ND 04 North, 44780 Bochum, Germany; Department of Biophysics, Chinese Academy of Sciences-Max-Planck Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences (SIBS), 320 Yue Yang Lu, 200031 Shanghai, PR China. Electronic address: gerwert@bph.rub.de.
Klaus
K
Gerwert
Department of Biophysics, University of Bochum, ND 04 North, 44780 Bochum, Germany.
Erik
E
Freier
Department of Biophysics, Chinese Academy of Sciences-Max-Planck Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences (SIBS), 320 Yue Yang Lu, 200031 Shanghai, PR China.
Steffen
S
Wolf
D001436:Bacteriorhodopsins / Q000737:chemistry* / Q000378:metabolism; D019605:Euryarchaeota / Q000737:chemistry / Q000502:physiology; D025602:Halorhodopsins / Q000737:chemistry* / Q000378:metabolism; D006860:Hydrogen Bonding; D017136:Ion Transport; D008027:Light; D008958:Models, Molecular; D011487:Protein Conformation; D011522:Protons; D012545:Schiff Bases / Q000737:chemistry* / Q000378:metabolism; D025603:Sensory Rhodopsins / Q000737:chemistry* / Q000378:metabolism; D014867:Water / Q000737:chemistry*
D025602:Halorhodopsins; D011522:Protons; D012545:Schiff Bases; D025603:Sensory Rhodopsins; D014867:Water; D001436:Bacteriorhodopsins
Biomolecular simulations; Fourier transform infrared spectroscopy; Grotthuss proton transfer; Microbial rhodopsins; Protein-bound water molecules