Insights into the molecular interaction between sucrose and α-chymotrypsin

© 2018 Elsevier B.V. One of the most important purposes of enzyme engineering is to increase the thermal and kinetic stability of enzymes, which is an important factor for using enzymes in industry. The purpose of the present study is to achieve a higher thermal stability of α-chymotrypsin (α-Chy) by modification of the solvent environment. The influence of sucrose was investigated using thermal denaturation analysis, fluorescence spectroscopy, circular dichroism, molecular docking and molecular dynamics (MD) simulations. The results point to the effect of sucrose in enhancing the α-Chy stability. Fluorescence spectroscopy revealed one binding site that is dominated by static quenching. Molecular docking and MD simulation results indicate that hydrogen bonding and van der Waals forces play a major role in stabilizing the complex. Tm of this complex was enhanced due to the higher H-bond formation and the lower surface hydrophobicity after sucrose modification. The results show the ability of sucrose in protecting the native structural conformation of α-Chy. Sucrose was preferentially excluded from the surface of α-Chy which is explained by the higher tendency of water toward favorable interactions with the functional groups of α-Chy than with sucrose

Stable stem enabled Shannon entropies distinguish non-coding RNAs from random backgrounds

<p>Abstract</p> <p>Background</p> <p>The computational identification of RNAs in genomic sequences requires the identification of signals of RNA sequences. Shannon base pairing entropy is an indicator for RNA secondary structure fold certainty in detection of structural, non-coding RNAs (ncRNAs). Under the Boltzmann ensemble of secondary structures, the probability of a base pair is estimated from its frequency across all the alternative equilibrium structures. However, such an entropy has yet to deliver the desired performance for distinguishing ncRNAs from random sequences. Developing novel methods to improve the entropy measure performance may result in more effective ncRNA gene finding based on structure detection.</p> <p>Results</p> <p>This paper shows that the measuring performance of base pairing entropy can be significantly improved with a constrained secondary structure ensemble in which only canonical base pairs are assumed to occur in energetically stable stems in a fold. This constraint actually reduces the space of the secondary structure and may lower the probabilities of base pairs unfavorable to the native fold. Indeed, base pairing entropies computed with this constrained model demonstrate substantially narrowed gaps of Z-scores between ncRNAs, as well as drastic increases in the Z-score for all 13 tested ncRNA sets, compared to shuffled sequences.</p> <p>Conclusions</p> <p>These results suggest the viability of developing effective structure-based ncRNA gene finding methods by investigating secondary structure ensembles of ncRNAs.</p

Urease Activity Protection With EDTA Against Nanoparticles (Fe2O3 and Fe3O4) Inactivation

In this study the effects of Fe2O3 and Fe3O4 magnetic nanoparticles and EDTA on urease activity was investigated. The effect of nano-Fe2O3 and nano-Fe3O4 on urease activity were investigated. Urease activity was studies by UV-Vis spectrophotometry at 40 °C at pH = 7.2 using sodium phosphate as buffer. Measurements were carried out using 0.075 mg/ml of urease and a range of nano-Fe2O3 and nano-Fe3O4 concentrations between 0.002-0.006 mg/ml. It was found that by increasing the concentration of nano-Fe2O3 and nano-Fe3O4, urease activity will be decreased. On the other hand, nano-Fe2O3 and nano-Fe3O4 act as non competitive inhibitor for urease. Urease protection studies were corried out by using different concentration of EDTA (0.004-0.008 mg/ml). It was shown by increasing the concentration of EDTA, the activity of enzyme increased

Structural studies on the interaction of nano-SiO2 with lysozyme

The interaction between nano-SiO2 and lysozyme was investigated by the method of UV-Visible  detection and fluorescence spectroscopic techniques. The thermal denaturation of lysozyme has been investigated in the presence and absence of nano-SiO2 over the temperature range (293-373) K in different buffers and pH values, using temperature scanning spectroscopy. The presence of nano-SiO2 caused the destabilization of lysozyme resulting in a decrease in the temperature of unfolding with an increase in nano-SiO2 concentration

Spectroscopic Studies on the Interaction of Nano-TiO2 with Lysozyme

In the present study, the interaction between nano-TiO2 and lysozyme was investigated by the method of UV-Vis detection and fluorescence spectroscopic techniques. The thermal denaturation of lysozyme has been investigated in the presence and absence of nano-TiO2 over the temperature range (293-373) K in different buffer and pH, using temperature scanning spectroscopy. The presence of nano-TiO2 caused the destabilization of lysozyme resulting in a decrease in the temperature of unfolding with an increase in nano-TiO2 concentration

Thermal Inactivation and Aggregation of Lysozyme in the Presence of Nano- TiO2 and Nano-SiO2 in Neutral pH

Protein aggregation is a problem in biotechnology. High temperature is one of the most important reasons to enhance enzyme inactivation and aggregation in industrial systems. This work focuses on the effect of TiO2 and SiO2 nanoparticles on refolding and reactivation of lysozyme. In the presence of TiO2 and SiO2 nanoparticles, after enzyme heat treatment at 98◦C for 30 min, not only aggregates were observed, but the amount of those increased. Hence the residual activity of lysozyme (without additives) and even in the presence of TiO2 and SiO2 nanoparticles after heat treatment was very low