PREdator: a python based GUI for data analysis, evaluation and fitting

Christoph Wiedemann,Matthias Görlach,Peter Bellstedt

doi:10.1186/1751-0473-9-21

Christoph Wiedemann, Matthias Görlach + Show 1 more

Open Access

https://doi.org/10.1186/1751-0473-9-21

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Abstract

The analysis of a series of experimental data is an essential procedure in virtually every field of research. The information contained in the data is extracted by fitting the experimental data to a mathematical model. The type of the mathematical model (linear, exponential, logarithmic, etc.) reflects the physical laws that underlie the experimental data. Here, we aim to provide a readily accessible, user-friendly python script for data analysis, evaluation and fitting. PREdator is presented at the example of NMR paramagnetic relaxation enhancement analysis.

Highlights

In most fields of physical, chemical or biological research it is requiered to convert experimental data into mathematical expressions
paramagnetic relaxation enhancement (PRE) can experimentally be derived from longitudinal (R1) or transverse (R2) relaxation rate measurements
A sensitive and reliable measure of transverse PREs can be obtained from cross-peak intensities for the state with and without the paramagnetic cosolvent

Summary

Introduction

In most fields of physical, chemical or biological research it is requiered to convert experimental data into mathematical expressions. The determination of longitudinal (R1) or transverse (R2) relaxation rates of protons in biological macromolecules deliver valuable molecular dynamics information on the system under investigation This information can be used to determine the interaction interface between individual domains or subunits on the basis of surface accessibility studies in situations where no other NMR parameters, e.g. nuclear Overhauser enhancement (NOE) or chemical shift perturbation data, are observable. In such cases, surface accessibility studies can be performed by using of chemically inert paramagnetic probes, e.g. paramagnetic metals, oxygen or PRE can experimentally be derived from longitudinal (R1) or transverse (R2) relaxation rate measurements. The PRE is calculated and is represented by the slope of the relaxation rate as a function of the concentration of the paramagnetic agent [3,4,5]

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Conclusion