Experimental and Molecular Dynamics Simulation Insights into Adsorption of Co(II), Cr(III), and Cu(II) on Chitosan and Chitosan/Tripolyphosphate Nanoparticles.

Chitosan (CS)/tripolyphosphate (TPP) nanoparticles were synthesized using the ionic gelation method based on the mass ratio and volume ratio between CS and TPP and then subsequently characterized using XRD, FT-IR, and SEM. The interaction between the metal ions Co(II), Cr(III), and Cu(II) on CS and 2CS/TPP was simulated using molecular dynamics (MD), and the findings were compared with the experimental data. CS/TPP nanoparticles were more favorable than using pure chitosan at a % removal efficiency of 91.47, 89.11, and 78.11 for Cu(II), Cr(III), and Co(II), respectively. The binding energy between 2CS/TPP and the metals was more favorable than that for CS at -214.95, -106.87, and -58.11 kcal/mol for Cr(III), Co(II), and Cu(II), respectively. The CS/TPP nanoparticles greatly affect metal adsorption and are therefore considered materials for wastewater treatment.

Production of biomaterials from seafood waste for application as vegetable wash disinfectant.

The production of seafood waste was studied by analyzing calcium oxide from the shells of tropical oyster and chitosan from the shells of white shrimp to use as a vegetable wash disinfectant. The preparations used were: natural oyster shell powder (NOSP), calcined tropical oyster shell powder in a programmable furnace for 2 h at 700 °C (OSP700), 800 °C (OSP800) and 900 °C (OSP900) including white shrimp shell chitosan (CS). The physical properties of all biomaterials were analyzed using Thermogravimetric analysis, X-ray diffraction and Fourier-transformed infrared spectrometry. The results showed that NOSP and OSP700 were calcite calcium carbonate crystal, but OSP800 and OSP900 were transformed to calcium oxide and calcium hydroxide. The amino group found in the chitin from white shrimp shell was deacetylated to chitosan. By investigating the qualitative antibacterial activity of OSP900 and CS, the inhibition zone of OSP900 against E. coli was higher than that of CS (p < 0.05); however, the inhibition zone of CS against S. aureus was higher than that of OSP900 (p < 0.05). In addition, OSP900 had significantly higher quantitative antibacterial activity against E. coli than S. aureus. The MIC of OSP900 against E. coli and S. aureus for 15 min were 2.5 and 5 mg/mL, respectively; furthermore, the MBC of OSP900 against E. coli and S. aureus were 5 and 10 mg/mL, respectively. However, the inhibitory activity of CS against S. aureus was higher than against E. coli with MIC and MBC values of 5 and 10 mg/mL, respectively, for 15 min. When testing the biomaterials, OSP900 and CS, to inhibit the bacteria on kale and lettuce, 2.5 mg/mL of OSP900 for a vegetable-washing time of 15 min had the highest E. coli inhibition for both vegetables, while 2.5 mg/mL of CS for the same washing time had the highest S. aureus inhibition for both vegetables. Therefore, this research indicated that biomaterials prepared from tropical oyster shell and white shrimp shell wastes could be used as effective wash disinfectants to eliminate contaminated bacteria on vegetables.

Structural analysis of rice Os4BGlu18 monolignol ß-glucosidase.

Monolignol glucosides are storage forms of monolignols, which are polymerized to lignin to strengthen plant cell walls. The conversion of monolignol glucosides to monolignols is catalyzed by monolignol ß-glucosidases. Rice Os4BGlu18 ß-glucosidase catalyzes hydrolysis of the monolignol glucosides, coniferin, syringin, and p-coumaryl alcohol glucoside more efficiently than other natural substrates. To understand more clearly the basis for substrate specificity of a monolignol ß-glucosidase, the structure of Os4BGlu18 was determined by X-ray crystallography. Crystals of Os4BGlu18 and its complex with δ-gluconolactone diffracted to 1.7 and 2.1 Å resolution, respectively. Two protein molecules were found in the asymmetric unit of the P212121 space group of their isomorphous crystals. The Os4BGlu18 structure exhibited the typical (ß/α)8 TIM barrel of glycoside hydrolase family 1 (GH1), but the four variable loops and two disulfide bonds appeared significantly different from other known structures of GH1 ß-glucosidases. Molecular docking studies of the Os4BGlu18 structure with monolignol substrate ligands placed the glycone in a similar position to the δ-gluconolactone in the complex structure and revealed the interactions between protein and ligands. Molecular docking, multiple sequence alignment, and homology modeling identified amino acid residues at the aglycone-binding site involved in substrate specificity for monolignol ß-glucosides. Thus, the structural basis of substrate recognition and hydrolysis by monolignol ß-glucosidases was elucidated.

Asymmetry in structural response of inner and outer transmembrane segments of CorA protein by a coarse-grain model.

Structure of CorA protein and its inner (i.corA) and outer (o.corA) transmembrane (TM) components are investigated as a function of temperature by a coarse-grained Monte Carlo simulation. Thermal response of i.corA is found to differ considerably from that of the outer component, o.corA. Analysis of the radius of gyration reveals that the inner TM component undergoes a continuous transition from a globular conformation to a random coil structure on raising the temperature. In contrast, the outer transmembrane component exhibits an abrupt (nearly discontinuous) thermal response in a narrow range of temperature. Scaling of the structure factor shows a globular structure of i.corA at a low temperature with an effective dimension D ∼ 3 and a random coil at a high temperature with D ∼ 2. The residue distribution in o.corA is slightly sparser than that of i.corA in a narrow thermos-responsive regime. The difference in thermos-response characteristics of these components (i.corA and o.corA) may reflect their unique transmembrane functions.

Inner and Outer Coordination Shells of Mg(2+) in CorA Selectivity Filter from Molecular Dynamics Simulations.

Structural data of CorA Mg(2+) channels show that the five Gly-Met-Asn (GMN) motifs at the periplasmic loop of the pentamer structure form a molecular scaffold serving as a selectivity filter. Unfortunately, knowledge about the cation selectivity of Mg(2+) channels remains limited. Since Mg(2+) in aqueous solution has a strong first hydration shell and apparent second hydration sphere, the coordination structure of Mg(2+) in a CorA selectivity filter is expected to be different from that in bulk water. Hence, this study investigated the hydration structure and ligand coordination of Mg(2+) in a selectivity filter of CorA using molecular dynamics (MD) simulations. The simulations reveal that the inner-shell structure of Mg(2+) in the filter is not significantly different from that in aqueous solution. The major difference is the characteristic structural features of the outer shell. The GMN residues engage indirectly in the interactions with the metal ion as ligands in the second shell of Mg(2+). Loss of hydrogen bonds between inner- and outer-shell waters observed from Mg(2+) in bulk water is mostly compensated by interactions between waters in the first solvation shell and the GMN motif. Some water molecules in the second shell remain in the selectivity filter and become less mobile to support the metal binding. Removal of Mg(2+) from the divalent cation sensor sites of the protein had an impact on the structure and metal binding of the filter. From the results, it can be concluded that the GMN motif enhances the affinity of the metal binding site in the CorA selectivity filter by acting as an outer coordination ligand.

Transmembrane Helix Assembly by Max-Min Ant System Algorithm.

Because of the rapid progress in biochemical and structural studies of membrane proteins, considerable attention has been given on developing efficient computational methods for solving low-to-medium resolution structures using sparse structural data. In this study, we demonstrate a novel algorithm, max-min ant system (MMAS), designed to find an assembly of α-helical transmembrane proteins using a rigid helix arrangement guided by distance constraints. The new algorithm generates a large variety with finite number of orientations of transmembrane helix bundle and finds the solution that is matched with the provided distance constraints based on the behavior of ants to search for the shortest possible path between their nest and the food source. To demonstrate the efficiency of the novel search algorithm, MMAS is applied to determine the transmembrane packing of KcsA and MscL ion channels from a limited distance information extracted from the crystal structures, and the packing of KvAP voltage sensor domain using a set of 10 experimentally determined constraints, and the results are compared with those of two popular used stochastic methods, simulated annealing Monte Carlo method and genetic algorithm.

Shaping the water crevice to accommodate the voltage sensor in a down conformation: a molecular dynamics simulation study.

Voltage sensor domains (VSD) of voltage-dependent ion channels share a basic molecular structure with a voltage-sensing phosphatase and a voltage-gated proton channel. The VSD senses and responds to changes in the membrane potential by undergoing conformational changes associated with the movement of the charged arginines located on the S4 segment. Although several functional and structural studies have provided useful information about the conformational changes in many ion channels, a detailed and unambiguous explanation has not been published. Therefore, understanding the principle of voltage-dependent gating at an atomic level is required. In this study, we took advantage of the available spin labeling electron paramagnetic resonance spectrometry data and computational methods to investigate the structure and dynamic properties of the Up-state (activated) and Down-state (resting) conformations of the VSD by means of all-atom molecular dynamics (MD) simulations. The MD results of the Down conformation determined in bilayers with and without lipid phosphates both revealed a different shape of the aqueous crevice, in which more water molecules surround and fill the intracellular crevice in its Down state than in its Up state. The solvent accessible surface within the crevice has a complementary shape that can account for water-mediated interactions between the voltage sensor and the lipid bilayer. The results support the previously reported experimental data.