scholarly journals ThermoSlope: A Software for Determining Thermodynamic Parameters from Single Steady-State Experiments

Molecules ◽  
2021 ◽  
Vol 26 (23) ◽  
pp. 7155
Author(s):  
Bjarte Aarmo Lund ◽  
Bjørn Olav Brandsdal
Keyword(s):  
Temperature Dependence ◽  
Thermodynamic Parameters ◽  
Enzyme Catalysis ◽  
Traditional Approach ◽  
Extreme Environments ◽  
Valence Bond ◽  
Activation Parameters ◽  
Gradual Change ◽  
Empirical Valence Bond ◽  
Wide Range

The determination of the temperature dependence of enzyme catalysis has traditionally been a labourious undertaking. We have developed a new approach to the classical Arrhenius parameter estimation by fitting the change in velocity under a gradual change in temperature. The evaluation with a simulated dataset shows that the approach is valid. The approach is demonstrated as a useful tool by characterizing the Bacillus pumilus LipA enzyme. Our results for the lipase show that the enzyme is psychrotolerant, with an activation energy of 15.3 kcal/mol for the chromogenic substrate para-nitrophenyl butyrate. Our results demonstrate that this can produce equivalent curves to the traditional approach while requiring significantly less sample, labour and time. Our method is further validated by characterizing three α-amylases from different species and habitats. The experiments with the α-amylases show that the approach works over a wide range of temperatures and clearly differentiates between psychrophilic, mesophilic and thermophilic enzymes. The methodology is released as an open-source implementation in Python, available online or used locally. This method of determining the activation parameters can make studies of the temperature dependence of enzyme catalysis more widely adapted to understand how enzymes have evolved to function in extreme environments. Moreover, the thermodynamic parameters that are estimated serve as functional validations of the empirical valence bond calculations of enzyme catalysis.

scholarly journals Kinetic and Mechanistic Studies on the Reaction of DL-Methionine with in Aqueous Medium at Physiological pH

2009 ◽  
Vol 2009 ◽  
pp. 1-5 ◽  
Author(s):  
Tandra Das ◽  
A. K. Datta ◽  
A. K. Ghosh
Keyword(s):  
Temperature Dependence ◽  
Aqueous Medium ◽  
Equilibrium Constant ◽  
Thermodynamic Parameters ◽  
Activation Parameters ◽  
Outer Sphere ◽  
Ligand Concentration ◽  
Mechanistic Studies ◽  
Association Equilibrium

The reaction has been studied spectrophotometrically; the reaction shows two steps, both of which are dependent on ligand concentration and show a limiting nature. An associative interchange mechanism is proposed. Kinetic and activation parameters ( and ) and (, , , and ) have been calculated. From the temperature dependence of the outer sphere association equilibrium constant, thermodynamic parameters ( and ; and ) have also been calculated.

scholarly journals Histidine protonation states are key in the LigI catalytic reaction mechanism

2021 ◽  
Author(s):  
LINA ZHAO ◽  
Dibyendu Mondal ◽  
Weifeng Li ◽  
Yuguang Mu ◽  
Philipp Kaldis
Keyword(s):  
Active Site ◽  
Enzyme Catalysis ◽  
Valence Bond ◽  
Free Energy Calculations ◽  
Active Site Residues ◽  
Protonation State ◽  
Empirical Valence Bond ◽  
Hydrolysis Of ◽  
Catalytic Reaction Mechanism

Lignin is one of the world’s most abundant organic polymers, and 2-pyrone-4,6-dicarboxylate lactonase (LigI) catalyzes the hydrolysis of 2-pyrone-4,6-dicarboxylate (PDC) in the degradation of lignin. The pH has profound effects on enzyme catalysis and therefore we studied this in the context of LigI. We found that changes of the pH mostly affects surface residues, while the residues at the active site are more subject to changes of the surrounding microenvironment. In accordance with this, a high pH facilitates the deprotonation of the substrate. Detailed free energy calculations by the empirical valence bond (EVB) approach revealed that the overall hydrolysis reaction is more likely when the three active site histidines (His31, His33 and His180) are protonated at the ɛ site, however, protonation at the δ site may be favored during specific steps of reaction. Our studies have uncovered the determinant role of the protonation state of the active site residues His31, His33 and His180 in the hydrolysis of PDC.

scholarly journals Biodiversity of Secondary Metabolites Compounds Isolated from Phylum Actinobacteria and Its Therapeutic Applications

Molecules ◽  
2021 ◽  
Vol 26 (15) ◽  
pp. 4504
Author(s):  
Muhanna Al-shaibani ◽  
Radin Maya Saphira Radin Mohamed ◽  
Nik Sidik ◽  
Hesham Enshasy ◽  
Adel Al-Gheethi ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Bioactive Compounds ◽  
Extreme Environments ◽  
Software Tool ◽  
Gene Clusters ◽  
Well Being ◽  
Bioactive Substances ◽  
Diverse Range ◽  
Wide Range ◽  
Potential Applications

The current review aims to summarise the biodiversity and biosynthesis of novel secondary metabolites compounds, of the phylum Actinobacteria and the diverse range of secondary metabolites produced that vary depending on its ecological environments they inhabit. Actinobacteria creates a wide range of bioactive substances that can be of great value to public health and the pharmaceutical industry. The literature analysis process for this review was conducted using the VOSviewer software tool to visualise the bibliometric networks of the most relevant databases from the Scopus database in the period between 2010 and 22 March 2021. Screening and exploring the available literature relating to the extreme environments and ecosystems that Actinobacteria inhabit aims to identify new strains of this major microorganism class, producing unique novel bioactive compounds. The knowledge gained from these studies is intended to encourage scientists in the natural product discovery field to identify and characterise novel strains containing various bioactive gene clusters with potential clinical applications. It is evident that Actinobacteria adapted to survive in extreme environments represent an important source of a wide range of bioactive compounds. Actinobacteria have a large number of secondary metabolite biosynthetic gene clusters. They can synthesise thousands of subordinate metabolites with different biological actions such as anti-bacterial, anti-parasitic, anti-fungal, anti-virus, anti-cancer and growth-promoting compounds. These are highly significant economically due to their potential applications in the food, nutrition and health industries and thus support our communities’ well-being.

Corrosion resistant metal-ceramic composite coatings for tribological applications

2021 ◽  
pp. 1-34
Author(s):  
Peter Renner ◽  
Swarn Jha ◽  
Yan Chen ◽  
Tariq Chagouri ◽  
Serge Kazadi ◽  
...  
Keyword(s):  
Ceramic Composite ◽  
Low Cost ◽  
Composite Coatings ◽  
Salt Spray ◽  
Extreme Environments ◽  
Safe Procedure ◽  
Corrosion Resistant ◽  
Wide Range ◽  
Metal Ceramic ◽  
Corrosion Resistant Coatings

Abstract Effective design of corrosion-resistant coatings is critical for the protection of metals and alloys. Many state-of-the-art corrosion-resistant coatings are unable to satisfy the challenges in extreme environments for tribological applications, such as elevated or cryogenic temperatures, high mechanical loads and impacts, severe wear, chemical attack, or a combination of these. The nature of challenging conditions demands that coatings have high corrosion and wear resistance, sustained friction control, and maintain surface integrity. In this research, multi-performance metal-ceramic composite coatings were developed for applications in harsh environments. These coatings were developed with an easy to fabricate, low-cost, and safe procedure. The coating consisted of boron nitride, graphite, silicon carbide, and transition metals such as chromium or nickel using epoxy as vehicle and bonding agent. Salt spray corrosion tests showed that 1010 carbon steel (1/4 hard temper) substrates lost 20-100× more mass than the coatings. The potentiodynamic polarization study showed better performance of the coatings by seven orders of magnitude in terms of corrosion relative to the substrate. Additionally, the corrosion rates of the coatings with Ni as an additive were five orders of magnitude lower than reported. The coefficient of friction of coatings was as low as 0.1, five to six times lower than that of epoxy and lower than a wide range of epoxy resin-based coatings found in literature. Coatings developed here exhibited potential in applications in challenging environments for tribological applications.

scholarly journals The role of enzyme dynamics and tunnelling in catalysing hydride transfer: studies of distal mutants of dihydrofolate reductase

2006 ◽  
Vol 361 (1472) ◽  
pp. 1307-1315 ◽  
Author(s):  
Lin Wang ◽  
Nina M Goodey ◽  
Stephen J Benkovic ◽  
Amnon Kohen
Keyword(s):  
Temperature Dependence ◽  
Dihydrofolate Reductase ◽  
Isotope Effects ◽  
Hydride Transfer ◽  
Activation Parameters ◽  
Physical Nature ◽  
Enzyme Dynamics ◽  
Temperature Dependences ◽  
Donor Acceptor ◽  
Significant Temperature

Residues M42 and G121 of Escherichia coli dihydrofolate reductase ( ec DHFR) are on opposite sides of the catalytic centre (15 and 19 Å away from it, respectively). Theoretical studies have suggested that these distal residues might be part of a dynamics network coupled to the reaction catalysed at the active site. The ec DHFR mutant G121V has been extensively studied and appeared to have a significant effect on rate, but only a mild effect on the nature of H-transfer. The present work examines the effect of M42W on the physical nature of the catalysed hydride transfer step. Intrinsic kinetic isotope effects (KIEs), their temperature dependence and activation parameters were studied. The findings presented here are in accordance with the environmentally coupled hydrogen tunnelling. In contrast to the wild-type (WT), fluctuations of the donor–acceptor distance were required, leading to a significant temperature dependence of KIEs and deflated intercepts. A comparison of M42W and G121V to the WT enzyme revealed that the reduced rates, the inflated primary KIEs and their temperature dependences resulted from an imperfect potential surface pre-arrangement relative to the WT enzyme. Apparently, the coupling of the enzyme's dynamics to the reaction coordinate was altered by the mutation, supporting the models in which dynamics of the whole protein is coupled to its catalysed chemistry.

Solvolysis of isopropyl bromide in ethanol–water mixtures. Dissection into initial state and transition state contributions

1976 ◽  
Vol 54 (24) ◽  
pp. 3944-3948 ◽  
Author(s):  
Wiendelt Drenth ◽  
Michael Cocivera
Keyword(s):  
Vapor Pressure ◽  
Transition State ◽  
Thermodynamic Parameters ◽  
Activation Parameters ◽  
Solvent Composition ◽  
Initial State ◽  
Partial Vapor Pressure ◽  
State Variation

Rates were determined for the solvolysis of isopropyl bromide in ethanol–water mixtures (20 to 80% by volume of ethanol) at 50 and 75 °C and the corresponding activation parameters calculated. From the partial vapor pressure of isopropyl bromide over the various solutions at 50 and 75 °C, the variations in its initial state thermodynamic parameters were calculated. Thus, the variation in the activation parameters with solvent composition could be analyzed in terms of initial and transition state contributions. The initial state variation dominates according to a unimolecular as well as to a bimolecular treatment of data.

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