title: Channelrhodopsins: a bioinformatics perspective.
abstract: Channelrhodopsins are microbial-type rhodopsins that function as light-gated cation channels. Understanding how the detailed architecture of the protein governs its dynamics and specificity for ions is important, because it has the potential to assist in designing site-directed channelrhodopsin mutants for specific neurobiology applications. Here we use bioinformatics methods to derive accurate alignments of channelrhodopsin sequences, assess the sequence conservation patterns and find conserved motifs in channelrhodopsins, and use homology modeling to construct three-dimensional structural models of channelrhodopsins. The analyses reveal that helices C and D of channelrhodopsins contain Cys, Ser, and Thr groups that can engage in both intra- and inter-helical hydrogen bonds. We propose that these polar groups participate in inter-helical hydrogen-bonding clusters important for the protein conformational dynamics and for the local water interactions. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.
authors.affiliation: Department of Computer Science and Artificial Intelligence, University of Granada, 18071 Granada, Spain. Electronic address: c.delval@decsai.ugr.es.
authors.forename: Coral
authors.initials: C
authors.lastname: Del Val
authors.affiliation: Theoretical Molecular Biophysics, Department of Physics, Freie Universitaet Berlin, 14195 Berlin, Germany.
authors.forename: José
authors.initials: J
authors.lastname: Royuela-Flor
authors.affiliation: Theoretical Molecular Biophysics, Department of Physics, Freie Universitaet Berlin, 14195 Berlin, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Milenkovic
authors.affiliation: Theoretical Molecular Biophysics, Department of Physics, Freie Universitaet Berlin, 14195 Berlin, Germany. Electronic address: nbondar@zedat.fu-berlin.de.
authors.forename: Ana-Nicoleta
authors.initials: AN
authors.lastname: Bondar
mesh_terms: D000595:Amino Acid Sequence; D016825:Chlamydomonas reinhardtii / Q000737:chemistry / Q000502:physiology; D019295:Computational Biology; D006860:Hydrogen Bonding; D017136:Ion Transport; D008027:Light; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D020560:Proteobacteria / Q000737:chemistry / Q000502:physiology; D012172:Retinaldehyde / Q000737:chemistry* / Q000378:metabolism; D025604:Rhodopsins, Microbial / Q000737:chemistry* / Q000378:metabolism; D016415:Sequence Alignment; D040681:Structural Homology, Protein; D014867:Water / Q000737:chemistry* / Q000378:metabolism
chemical_list: D025604:Rhodopsins, Microbial; D014867:Water; D012172:Retinaldehyde
keywords: Bioinformatics; Channelrhodopsin; Membrane protein; Protein structure and dynamics