BLUF Domain Function Does Not Require a Metastable Radical Intermediate State

BLUF (blue light using flavin) domain proteins are an important family of blue light-sensing proteins which control a wide variety of functions in cells. The primary light-activated step in the BLUF domain is not yet established. A number of experimental and theoretical studies points to a role for photoinduced electron transfer (PET) between a highly conserved tyrosine and the flavin chromophore to form a radical intermediate state. Here we investigate the role of PET in three different BLUF proteins, using ultrafast broadband transient infrared spectroscopy. We characterize and identify infrared active marker modes for excited and ground state species and use them to record photochemical dynamics in the proteins. We also generate mutants which unambiguously show PET and, through isotope labeling of the protein and the chromophore, are able to assign modes characteristic of both flavin and protein radical states. We find that these radical intermediates are not observed in two of the three BLUF domains studied, casting doubt on the importance of the formation of a population of radical intermediates in the BLUF photocycle. Further, unnatural amino acid mutagenesis is used to replace the conserved tyrosine with fluorotyrosines, thus modifying the driving force for the proposed electron transfer reaction; the rate changes observed are also not consistent with a PET mechanism. Thus, while intermediates of PET reactions can be observed in BLUF proteins they are not correlated with photoactivity, suggesting that radical intermediates are not central to their operation. Alternative nonradical pathways including a keto–enol tautomerization induced by electronic excitation of the flavin ring are considered

Super-sieving effect in phenol adsorption from aqueous solutions on nanoporous carbon beads

Removal of aromatic contaminants, like phenol, from water can be efficiently achieved by preferential adsorption on porous carbons which exhibit molecular sieving properties. Here, we present nanoporous carbon beads exhibiting an outstanding sieving effect in phenol adsorption from aqueous solution at neutral pH, which is evidenced experimentally and theoretically. The molecular sieving with pure phenol adsorbed phase is achieved by tuning the pore size and surface chemistry of the adsorbent. This study elucidates the essential role of hydrophobic interactions in narrow carbon micropores in removal and clean-up of water from organic pollutants. Furthermore, we suggest a new theoretical approach for evaluation of phenol adsorption capacity that is based on the Monte Carlo simulation of phenol adsorption with the relevance to the pore size distribution function determined by the density functional theory method from low temperature nitrogen adsorption

Simple model of adsorption on external surface of carbon nanotubes: a new analytical approach basing on molecular simulation data

Nitrogen adsorption on carbon nanotubes is wide- ly studied because nitrogen adsorption isotherm measurement is a standard method applied for porosity characterization. A further reason is that carbon nanotubes are potential adsorbents for separation of nitrogen from oxygen in air. The study presented here describes the results of GCMC simulations of nitrogen (three site model) adsorption on single and multi walled closed nanotubes. The results obtained are described by a new adsorption isotherm model proposed in this study. The model can be treated as the tube analogue of the GAB isotherm taking into account the lateral adsorbate-adsorbate interactions. We show that the model describes the simulated data satisfactorily. Next this new approach is applied for a description of experimental data measured on different commercially available (and characterized using HRTEM) carbon nanotubes. We show that generally a quite good fit is observed and therefore it is suggested that the observed mechanism of adsorption in the studied materials is mainly determined by adsorption on tubes separated at large distances, so the tubes behave almost independently

Morphologically disordered pore model for characterization of micro-mesoporous carbons

We present a new morphologically disordered slit-shaped pore (MDSP) model for simulating gas adsorption in micro-mesoporous carbonaceous materials. The MDSP model qualitatively accounts for the inherent roughness of carbon pore walls in accord with the atomistic structural model of LMA10 reference carbon material. The MDSP model is applied to pore size distribution (PSD) calculations from nitrogen adsorption isotherms measured at 77.4 K in the range of pore widths from 0.72 to 40 nm. The MDSP model improves significantly the nitrogen adsorption porosimetry and, being fully atomistic, it is transferable to study various adsorbate-adsorbent systems. Computations of PSD functions for a series of carbonaceous materials, including activated carbon fiber, granular activated carbons, synthetic activated carbons showed that MDSP generates smooth Gaussian-type PSD functions with a well-defined average pore size. Furthermore, PSD functions computed from the MDSP model are free from the artificial gaps in the region of narrow micropores (∼1 nm and ∼2 nm) predicted from the standard slit-shaped pore models with ideal graphite-like walls. MDSP is not only a complementary model to existing approaches, such as quench-solid density functional theory method, but it paves the way to efficient atomistic simulations of various compounds within morphologically disordered carbon nanopores

Low-temperature and time-resolved spectroscopic characterization of the LOV2 domain of Avena sativa phototropin.

ABSTRACT The phototropins are plant blue-light receptors that base their light-dependent action on the reversible formation of a covalent bond between a flavin mononucleotide (FMN) cofactor and a conserved cysteine residue in light, oxygen or voltage (LOV) domains. The spectroscopic properties of the LOV2 domain of phototropin 1 of Avena sativa (oat) have been investigated by means of low-temperature absorption and fluorescence spectroscopy and by time-resolved fluorescence spectroscopy. The low-temperature absorption spectrum of the LOV2 domain showed a fine structure around 473 nm, indicating heterogeneity in the flavin binding pocket. The fluorescence quantum yield of the flavin cofactor increased from 0.13 to 0.41 upon cooling the sample from room temperature to 77 K. A pronounced phosphorescence emission around 600 nm was observed in the LOV2 domain between 77 and 120 K, allowing for an accurate positioning of the flavin triplet state in the LOV2 domain at 16900 cm -1 . Fluorescence from the cryotrapped covalent adduct state was extremely weak, with a fluorescence spectrum showing a maximum at 440 nm. Time-resolved fluorescence experiments utilizing a synchroscan streak camera revealed a singlet-excited state lifetime of the LOV2 domain of 2.4 ns. FMN dissolved in aqueous solution showed a pH-dependent lifetime ranging between 2.9 ns at pH 2.0 to 4.7 ns at pH 8.0. No spectral shifting of the flavin emission was observed in the LOV2 domain nor in FMN in aqueous solution

Porosity of closed carbon nanotubes compressed using hydraulic pressure

Experimental data of nitrogen adsorption (T = 77.3 K) from gaseous phase measured on commercial closed carbon nanotubes are presented. Additionally, we show the results of N2 adsorption on compressed (using hydraulic press) CNTs. In order to explain the experimental observations the results of GCMC simulations of N2 adsorption on isolated or bundled multi-walled closed nanotubes (four models of bundles) are discussed. We show that the changes of the experimental adsorption isotherms are related to the compression of the investigated adsorbents. They are qualitatively similar to the theoretical observations. Taking into account all results it is concluded that in the "architecture" of nanotubes very important role has been played by isolated nanotubes

Behavioral response of dissimilatory perchlorate-reducing bacteria to different electron acceptors

The response behavior of three dissimilatory perchlorate-reducing bacteria to different electron acceptors (nitrate, chlorate, and perchlorate) was investigated with two different assays. The observed response was species-specific, dependent on the prior growth conditions, and was inhibited by oxygen. We observed attraction toward nitrate when Dechloromonas aromatica strain RCB and Azospira suillum strain PS were grown with nitrate. When D. aromatica and Dechloromonas agitata strain CKB were grown with perchlorate, both responded to nitrate, chlorate, and perchlorate. When A. suillum was grown with perchlorate, the organism responded to chlorate and perchlorate but not nitrate. A gene replacement mutant in the perchlorate reductase subunit (pcrA) of D. aromatica resulted in a loss of the attraction response toward perchlorate but had no impact on the nitrate response. Washed-cell suspension studies revealed that the perchlorate grown cells of D. aromatica reduced both perchlorate and nitrate, while A. suillum cells reduced perchlorate only. Based on these observations, energy taxis was proposed as the underlying mechanism for the responses to (per)chlorate by D. aromatica. To the best of our knowledge, this study represents the first investigation of the response behavior of perchlorate-reducing bacteria to environmental stimuli. It clearly demonstrates attraction toward chlorine oxyanions and the unique ability of these organisms to distinguish structurally analogous compounds, nitrate, chlorate, and perchlorate and respond accordingly