Ionised concentrations in calcium and magnesium buffers: Standards and precise measurement are mandatory

PyChelator: a Python-based Colab and web application for metal chelator calculations

BACKGROUND

Metal ions play vital roles in regulating various biological systems, making it essential to control the concentration of free metal ions in solutions during experimental procedures. Several software applications exist for estimating the concentration of free metals in the presence of chelators, with MaxChelator being the easily accessible choice in this domain. This work aimed at developing a Python version of the software with arbitrary precision calculations, extensive new features, and a user-friendly interface to calculate the free metal ions.

RESULTS

We introduce the open-source PyChelator web application and the Python-based Google Colaboratory notebook, PyChelator Colab. Key features aim to improve the user experience of metal chelator calculations including input in smaller units, selection among stability constants, input of user-defined constants, and convenient download of all results in Excel format. These features were implemented in Python language by employing Google Colab, facilitating the incorporation of the calculator into other Python-based pipelines and inviting the contributions from the community of Python-using scientists for further enhancements. Arbitrary-precision arithmetic was employed by using the built-in Decimal module to obtain the most accurate results and to avoid rounding errors. No notable differences were observed compared to the results obtained from the PyChelator web application. However, comparison of different sources of stability constants showed substantial differences among them.

CONCLUSIONS

PyChelator is a user-friendly metal and chelator calculator that provides a platform for further development. It is provided as an interactive web application, freely available for use at https://amrutelab.github.io/PyChelator , and as a Python-based Google Colaboratory notebook at https://colab.

RESEARCH

google.com/github/AmruteLab/PyChelator/blob/main/PyChelator_Colab.ipynb .

Ionized concentrations in Ca2+ and Mg2+ buffers must be measured, not calculated

NEW FINDINGS

What is the topic of this review? The [Ca²⁺ ]/[Mg²⁺ ] in buffers are usually calculated using one of eight programs. These all give different values, thus [Ca²⁺ ]/[Mg²⁺ ] must be measured. What advances does it highlight? The ligand optimization method (LOM) using electrodes is an accurate method to do this. The limitations of the method are described. The LOM has been generalized to include calibration of fluorochromes and aequorin. It is the method of choice to measure intracellular equilibrium constants. Owing to the uncertainties for the values of resting [Ca²⁺ ], ∆[Ca²⁺ ] and the pK' values for intracellular Ca²⁺ /Mg²⁺ binding used in modelling, these values must now be re-examined critically.

ABSTRACT

Modelling intracellular regulation of Ca²⁺ /Mg²⁺ is now an established part of physiology. However, the conclusions drawn from such studies depend on accurate knowledge of intracellular [Ca²⁺ ], ∆[Ca²⁺ ] and the pK' values for the intracellular binding of Ca²⁺ /Mg²⁺ . Calculation of [Ca²⁺ ]/[Mg²⁺ ] in buffers is normal. The eight freely available programs all give different values for the [Ca²⁺ ]/[Mg²⁺ ] in the buffer solutions, varying by up to a factor of 4.3. As a result, concentrations must be measured. There are two methods to do this, both based on the ligand optimization method (LOM): (1) calibration solutions from 0.5 to 4 mmol l^-1 ; and (2) calibration solutions from 0.1 µmol l^-1 to 2 mmol l^-1 . Both methods can be used to calibrate Ca²⁺ /Mg²⁺ electrodes. Only Method 2 can be used directly to calibrate fluorochromes and aequorin. Software in the statistical program R to calculate the [Ca²⁺ ]/[Mg²⁺ ] in buffers is provided for both methods. The LOM has now been generalized for use with electrodes, fluorochromes and aequorin, making it the ideal method to determine the pK' values for intracellular binding of Ca²⁺ /Mg²⁺ . The [Ca²⁺ ]/[Mg²⁺ ] in buffers must be measured routinely, which is best done by calibrating electrodes with the LOM and software written in R. If [Ca²⁺ ]/[Mg²⁺ ] in buffers are calculated, the parameters used in modelling show the same degree of variability as the software programs. Uncritical acceptance of such parameters means that conclusions reached from such studies are relative, not absolute, and must now be re-examined.

Self-Correcting Method for the Measurement of Free Calcium and Magnesium Concentrations by 1H NMR

A method for the direct measurement of free Ca2+ and Mg2+ concentrations in the range of 1-100 mM by NMR spectroscopy is demonstrated. The method automatically corrects for the effect of ionic strength on the activity of the species in solution and works satisfactorily even when significant concentrations of competitive ions are present. The method requires only the measurement of the 1H chemical shifts of our reporter ligands, glycolate and sulfoacetate, and is easily implemented using NMR imaging techniques. As a proof of concept, we extract the thermodynamic binding constants and conformer distributions of analyte ligands using an in situ ion gradient. Existing approaches for the measurement of free Ca2+ or Mg2+ concentrations by NMR operate only at very low ion concentrations or else require careful recalibration for different sample conditions. By providing the free Ca2+ or Mg2+ concentrations, the proposed methodology significantly enhances the information obtainable via NMR investigations of ion-responsive systems.

A practical guide to the preparation and use of metal ion-buffered systems for physiological research

Recent recognition that mobile pools of Zn²⁺ and Cu²⁺ are involved in the regulation of neuronal, endocrine and other cells has stimulated the development of tools to visualize and quantify the level of free trace metal ions. Most of the methods used to measure or control loosely bound metals require reference media that contain exactly defined free concentrations of the target ions. Despite the central importance of proper metal ion buffering, there is still a lack of international standards and beginners in the field may have difficulties finding a coherent description of how to prepare trace metal ion buffers, especially when experiments are to be performed in multimetal systems. To close this gap, we provide a guide for the design, preparation and use of metal ion-buffered systems that facilitate immediate application under physiologically relevant ionic conditions. Thermodynamic and kinetic concepts of chemical speciation as well as general protocols and specific examples are outlined for the accurate preparation of single- and dual-metal ion buffers. In addition, experiments have been performed with FluoZin-3 to illustrate that metal ion-buffered systems are required for reliable preparation of nanomolar Zn²⁺ solutions and that dual-metal ion buffers can be used to calibrate suitable fluorescent Zn²⁺ sensors in the presence of millimolar Ca²⁺ concentrations. Together, the information provided should sensitize readers to the many potential pitfalls and uncertainties that exist when working with physiologically relevant concentrations of trace metal ions and enable them to formulate their own metal ion buffers for most in vitro applications.