Enzymology and thermal stability of phytase appA mutants

RSC Advances ◽  
2015 ◽  
Vol 5 (54) ◽  
pp. 43863-43872 ◽  
Author(s):  
Xi Wang ◽  
Mingze Yao ◽  
Binsheng Yang ◽  
Yuejun Fu ◽  
Fengyun Hu ◽  
...  
Keyword(s):  
Thermal Stability ◽  
Melting Temperature ◽  
Titration Curves ◽  
Thermal Stability Of

(A) The comparison of different melting temperature (Tm) of appA (), appAM8 () and appAM10 (). TheTmvalues were 60 °C for appA, 64.1 °C for appAM8, and 67.5 °C for appAM10. (B) Titration curves of the addition TNS to appAM10 (a) and appA (b).

Thermal stability of marks gold nanoparticles: A molecular dynamics simulation

2017 ◽  
Vol 31 (07) ◽  
pp. 1741001
Author(s):  
Yanlin Jia ◽  
Siqi Li ◽  
Weihong Qi ◽  
Mingpu Wang ◽  
Zhou Li ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Thermal Stability ◽  
Melting Temperature ◽  
Cohesive Energy ◽  
Au Nanoparticles ◽  
Mean Square Displacement ◽  
Dynamics Simulation ◽  
Structure Variation ◽  
Deformation Parameters ◽  
Thermal Stability Of

Molecular dynamics (MDs) simulations were used to explore the thermal stability of Au nanoparticles (NPs) with decahedral, cuboctahedral, icosahedral and Marks NPs. According to the calculated cohesive energy and melting temperature, the Marks NPs have a higher cohesive energy and melting temperature compared to these other shapes. The Lindemann index, radial distribution function, deformation parameters, mean square displacement and self-diffusivity have been used to characterize the structure variation during heating. This work may inspire researchers to prepare Marks NPs and apply them in different fields.

scholarly journals Predicting protein thermal stability changes upon point mutations using statistical potentials: Introducing HoTMuSiC

2016 ◽  
Author(s):  
Fabrizio Pucci ◽  
Raphaël Bourgeas ◽  
Marianne Rooman
Keyword(s):  
Thermal Stability ◽  
Melting Temperature ◽  
Point Mutations ◽  
Model Structure ◽  
Temperature Dependent ◽  
Statistical Potentials ◽  
Validation Procedure ◽  
The Impact ◽  
Fold Cross Validation ◽  
Thermal Stability Of

The accurate prediction of the impact of an amino acid substitution on the thermal stability of a protein is a central issue in protein science, and is of key relevance for the rational optimization of various bioprocesses that use enzymes in unusual conditions. Here we present one of the first computational tools to predict the change in melting temperature ΔTmupon point mutations, given the protein structure and, when available, the melting temperature Tmof the wild-type protein. The key ingredients of our model structure are standard and temperature-dependent statistical potentials, which are combined with the help of an artificial neural network. The model structure was chosen on the basis of a detailed thermodynamic analysis of the system. The parameters of the model were identified on a set of more than 1,600 mutations with experimentally measured ΔTm. The performance of our method was tested using a strict 5-fold cross-validation procedure, and was found to be significantly superior to that of competing methods. We obtained a root mean square deviation between predicted and experimental ΔTmvalues of 4.2°C that reduces to 2.9°C when ten percent outliers are removed. A webserver-based tool is freely available for non-commercial use at soft.dezyme.com.

scholarly journals Second generation silver(I)-mediated imidazole base pairs

2014 ◽  
Vol 10 ◽  
pp. 2139-2144 ◽  
Author(s):  
Susanne Hensel ◽  
Nicole Megger ◽  
Kristina Schweizer ◽  
Jens Müller
Keyword(s):  
Thermal Stability ◽  
Melting Temperature ◽  
Base Pair ◽  
Metal Ion ◽  
Second Generation ◽  
Dna Duplex ◽  
Base Pairs ◽  
Double Helices ◽  
Thermal Stability Of

The imidazole–Ag(I)–imidazole base pair is one of the best-investigated artificial metal-mediated base pairs. We show here that its stability can be further improved by formally replacing the imidazole moiety by a 2-methylimidazole or 4-methylimidazole moiety. A comparison of the thermal stability of several double helices shows that the addition of one equivalent of Ag(I) leads to a 50% larger increase in the melting temperature when a DNA duplex with methylated imidazole nucleosides is applied. This significant effect can likely be attributed to a better steric shielding of the metal ion within the metal-mediated base pair.

A Comparative Study of the Influence of Aquaous 2,2,2-Trifluoroethanol And Ethanol on the Structural Organization, the Kinetic and Thermodynamic Properties of Oligodeoxyribonucleotides Intermolecular Complex Formation

2013 ◽  
Vol 8 (1) ◽  
pp. 115-124
Author(s):  
Aleksandr Lomzov ◽  
Kseniya Ivanova ◽  
Inna Pyshnaya ◽  
Elena Dmitrienko ◽  
Dmitriy Pyshnyi
Keyword(s):  
Thermal Stability ◽  
Aqueous Solution ◽  
Comparative Study ◽  
Melting Temperature ◽  
Structural Organization ◽  
Volume Fraction ◽  
Dna Duplexes ◽  
Intermolecular Complex ◽  
Linear Decrease ◽  
Thermal Stability Of

A comparative study of the structural organization, thermodynamic and kinetic properties of the oligodeoxynucleotides complexes formation in the presence of 2,2,2-trifluoroethanol and ethanol in aqueous solution (volume fraction of alcohol 0 to 50 %) was performed. No significant changes in the circular dichroism spectra of oligonucleotides and their complexes at the adding of 50 % v/v alcohol into a solution, was observed, and they retain the profile typical for B-form DNA. The study of the thermal stability of DNA duplexes showed that the increase in the volume fraction of ethanol in the aqueous solution up to 50 % results in a linear decrease in the melting temperature of the intermolecular DNA complexes. In the case of the 2,2,2-trifluoroethanol we observed atypical dependence of thermal stability of DNA duplexes on the fraction of the fluorine-containing co-solvent. Increasing the alcohol fraction from 0 to 20% v/v led to a linear decrease of the melting point of the complex. A further increase in the volume fraction of alcohol (up to 50 %) did not change the thermal stability of the duplexes. It was shown, that the destabilizing effect of the two co-solvents is due to the increase of the dissociation rate constant of the complex and has mainly entropic nature. On the example of oligonucleotides complexes of 8, 12, 15 and 20 base pairs length the possibility of prediction DNA duplexes thermal stability was shown. A model taking into account the change of a number solvent molecules interacting with nucleic acids at the duplex formation in aqueous ethanol (50 % v/v) or trifluoroethanol (20 % v/v) was applied. An accuracy of melting temperature prediction was 1.3 and 0.6 degrees. Using this model, we found that the addition of alcohols in solution leads to an increase in the number of water molecules that bind to a complementary pair of nucleotides at the formation of intermolecular complex (in the presence of ethanol or trifluoroethanol 0.51 ± 0.09 and 1.33 ± 0.12, respectively). At the same time, alcohols interacted with single-stranded oligonucleotides and double-stranded in the same way

Anomaly in Thermal Stability of Nanostructured Materials

2010 ◽  
Vol 653 ◽  
pp. 23-30 ◽  
Author(s):  
Karuna Kar Nanda
Keyword(s):  
Thermal Stability ◽  
Particle Size ◽  
Melting Temperature ◽  
Nanostructured Materials ◽  
Vapour Pressure ◽  
Elevated Temperatures ◽  
Volume Ratio ◽  
Local Maxima ◽  
Embedded Nanoparticles ◽  
Thermal Stability Of

Understanding of the melting temperature of nanostructures is beneficial to exploit phase transitions and their applications at elevated temperatures. The melting temperature of nanostructured materials depends on particle size, shape and dimensionality and has been well established both experimentally and theoretically. The large surface-to-volume ratio is the key for the low melting temperature of nanostructured materials. The melting temperature of almost free nanoparticles decreases with decreasing size although there are anomalies for some cases. Superheating has been reported for some embedded nanoparticles. Local maxima and minima in the melting temperature have been reported for particles with fewer atoms. Another quantity that is influenced by large surface-to-volume ratio and related to the thermal stability, is the vapour pressure. The vapour pressure of nanoparticles is shown to be enhanced for smaller particles. In this article, we have discussed the anomaly in thermal stability of nanostructured materials.

New Porphyrins/Calf Thymus DNA Complexes - Their Thermostability

2015 ◽  
Vol 1084 ◽  
pp. 554-558
Author(s):  
Lusine Aloyan ◽  
Yeva Dalyan ◽  
Aleksey Gogolev
Keyword(s):  
Thermal Stability ◽  
Melting Temperature ◽  
Relative Concentration ◽  
Melting Curve ◽  
Water Soluble ◽  
Dna Melting ◽  
Binding Mechanism ◽  
Dna Complexes ◽  
Calf Thymus ◽  
Thermal Stability Of

The paper studies the melting parameters of the complexes of water soluble cationic 3N- and 4N-pyridyl porphyrins with different peripheral substituents (oxyethyl, buthyl, allyl, metallyl) with DNA. The results indicate that the presence of porphyrin changes the shape and parameters of DNA melting curve. The porphyrin concentration increase results in the increase of the melting temperature (Tm) and melting interval (ΔT) of DNA. With the porphyrin-DNA concentration ratio ν = 0.01, changes of melting temperature have not been observed. The melting intervals almost do not change upon the addition of the 4N- porphyrins, while the decrease of ΔT is observed in the presence of 3N-porphyrins. Because of the intercalation binding mechanism occurring in GC-rich regions of DNA, we assume that 3N-porphyrins intercalated in GC-rich regions, reduce the thermal stability of these sites, bringing them closer to the thermal stability of the AT-sites, which is the reason for the decrease in melting interval. While with the relative concentration ν = 0.01 for 4-N porphyrins the external binding mechanism “turns on” and destabilizing effect of porphyrins on GC-pairs compensated by their stabilizing effect on AT-pairs. As a result, no change in the melting parameters of DNA is observed upon complexation with these porphyrins.

Calculating Melting Temperature of Native and Modified Oligonucleotide Complexes at Various Cation Concentrations with the Use of Enhanced Counterion Condensation Model

2010 ◽  
Vol 3 (2) ◽  
pp. 61-75
Author(s):  
Aleksandr A. Lomzov ◽  
Dmitriy V. Pyshnyi
Keyword(s):  
Thermal Stability ◽  
Ionic Strength ◽  
Melting Temperature ◽  
Binding Constants ◽  
Data Sets ◽  
Dna Duplexes ◽  
Counterion Binding ◽  
Cation Concentration ◽  
Wide Range ◽  
Thermal Stability Of

A new model describing the influence of ionic strength on thermal stability of DNA comlexes of oligonucleotides is proposed. This model assumes that binding of cations with DNA polyanions influences solely the entropy of hybridization and has a saturating mode. The efficacy of counterion binding with single- and double-stranded DNA is different, and the number of cations which bind additionally with the oligonucleotide at duplex formation depends on bulk cation concentration. Analytical equations describing the influence of cation concentration on melting temperature of DNA-duplexes as function of the length of oligonucleotide, its GC-composition and presence of the modification (non-nucleotide insert) were obtained. The values of melting temperature (Tm ) and thermodynamic parameters ( o ∆H , o ∆S ) characterizing the hybridization of both native and «bridged» oligonucleotides (bearing non-nucleotide insert on the basis of diethylene glycol phosphodiester) with DNA in various concentrations of NaCl (0,01÷1 М) were obtained using the UV-melting technique. Based on both the data obtained and presented in literature the database (695 data sets) characterizing the influence of ionic strength on the thermal stability of oligonucleotide complexes of various structure is developed. The database analysis allows us to obtain the values of the equilibrium binding constants for condensation of caions on DNA and the number of ions required for saturation of a discrete binding site. The proposed enhanced model of cation condensation utilizing unified thermodynamic increments of dsDNA formation allows us to calculate melting temperatures of DNAduplexes in the wide range of ionic strength ([Na+] = 0,01÷1 М) with high accuracy.

scholarly journals Assessment for Melting Temperature Measurement of Nucleic Acid by HRM

2016 ◽  
Vol 2016 ◽  
pp. 1-8 ◽  
Author(s):  
Jing Wang ◽  
Xiaoming Pan ◽  
Xingguo Liang
Keyword(s):  
Thermal Stability ◽  
Nucleic Acid ◽  
Melting Temperature ◽  
High Sensitivity ◽  
Structural Elements ◽  
Sequence Dependence ◽  
Mutation Scanning ◽  
Dna Triplex ◽  
Uv Melting ◽  
Thermal Stability Of

High resolution melting (HRM), with a high sensitivity to distinguish the nucleic acid species with small variations, has been widely applied in the mutation scanning, methylation analysis, and genotyping. For the aim of extending HRM for the evaluation of thermal stability of nucleic acid secondary structures on sequence dependence, we investigated effects of the dye of EvaGreen, metal ions, and impurities (such as dNTPs) on melting temperature (Tm) measurement by HRM. The accuracy of HRM was assessed as compared with UV melting method, and little difference between the two methods was found when the DNA Tm was higher than 40°C. Both insufficiency and excessiveness of EvaGreen were found to give rise to a little bit higher Tm, showing that the proportion of dye should be considered for precise Tm measurement of nucleic acids. Finally, HRM method was also successfully used to measure Tms of DNA triplex, hairpin, and RNA duplex. In conclusion, HRM can be applied in the evaluation of thermal stability of nucleic acid (DNA or RNA) or secondary structural elements (even when dNTPs are present).

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