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PELDOR Measurements on Nitroxide-Labeled Oligonucleotides

PELDOR Measurements on Nitroxide-Labeled Oligonucleotides

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作者： Tobias Hett Olav Schiemann

In the past decades, pulsed dipolar electron paramagnetic resonance spectroscopy (PDS) has emerged as a powerful tool in biophysical chemistry to study the structure, dynamics, and function of biomolecules like oligonucleotides and proteins. Structural information is obtained from PDS methods in form of a distribution of distances between spin centers. Such spin centers can either be intrinsically present paramagnetic metal ions and organic radicals or may be attached to the biomolecule by means of site-directed spin labeling. The most common PDS experiment for probing interspin distances in the nanometer range is pulsed electron–electron double resonance (PELDOR or DEER). In the protocol presented here, we provide a step-by-step workflow on how to set up a PELDOR experiment on a commercially available pulsed EPR spectrometer, outline the data analysis, and highlight potential pitfalls. We suggest PELDOR measurements on nitroxide-labeled oligonucleotides to study the structure of either RNA-cleaving DNAzymes in complex with their RNA targets or modified DNAzymes with different functions and targets, in which deoxynucleotides are substituted by nitroxide-labeled nucleotides. less

关键词： Spectroscopy electron spin Resonance Spectroscopy two-pulse electron spin-echo envelope modulation electron spin echo envelope modulation Spectroscopy Phase Cycle Rutherford Backscattering Spectroscopy Deep learning MATLAB Data analysis Programming Language electron paramagnetic resonance (EPR) spin label electron spin resonance (ESR) Double electron–electron resonance (DEER) pulsed electron–electron double resonance (PELDOR)

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PELDOR/DEER: An electron Paramagnetic Resonance Method to Study Membrane Proteins in Lipid Bilayers

PELDOR/DEER: An Electron Paramagnetic Resonance Method to St...

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作者： Martin F. Peter Kiran Bountra Konstantinos Beis Gregor Hagelueken

Every membrane protein is involved in close interactions with the lipid environment of cellular membranes. The annular lipids, that are in direct contact with the polypeptide, can in principle be seen as an integral part of its structure, akin to the first hydration shell of soluble proteins. It is therefore desirable to investigate the structure of membrane proteins and especially their conformational flexibility under conditions that are as close as possible to their native state. This can be achieved by reconstituting the protein into proteoliposomes, nanodiscs, or bicelles. In recent years, PELDOR/DEER spectroscopy has proved to be a very useful method to study the structure and function of membrane proteins in such artificial membrane environments. The technique complements both X-ray crystallography and cryo-EM and can be used in combination with virtually any artificial membrane environment and under certain circumstances even in native membranes. Of the above-mentioned membrane mimics, bicelles are currently the least often used for PELDOR studies, although they offer some advantages, especially their ease of use. Here, we provide a step-by-step protocol for studying a bicelle reconstituted membrane protein with PELDOR/DEER spectroscopy. less

关键词： electron spin Resonance Spectroscopy Continuous-wave EPR Spectroscopy X-ray Crystallography Cryo-EM Protease Cleavage Site-directed Mutagenesis Cell And Tissue Culture Nickel Affinity Chromatography FPLC Size-exclusion Chromatography SDS-PAGE Sonication pulsed electron-electron Double Resonance Spectroscopy two-pulse electron spin-echo envelope modulation Chromatography PCR Membrane protein EPR PELDOR DEER Bicelle

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EPR Techniques to Probe Insertion and Conformation of spin-Labeled Proteins in Lipid Bilayers

EPR Techniques to Probe Insertion and Conformation of Spin-L...

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作者： Enrica Bordignon Svetlana Kucher Yevhen Polyhach

electron paramagnetic resonance (EPR) spectroscopy of spin-labeled membrane proteins is a valuable biophysical technique to study structural details and conformational transitions of proteins close to their physiological environment, for example, in liposomes, membrane bilayers, and nanodiscs. Unlike in nuclear magnetic resonance (NMR) spectroscopy, having only one or few specific side chains labeled at a time with paramagnetic probes makes the size of the object under investigation irrelevant in terms of technique sensitivity. As a drawback, extensive site-directed mutagenesis is required in order to analyze the properties of the protein under investigation. EPR can provide detailed information on side chain dynamics of large membrane proteins or protein complexes embedded in membranes with an exquisite sensitivity for flexible regions and on water accessibility profiles across the membrane bilayer. Moreover, distances between the two spin-labeled side chains in membrane proteins can be detected with high precision at cryogenic temperatures. The application of EPR to membrane proteins still presents some challenges in terms of sample preparation, sensitivity and data interpretation, thus it is difficult to give ready-to-go methodological recipes. However, new technological developments (arbitrary waveform generators) and new spin labels spectroscopically orthogonal to nitroxides increased the range of applicability from in vitro toward in-cell EPR experiments. This chapter is an updated version of the one published in the first edition of the book and describes the state of the art in the application of nitroxide-based site-directed spin labeling EPR to membrane proteins, addressing new tools such as arbitrary waveform generators and spectroscopically orthogonal labels, such as Gd(III)-based labels. We will present challenges in sample preparation and data analysis for functional and structural membrane protein studies using site-directed spin labeling techniques a

关键词： electron spin Resonance Spectroscopy NMR Site-directed Mutagenesis Spectroscopy Protein Secondary Structure Mutagenesis DNP NMR spectroscopy Proton NMR pulse EPR pulsed electron-electron Double Resonance Spectroscopy Rutherford Backscattering Spectroscopy two-pulse electron spin-echo envelope modulation Molecular Dynamics Simulation Microscopy electron spin echo envelope modulation Spectroscopy Data analysis Membrane proteins EPR Mobility Bilayer Gadolinium High field Site-directed spin labeling Nitroxide Arbitrary waveform generator Water accessibility Distances Double electron–electron resonance (DEER) ODNP

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