Biophysical properties of DNA in hydrated ionic liquids

The biophysical properties and behavior of natural calf thymus DNA in hydrated 1-ethyl-3-butylimidazolium bromide ionic liquid ([C2bim]Br) have been studied using spectroscopy technique. The effect of ionic liquid concentration and temperature towards the duplex B-DNA conformation were determined. The presence of ionic liquid causes higher duplex DNA stability with the DNA melting temperature of ∼56°C without any addition of buffer solutions. The electrostatic attraction between ionic liquid’s cation and DNA phosphates groups was found play a main role in stabilizing native DNA structure. Understanding of the biophysical properties of DNA in this ionic media could be used as a platform for future development of specific solvent for nucleic acid nanotechnology

Comparison of estimation capabilities of response surface methodology (RSM) with artificial neural network (ANN) in lipase-catalyzed synthesis of palm-based wax ester

<p>Abstract</p> <p>Background</p> <p>Wax esters are important ingredients in cosmetics, pharmaceuticals, lubricants and other chemical industries due to their excellent wetting property. Since the naturally occurring wax esters are expensive and scarce, these esters can be produced by enzymatic alcoholysis of vegetable oils. In an enzymatic reaction, study on modeling and optimization of the reaction system to increase the efficiency of the process is very important. The classical method of optimization involves varying one parameter at a time that ignores the combined interactions between physicochemical parameters. RSM is one of the most popular techniques used for optimization of chemical and biochemical processes and ANNs are powerful and flexible tools that are well suited to modeling biochemical processes.</p> <p>Results</p> <p>The coefficient of determination (R²) and absolute average deviation (AAD) values between the actual and estimated responses were determined as 1 and 0.002844 for ANN training set, 0.994122 and 1.289405 for ANN test set, and 0.999619 and 0.0256 for RSM training set respectively. The predicted optimum condition was: reaction time 7.38 h, temperature 53.9°C, amount of enzyme 0.149 g, and substrate molar ratio 1:3.41. The actual experimental percentage yield was 84.6% at optimum condition, which compared well to the maximum predicted value by ANN (83.9%) and RSM (85.4%). The order of effective parameters on wax ester percentage yield were; respectively, time with 33.69%, temperature with 30.68%, amount of enzyme with 18.78% and substrate molar ratio with 16.85%, whereas R²and AAD were determined as 0.99998696 and 1.377 for ANN, and 0.99991515 and 3.131 for RSM respectively.</p> <p>Conclusion</p> <p>Though both models provided good quality predictions in this study, yet the ANN showed a clear superiority over RSM for both data fitting and estimation capabilities.</p

An insight into structure and stability of DNA in ionic liquids from molecular dynamics simulation and experimental studies

Molecular dynamics simulation and biophysical analysis were employed to reveal the characteristics and the influence of ionic liquids (ILs) on the structural properties of DNA. Both computational and experimental evidence indicate that DNA retains its native B-conformation in ILs. Simulation data show that the hydration shells around the DNA phosphate group were the main criteria for DNA stabilization in this ionic media. Stronger hydration shells reduce the binding ability of ILs' cations to the DNA phosphate group, thus destabilizing the DNA. The simulation results also indicated that the DNA structure maintains its duplex conformation when solvated by ILs at different temperatures up to 373.15 K. The result further suggests that the thermal stability of DNA at high temperatures is related to the solvent thermodynamics, especially entropy and enthalpy of water. All the molecular simulation results were consistent with the experimental findings. The understanding of the properties of IL–DNA could be used as a basis for future development of specific ILs for nucleic acid technology

High yield lipase-catalyzed synthesis of Engkabang fat esters for the cosmetic industry

Engkabang fat esters were produced via alcoholysis reaction between Engkabang fat and oleyl alcohol, catalyzed by Lipozyme RM IM. The reaction was carried out in a 500 ml Stirred tank reactor using heptane and hexane as solvents. Response surface methodology (RSM) based on a four-factor-five-level Central composite design (CCD) was applied to evaluate the effects of synthesis parameters, namely temperature, substrate molar ratio (oleyl alcohol: Engkabang fat), enzyme amount and impeller speed. The optimum yields of 96.2% and 91.4% were obtained for heptane and hexane at the optimum temperature of 53.9 °C, impeller speeds of 309.5 and 309.0 rpm, enzyme amounts of 4.82 and 5.65 g and substrate molar ratios of 2.94 and 3.39:1, respectively. The actual yields obtained compared well with the predicted values of 100.0% and 91.5%, respectively. Meanwhile, the properties of the esters show that they are suitable to be used as ingredient for cosmetic applications

Solution structure and in Silico binding of a cyclic peptide with hepatitis B surface antigen

A specific ligand targeting the immunodominant region of hepatitis B virus is desired in neutralizing the infectivity of the virus. In a previous study, a disulfide constrained cyclic peptide cyclo S1,S9 Cys-Glu-Thr-Gly-Ala-Lys-Pro-His-Cys (S1, S9-cyclo-CETGAKPHC) was isolated from a phage displayed cyclic peptide library using an affinity selection method against hepatitis B surface antigen. The cyclic peptide binds tightly to hepatitis B surface antigen with a relative dissociation constant (KDrel) of 2.9 nm. The binding site of the peptide was located at the immunodominant region on hepatitis B surface antigen. Consequently, this study was aimed to elucidate the structure of the cyclic peptide and its interaction with hepatitis B surface antigen in silico. The solution structure of this cyclic peptide was solved using 1H, 13C, and 15N NMR spectroscopy and molecular dynamics simulations with NMR-derived distance and torsion angle restraints. The cyclic peptide adopted two distinct conformations due to the isomerization of the Pro residue with one structured region in the ETGA sequence. Docking studies of the peptide ensemble with a model structure of hepatitis B surface antigen revealed that the cyclic peptide can potentially be developed as a therapeutic drug that inhibits the virus–host interactions

Novel octapeptide as an asymmetric catalyst for Michael reaction in aqueous media

In this work, three forms of a novel octapeptide have been evaluated as asymmetric catalysts for the Michael reaction. Low quantity catalyst loading, ecofriendly solvents, and reusability of organocatalyst successfully applied to attain excellent yields and moderate enantioselectivities in the Michael reaction

Asymmetric Michael reaction catalyzed by mimicked peptides

Peptides mimicked from active site of promiscuous aldo-ketoreductase were synthesized and tested as asymmetry catalysts in the Michael adduct reaction of aldehydes or ketones with nitroolefins to furnish the corresponding γ-nitroaldehydes, γ-nitroketones with up to 93 % yield, 99:1 dr and 71 % ee at room temperature and on eco-friendly solvents. Aspartic acid residue as second amino acid produced greater enantioselectivity

Enantioselectivity investigation of short polar peptides with different positions in the Michael reaction

This work reports the effectiveness of short polar peptides as asymmetric catalysts in Michael reactions to attain good yields of enantio- and diastereoselective isomers. In a comparison, glutamic acid and histidine produced greater ee and yields when they were applied as the second amino acid in short trimeric peptides. These short polar peptides were found to be efficient organocatalysts for the asymmetric Michael addition reaction in water

Rational design of mimetic peptides based on aldo-ketoreductase enzyme as asymmetric organocatalysts in aldol reactions

Peptides as a kind of important chiral scaffold are broadly identified for their obvious advantages, diverse structures and accessibility. Based on promiscuous aldo-keto-reductase enzymes, several mimetic peptides were designed which were synthesized and tested as multifunctional organocatalysts in direct asymmetric aldol reactions. The corresponding aldol products were produced with high yields (up to 97%) and excellent diastereoselectivities (up to 99/1) and enantioselectivities (>98%) under mild reaction selectivity and enantioselectivity. The secondary structures of peptide catalysts provide an understanding of their mechanism

Structural conformation of Bacillus stearothermophilus F1 protease and effect of modification on its thermostability

The extracellular F1 serine protease, produced by a thermophilic Bacillus stearothermophilus F1, has been isolated and characterized as one of a serine protease. F1 protease was stable in the pH range of 8.0 to 10.0, with an optimum activity at pH 9.0. The enzyme was stable for 24h at 70°C (Rahman et al., 1994)