scholarly journals Bayesian analysis of isothermal titration calorimetry for binding thermodynamics

2018 ◽  
Author(s):  
Trung Hai Nguyen ◽  
Ariën S. Rustenburg ◽  
Stefan G. Krimmer ◽  
Hexi Zhang ◽  
John D. Clark ◽  
...  

AbstractIsothermal titration calorimetry (ITC) is the only technique able to determine both the enthalpy and entropy of noncovalent association in a single experiment. The standard data analysis method based on nonlinear regression, however, provides unrealistically small uncertainty estimates due to its neglect of dominant sources of error. Here, we present a Bayesian framework for sampling from the posterior distribution of all thermodynamic parameters and other quantities of interest from one or more ITC experiments, allowing uncertainties and correlations to be quantitatively assessed. For a series of ITC measurements on metal:chelator and protein:ligand systems, the Bayesian approach yields uncertainties which represent the variability from experiment to experiment more accurately than the standard data analysis. In some datasets, the median enthalpy of binding is shifted by as much as 1.5 kcal/mol. A Python implementation suitable for analysis of data generated by MicroCal instruments (and adaptable to other calorimeters) is freely available online.

2015 ◽  
Author(s):  
Sarah E. Boyce ◽  
Joel Tellinghuisen ◽  
John D. Chodera

Isothermal titration calorimetry (ITC) can yield precise (±3%) estimates of the thermodynamic parameters describing biomolecular association (affinity, enthalpy, and entropy), making it an indispensable tool for biochemistry and drug discovery. Surprisingly, interlaboratory comparisons suggest that errors of ∼20% are common and widely underreported. Here, we show how to reduce precision- and accuracy-limiting errors while obtaining good estimates and minimizing material and time consumed by an experiment. We provide a simple spreadsheet that allows practitioners to identify precision-limiting operations during protocol design, track precision during the experiment, and propagate error to yield realistic final uncertainties.


PLoS ONE ◽  
2018 ◽  
Vol 13 (9) ◽  
pp. e0203224 ◽  
Author(s):  
Trung Hai Nguyen ◽  
Ariën S. Rustenburg ◽  
Stefan G. Krimmer ◽  
Hexi Zhang ◽  
John D. Clark ◽  
...  

2021 ◽  
Author(s):  
Felix Ott ◽  
Kersten S. Rabe ◽  
Christof M Niemeyer ◽  
Gudrun Gygli

<div> <p>An experimental workflow to provide detailed information of the molecular mechanisms of enzymes is described. This workflow will help in the application of enzymes in technical processes by providing crucial parameters needed to plan, model and implement biocatalytic processes more efficiently. These parameters are homogeneity of the enzyme sample (HES), kinetic and thermodynamic parameters of enzyme kinetics and binding of reactants to enzymes. The techniques used to measure these properties are dynamic light scattering (DLS), UV-Vis spectrophotometry and isothermal titration calorimetry (ITC) respectively. The workflow is standardized by the use of SOPs and python-scripted data analysis. </p> <p>We have used the NADPH-dependent alcohol dehydrogenase Gre2p as a challenging enzyme to demonstrate the power of this workflow. Our work highlights the utility for combined binding and kinetic studies for such complex multi-substrate reactions and the importance of sample quality control during experiments.</p> </div>


2021 ◽  
Author(s):  
Felix Ott ◽  
Kersten S. Rabe ◽  
Christof M Niemeyer ◽  
Gudrun Gygli

<div> <p>An experimental workflow to provide detailed information of the molecular mechanisms of enzymes is described. This workflow will help in the application of enzymes in technical processes by providing crucial parameters needed to plan, model and implement biocatalytic processes more efficiently. These parameters are homogeneity of the enzyme sample (HES), kinetic and thermodynamic parameters of enzyme kinetics and binding of reactants to enzymes. The techniques used to measure these properties are dynamic light scattering (DLS), UV-Vis spectrophotometry and isothermal titration calorimetry (ITC) respectively. The workflow is standardized by the use of SOPs and python-scripted data analysis. </p> <p>We have used the NADPH-dependent alcohol dehydrogenase Gre2p as a challenging enzyme to demonstrate the power of this workflow. Our work highlights the utility for combined binding and kinetic studies for such complex multi-substrate reactions and the importance of sample quality control during experiments.</p> </div>


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