The hairpin extension controls solvent access to the chromophore binding pocket in a bacterial phytochrome: a UV–vis absorption spectroscopy study

Solvent access to the protein interior plays an important role in the function of many proteins. Phytochromes contain a specific structural feature, a hairpin extension that appears to relay structural information from the chromophore to the rest of the protein. The extension interacts with amino acids near the chromophore, and hence shields the chromophore from the surrounding solvent. We envision that the detachment of the extension from the protein surface allows solvent exchange reactions in the vicinity of the chromophore. This can facilitate for example, proton transfer processes between solvent and the protein interior. To test this hypothesis, the kinetics of the protonation state of the biliverdin chromophore from Deinococcus radiodurans bacteriophytchrome, and thus, the pH of the surrounding solution, is determined. The observed absorbance changes are related to the solvent access of the chromophore binding pocket, gated by the hairpin extension. We therefore propose a model with an “open” (solvent-exposed, deprotonation-active on a (sub)second time-scale) state and a “closed” (solvent-gated, deprotonation inactive) state, where the hairpin fluctuates slowly between these conformations thereby controlling the deprotonation process of the chromophore on a minute time scale. When the connection between the hairpin and the biliverdin surroundings is destabilized by a point mutation, the amplitude of the deprotonation phase increases considerably. In the absence of the extension, the chromophore deprotonates essentially without any “gating”. Hence, we introduce a straightforward method to study the stability and fluctuation of the phytochrome hairpin in its photostationary state. This approach can be extended to other chromophore-protein systems where absorption changes reflect dynamic processes of the protein.

Development of an atmospheric chemistry model coupled to the PALM model system 6.0: implementation and first applications

In this article we describe the implementation of an online-coupled gas-phase chemistry model in the turbulence-resolving PALM model system 6.0 (formerly an abbreviation for Parallelized Large-eddy Simulation Model and now an independent name). The new chemistry model is implemented in the PALM model as part of the PALM-4U (PALM for urban applications) components, which are designed for application of the PALM model in the urban environment (Maronga et al., 2020). The latest version of the Kinetic PreProcessor (KPP, 2.2.3) has been utilized for the numerical integration of gas-phase chemical reactions. A number of tropospheric gas-phase chemistry mechanisms of different complexity have been implemented ranging from the photostationary state (PHSTAT) to mechanisms with a strongly simplified volatile organic compound (VOC) chemistry (e.g. the SMOG mechanism from KPP) and the Carbon Bond Mechanism 4 (CBM4; Gery et al., 1989), which includes a more comprehensive, but still simplified VOC chemistry. Further mechanisms can also be easily added by the user. In this work, we provide a detailed description of the chemistry model, its structure and input requirements along with its various features and limitations. A case study is presented to demonstrate the application of the new chemistry model in the urban environment. The computation domain of the case study comprises part of Berlin, Germany. Emissions are considered using street-type-dependent emission factors from traffic sources. Three chemical mechanisms of varying complexity and one no-reaction (passive) case have been applied, and results are compared with observations from two permanent air quality stations in Berlin that fall within the computation domain. Even though the feedback of the model's aerosol concentrations on meteorology is not yet considered in the current version of the model, the results show the importance of online photochemistry and dispersion of air pollutants in the urban boundary layer for high spatial and temporal resolutions. The simulated NOx and O3 species show reasonable agreement with observations. The agreement is better during midday and poorest during the evening transition hours and at night. The CBM4 and SMOG mechanisms show better agreement with observations than the steady-state PHSTAT mechanism.

Improvement of Growth and Morphology of Vegetable Seedlings with Supplemental Far-Red Enriched LED Lights in a Plant Factory

Although light-emitting diode (LED) lamps have been broadly applied in horticultural production to improve plant yield and quality, compared to natural light there is a disadvantage in the lack of far-red light in the LED spectrum. Far-red light has been studied widely to control plant growth and development. Therefore, this study aimed to find the effect of supplemental far-red-enriched LED lights to control the growth of tomato, red pepper, cucumber, gourd, watermelon and bottle gourd seedlings. The treatments were cool white LED:far-red LED at ratios of 5:0, 5:1, 5:2 and 5:3. The growth of tomato and red pepper seedlings, including hypocotyl length, was correlated to far-red light and light intensity. The phytochrome photostationary state (PSS) value of maximum hypocotyl length by supplemental far-red-enriched light ranged from 0.69 to 0.77 in tomato and red pepper seedlings. Although hypocotyl lengths of cucumber and watermelon were greatly affected by PSS, the PSS value for maximum hypocotyl length was lower than for tomato and red pepper. These results show that manipulating supplemental far-red enrichment can be used to control vegetable seedling growth with some variation among plant species.

Development of an atmospheric chemistry model coupled to the PALM model system 6.0: Implementation and first applications

In this article we describe the implementation of an online-coupled gas-phase chemistry model in the turbulence resolving PALM model system 6.0. The new chemistry model is part of the PALM-4U components (read: PALM for you; PALM for urban applications) which are designed for application of PALM model in the urban environment (Maronga et al., 2020). The latest version of the Kinetic PreProcessor (KPP, 2.2.3), has been utilised for the numerical integration of gas-phase chemical reactions. A number of tropospheric gas-phase chemistry mechanisms of different complexity have been implemented ranging from the photostationary state to more complex mechanisms such as CBM4, which includes major pollutants namely O3, NO, NO2, CO, a simplified VOC chemistry and a small number of products. Further mechanisms can also be easily added by the user. In this work, we provide a detailed description of the chemistry model, its structure along with its various features, input requirements, its application and limitations. A case study is presented to demonstrate the application of the new chemistry model in the urban environment. The computation domain of the case study is comprised of part of Berlin, Germany, covering an area of 6.71 × 6.71 km with a horizontal resolution of 10 m. We used "PARAMETERIZED" emission mode of the chemistry model that only considers emissions from traffic sources. Three chemical mechanisms of varying complexity and one no-reaction (passive) case have been applied and results are compared with observations from two permanent air quality stations in Berlin that fall within the computation domain. The results show importance of online photochemistry and dispersion of air pollutants in the urban boundary layer. The simulated NOx and O3 species show reasonable agreement with observations. The agreement is better during midday and poorest during the evening transition hours and at night. CBM4 and SMOG mechanisms show better agreement with observations than the steady state PHSTAT mechanism.

Ozone Trends from Two Decades of Ground Level Observation in Malaysia

We examine the change in surface ozone and its precursor behavior over 20 years at four locations in western Peninsular Malaysia which have undergone urban-commercial development. Trend and correlation analyses were carried out on ozone and oxides of nitrogen observation data over the periods of 1997–2016 as well as the decadal intervals of 1997–2006 and 2007–2016. Diurnal variation composites for decadal intervals were also plotted. Significant increasing ozone concentrations were observed at all locations for the 20-year period, with a range between 0.09 and 0.21 ppb yr−1. The most urbanized location (S3) showed the highest ozone trend. Decadal intervals show that not all stations record significant increasing trends of ozone, with S1 recording decreasing ozone at a rate of −0.44 ppb yr−1 during the latter decade. Correlation analysis showed that only oxides of nitrogen ratios (NO/NO2) had significant inverse relationships with ozone at all stations corresponding to control of ozone by photostationary state reactions. The diurnal composites show that decadal difference in NO/NO2 is mostly influenced by change in nitric oxide concentrations.

Synthesis of 4-Chloro-1,3-Diazobenzene Bent-Cores Liquid Crystal and Characterizations of Its Mesogenic Behaviors and Photosensitivity

<p></p><p>Azobenzene-based bent-core liquid crystals demonstrate a variety of mesomorphic behaviours and photochromic properties which are desirable for optical switching. In this study, a novel compound <b>4c</b> was synthesised by adding azo functional groups and chlorine substituent to the central bent-core. The structure, mesogenic properties, and photosensitivity of <b>4c</b> was characterised by fourier-transform infrared spectroscopy (FTIR), ¹H and ¹³C nuclear magnetic resonance (NMR), mass spectrometry (MS), differential scanning calorimetry (DSC), polarised optical microscopy (POM), and ultraviolet–visible spectroscopy (UV-Vis). The experimental results show that <b>4c</b> exhibited a broad temperature window of nematic phase (63.8 °C), rapid <i>trans – cis</i> photoisomerisation in seconds, and high <i>cis</i> fraction of 0.81. At room temperature, <b>4c </b>dissolved in ethyl acetate can reach photostationary state in 10 seconds. At 95 °C, nematic <b>4c</b> became isotropic under UV irradiation in 3 seconds and can be restored to be nematic under natural visible light in 5 seconds. Quantum mechanics calculations confirm that using azos instead of esters as the central linkages can effectively reduce the molecular dipole moment and enhance the overall molecular polarisabilities, which promotes favourable mesogenic and photonic behaviours. This study provides novel synthesis route and synergistic approach to advance the design of azobenzene bent-core liquid crystals.</p><p></p>

Synthesis of 4-Chloro-1,3-Diazobenzene Bent-Cores Liquid Crystal and Characterizations of Its Mesogenic Behaviors and Photosensitivity

<p></p><p>Azobenzene-based bent-core liquid crystals demonstrate a variety of mesomorphic behaviours and photochromic properties which are desirable for optical switching. In this study, a novel compound <b>4c</b> was synthesised by adding azo functional groups and chlorine substituent to the central bent-core. The structure, mesogenic properties, and photosensitivity of <b>4c</b> was characterised by fourier-transform infrared spectroscopy (FTIR), ¹H and ¹³C nuclear magnetic resonance (NMR), mass spectrometry (MS), differential scanning calorimetry (DSC), polarised optical microscopy (POM), and ultraviolet–visible spectroscopy (UV-Vis). The experimental results show that <b>4c</b> exhibited a broad temperature window of nematic phase (63.8 °C), rapid <i>trans – cis</i> photoisomerisation in seconds, and high <i>cis</i> fraction of 0.81. At room temperature, <b>4c </b>dissolved in ethyl acetate can reach photostationary state in 10 seconds. At 95 °C, nematic <b>4c</b> became isotropic under UV irradiation in 3 seconds and can be restored to be nematic under natural visible light in 5 seconds. Quantum mechanics calculations confirm that using azos instead of esters as the central linkages can effectively reduce the molecular dipole moment and enhance the overall molecular polarisabilities, which promotes favourable mesogenic and photonic behaviours. This study provides novel synthesis route and synergistic approach to advance the design of azobenzene bent-core liquid crystals.</p><p></p>