Application of chemically modified beach sand as low cost efficient adsorbent for dye removal

In the current work, beach sand (BS) and beach sand coated with polyaniline (BS/Pani) were used as an efficient green adsorbent for dye removal from aqueous solutions. Methylene blue (MB) was chosen as a test probe for the evaluation of the selected adsorbents for dye removal efficiency. The adsorption experiments were carried out in batch system and the effect of some important empirical parameters affecting adsorption processes were then investigated. The experimental data were also analyzed by Langmuir and Freundlich adsorption models. Based on the correlation coefficient values obtained (R2), it was found that equilibrium data for both adsorbents fitted well with both models. Adsorption data were also examined by pseudo-first-order and pseudo-second-order models and their respective rate constants were estimated. It was found that sorption of MB dye onto BS/Pani is fitted very well with pseudo-second-order kinetic model. Using the equilibrium concentration constants obtained at different temperatures, important thermodynamic parameters of the sorption process were calculated. It was found that the chemically modified beach sand is an effective and low cost adsorbent for dye removal from aqueous solutions

Designing with biobased composites: understanding digital material perception through semiotic attributes

Biobased composites, which are considered a sustainable alternative to plastics, are yet to create a significant influence on product design and manufacturing. A key reason for this is perceptual handicaps associated with biobased composites and this study was aimed at understanding the mechanisms behind biocomposite perception, in the context of digital visuals. This study of digital biocomposite visuals demonstrated that material perception is influenced by the visual characteristics of the material. Data analysis of the perceptual attributes of the materials pointed towards clear ‘clustering’ of the materials against these attributes. Analysis shows that visual features like fibres and surface appearance may impact aesthetic and functional evaluation and there is no effect on age, gender or polymer type. We also propose a reference framework to categorise biobased composites based on visual order

The Functional Unit of Neisseria meningitidis 3-Deoxy-ᴅ-Arabino-Heptulosonate 7-Phosphate Synthase Is Dimeric.

Neisseria meningitidis 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (NmeDAH7PS) adopts a homotetrameric structure consisting of an extensive and a less extensive interface. Perturbation of the less extensive interface through a single mutation of a salt bridge (Arg126-Glu27) formed at the tetramer interface of all chains resulted in a dimeric DAH7PS in solution, as determined by small angle X-ray scattering, analytical ultracentrifugation and analytical size-exclusion chromatography. The dimeric NmeDAH7PSR126S variant was shown to be catalytically active in the aldol-like condensation reaction between D-erythrose 4-phosphate and phosphoenolpyruvate, and allosterically inhibited by L-phenylalanine to the same extent as the wild-type enzyme. The dimeric NmeDAH7PSR126S variant exhibited a slight reduction in thermal stability by differential scanning calorimetry experiments and a slow loss of activity over time compared to the wild-type enzyme. Although NmeDAH7PSR126S crystallised as a tetramer, like the wild-type enzyme, structural asymmetry at the less extensive interface was observed consistent with its destabilisation. The tetrameric association enabled by this Arg126-Glu27 salt-bridge appears to contribute solely to the stability of the protein, ultimately revealing that the functional unit of NmeDAH7PS is dimeric

A dimeric catalytic core relates the short and long forms of ATP-phosphoribosyltransferase

Adenosine triphosphate (ATP) phosphoribosyltransferase (ATP-PRT) catalyses the first committed step of histidine biosynthesis in plants and microorganisms. Two forms of ATP-PRT have been reported, which differ in their molecular architecture and mechanism of allosteric regulation. The short-form ATP-PRT is a hetero-octamer, with four HisG chains that comprise only the catalytic domains and four separate chains of HisZ required for allosteric regulation by histidine. The long-form ATP-PRT is homo-hexameric, with each chain comprising two catalytic domains and a covalently linked regulatory domain that binds histidine as an allosteric inhibitor. Here, we describe a truncated long-form ATP-PRT from Campylobacter jejuni devoid of its regulatory domain (CjeATP-PRT). Results showed that CjeATP-PRT is dimeric, exhibits attenuated catalytic activity, and is insensitive to histidine, indicating that the covalently linked regulatory domain plays a role in both catalysis and regulation. Crystal structures were obtained for CjeATP-PRT in complex with both substrates, and for the first time, the complete product of the reaction. These structures reveal the key features of the active site and provide insights into how substrates move into position during catalysis

Analysis of the dimer and tetramer interfaces in <i>Mtu</i>DAH7PS.

<p>(A) Surface representation of the dimer interface of <i>Mtu</i>DAH7PS (PDB 3NV8). Residues contributing to this interface are displayed as red sticks. Residues identified to contribute to the dimer interface by PISA include residues 2–13, 15, 44, 47–48, 51, 54–58, 60, 62–63, 92, 94–96, 99, 165–167, 170–171, 173–175, 177–178, 180–182, 184–186, 189, 260, 263 and 265 of chain A, and residues 1, 3–13, 47–48, 51, 54–58, 60, 62–63, 91–92, 94–97, 99–100, 165, 167–168, 170–171, 173–175, 177–182, 184–186, 188–190,296, and 260 of chain B. (B) Surface representation of the tetramer interface of <i>Mtu</i>DAH7PS (PDB 3NV8). Residues contributing to this interface are displayed as blue sticks. Residue numbers are described in the main text. (C) Hydrophobic grove in the tetramer interface and the interaction with Phe227 from the other chain. (D) Positions of the two Gly232 residues on the tetramer interface, succeeding helices α2a and α2b.</p

Crystal structure of <i>Mtu</i>DAH7PS.

<p>(A) Tetramer of <i>Mtu</i>DAH7PS (PDB 5CKV), dimer and tetramer interfaces are indicated with dashed lines. Residues contributing to the dimer and tetramer interfaces are colored pink and blue respectively. (B) Monomeric unit of <i>Mtu</i>DAH7PS in complex with allosteric ligands Phe, Trp and Tyr (PDB 5CKV), the three aromatic amino acids are displayed as spheres with green carbon atoms, the active site metal ion Mn²⁺ is shown as cyan sphere.</p

Quaternary structure is an essential component that contributes to the sophisticated allosteric regulation mechanism in a key enzyme from <i>Mycobacterium tuberculosis</i>

<div><p>The first enzyme of the shikimate pathway, 3-deoxy-D-<i>arabino</i>-heptulosonate 7-phosphate synthase (DAH7PS), adopts a range of distinct allosteric regulation mechanisms in different organisms, related to different quaternary assemblies. DAH7PS from <i>Mycobacterium tuberculosis</i> (<i>Mtu</i>DAH7PS) is a homotetramer, with the allosteric sites in close proximity to the interfaces. Here we examine the importance of the quaternary structure on catalysis and regulation, by amino acid substitution targeting the tetramer interface of <i>Mtu</i>DAH7PS. Using only single amino acid substitutions either in, or remote from the interface, two dimeric variants of <i>Mtu</i>DAH7PS (<i>Mtu</i>DAH7PS_F227D and <i>Mtu</i>DAH7PS_G232P) were successfully generated. Both dimeric variants maintained activity due to the distance between the sites of amino acid substitution and the active sites, but attenuated catalytic efficiency was observed. Both dimeric variants showed significantly disrupted allosteric regulation with greatly impaired binding affinity for one of the allosteric ligands. Molecular dynamics simulations revealed changes in protein dynamics and average conformations in the dimeric variant caused by amino acid substitution remote to the tetramer interface (<i>Mtu</i>DAH7PS_G232P), which are consistent with the observed reduction in catalytic efficiency and loss of allosteric response.</p></div

Analysis of conformational ensembles from MD simulations.

<p>(A) MD conformational ensemble sampled by loop 2 (residues 130 to 153) during equilibrated time period of MD simulations for tetrameric <i>Mtu</i>DAH7PS_WT (blue), dimeric variant <i>Mtu</i>DAH7PS_G232P (red) and the theoretical dimer <i>Mtu</i>DAH7PS_WT^dimer (green). RMSD values of Cα atoms on loop 2 residues (130 to 153) were measured in reference to both the MD average of <i>Mtu</i>DAH7PS_G232P variant and crystal structure of ligand free <i>Mtu</i>DAH7PS_WT. (B) Chain-averaged α-carbon RMSD values of MD average conformations of <i>Mtu</i>DAH7PS_WT, <i>Mtu</i>DAH7PS_wt^dimer, and <i>Mtu</i>DAH7PS_G232P in comparison with crystal structure of ligand free <i>Mtu</i>DAH7PS (PDB 3NV8), for residue range 189–247. (C) Superimposition between ligand free crystal structure of <i>Mtu</i>DAH7PS (PDB 3NV8, grey) and MD average conformations of each chain from MD simulations of <i>Mtu</i>DH7PS_WT (blue), <i>Mtu</i>DAH7PS_G232P (red) and <i>Mtu</i>DAH7PS_WT^dimer (green), only residues 190–243 are displayed for clarity. Regions that are responsible for forming the tetramer interface are highlighted in black circles.</p