Effects of helix and fingertip mutations on the thermostability of xyn11A investigated by molecular dynamics simulations and enzyme activity assays

Local conformational changes and global unfolding pathways of wildtype xyn11A recombinant and its mutated structures were studied through a series of atomistic molecular dynamics (MD) simulations, along with enzyme activity assays at three incubation temperatures to investigate the effects of mutations at three different sites to the thermostability. The first mutation was to replace an unstable negatively charged residue at a surface beta turn near the active site (D32G) by a hydrophobic residue. The second mutation was to create a disulphide bond (S100C/N147C) establishing a strong connection between an alpha helix and a distal beta hairpin associated with the thermally sensitive Thumb loop, and the third mutation add an extra hydrogen bond (A155S) to the same alpha helix. From the MD simulations performed, MM/PBSA energy calculations of the unfolding energy were in a good agreement with the enzyme activities measured from the experiment, as all mutated structures demonstrated the improved thermostability, especially the S100C/N147C proved to be the most stable mutant both by the simulations and the experiment. Local conformational analysis at the catalytic sites and the xylan access region also suggested that mutated xyn11A structures could accommodate xylan binding. However, the analysis of global unfolding pathways showed that structural disruptions at the beta sheet regions near the N-terminal were still imminent. These findings could provide the insight on the molecular mechanisms underlying the enhanced thermostability due to mutagenesis and changes in the protein unfolding pathways for further protein engineering of the GH11 family xylanase enzymes.     

Response surface methodology to supercritical carbon dioxide extraction of astaxanthin from Haematococcus pluvialis

Experimental design was used to investigate the effect of operating temperature (40-80 degrees C), operating pressure (30-50 MPa), and extraction time (1-4h) of supercritical carbon dioxide (SC-CO2) extraction on astaxanthin yields and the extract antioxidant activity (IC50). The ranges of the factors investigated were 40-80 degrees C for the operating temperature (X1), 30-50 MPa for the operating pressure (X2), and 1-4h for the extraction time (X3). The statistical analysis of the experiment indicated that pressure, extraction time, and the interaction between temperature and pressure (X1X2) had significant effect on astaxanthin yields. The central composite design showed that polynomial regression models were in good agreement with the experimental results with the coefficients of determination of 0.924 and 0.846 for astaxanthin yield and antioxidant activity, respectively. The optimal condition for astaxanthin yield within the experimental range of the variables studied was at 70 degrees C, 50 MPa, and 4h. At this condition, the predicted amount of astaxanthin extracted was 23.04 mg/g (2.3 wt% or 83.78% recovery). For the effect of experimental extraction conditions on antioxidant activity, IC50 was used as an index, which is the concentration that gives a 50% reduction in the absorbance of the ABTS free radical. The analysis of the results showed that the interaction between the operating temperature and operating pressure (X1X2) was the only significant factor affecting the extract antioxidant activity. The statistical model gave the minimum point for antioxidant activity at 67 degrees C, 40.3 MPa, and 1.86 h of extraction, at which the value for 1/IC50 was 0.39 l/mg (or IC50 was 2.57 mg/l).     

Fast drops: a high-throughput approach for setting up protein crystal screens.

There is significant demand to rapidly obtain protein structure information for both structural genomics and drug discovery applications. To meet this demand, all steps in the process of determining protein structure by X-ray crystallography need to be optimized and streamlined with high-throughput methodologies. This communication describes a method that brings high-throughput technology to protein crystallization in both manual and automated modes, suitable for virtually every crystallography laboratory.     

The first report of RNA U to C or G editing in the mitochondrial NADH dehydrogenase subunit 5 (Nad5) transcript of wild barley

Molecular Biology Reports - Nad dehydrogenase complex in mtDNA has a significant role in cellular respiration. One of the largest subunits in the complex is subunit 5 (Nad5). Four cDNAs of the...     

Absorptive removal of biomass tar using water and oily materials

Water is the most common choice of absorption medium selected in many gasification systems. Because of poor solubility of tar in water, hydrophobic absorbents (diesel fuel, biodiesel fuel, vegetable oil, and engine oil) were studied on their absorption efficiency of biomass tar and compared with water. The results showed that only 31.8% of gravimetric tar was removed by the water scrubber, whereas the highest removal of gravimetric tar was obtained by a vegetable oil scrubber with a removal efficiency of 60.4%. When focusing on light PAH tar removal, the absorption efficiency can be ranked in the following order; diesel fuel > vegetable oil > biodiesel fuel > engine oil > water. On the other hand, an increase in gravimetric tar was observed for diesel fuel and biodiesel fuel scrubbers because of their easy evaporation. Therefore, the vegetable oil is recommended as the best absorbent to be used in gasification systems.     

AGGLUTINATION OF THE CHLOROPHYCEAN FLAGELLATE DUNALIELLA TERTIOLECTA BY TREATMENT WITH LECTINS OR DIVALENT CATIONS AT ALKALINE pH1

Washed cells of Dunaliella tertiolecta Butcher became immobile and agglutinated upon exposure to 100–400 μ/mL lectins in NaCl solution. The agglutinations were strongest with Limulus polyphemus agglutinin and wheat-germ agglutinin, moderate with soybean agglutinin and weakest with Concanavalin A. All lectin-induced agglutinations were inhibited or mitigated by the simultaneous presence of specific lectin-binding sugars. The differential sensitivity of the alga to these lectins suggested that sialic acid and/or N-acetyl-D-glucosamine might be the predominant lectin-receptor sugars in the algal surface coat, with N-acetyl-D-galactosamine likely present as a lesser component. In the absence of lectins, the divalent cations Mg²⁺, Ca²⁺ or Mn²⁺ also caused agglutination, but this process required an alkaline pH of at least ca. 8.6–8.9. Such cation-induced agglutination was reversibly inhibited by the cation complexing agent EDTA as well as by lowering the pH below 8.0. SEM observations of the agglutinations revealed random flagellar attachments as well as direct body contact between agglutinated cells.     

Ultrastructural,cytochemical, and enzymatic studies on the adhesive “plaques” of the brown algaeLaminaria saccharina (L.) lamour. andNereocystis luetkeana (nert.) post. et rupr. 1

Summary Newly settled zoospores of bothLaminaria saccharina andNereocystis luetkeana are surrounded by adhesive plaques. At this stage cell wall deposition has not occurred and similar structures cannot be detected in the cytoplasm. In free swimming zoospores, however, plaques are observed exclusively in small vesicles within the cytoplasm. Enzymatic extractions and cytochemical tests indicate that plaques are glycoproteid in nature. Studies on the influence of several enzymes on the attachment of zoospores show that plaques are involved in the adhesion of zoospores to the substratum.Project supported by NRC grant #A2288. Nereocystis data are part of a Ph.D. dissertation presented by this author to the University of British Columbia.