Understanding Thermostability Factors of <Emphasis Type="Italic">Aspergillus niger</Emphasis> PhyA Phytase: A Molecular Dynamics Study

Molecular dynamics simulation was used to study the dynamic differences between native Aspergillus niger PhyA phytase and a mutant with 20 % greater thermostability. Atomic root mean square deviation, radius of gyration, and number of hydrogen bonds and salt bridges are examined to determine thermostability factors. The results suggest that, among secondary structure elements, loops have the most impact on the thermal stability of A. niger phytase. In addition, the location rather than the number of hydrogen bonds is found to have an important contribution to thermostability. The results also show that salt bridges may have stabilizing or destabilizing effect on the enzyme and influence its thermostability accordingly.     

Molecular dynamics simulation of oleyl oleate swollen micelles system

Problems with transdermal drug delivery were directly associated with the skin barrier which is the lipid bilayer at the stratum corneum. Chemical penetration enhancers such as swollen micelles that formed from the solubilisation of the surfactants in the nano-emulsion system could provide an effective solution. However, the structural properties of swollen micelles from nano-emulsions of palm-oil esters, whose behaviour is related to colloidal systems, have not been studied in great detail. In this paper, we report on the use of molecular dynamics (MD) simulations to investigate the structural properties of swollen micelles of oleyl oleate (OE). Five series of 10 ns MD simulations were performed at different micelle compositions to determine the structural evolution of OE/Span20 (S20) swollen micelles. We also carried out four MD simulations on the structure of S20, OE/S20, Tween80 (T80) and OE/T80 micelles to study the effect of different surfactants and the addition of OE into the systems. The shapes of the swollen micelles were observed to vary by the difference in the micelle composition, the surfactants used and the addition of OE. The results were correlated with published theory, and consistent with experimental results on the phase behaviour of the nano-emulsion system.     

Screening and docking chemical ligands onto pocket cavities of a protease for designing a biocatalyst

A detailed study of the trypsin surface has been carried out to gain insight into its biological functions and interactions which helped to determine the binding specificity. Twenty-four cavity pockets were automatically identified on trypsin from PDB file entry 1AUJ using CASTp (Computed Atlas of Surface Topography of proteins). Molecular docking was exploited as an efficient in silico screening tool for studying protein–ligand interactions. A systematic docking study using Autodock 3.05 has been performed on the five largest binding pockets in trypsin. A set of ten putative chemical ligands was used to dock into selected binding pockets. Docking of ligands into the five largest pockets in trypsin showed that 1,10-phenanthroline and ethanolamine preferentially bound at pocket 24 and benzamidine at pocket 22. Thermodynamically, we also found that ethanol, propanol, propandiol and phosphoethanolamine preferentially bound at pocket 21 whereas p-aminobenzamidine, phenylacetic acid and phenylalanine interacted mainly at pocket 20 based on their lowest interaction free energy.     

Application of advanced materials as support for immobilisation of lipase from Candida rugosa

Ni/Al-layered double hydroxides (Ni-LDHs) and Ni/Al-sodium dodecyl sulfonate layered double hydroxide nanocomposites (Ni-SDS-LDHs) with a molar ratio of Ni:Al (4:1) have been prepared by a co-precipitation (or salt-base) method. Their structures were determined using Powder X-Ray Diffractometer (PXRD) and the spectra showed that basal spacings for Ni-LDHs and Ni-SDS-LDHs synthesised were around 8.1?Å and 34.8?Å, respectively. Lipase from Candida rugosa was immobilised onto these advanced materials, by physical adsorption. The activity of immobilised lipase was investigated through esterification of palmitic acid and isopropyl alcohol in hexane. The effects of reaction temperature, thermostability, stability in organic solvent, operational stability, leaching and storage studies of the immobilised lipase were investigated. These biocatalysts exhibited higher activities than the native lipase with an optimum temperature of 40°C. Immobilised lipases showed higher storage stability than native lipase (up to 60 days) and during operational studies at 30°C for 5?h, more than 50% of its activity was retained. Leaching studies showed that physical adsorption is suitable for the attachment of enzymes onto LDHs.     

Nutrient Amendments of Inorganic Fertiliser and Oil Palm Empty Fruit Bunch and Their Influence on Bacterial Species Dominance and Degradation of the Associated Crude Oil Constituents

The effects of inorganic commercial fertiliser (N:P:K = 8:8:1) and oil palm empty fruit bunch (EFB) as nutrient amendments for crude oil degradation and microbial population shift by a microbial consortium [Pseudomonas sp. (UKMP-14T), Acinetobacter sp. (UKMP-12T), Trichoderma sp. (TriUKMP-1M and TriUKMP-2M)] were assessed. The bacterial populations present during crude oil degradation were analysed by spread plate method and 16S rRNA sequences, whereas the presence of fungi was assessed by growth on potato dextrose agar. Crude oil degradation analysed using gas chromatography-flame ionisation detection showed total petroleum hydrocarbon reduced between 70 and 100%, depending on the type of amendments compared to control (≈55%) after 30 days of incubation. Nutrient amendments using NPK fertiliser or EFB were found to influence the domination of different bacterial species, which in turn preferentially utilised different hydrocarbons. This study suggested different nutrient amendments could be used to preferentially select bacteria to degrade different components of crude oil, particularly pertaining to the recalcitrant phytane. This information is very useful for application of in situ bioremediation of soil hydrocarbon contamination.     

Purification and Characterisation of an F16L Mutant of a Thermostable Lipase

A mutant of the lipase from Geobacillus sp. strain T1 with a phenylalanine to leucine substitution at position 16 was overexpressed in Escherichia coli strain BL21(De3)pLysS. The crude enzyme was purified by two-step affinity chromatography with a final recovery and specific activity of 47.4 and 6,315.8 U/mg, respectively. The molecular weight of the purified F16L lipase was approximately 43 kDa by 12% SDS-PAGE analysis. The F16L lipase was demonstrated to be a thermophilic enzyme due its optimum temperature at 70 °C and showed stability over a temperature range of 40–60 °C. The enzyme exhibited an optimum pH 7 in phosphate buffer and was relatively stable at an alkaline pH 8–9. Metal ions such as Ca²⁺, Mn²⁺, Na⁺, and K⁺ enhanced the lipase activity, but Mg²⁺, Zn²⁺, and Fe²⁺ inhibited the lipase. All surfactants tested, including Tween 20, 40, 60, 80, Triton X-100, and SDS, significantly inhibited the lipolytic action of the lipase. A high hydrolytic rate was observed on long-chain natural oils and triglycerides, with a notable preference for olive oil (C18:1; natural oil) and triolein (C18:1; triglyceride). The F16L lipase was deduced to be a metalloenzyme because it was strongly inhibited by 5 mM EDTA. Moderate inhibition was observed in the presence of PMSF at a similar concentration, indicating that serine residues are involved in its catalytic action. Further, the activity was not impaired by water-miscible solvents, including methanol, ethanol, and acetone.     

Solution Structures,Dynamics, and Ice Growth Inhibitory Activity of Peptide Fragments Derived from an Antarctic Yeast Protein

Exotic functions of antifreeze proteins (AFP) and antifreeze glycopeptides (AFGP) have recently been attracted with much interest to develop them as commercial products. AFPs and AFGPs inhibit ice crystal growth by lowering the water freezing point without changing the water melting point. Our group isolated the Antarctic yeast Glaciozyma antarctica that expresses antifreeze protein to assist it in its survival mechanism at sub-zero temperatures. The protein is unique and novel, indicated by its low sequence homology compared to those of other AFPs. We explore the structure-function relationship of G. antarctica AFP using various approaches ranging from protein structure prediction, peptide design and antifreeze activity assays, nuclear magnetic resonance (NMR) studies and molecular dynamics simulation. The predicted secondary structure of G. antarctica AFP shows several α-helices, assumed to be responsible for its antifreeze activity. We designed several peptide fragments derived from the amino acid sequences of α-helical regions of the parent AFP and they also showed substantial antifreeze activities, below that of the original AFP. The relationship between peptide structure and activity was explored by NMR spectroscopy and molecular dynamics simulation. NMR results show that the antifreeze activity of the peptides correlates with their helicity and geometrical straightforwardness. Furthermore, molecular dynamics simulation also suggests that the activity of the designed peptides can be explained in terms of the structural rigidity/flexibility, i.e., the most active peptide demonstrates higher structural stability, lower flexibility than that of the other peptides with lower activities, and of lower rigidity. This report represents the first detailed report of downsizing a yeast AFP into its peptide fragments with measurable antifreeze activities.     

Cloning of a DNA region of aPseudomonas plasmid that codes for detoxification of the herbicide paraquat

A newly isolatedPseudomonas plasmid coding for detoxification of the herbicide paraquat (Pq^r) was characterized. AnEcoR1-generated fragment derived from the plasmid carrying the Pq^r determinant was cloned intoEscherichia coli. Subsequent subclonings, followed by exonuclease III-mediated deletion analysis, localized the Pq^r gene(s) to a 1.8-kb segment within a 4.2Pst1 subfragment. The cloning and apparent expression of the Pq^r gene(s) inE. coli will enable its structural organization and function to be analyzed in detail.