On the coupling between the dynamics of protein and water

2017 ◽  
Vol 19 (12) ◽  
pp. 8243-8257 ◽  
Author(s):  
Yulian Gavrilov ◽  
Jessica D. Leuchter ◽  
Yaakov Levy
Keyword(s):  
Thermodynamic Stability ◽  
Flexible Protein ◽  
Solvation Entropy

The solvation entropy of flexible protein regions is higher than that of rigid regions and contributes differently to the overall thermodynamic stability.

Using a Software Application to Evaluation Thermodynamic Stability on the Example of Iron

2019 ◽  
Vol 24 (3) ◽  
pp. 309-312
Author(s):  
Aleksandr S. Gulyaev ◽  
◽  
Vladimir B. Koltsov ◽  
Elena A. Sevryukova ◽  
◽  
...  
Keyword(s):  
Thermodynamic Stability ◽  
Software Application

Theoretical and Experimental Evaluation of the Effect of Fluorinated Substituent on the Topological Landscape and Thermodynamic Stability of Zeolitic Imidazolate Framework Polymorphs

2018 ◽  
Author(s):  
Mihails Arhangelskis ◽  
Athanassis Katsenis ◽  
Novendra Novendra ◽  
Zamirbek Akimbekov ◽  
Dayaker Gandrath ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Mechanochemical Synthesis ◽  
Thermodynamic Stability ◽  
Experimental Evaluation ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Zeolitic Imidazolate Framework ◽  
Functional Theory ◽  
Calorimetric Measurements ◽  
And Calorimetry

By combining mechanochemical synthesis and calorimetry with theoretical calculations, we demonstrate that dispersion-corrected periodic density functional theory (DFT) can accurately survey the topological landscape and predict relative energies of polymorphs for a previously inaccessible fluorine-substituted zeolitic imidazolate framework (ZIF). Experimental screening confirmed two out of three theoretically anticipated polymorphs, and the calorimetric measurements provided an excellent match to theoretically calculated energetic difference between them.<br>

Thermodynamic Stability of Hexagonal and Rhombohedral Bn at Cvd Conditions from Van der Waals Corrected First Principles Calculations

2019 ◽  
Author(s):  
Henrik Pedersen ◽  
Björn Alling ◽  
Hans Högberg ◽  
Annop Ektarawong
Keyword(s):  
Thin Films ◽  
Thermodynamic Stability ◽  
First Principles ◽  
Thermal Equilibrium ◽  
Density Functional ◽  
Van Der Waals ◽  
Chemical Vapor ◽  
First Principles Calculations ◽  
Functional Theory ◽  
The Stability

Thin films of boron nitride (BN), particularly the sp<sup>2</sup>-hybridized polytypes hexagonal BN (h-BN) and rhombohedral BN (r-BN) are interesting for several electronic applications given band gaps in the UV. They are typically deposited close to thermal equilibrium by chemical vapor deposition (CVD) at temperatures and pressures in the regions 1400-1800 K and 1000-10000 Pa, respectively. In this letter, we use van der Waals corrected density functional theory and thermodynamic stability calculations to determine the stability of r-BN and compare it to that of h-BN as well as to cubic BN and wurtzitic BN. We find that r-BN is the stable sp<sup>2</sup>-hybridized phase at CVD conditions, while h-BN is metastable. Thus, our calculations suggest that thin films of h-BN must be deposited far from thermal equilibrium.

Modelling Flexible Protein-Ligand Binding in p38α MAP Kinase using the QUBE Force Field

2019 ◽  
Author(s):  
Joshua Horton ◽  
Alice Allen ◽  
Daniel Cole
Keyword(s):  
Quantum Mechanics ◽  
Force Field ◽  
Map Kinase ◽  
Binding Free Energy ◽  
Quantum Mechanical ◽  
Enhanced Sampling ◽  
Relative Binding ◽  
Stringent Test ◽  
Flexible Protein ◽  
P38α Map Kinase

<div><div><div><p>The quantum mechanical bespoke (QUBE) force field is used to retrospectively calculate the relative binding free energy of a series of 17 flexible inhibitors of p38α MAP kinase. The size and flexibility of the chosen molecules represent a stringent test of the derivation of force field parameters from quantum mechanics, and enhanced sampling is required to reduce the dependence of the results on the starting structure. Competitive accuracy with a widely-used biological force field is achieved, indicating that quantum mechanics derived force fields are approaching the accuracy required to provide guidance in prospective drug discovery campaigns.</p></div></div></div>

Nε-Acetyl L-α Lysine Improves Activity and Stability of α-Amylase at Acidic Conditions: A Comparative Study with other Osmolytes

2020 ◽  
Vol 27 (6) ◽  
pp. 551-556
Author(s):  
Nidhya N. Joghee ◽  
Gurunathan Jayaraman ◽  
Masilamani Selladurai
Keyword(s):  
Enzyme Activity ◽  
Amino Acid ◽  
Thermodynamic Stability ◽  
Protective Effects ◽  
Residual Enzyme Activity ◽  
Functional Stability ◽  
Biotechnological Applications ◽  
Optimal Temperature ◽  
Acidic Conditions ◽  
Cellular Components

Background: Nε-acetyl L-α lysine is an unusual acetylated di-amino acid synthesized and accumulated by certain halophiles under osmotic stress. Osmolytes are generally known to protect proteins and other cellular components under various stress conditions. Objective: The structural and functional stability imparted by Nε-acetyl L-lysine on proteins were unknown and hence was studied and compared to other commonly known bacterial osmolytes - ectoine, proline, glycine betaine, trehalose and sucrose. Methods: Effects of osmolytes on the temperature and pH profiles, pH stability and thermodynamic stability of the model enzyme, α-amylase were analyzed. Results: At physiological pH, all the osmolytes under study increased the optimal temperature for enzyme activity and improved the thermodynamic stability of the enzyme. At acidic conditions (pH 3.0), Nε-acetyl L-α lysine and ectoine improved both the catalytic and thermodynamic stability of the enzyme; it was reflected in the increase in residual enzyme activity after incubation of the enzyme at pH 3.0 for 15 min by 60% and 63.5% and the midpoint temperature of unfolding transition by 11°C and 10°C respectively. Conclusion: Such significant protective effects on both activity and stability of α-amylase imparted by addition of Nε-acetyl L-α lysine and ectoine at acidic conditions make these osmolytes interesting candidates for biotechnological applications.

Formation, Physicochemical Characterization, and Thermodynamic Stability of the Amorphous State of Drugs and Excipients

2016 ◽  
Vol 22 (32) ◽  
pp. 4959-4974 ◽  
Author(s):  
Piera Di Martino ◽  
Federico Magnoni ◽  
Dolores Vargas Peregrina ◽  
Maria Rosa Gigliobianco ◽  
Roberta Censi ◽  
...  
Keyword(s):  
Thermodynamic Stability ◽  
Physicochemical Characterization ◽  
Amorphous State
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