Abstract
The ability of high-resolution NMR spectroscopy to readout the response of molecular interactions at multiple atomic sites presents a unique capability to define thermodynamic equilibrium constants and kinetic rate constants for complex, multiple-step biological interactions. Nonetheless, the extraction of the relevant equilibrium binding and rate constants requires the appropriate analysis of not only a readout that follows the equilibrium concentrations of typical binding titration curves, but also the lineshapes of NMR spectra. To best take advantage of NMR data for characterizing molecular interactions, we developed NmrLineGuru, a software tool with a user-friendly graphical user interface (GUI) to model two-state, three-state, and four-state binding processes. Application of NmrLineGuru is through stand-alone GUIs, with no dependency on other software and no scripted input. NMR spectra can be fitted or simulated starting with user-specified input parameters and a chosen kinetic model. The ability to both simulate and fit NMR spectra provides the user the opportunity to not only determine the binding parameters that best reproduce the measured NMR spectra for the selected kinetic model, but to also query the possibility that alternative models agree with the data. NmrLineGuru is shown to provide an accurate, quantitative analysis of complex molecular interactions.
Highlights
To study binding interactions by NMR, a titration experiment is usually performed
None of the listed software packages is fully based on a graphical user interface (GUI) for both lineshape simulation and fitting; running the script-based simulation or fitting requires a certain level of programming knowledge for MATLAB
Based on our previous work in NMR lineshape analysis utilizing multi-state equilibrium models3, we developed NmrLineGuru, a standalone and user-friendly NMR lineshape software containing six GUIs for simulating and fitting NMR lineshape with two, three, and four-state binding models
Summary
To study binding interactions by NMR, a titration experiment is usually performed. At each titration point, an NMR-observable molecule (P) is mixed with its binding partner (L) at a certain ratio and 1D or 2D NMR spectra are recorded. Lineshape analysis can extract both thermodynamics and kinetics parameters for multi-state equilibrium binding models and all types of exchange regimes, the calculation steps are more complicated by involving both the equilibrium binding constants and kinetics rate constants. This complication limits the wide application of NMR lineshape analysis method. Based on our previous work in NMR lineshape analysis utilizing multi-state equilibrium models, we developed NmrLineGuru, a standalone and user-friendly NMR lineshape software containing six GUIs for simulating and fitting NMR lineshape with two-, three-, and four-state binding models These GUIs have no dependency on other software; NmrLineGuru is developed in the MATLAB environment, but does not require separate installation of MATLAB. NmrLineGuru aims to be extremely user-friendly for non-experts and time-saving with the hope of promoting the application of NMR lineshape analysis in research
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