scholarly journals Thermodynamics and kinetics of the F o F 1 -ATPase: application of the probability isotherm

2016 ◽  
Vol 3 (2) ◽  
pp. 150379 ◽  
Author(s):  
Brian Chapman ◽  
Denis Loiselle
Keyword(s):  
Free Energy ◽  
Numerical Solution ◽  
Atp Synthesis ◽  
Enzyme Activation ◽  
Thermodynamic Efficiency ◽  
Second Law ◽  
Metabolic Rates ◽  
Thermodynamics And Kinetics ◽  
Rotary Mechanism ◽  
Kinetics Of

We use the results of recent publications as vehicles with which to discuss the thermodynamics of the proton-driven mitochondrial F o F 1 -ATP synthase, focusing particularly on the possibility that there may be dissociation between rotatory steps and ATP synthesis/hydrolysis. Such stoichiometric ‘slippage’ has been invoked in the literature to explain observed non-ideal behaviour. Numerical solution of the Rate Isotherm (the kinetic equivalent of the more fundamental Probability Isotherm) suggests that such ‘slippage’ is an unlikely explanation; instead, we suggest that the experimental results may be more consistent with damage to the enzyme caused by its isolation from the biomembrane and its experimental fixation, resulting in non-physiological friction within the enzyme's rotary mechanism. We emphasize the unavoidable constraint of the Second Law as instantiated by the obligatory dissipation of Gibbs Free Energy if the synthase is to operate at anything other than thermodynamic equilibrium. We use further numerical solution of the Rate Isotherm to demonstrate that there is no necessary association of low thermodynamic efficiency with high metabolic rates in a bio-world in which the dominating mechanism of metabolic control is multifactorial enzyme activation.

Macromolecular conformations and interactions

2018 ◽  
Author(s):  
Dennis Sherwood ◽  
Paul Dalby
Keyword(s):  
Amino Acids ◽  
Free Energy ◽  
Protein Folding ◽  
Energy Minimum ◽  
Huge Number ◽  
Thermodynamics And Kinetics ◽  
Ligand Interactions ◽  
Kinetics Of ◽  
Single Configuration ◽  
Over Time

As a polymer of many amino acids, any given protein can, in principle, adopt a huge number of configurations. In reality, however, the biologically stable protein adopts a single configuration that is stable over time. Thermodynamically, this configuration must represent a Gibbs free energy minimum. This chapter therefore explores how the thermodynamics and kinetics of protein folding and unfolding can be investigated experimentally (using, for example, chaotropes, heating or ligand interactions), and how these measurements can be used to enrich our understanding of protein configurations and stability.

scholarly journals Thermodynamics and Kinetics in Antibody Resistance of the 501Y.V2 SARS-CoV-2 Variant

2021 ◽  
Author(s):  
Son Tung Ngo ◽  
Trung Hai Nguyen ◽  
Duc-Hung Pham ◽  
Nguyen Thanh Tung ◽  
Pham Cam Nam
Keyword(s):  
Free Energy ◽  
South African ◽  
Binding Free Energy ◽  
Energy Landscape ◽  
Neutralizing Antibody ◽  
Receptor Binding Domain ◽  
The South ◽  
Thermodynamics And Kinetics ◽  
Antibody Resistance ◽  
Kinetics Of

Understanding thermodynamics and kinetics of the binding process of antibody to SARS-CoV-2 receptor-binding domain (RBD) of Spike protein is very important for the development of COVID19 vaccines. Especially, it is essential to understand how the binding mechanism may change under the effects of RBD mutations. In this context, we have demonstrated that the South African variant (B1.351 or 501Y.V2) can resist the neutralizing antibody (NAb). Three substitutions in RBD including K417N, E484K, and N501Y alters the free energy landscape, binding pose, binding free energy, binding kinetics, and unbinding pathway of RBD + NAb complexes. The low binding affinity of NAb to 501Y.V2 RBD confirms the antibody resistance of the South African variant.

scholarly journals Thermodynamics and Kinetics in Antibody Resistance of the 501Y.V2 SARS-CoV-2 Variant

2021 ◽  
Author(s):  
Son Tung Ngo ◽  
Trung Hai Nguyen ◽  
Duc-Hung Pham ◽  
Nguyen Thanh Tung ◽  
Pham Cam Nam
Keyword(s):  
Free Energy ◽  
South African ◽  
Binding Free Energy ◽  
Energy Landscape ◽  
Neutralizing Antibody ◽  
Receptor Binding Domain ◽  
The South ◽  
Thermodynamics And Kinetics ◽  
Antibody Resistance ◽  
Kinetics Of

Understanding thermodynamics and kinetics of the binding process of antibody to SARS-CoV-2 receptor-binding domain (RBD) of Spike protein is very important for the development of COVID19 vaccines. Especially, it is essential to understand how the binding mechanism may change under the effects of RBD mutations. In this context, we have demonstrated that the South African variant (B1.351 or 501Y.V2) can resist the neutralizing antibody (NAb). Three substitutions in RBD including K417N, E484K, and N501Y alters the free energy landscape, binding pose, binding free energy, binding kinetics, and unbinding pathway of RBD + NAb complexes. The low binding affinity of NAb to 501Y.V2 RBD confirms the antibody resistance of the South African variant.

Benefits of Modeling of Melting for the Understanding of Solidification Processes

2010 ◽  
Vol 649 ◽  
pp. 53-59
Author(s):  
Markus Rettenmayr
Keyword(s):  
Free Energy ◽  
Phase Transformation ◽  
Diffusion Coefficients ◽  
Solid Phase ◽  
Local Equilibrium ◽  
Kinetic Equations ◽  
Thermodynamics And Kinetics ◽  
Solidification Processes ◽  
Kinetics Of ◽  
Melting And Solidification

Melting and solidification are both phase transformations involving a liquid and a solid phase. In a simplifying procedure melting could be treated as the inverse process of solidification. However, there are substantial differences in the thermodynamics and kinetics of melting and solidification. The elaboration of a model for melting of binary alloys has lead to the possibility to also describe solidification processes more consistently. Input parameters in the model are the Gibbs Free Energy curves and the diffusion coefficients in the liquid and solid phase, respectively. Assumptions about the thermodynamic state of the interface like local equilibrium are not necessary, recently developed interface thermodynamics is coupled with the kinetic equations. Simulations results for steady-state melting and solidification are compared. The treatment of both solidification and melting yields some insight in the proper¬ties of the liquid/solid interface and its role during the phase transformation.

scholarly journals Determination of thermodynamics and kinetics of RNA reactions by force

2006 ◽  
Vol 39 (4) ◽  
pp. 325-360 ◽  
Author(s):  
Ignacio Tinoco ◽  
Pan T. X. Li ◽  
Carlos Bustamante
Keyword(s):  
Free Energy ◽  
Single Molecule ◽  
Rate Constants ◽  
Magnetic Tweezers ◽  
Constant Force ◽  
Thermodynamics And Kinetics ◽  
Wide Range ◽  
Kinetic Mechanisms ◽  
Kinetics Of ◽  
Force Drop

1. Introduction 3262. Instrumentation 3282.1 Instruments to study mechanical properties of RNA 3282.1.1 AFM 3282.1.2 Magnetic tweezers 3282.1.3 Optical tweezers 3302.2 Optical trap instrumentation 3302.3 Calibrations 3322.3.1 Calibration of trap stiffness 3322.3.2 Calibration of force 3332.3.3 Calibration of distance 3342.4 Types of experiments 3342.4.1 Force-ramp 3342.4.2 Force-clamp or constant-force experiments 3352.4.3 Extension-clamp or constant extension experiments 3352.4.4 Force-jump, Force-drop 3362.4.5 Passive mode 3363. Thermodynamics 3363.1 Reversibility 3363.2 Gibbs free energy 3373.2.1 Stretching free energy 3383.2.1.1 Rigid molecules 3383.2.1.2 Compliant or flexible molecules 3393.2.2 Free energy of a reversible unfolding transition 3393.2.3 Free energy of unfolding at zero force 3403.2.4 Free energy of an irreversible unfolding transition 3403.2.4.1 Jarzynski's method 3413.2.4.2 Crooks fluctuation theorem 3434. Kinetics 3454.1 Measuring rate constants 3454.1.1 Hopping 3454.1.2 Force-jump, Force-drop 3474.1.3 Force-ramp 3484.1.4 Instrumental effects 3504.2 Kinetic mechanisms 3514.2.1 Free-energy landscapes 3514.2.2 Kinetics of unfolding 3535. Relating force-measured data to other measurements 3545.1 Thermodynamics 3545.2 Kinetics 3576. Acknowledgements 3577. References 358Single-molecule methods have made it possible to apply force to an individual RNA molecule. Two beads are attached to the RNA; one is on a micropipette, the other is in a laser trap. The force on the RNA and the distance between the beads are measured. Force can change the equilibrium and the rate of any reaction in which the product has a different extension from the reactant. This review describes use of laser tweezers to measure thermodynamics and kinetics of unfolding/refolding RNA. For a reversible reaction the work directly provides the free energy; for irreversible reactions the free energy is obtained from the distribution of work values. The rate constants for the folding and unfolding reactions can be measured by several methods. The effect of pulling rate on the distribution of force-unfolding values leads to rate constants for unfolding. Hopping of the RNA between folded and unfolded states at constant force provides both unfolding and folding rates. Force-jumps and force-drops, similar to the temperature jump method, provide direct measurement of reaction rates over a wide range of forces. The advantages of applying force and using single-molecule methods are discussed. These methods, for example, allow reactions to be studied in non-denaturing solvents at physiological temperatures; they also simplify analysis of kinetic mechanisms because only one intermediate at a time is present. Unfolding of RNA in biological cells by helicases, or ribosomes, has similarities to unfolding by force.

scholarly journals Thermodynamics and Kinetics in Antibody Resistance of the 501Y.V2 SARS-CoV-2 Variant

2021 ◽  
Author(s):  
Son Tung Ngo ◽  
Trung Hai Nguyen ◽  
Duc-Hung Pham ◽  
Nguyen Thanh Tung ◽  
Pham Cam Nam
Keyword(s):  
Free Energy ◽  
South African ◽  
Binding Free Energy ◽  
Energy Landscape ◽  
Neutralizing Antibody ◽  
Receptor Binding Domain ◽  
The South ◽  
Thermodynamics And Kinetics ◽  
Antibody Resistance ◽  
Kinetics Of

Understanding thermodynamics and kinetics of the binding process of antibody to SARS-CoV-2 receptor-binding domain (RBD) of Spike protein is very important for the development of COVID19 vaccines. Especially, it is essential to understand how the binding mechanism may change under the effects of RBD mutations. In this context, we have demonstrated that the South African variant (B1.351 or 501Y.V2) can resist the neutralizing antibody (NAb). Three substitutions in RBD including K417N, E484K, and N501Y alters the free energy landscape, binding pose, binding free energy, binding kinetics, and unbinding pathway of RBD + NAb complexes. The low binding affinity of NAb to 501Y.V2 RBD confirms the antibody resistance of the South African variant.

scholarly journals Thermodynamics and Kinetics in Antibody Resistance of the 501Y.V2 SARS-CoV-2 Variant

2021 ◽  
Author(s):  
Son Tung Ngo ◽  
Trung Hai Nguyen ◽  
Duc-Hung Pham ◽  
Nguyen Thanh Tung ◽  
Pham Cam Nam
Keyword(s):  
Free Energy ◽  
South African ◽  
Binding Free Energy ◽  
Energy Landscape ◽  
Neutralizing Antibody ◽  
Receptor Binding Domain ◽  
The South ◽  
Thermodynamics And Kinetics ◽  
Antibody Resistance ◽  
Kinetics Of

Understanding thermodynamics and kinetics of the binding process of antibody to SARS-CoV-2 receptor-binding domain (RBD) of Spike protein is very important for the development of COVID19 vaccines. Especially, it is essential to understand how the binding mechanism may change under the effects of RBD mutations. In this context, we have demonstrated that the South African variant (B1.351 or 501Y.V2) can resist the neutralizing antibody (NAb). Three substitutions in RBD including K417N, E484K, and N501Y alters the free energy landscape, binding pose, binding free energy, binding kinetics, and unbinding pathway of RBD + NAb complexes. The low binding affinity of NAb to 501Y.V2 RBD confirms the antibody resistance of the South African variant.

scholarly journals Thermodynamics and Kinetics in Antibody Resistance of the 501Y.V2 SARS-CoV-2 Variant

2021 ◽  
Author(s):  
Son Tung Ngo ◽  
Trung Hai Nguyen ◽  
Duc-Hung Pham ◽  
Nguyen Thanh Tung ◽  
Pham Cam Nam
Keyword(s):  
Free Energy ◽  
South African ◽  
Binding Free Energy ◽  
Neutralizing Antibody ◽  
Receptor Binding Domain ◽  
The South ◽  
Binding Process ◽  
Thermodynamics And Kinetics ◽  
Antibody Resistance ◽  
Kinetics Of

<div> <p><a>Understanding thermodynamics and kinetics of the binding process of an antibody to SARS-CoV-2 receptor-binding domain (RBD) of Spike protein is very important for the development of COVID19 vaccines. Especially, it is essential to understand how the binding mechanism may change under the effects of RBD mutations. In this context, we have demonstrated that the South African variant (B1.351 or 501Y.V2) can resist the neutralizing antibody (NAb). Three substitutions in RBD including K417N, E484K, and N501Y alters the free energy landscape, binding pose, binding free energy, binding kinetics, hydrogen bond, nonbonded contacts, and unbinding pathway of RBD + NAb complexes. The low binding affinity of NAb to 501Y.V2 RBD confirms the antibody resistance of the South African variant.</a> Moreover, the fragment of NAb + RBD can be used as an affordable model to investigate the change of the binding process between mutations RBD and antibodies.</p></div>

Irradiation behavior of pyrolytic silicon carbide

1983 ◽  
Vol 41 ◽  
pp. 72-73
Author(s):  
R. J. Lauf
Keyword(s):  
Silicon Carbide ◽  
Fission Products ◽  
Thermodynamics And Kinetics ◽  
Neutron Fluences ◽  
Fuel Particles ◽  
Sic Coatings ◽  
Irradiation Behavior ◽  
Kinetics Of ◽  
Htgr Fuel

Fuel particles for the High-Temperature Gas-Cooled Reactor (HTGR) contain a layer of pyrolytic silicon carbide to act as a miniature pressure vessel and primary fission product barrier. Optimization of the SiC with respect to fuel performance involves four areas of study: (a) characterization of as-deposited SiC coatings; (b) thermodynamics and kinetics of chemical reactions between SiC and fission products; (c) irradiation behavior of SiC in the absence of fission products; and (d) combined effects of irradiation and fission products. This paper reports the behavior of SiC deposited on inert microspheres and irradiated to fast neutron fluences typical of HTGR fuel at end-of-life.

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