Dataset Information

Crystal structures of the L1, L2, N, and O states of pharaonis halorhodopsin.

ABSTRACT: Halorhodopsin from Natronomonas pharaonis (pHR) functions as a light-driven halide ion pump. In the presence of halide ions, the photochemical reaction of pHR is described by the scheme: K? L1 ? L2 ? N ? O ? pHR' ? pHR. Here, we report light-induced structural changes of the pHR-bromide complex observed in the C2 crystal. In the L1-to-L2 transition, the bromide ion that initially exists in the extracellular vicinity of retinal moves across the retinal Schiff base. Upon the formation of the N state with a bromide ion bound to the cytoplasmic vicinity of the retinal Schiff base, the cytoplasmic half of helix F moves outward to create a water channel in the cytoplasmic interhelical space, whereas the extracellular half of helix C moves inward. During the transition from N to an N-like reaction state with retinal assuming the 13-cis/15-syn configuration, the translocated bromide ion is released into the cytoplasmic medium. Subsequently, helix F relaxes into its original conformation, generating the O state. Anion uptake from the extracellular side occurs when helix C relaxes into its original conformation. These structural data provide insight into the structural basis of unidirectional anion transport.

SUBMITTER: Kouyama T

PROVIDER: S-EPMC4457492 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature

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Crystal structures of the L1, L2, N, and O states of pharaonis halorhodopsin.

Kouyama Tsutomu T Kawaguchi Haruki H Nakanishi Taichi T Kubo Hiroki H Murakami Midori M

Biophysical journal 20150601 11

Halorhodopsin from Natronomonas pharaonis (pHR) functions as a light-driven halide ion pump. In the presence of halide ions, the photochemical reaction of pHR is described by the scheme: K→ L1 → L2 → N → O → pHR' → pHR. Here, we report light-induced structural changes of the pHR-bromide complex observed in the C2 crystal. In the L1-to-L2 transition, the bromide ion that initially exists in the extracellular vicinity of retinal moves across the retinal Schiff base. Upon the formation of the N sta ...[more]

PMID: 26039169

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Project description:Active ion transport across membranes is vital to maintaining the electrochemical gradients of ions in cells and is mediated by transmembrane proteins. Halorhodopsin (HR) functions as a light-driven inward pump for chloride ions. The protein contains all-trans-retinal bound to a specific lysine residue through a protonated Schiff base. Interaction between the bound chloride ion and the protonated Schiff base is crucial for ion transport because chloride ion movement is driven by the flipping of the protonated Schiff base upon photoisomerization. However, it remains unknown how this interaction evolves in the HR photocycle. Here, we addressed the effect of the bound anion on the structure and dynamics of HR from Natronomonas pharaonis in the early stage of the photocycle. Comparison of the chloride-bound, formate-bound, and anion-depleted forms provided insights into the interaction between the bound anion and the chromophore/protein moiety. In the unphotolyzed state, the bound anion affects the ?-conjugation of the polyene chain and the hydrogen bond of the protonated Schiff base of the retinal chromophore. Picosecond time scale measurements showed that the band intensities of the W16 and W18 modes of the tryptophan residues decreased instantaneously upon photoexcitation of the formate-bound form. In contrast, these intensity decreases were delayed for the chloride-bound and anion-depleted forms. These observations suggest the stronger interactions of the bound formate ion with the retinal chromophore and the chromophore pocket. On the nanosecond to microsecond timescales, we found that the interaction between the protonated Schiff base and the bound ion is broken upon formation of the K intermediate and is recovered following translocation of the bound anion toward the protonated Schiff base in the L intermediate. Our results demonstrate that the hydrogen-bonding ability of the bound anion plays an essential role in the ion transport of light-driven anion pumps.

Project description:Multi-word expressions (MWEs) are fixed, conventional phrases often used by native speakers of a given language (L1). The type of MWEs investigated in this study were collocations. For bilinguals who have intensive contact with the second language (L2), collocational patterns can be transferred from the L2 to the L1 as a result of cross-linguistic influence (CLI). For example, bilingual migrants can accept collocations from their L2 translated to their L1 as correct. In this study, we asked whether such CLI is possible in native speakers living in the L1 environment and whether it depends on their L2 English proficiency. To this end, we created three lists of expressions in Polish: (1) well-formed Polish verb-noun collocations (e.g., ma sens - ∗has sense), (2) collocational calques from English (loan translations), where the English verb was replaced by a Polish translation equivalent (e.g., ∗ robi sens - makes sense), and, as a reference (3) absurd verb-noun expression, where the verb did not collocate with the noun (e.g., ∗ zjada sens - ∗eats sense). We embedded the three types of collocations in sentences and presented them to L1 Polish participants of varying L2 English proficiency in two experiments. We investigated whether L2 calques would (1) be explicitly judged as non-native in the L1; (2) whether they would evoke differential brain response than native L1 Polish equivalents in the event-related potentials (ERPs). We also explored whether the sensitivity to CLI in calques depended on participants' level of proficiency in L2 English. The results indicated that native speakers of Polish assessed the calques from English as less acceptable than the correct Polish collocations. Still, there was no difference in online processing of correct and calques collocations as measured by the ERPs. This suggests a dissociation between explicit offline judgments and indices of online language processing. Interestingly, English L2 proficiency did not modulate these effects. The results indicate that the influence of English on Polish is so pervasive that collocational calques from this language are likely to become accepted and used by Poles.

Dataset Information

Crystal structures of the L1, L2, N, and O states of pharaonis halorhodopsin.

Publications

Crystal structures of the L1, L2, N, and O states of pharaonis halorhodopsin.

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